14-Ptuh-miRNA-lncRNA-BLASTs-miRanda ================ Kathleen Durkin 2025-06-17 - 1 Prep for BLASTs - 1.1 Isolate the pre-mirna and mature mirna sequences - 1.2 Check miRNA lengths - 1.3 check lncRNAs - 2 BLASTs - 2.1 Make databases - 2.2 Run BLASTn - 3 Examine BLAST tables - 3.1 LncRNAs as miRNA precursors - 3.2 LncRNAs as miRNA sponges - 4 miRanda - 4.1 Run miRanda - 5 Summarize results ``` r library(dplyr) ``` ## ## Attaching package: 'dplyr' ## The following objects are masked from 'package:stats': ## ## filter, lag ## The following objects are masked from 'package:base': ## ## intersect, setdiff, setequal, union ``` r library(ggplot2) knitr::opts_chunk$set( echo = TRUE, # Display code chunks eval = FALSE # Evaluate code chunks ) ``` Two possible interactions between miRNA and lncRNA are: 1) lncRNA acting as a precursor molecule for miRNA(s), so that the lncRNA contains one or many pre-miRNA sequences and will be broken down into pre-miRNAs molecules, which will then be processed into mature miRNAs. 2) lncRNA acting as a “sponge” for miRNAs, so that an miRNA will bind to the lncRNA instead of being incorporated into an RISC complex to alter gene expression. In situation 1 we would expect one or several **pre-miRNA sequences to appear inside of a lncRNA**. This should be identifiable via BLASTn. In situation 2 we would expect the **mature miRNA sequence to appear inside a lncRNA**. Note that situation 2 is a bit more complicated, because we can’t say for certain what sequence similarity is required for binding. In cnidarians, miRNAs seem to act, like plants, through complementarity of the full mature miRNA (this is in contrast to e.g. mammals, where only binding of a short seed region is required) (Moran et al. ([2014](#ref-moran_cnidarian_2014)), Admoni et al. ([2023](#ref-admoni_target_2023))). However, for lncRNA acting as sponges, I don’t know whether to expect complementarity of the full mature miRNA or only a section, and I don’t know what degree of complementarity is required. **Work to identify lncRNA sponges could use BLASTn, but will likely need to include additional methods like miRanda to identify potential binding.** # 1 Prep for BLASTs ## 1.1 Isolate the pre-mirna and mature mirna sequences ``` bash full_mirna_fasta="../output/05-Ptuh-sRNA-ShortStack_4.1.0/ShortStack_out/mir.fasta" premirna_fasta="../output/14-Ptuh-miRNA-lncRNA-BLASTs-miRanda/Ptuh_ShortStack_4.1.0_precursor.fasta" mature_mirna_fasta="../output/14-Ptuh-miRNA-lncRNA-BLASTs-miRanda/Ptuh_ShortStack_4.1.0_mature.fasta" star_mirna_fasta="../output/14-Ptuh-miRNA-lncRNA-BLASTs-miRanda/Ptuh_ShortStack_4.1.0_star.fasta" # Pull out all sequences that DON'T contain "mature" or "star" in sequence name # Note the pre-miRNAs have sequences for both strands awk ' # If the line starts with ">", check the header /^>/ { if ($0 ~ /mature/ || $0 ~ /star/) { print_seq = 0 # Skip sequences with "mature" or "star" in the header } else { print_seq = 1 # Mark sequences for printing } } # Print the header and the next two lines if marked for printing print_seq { print if (!/^>/) { getline; print } # Capture second sequence line } ' "$full_mirna_fasta" > "$premirna_fasta" # Pull out all sequences that contain "mature" in sequence name grep -A 1 "mature" $full_mirna_fasta | grep -v "^--$" > $mature_mirna_fasta # Pull out all sequences that contain "star" in sequence name grep -A 1 "star" $full_mirna_fasta | grep -v "^--$" > $star_mirna_fasta ``` ``` bash premirna_fasta="../output/14-Ptuh-miRNA-lncRNA-BLASTs-miRanda/Ptuh_ShortStack_4.1.0_precursor.fasta" mature_mirna_fasta="../output/14-Ptuh-miRNA-lncRNA-BLASTs-miRanda/Ptuh_ShortStack_4.1.0_mature.fasta" star_mirna_fasta="../output/14-Ptuh-miRNA-lncRNA-BLASTs-miRanda/Ptuh_ShortStack_4.1.0_star.fasta" # Check we have appropriate headers, same number of sequences in each grep "^>" $premirna_fasta | head -2 echo "" grep "^>" $mature_mirna_fasta | head -2 echo "" grep "^>" $star_mirna_fasta | head -2 echo "" grep "^>" $premirna_fasta | wc -l echo "" grep "^>" $mature_mirna_fasta | wc -l echo "" grep "^>" $star_mirna_fasta | wc -l echo "" ``` ## >Cluster_21::Pocillopora_meandrina_HIv1___Sc0000000:818027-818120(+) ## >Cluster_21.mature::Pocillopora_meandrina_HIv1___Sc0000000:818049-818070(+) ## ## >Cluster_21.mature::Pocillopora_meandrina_HIv1___Sc0000000:818049-818070(+) ## >Cluster_36.mature::Pocillopora_meandrina_HIv1___Sc0000000:2872041-2872061(+) ## ## >Cluster_21.star::Pocillopora_meandrina_HIv1___Sc0000000:818079-818100(+) ## >Cluster_36.star::Pocillopora_meandrina_HIv1___Sc0000000:2872070-2872090(+) ## ## 111 ## ## 37 ## ## 37 ## 1.2 Check miRNA lengths ``` bash # Extract sequence lengths for precursors awk '/^>/ {if (seqlen){print seqlen}; printf $0" " ;seqlen=0;next; } { seqlen += length($0)}END{print seqlen}' ../output/14-Ptuh-miRNA-lncRNA-BLASTs-miRanda/Ptuh_ShortStack_4.1.0_precursor.fasta > ../output/14-Ptuh-miRNA-lncRNA-BLASTs-miRanda/Ptuh_ShortStack_4.1.0_precursor_lengths.txt # Sequence lengths for matures awk '/^>/ {if (seqlen){print seqlen}; printf $0" " ;seqlen=0;next; } { seqlen += length($0)}END{print seqlen}' ../output/14-Ptuh-miRNA-lncRNA-BLASTs-miRanda/Ptuh_ShortStack_4.1.0_mature.fasta > ../output/14-Ptuh-miRNA-lncRNA-BLASTs-miRanda/Ptuh_ShortStack_4.1.0_mature_lengths.txt ``` ``` r # Summary stats of precursor and mature lengths precursor_lengths <- read.table("../output/14-Ptuh-miRNA-lncRNA-BLASTs-miRanda/Ptuh_ShortStack_4.1.0_precursor_lengths.txt", sep = " ", header = FALSE, col.names = c("seqID", "length")) mature_lengths <- read.table("../output/14-Ptuh-miRNA-lncRNA-BLASTs-miRanda/Ptuh_ShortStack_4.1.0_mature_lengths.txt", sep = " ", header = FALSE, col.names = c("seqID", "length")) cat("Average pre-miRNA length: ", mean(precursor_lengths$length)) ``` ## Average pre-miRNA length: 46.25225 ``` r cat("\n") ``` ``` r cat("Range of pre-miRNA lengths: ", range(precursor_lengths$length)) ``` ## Range of pre-miRNA lengths: 21 101 ``` r cat("\n") ``` ``` r cat("Average mature miRNA length: ", mean(mature_lengths$length)) ``` ## Average mature miRNA length: 21.91892 ``` r cat("\n") ``` ``` r cat("Range of mature miRNA lengths: ", range(mature_lengths$length)) ``` ## Range of mature miRNA lengths: 21 23 ## 1.3 check lncRNAs LncRNAs were identified from Ptuh RNA-seq data Fasta of Ptuh lncRNAs stored at `https://gannet.fish.washington.edu/acropora/E5-deep-dive-expression/output/01.6-lncRNA-pipline/Ptuh_lncRNA.fasta` ``` bash curl -L https://gannet.fish.washington.edu/acropora/E5-deep-dive-expression/output/01.6-lncRNA-pipline/Ptuh_lncRNA.fasta -o ../output/14-Ptuh-miRNA-lncRNA-BLASTs-miRanda/Ptuh_lncRNA.fasta echo "Number of lncRNAs:" grep "^>" ../output/14-Ptuh-miRNA-lncRNA-BLASTs-miRanda/Ptuh_lncRNA.fasta | wc -l ``` ## % Total % Received % Xferd Average Speed Time Time Time Current ## Dload Upload Total Spent Left Speed ## 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 14 329M 14 47.8M 0 0 89.7M 0 0:00:03 --:--:-- 0:00:03 89.5M 47 329M 47 156M 0 0 101M 0 0:00:03 0:00:01 0:00:02 101M 80 329M 80 265M 0 0 104M 0 0:00:03 0:00:02 0:00:01 104M100 329M 100 329M 0 0 105M 0 0:00:03 0:00:03 --:--:-- 105M ## Number of lncRNAs: ## 56445 ``` bash # Extract sequence lengths for precursors awk '/^>/ {if (seqlen){print seqlen}; printf $0" " ;seqlen=0;next; } { seqlen += length($0)}END{print seqlen}' ../output/14-Ptuh-miRNA-lncRNA-BLASTs-miRanda/Ptuh_lncRNA.fasta > ../output/14-Ptuh-miRNA-lncRNA-BLASTs-miRanda/Ptuh_lncRNA_lengths.txt ``` ``` r # Summary stats of lncRNA lengths lncRNA_lengths <- read.table("../output/14-Ptuh-miRNA-lncRNA-BLASTs-miRanda/Ptuh_lncRNA_lengths.txt", sep = " ", header = FALSE, col.names = c("seqID", "length")) cat("Average lncRNA length: ", mean(lncRNA_lengths$length)) ``` ## Average lncRNA length: 5950.737 ``` r cat("\n") ``` ``` r cat("Range of lncRNA lengths: ", range(lncRNA_lengths$length)) ``` ## Range of lncRNA lengths: 201 235368 ``` r ggplot(lncRNA_lengths, aes(x = length)) + geom_histogram(binwidth = 500) + labs(title = "A. pulchra lncRNA sequence lengths", x = "Sequence Length [nucleotides]", y = "Frequency") + xlim(200, 50000) + ylim(0, 800) + theme_minimal() ``` ## Warning: Removed 452 rows containing non-finite outside the scale range ## (`stat_bin()`). ## Warning: Removed 19 rows containing missing values or values outside the scale range ## (`geom_bar()`). ![](14-Ptuh-miRNA-lncRNA-BLASTs-miRanda_files/figure-gfm/unnamed-chunk-5-1.png) # 2 BLASTs ## 2.1 Make databases Database of pre-miRNAs: ``` bash /home/shared/ncbi-blast-2.11.0+/bin/makeblastdb \ -in ../output/14-Ptuh-miRNA-lncRNA-BLASTs-miRanda/Ptuh_ShortStack_4.1.0_precursor.fasta \ -dbtype nucl \ -out ../output/14-Ptuh-miRNA-lncRNA-BLASTs-miRanda/blasts/Ptuh-db/Ptuh_ShortStack_4.1.0_precursor ``` Database of mature miRNAs: ``` bash /home/shared/ncbi-blast-2.11.0+/bin/makeblastdb \ -in ../output/14-Ptuh-miRNA-lncRNA-BLASTs-miRanda/Ptuh_ShortStack_4.1.0_mature.fasta \ -dbtype nucl \ -out ../output/14-Ptuh-miRNA-lncRNA-BLASTs-miRanda/blasts/Ptuh-db/Ptuh_ShortStack_4.1.0_mature ``` ## 2.2 Run BLASTn Generate a list of blast results. It seems plausible that a single lncRNA, which would be hundreds or thousands of nucleotides long, could interact with multiple miRNAs, so I will allow up to 10 hits (\~25% of Ptuh miRNAs) for each lncRNA. I want to see the top hits no matter how poor the match is, so I will not filter by e-value at this stage. I’ll also include the “-word_size 4” option, which reduces the required length of the initial match. Full pre-miRNAs: ``` bash /home/shared/ncbi-blast-2.11.0+/bin/blastn \ -task blastn \ -query ../output/14-Ptuh-miRNA-lncRNA-BLASTs-miRanda/Ptuh_lncRNA.fasta \ -db ../output/14-Ptuh-miRNA-lncRNA-BLASTs-miRanda/blasts/Ptuh-db/Ptuh_ShortStack_4.1.0_precursor \ -out ../output/14-Ptuh-miRNA-lncRNA-BLASTs-miRanda/blasts/lncRNA_to_precursor_blastn.tab \ -num_threads 40 \ -word_size 4 \ -max_target_seqs 10 \ -max_hsps 1 \ -outfmt 6 ``` ``` bash wc -l ../output/14-Ptuh-miRNA-lncRNA-BLASTs-miRanda/blasts/lncRNA_to_precursor_blastn.tab ``` ## 551650 ../output/14-Ptuh-miRNA-lncRNA-BLASTs-miRanda/blasts/lncRNA_to_precursor_blastn.tab Note we have less than (10 \* $$# of lncRNAs$$) output alignments because, while I did not set an evalue threshold, the default evalue threshold of evalue=10 is still in place. That means extremely poor matches were still excluded by default. Mature miRNAs: Note that I’m using the blastn-short option here because all of our mature miRNAs are less than 30 nucleotides long (recommended by [BLAST user manual](https://www.ncbi.nlm.nih.gov/books/NBK279684/table/appendices.T.blastn_application_options/)) ``` bash /home/shared/ncbi-blast-2.11.0+/bin/blastn \ -task blastn \ -query ../output/14-Ptuh-miRNA-lncRNA-BLASTs-miRanda/Ptuh_lncRNA.fasta \ -db ../output/14-Ptuh-miRNA-lncRNA-BLASTs-miRanda/blasts/Ptuh-db/Ptuh_ShortStack_4.1.0_mature \ -out ../output/14-Ptuh-miRNA-lncRNA-BLASTs-miRanda/blasts/lncRNA_to_mature_blastn.tab \ -num_threads 40 \ -word_size 4 \ -max_target_seqs 10 \ -max_hsps 1 \ -outfmt 6 ``` ``` bash wc -l ../output/14-Ptuh-miRNA-lncRNA-BLASTs-miRanda/blasts/lncRNA_to_mature_blastn.tab ``` ## 550258 ../output/14-Ptuh-miRNA-lncRNA-BLASTs-miRanda/blasts/lncRNA_to_mature_blastn.tab # 3 Examine BLAST tables Read into R and assign informative column labels ``` r precursor_lncRNA_BLASTn <- read.table("../output/14-Ptuh-miRNA-lncRNA-BLASTs-miRanda/blasts/lncRNA_to_precursor_blastn.tab", sep="\t", header=FALSE) mature_lncRNA_BLASTn <- read.table("../output/14-Ptuh-miRNA-lncRNA-BLASTs-miRanda/blasts/lncRNA_to_mature_blastn.tab", sep="\t", header=FALSE) colnames(precursor_lncRNA_BLASTn) <- c("qseqid", "sseqid", "pident", "length", "mismatch", "gapopen", "qstart", "qend", "sstart", "send", "evalue", "bitscore") colnames(mature_lncRNA_BLASTn) <- c("qseqid", "sseqid", "pident", "length", "mismatch", "gapopen", "qstart", "qend", "sstart", "send", "evalue", "bitscore") ``` ## 3.1 LncRNAs as miRNA precursors Are there any alignments of the full precursor miRNA to a lncRNA? Our precursor sequences are 90-98 nucleotides long, so let’s look for any alignments of at least 90 nucleotides with 0 mismatches. ``` r precursor_lncRNA_BLASTn %>% filter(length >= 90) %>% filter(mismatch == 0) %>% unique() %>% nrow() ``` ## [1] 50 ``` r precursor_lncRNA_BLASTn %>% filter(length >= 90) %>% filter(mismatch == 0) %>% select(qseqid) %>% unique() %>% nrow() ``` ## [1] 46 ``` r precursor_lncRNA_BLASTn %>% filter(length >= 90) %>% filter(mismatch == 0) %>% select(sseqid) %>% unique() %>% nrow() ``` ## [1] 20 ``` r precursor_lncRNA_BLASTn %>% filter(length >= 90) %>% filter(mismatch == 0) %>% unique() ``` ## qseqid ## 1 transcript::Pocillopora_meandrina_HIv1___Sc0000000:20369328-20376434 ## 2 transcript::Pocillopora_meandrina_HIv1___Sc0000000:20369596-20376434 ## 3 transcript::Pocillopora_meandrina_HIv1___Sc0000002:16098946-16109961 ## 4 transcript::Pocillopora_meandrina_HIv1___Sc0000002:16098969-16109961 ## 5 transcript::Pocillopora_meandrina_HIv1___Sc0000002:10843224-10849334 ## 6 transcript::Pocillopora_meandrina_HIv1___Sc0000002:10843224-10850210 ## 8 transcript::Pocillopora_meandrina_HIv1___Sc0000002:10843230-10850210 ## 9 transcript::Pocillopora_meandrina_HIv1___Sc0000002:10843249-10850210 ## 10 transcript::Pocillopora_meandrina_HIv1___Sc0000002:10843912-10850210 ## 11 transcript::Pocillopora_meandrina_HIv1___Sc0000002:15745570-15749355 ## 12 transcript::Pocillopora_meandrina_HIv1___Sc0000002:16103323-16107320 ## 13 transcript::Pocillopora_meandrina_HIv1___Sc0000005:10381740-10386428 ## 14 transcript::Pocillopora_meandrina_HIv1___Sc0000005:11254225-11264779 ## 15 transcript::Pocillopora_meandrina_HIv1___Sc0000005:11254225-11264779 ## 18 transcript::Pocillopora_meandrina_HIv1___Sc0000005:11254234-11264779 ## 19 transcript::Pocillopora_meandrina_HIv1___Sc0000005:11254234-11264779 ## 20 transcript::Pocillopora_meandrina_HIv1___Sc0000005:11255611-11264779 ## 21 transcript::Pocillopora_meandrina_HIv1___Sc0000005:11255611-11264779 ## 22 transcript::Pocillopora_meandrina_HIv1___Sc0000005:11258006-11264779 ## 23 transcript::Pocillopora_meandrina_HIv1___Sc0000005:11258006-11264779 ## 24 transcript::Pocillopora_meandrina_HIv1___Sc0000008:1780853-1785411 ## 25 transcript::Pocillopora_meandrina_HIv1___Sc0000008:1783244-1785411 ## 26 transcript::Pocillopora_meandrina_HIv1___Sc0000008:3565328-3586776 ## 27 transcript::Pocillopora_meandrina_HIv1___Sc0000008:3565450-3586776 ## 28 transcript::Pocillopora_meandrina_HIv1___Sc0000008:3614527-3621648 ## 29 transcript::Pocillopora_meandrina_HIv1___Sc0000008:5381562-5389641 ## 30 transcript::Pocillopora_meandrina_HIv1___Sc0000008:5382168-5389641 ## 31 transcript::Pocillopora_meandrina_HIv1___Sc0000008:5382569-5389641 ## 32 transcript::Pocillopora_meandrina_HIv1___Sc0000010:8008539-8014109 ## 33 transcript::Pocillopora_meandrina_HIv1___Sc0000010:8010601-8014109 ## 34 transcript::Pocillopora_meandrina_HIv1___Sc0000010:8008765-8013853 ## 35 transcript::Pocillopora_meandrina_HIv1___Sc0000010:8009039-8013853 ## 36 transcript::Pocillopora_meandrina_HIv1___Sc0000010:8009189-8013853 ## 37 transcript::Pocillopora_meandrina_HIv1___Sc0000012:6412836-6456125 ## 38 transcript::Pocillopora_meandrina_HIv1___Sc0000012:6453048-6455906 ## 39 transcript::Pocillopora_meandrina_HIv1___Sc0000014:2590221-2602242 ## 40 transcript::Pocillopora_meandrina_HIv1___Sc0000014:2593067-2602242 ## 41 transcript::Pocillopora_meandrina_HIv1___Sc0000014:9359559-9367897 ## 42 transcript::Pocillopora_meandrina_HIv1___Sc0000017:5040660-5060662 ## 43 transcript::Pocillopora_meandrina_HIv1___Sc0000018:6845867-6863996 ## 44 transcript::Pocillopora_meandrina_HIv1___Sc0000018:6845930-6863996 ## 45 transcript::Pocillopora_meandrina_HIv1___Sc0000018:6851678-6863996 ## 46 transcript::Pocillopora_meandrina_HIv1___Sc0000018:6852954-6863996 ## 47 transcript::Pocillopora_meandrina_HIv1___Sc0000021:4343937-4359207 ## 48 transcript::Pocillopora_meandrina_HIv1___Sc0000021:4343945-4359207 ## 49 transcript::Pocillopora_meandrina_HIv1___Sc0000021:4346471-4359207 ## 50 transcript::Pocillopora_meandrina_HIv1___Sc0000021:4346968-4359207 ## 51 transcript::Pocillopora_meandrina_HIv1___Sc0000024:4797252-4815862 ## 52 transcript::Pocillopora_meandrina_HIv1___Sc0000024:4797853-4815862 ## 53 transcript::Pocillopora_meandrina_HIv1___Sc0000026:1150884-1161746 ## sseqid ## 1 Cluster_360::Pocillopora_meandrina_HIv1___Sc0000000:20372416-20372510(-) ## 2 Cluster_360::Pocillopora_meandrina_HIv1___Sc0000000:20372416-20372510(-) ## 3 Cluster_1080::Pocillopora_meandrina_HIv1___Sc0000002:16106559-16106650(+) ## 4 Cluster_1080::Pocillopora_meandrina_HIv1___Sc0000002:16106559-16106650(+) ## 5 Cluster_1015::Pocillopora_meandrina_HIv1___Sc0000002:10845722-10845816(-) ## 6 Cluster_1015::Pocillopora_meandrina_HIv1___Sc0000002:10845722-10845816(-) ## 8 Cluster_1015::Pocillopora_meandrina_HIv1___Sc0000002:10845722-10845816(-) ## 9 Cluster_1015::Pocillopora_meandrina_HIv1___Sc0000002:10845722-10845816(-) ## 10 Cluster_1015::Pocillopora_meandrina_HIv1___Sc0000002:10845722-10845816(-) ## 11 Cluster_1068::Pocillopora_meandrina_HIv1___Sc0000002:15749261-15749351(+) ## 12 Cluster_1080::Pocillopora_meandrina_HIv1___Sc0000002:16106559-16106650(+) ## 13 Cluster_1938::Pocillopora_meandrina_HIv1___Sc0000005:10385497-10385597(+) ## 14 Cluster_1953::Pocillopora_meandrina_HIv1___Sc0000005:11261356-11261449(+) ## 15 Cluster_1952::Pocillopora_meandrina_HIv1___Sc0000005:11260734-11260823(+) ## 18 Cluster_1953::Pocillopora_meandrina_HIv1___Sc0000005:11261356-11261449(+) ## 19 Cluster_1952::Pocillopora_meandrina_HIv1___Sc0000005:11260734-11260823(+) ## 20 Cluster_1953::Pocillopora_meandrina_HIv1___Sc0000005:11261356-11261449(+) ## 21 Cluster_1952::Pocillopora_meandrina_HIv1___Sc0000005:11260734-11260823(+) ## 22 Cluster_1953::Pocillopora_meandrina_HIv1___Sc0000005:11261356-11261449(+) ## 23 Cluster_1952::Pocillopora_meandrina_HIv1___Sc0000005:11260734-11260823(+) ## 24 Cluster_2793::Pocillopora_meandrina_HIv1___Sc0000008:1783802-1783891(+) ## 25 Cluster_2793::Pocillopora_meandrina_HIv1___Sc0000008:1783802-1783891(+) ## 26 Cluster_2837::Pocillopora_meandrina_HIv1___Sc0000008:3576420-3576514(+) ## 27 Cluster_2837::Pocillopora_meandrina_HIv1___Sc0000008:3576420-3576514(+) ## 28 Cluster_2839::Pocillopora_meandrina_HIv1___Sc0000008:3619341-3619435(-) ## 29 Cluster_2859::Pocillopora_meandrina_HIv1___Sc0000008:5387738-5387830(-) ## 30 Cluster_2859::Pocillopora_meandrina_HIv1___Sc0000008:5387738-5387830(-) ## 31 Cluster_2859::Pocillopora_meandrina_HIv1___Sc0000008:5387738-5387830(-) ## 32 Cluster_3392::Pocillopora_meandrina_HIv1___Sc0000010:8012916-8013008(+) ## 33 Cluster_3392::Pocillopora_meandrina_HIv1___Sc0000010:8012916-8013008(+) ## 34 Cluster_3392::Pocillopora_meandrina_HIv1___Sc0000010:8012916-8013008(+) ## 35 Cluster_3392::Pocillopora_meandrina_HIv1___Sc0000010:8012916-8013008(+) ## 36 Cluster_3392::Pocillopora_meandrina_HIv1___Sc0000010:8012916-8013008(+) ## 37 Cluster_3661::Pocillopora_meandrina_HIv1___Sc0000012:6455183-6455276(+) ## 38 Cluster_3661::Pocillopora_meandrina_HIv1___Sc0000012:6455183-6455276(+) ## 39 Cluster_4040::Pocillopora_meandrina_HIv1___Sc0000014:2594743-2594833(+) ## 40 Cluster_4040::Pocillopora_meandrina_HIv1___Sc0000014:2594743-2594833(+) ## 41 Cluster_4118::Pocillopora_meandrina_HIv1___Sc0000014:9365459-9365552(-) ## 42 Cluster_4572::Pocillopora_meandrina_HIv1___Sc0000017:5050908-5051000(-) ## 43 Cluster_4823::Pocillopora_meandrina_HIv1___Sc0000018:6855499-6855592(+) ## 44 Cluster_4823::Pocillopora_meandrina_HIv1___Sc0000018:6855499-6855592(+) ## 45 Cluster_4823::Pocillopora_meandrina_HIv1___Sc0000018:6855499-6855592(+) ## 46 Cluster_4823::Pocillopora_meandrina_HIv1___Sc0000018:6855499-6855592(+) ## 47 Cluster_5253::Pocillopora_meandrina_HIv1___Sc0000021:4351817-4351909(+) ## 48 Cluster_5253::Pocillopora_meandrina_HIv1___Sc0000021:4351817-4351909(+) ## 49 Cluster_5253::Pocillopora_meandrina_HIv1___Sc0000021:4351817-4351909(+) ## 50 Cluster_5253::Pocillopora_meandrina_HIv1___Sc0000021:4351817-4351909(+) ## 51 Cluster_5612::Pocillopora_meandrina_HIv1___Sc0000024:4808666-4808760(+) ## 52 Cluster_5612::Pocillopora_meandrina_HIv1___Sc0000024:4808666-4808760(+) ## 53 Cluster_5740::Pocillopora_meandrina_HIv1___Sc0000026:1154719-1154813(-) ## pident length mismatch gapopen qstart qend sstart send evalue bitscore ## 1 100 95 0 0 3088 3182 95 1 2.44e-45 172 ## 2 100 95 0 0 2820 2914 95 1 2.35e-45 172 ## 3 100 92 0 0 7613 7704 1 92 1.55e-43 167 ## 4 100 92 0 0 7590 7681 1 92 1.55e-43 167 ## 5 100 95 0 0 2498 2592 95 1 2.10e-45 172 ## 6 100 95 0 0 2498 2592 95 1 2.40e-45 172 ## 8 100 95 0 0 2492 2586 95 1 2.40e-45 172 ## 9 100 95 0 0 2473 2567 95 1 2.39e-45 172 ## 10 100 95 0 0 1810 1904 95 1 2.16e-45 172 ## 11 100 91 0 0 3691 3781 1 91 1.99e-43 165 ## 12 100 92 0 0 3236 3327 1 92 6.03e-44 167 ## 13 100 101 0 0 3757 3857 1 101 9.20e-49 183 ## 14 100 94 0 0 7131 7224 1 94 1.27e-44 170 ## 15 100 90 0 0 6509 6598 1 90 1.88e-42 163 ## 18 100 94 0 0 7122 7215 1 94 1.26e-44 170 ## 19 100 90 0 0 6500 6589 1 90 1.88e-42 163 ## 20 100 94 0 0 5745 5838 1 94 1.10e-44 170 ## 21 100 90 0 0 5123 5212 1 90 1.63e-42 163 ## 22 100 94 0 0 3350 3443 1 94 8.11e-45 170 ## 23 100 90 0 0 2728 2817 1 90 1.20e-42 163 ## 24 100 90 0 0 2949 3038 1 90 8.38e-43 163 ## 25 100 90 0 0 558 647 1 90 3.97e-43 163 ## 26 100 95 0 0 11092 11186 1 95 7.11e-45 172 ## 27 100 95 0 0 10970 11064 1 95 7.07e-45 172 ## 28 100 95 0 0 4814 4908 95 1 2.44e-45 172 ## 29 100 93 0 0 6176 6268 93 1 3.38e-44 168 ## 30 100 93 0 0 5570 5662 93 1 3.13e-44 168 ## 31 100 93 0 0 5169 5261 93 1 2.96e-44 168 ## 32 100 93 0 0 4377 4469 1 93 2.33e-44 168 ## 33 100 93 0 0 2315 2407 1 93 1.52e-44 168 ## 34 100 93 0 0 4151 4243 1 93 2.13e-44 168 ## 35 100 93 0 0 3877 3969 1 93 2.01e-44 168 ## 36 100 93 0 0 3727 3819 1 93 2.02e-44 168 ## 37 100 94 0 0 42347 42440 1 94 4.83e-44 170 ## 38 100 94 0 0 2135 2228 1 94 3.53e-45 170 ## 39 100 91 0 0 4522 4612 1 91 5.91e-43 165 ## 40 100 91 0 0 1676 1766 1 91 4.68e-43 165 ## 41 100 94 0 0 5900 5993 94 1 9.99e-45 170 ## 42 100 93 0 0 10248 10340 93 1 8.08e-44 168 ## 43 100 94 0 0 9632 9725 1 94 2.10e-44 170 ## 44 100 94 0 0 9569 9662 1 94 2.09e-44 170 ## 45 100 94 0 0 3821 3914 1 94 1.42e-44 170 ## 46 100 94 0 0 2545 2638 1 94 1.28e-44 170 ## 47 100 93 0 0 7880 7972 1 93 6.17e-44 168 ## 48 100 93 0 0 7872 7964 1 93 6.16e-44 168 ## 49 100 93 0 0 5346 5438 1 93 5.14e-44 168 ## 50 100 93 0 0 4849 4941 1 93 4.94e-44 168 ## 51 100 95 0 0 11414 11508 1 95 6.17e-45 172 ## 52 100 95 0 0 10813 10907 1 95 5.97e-45 172 ## 53 100 95 0 0 3835 3929 95 1 3.60e-45 172 We have 50 alignments of a full pre-miRNA to a lncRNA with no mismatches. 46 lncRNA and 20 miRNA are represented. Note that, as in A.pulchra and P.evermanni, there are instances of a single pre-miRNA matching to several overlapping lncRNA, potentially representing multiple isoforms of a single lncRNA gene. Save these results ``` r precursor_lncRNAs <- precursor_lncRNA_BLASTn %>% filter(length >= 90) %>% filter(mismatch == 0) write.table(precursor_lncRNAs, "../output/14-Ptuh-miRNA-lncRNA-BLASTs-miRanda/lncRNAs_as_miRNA_precursors.txt") ``` ## 3.2 LncRNAs as miRNA sponges I’m not sure whether to expect lncRNAs to bind miRNAs in the same way cnidarian miRNA-mRNA binding occurs (nearly perfect complementarity of mature sequence), or whether the mechanism could differ (e.g., requires only a complementary seed region, as in vertebrate miRNA-mRNA binding). that means I don’t know what alignment parameters to require for our BLAST results. For now let’s say the aligned region must be at least 8 nucleotides (the expected length of an miRNA seed region), and let’s require a low evalue of 1e-3, to generally restrict results to those with high complementarity. ``` r mature_lncRNA_BLASTn %>% filter(length >= 8) %>% filter(evalue <= 0.001) %>% unique() ``` ## qseqid ## 1 transcript::Pocillopora_meandrina_HIv1___Sc0000000:9460120-9468105 ## 2 transcript::Pocillopora_meandrina_HIv1___Sc0000000:21384040-21389137 ## 3 transcript::Pocillopora_meandrina_HIv1___Sc0000000:5576917-5586430 ## 4 transcript::Pocillopora_meandrina_HIv1___Sc0000000:9832996-9834378 ## 5 transcript::Pocillopora_meandrina_HIv1___Sc0000000:15414465-15415251 ## 6 transcript::Pocillopora_meandrina_HIv1___Sc0000000:20369328-20376434 ## 7 transcript::Pocillopora_meandrina_HIv1___Sc0000000:20369596-20376434 ## 8 transcript::Pocillopora_meandrina_HIv1___Sc0000000:9631539-9631850 ## 9 transcript::Pocillopora_meandrina_HIv1___Sc0000000:10412213-10412438 ## 10 transcript::Pocillopora_meandrina_HIv1___Sc0000001:2796979-2901870 ## 11 transcript::Pocillopora_meandrina_HIv1___Sc0000001:2796983-2878479 ## 12 transcript::Pocillopora_meandrina_HIv1___Sc0000001:2798685-2819647 ## 13 transcript::Pocillopora_meandrina_HIv1___Sc0000001:2816869-2819647 ## 14 transcript::Pocillopora_meandrina_HIv1___Sc0000001:2858237-2901870 ## 15 transcript::Pocillopora_meandrina_HIv1___Sc0000001:2839579-2879069 ## 17 transcript::Pocillopora_meandrina_HIv1___Sc0000001:2863981-2890925 ## 18 transcript::Pocillopora_meandrina_HIv1___Sc0000001:2864560-2890444 ## 19 transcript::Pocillopora_meandrina_HIv1___Sc0000001:2879403-2905618 ## 20 transcript::Pocillopora_meandrina_HIv1___Sc0000001:2879403-2905618 ## 21 transcript::Pocillopora_meandrina_HIv1___Sc0000001:2892893-2905618 ## 22 transcript::Pocillopora_meandrina_HIv1___Sc0000001:2901956-2903096 ## 23 transcript::Pocillopora_meandrina_HIv1___Sc0000001:2901969-2903096 ## 24 transcript::Pocillopora_meandrina_HIv1___Sc0000001:9515025-9516170 ## 25 transcript::Pocillopora_meandrina_HIv1___Sc0000001:10636463-10636733 ## 26 transcript::Pocillopora_meandrina_HIv1___Sc0000001:15129619-15133203 ## 27 transcript::Pocillopora_meandrina_HIv1___Sc0000001:15130626-15133203 ## 28 transcript::Pocillopora_meandrina_HIv1___Sc0000001:15130744-15133203 ## 29 transcript::Pocillopora_meandrina_HIv1___Sc0000001:19836178-19836634 ## 30 transcript::Pocillopora_meandrina_HIv1___Sc0000001:2237534-2237938 ## 31 transcript::Pocillopora_meandrina_HIv1___Sc0000001:2237534-2237938 ## 32 transcript::Pocillopora_meandrina_HIv1___Sc0000001:2814548-2836948 ## 33 transcript::Pocillopora_meandrina_HIv1___Sc0000001:2837727-2878297 ## 34 transcript::Pocillopora_meandrina_HIv1___Sc0000001:2858211-2901870 ## 35 transcript::Pocillopora_meandrina_HIv1___Sc0000001:2866158-2890444 ## 36 transcript::Pocillopora_meandrina_HIv1___Sc0000001:2877566-2901222 ## 37 transcript::Pocillopora_meandrina_HIv1___Sc0000001:2877566-2901222 ## 38 transcript::Pocillopora_meandrina_HIv1___Sc0000001:2891317-2894653 ## 39 transcript::Pocillopora_meandrina_HIv1___Sc0000001:2891317-2894653 ## 40 transcript::Pocillopora_meandrina_HIv1___Sc0000001:4516090-4522563 ## 41 transcript::Pocillopora_meandrina_HIv1___Sc0000001:4517219-4521793 ## 42 transcript::Pocillopora_meandrina_HIv1___Sc0000001:8363105-8365676 ## 43 transcript::Pocillopora_meandrina_HIv1___Sc0000001:9595757-9596796 ## 44 transcript::Pocillopora_meandrina_HIv1___Sc0000001:9613910-9614369 ## 45 transcript::Pocillopora_meandrina_HIv1___Sc0000001:13523995-13524328 ## 46 transcript::Pocillopora_meandrina_HIv1___Sc0000002:16098946-16109961 ## 47 transcript::Pocillopora_meandrina_HIv1___Sc0000002:16098969-16109961 ## 48 transcript::Pocillopora_meandrina_HIv1___Sc0000002:2422287-2451232 ## 49 transcript::Pocillopora_meandrina_HIv1___Sc0000002:2426774-2451232 ## 50 transcript::Pocillopora_meandrina_HIv1___Sc0000002:10843224-10849334 ## 51 transcript::Pocillopora_meandrina_HIv1___Sc0000002:10843224-10850210 ## 53 transcript::Pocillopora_meandrina_HIv1___Sc0000002:10843230-10850210 ## 54 transcript::Pocillopora_meandrina_HIv1___Sc0000002:10843249-10850210 ## 55 transcript::Pocillopora_meandrina_HIv1___Sc0000002:10843912-10850210 ## 56 transcript::Pocillopora_meandrina_HIv1___Sc0000002:15745570-15749355 ## 57 transcript::Pocillopora_meandrina_HIv1___Sc0000002:16103323-16107320 ## 58 transcript::Pocillopora_meandrina_HIv1___Sc0000003:17486962-17492303 ## 60 transcript::Pocillopora_meandrina_HIv1___Sc0000003:17856338-17862013 ## 61 transcript::Pocillopora_meandrina_HIv1___Sc0000003:17856393-17862013 ## 62 transcript::Pocillopora_meandrina_HIv1___Sc0000003:17856394-17862013 ## 63 transcript::Pocillopora_meandrina_HIv1___Sc0000004:1926613-2032729 ## 64 transcript::Pocillopora_meandrina_HIv1___Sc0000004:2026148-2098694 ## 65 transcript::Pocillopora_meandrina_HIv1___Sc0000004:2028927-2098694 ## 66 transcript::Pocillopora_meandrina_HIv1___Sc0000004:2028961-2098694 ## 68 transcript::Pocillopora_meandrina_HIv1___Sc0000004:6086741-6087707 ## 69 transcript::Pocillopora_meandrina_HIv1___Sc0000004:1971355-1995126 ## 70 transcript::Pocillopora_meandrina_HIv1___Sc0000004:2032024-2098677 ## 71 transcript::Pocillopora_meandrina_HIv1___Sc0000004:2284236-2284529 ## 72 transcript::Pocillopora_meandrina_HIv1___Sc0000005:1364073-1370803 ## 73 transcript::Pocillopora_meandrina_HIv1___Sc0000005:7183655-7185109 ## 74 transcript::Pocillopora_meandrina_HIv1___Sc0000005:10381740-10386428 ## 75 transcript::Pocillopora_meandrina_HIv1___Sc0000005:11254225-11264779 ## 76 transcript::Pocillopora_meandrina_HIv1___Sc0000005:11254225-11264779 ## 79 transcript::Pocillopora_meandrina_HIv1___Sc0000005:11254234-11264779 ## 80 transcript::Pocillopora_meandrina_HIv1___Sc0000005:11254234-11264779 ## 81 transcript::Pocillopora_meandrina_HIv1___Sc0000005:11255611-11264779 ## 82 transcript::Pocillopora_meandrina_HIv1___Sc0000005:11255611-11264779 ## 83 transcript::Pocillopora_meandrina_HIv1___Sc0000005:11258006-11264779 ## 84 transcript::Pocillopora_meandrina_HIv1___Sc0000005:11258006-11264779 ## 85 transcript::Pocillopora_meandrina_HIv1___Sc0000005:7085401-7086955 ## 86 transcript::Pocillopora_meandrina_HIv1___Sc0000006:1194570-1200633 ## 87 transcript::Pocillopora_meandrina_HIv1___Sc0000006:1284114-1290097 ## 88 transcript::Pocillopora_meandrina_HIv1___Sc0000006:2618832-2627995 ## 90 transcript::Pocillopora_meandrina_HIv1___Sc0000006:2618914-2627995 ## 92 transcript::Pocillopora_meandrina_HIv1___Sc0000006:2618915-2627995 ## 94 transcript::Pocillopora_meandrina_HIv1___Sc0000006:2619005-2627995 ## 95 transcript::Pocillopora_meandrina_HIv1___Sc0000006:2619706-2627995 ## 96 transcript::Pocillopora_meandrina_HIv1___Sc0000006:7049052-7055016 ## 97 transcript::Pocillopora_meandrina_HIv1___Sc0000006:5847740-5848989 ## 98 transcript::Pocillopora_meandrina_HIv1___Sc0000007:358827-364739 ## 99 transcript::Pocillopora_meandrina_HIv1___Sc0000007:358833-364739 ## 100 transcript::Pocillopora_meandrina_HIv1___Sc0000007:4276948-4277256 ## 101 transcript::Pocillopora_meandrina_HIv1___Sc0000008:1780853-1785411 ## 102 transcript::Pocillopora_meandrina_HIv1___Sc0000008:1783244-1785411 ## 103 transcript::Pocillopora_meandrina_HIv1___Sc0000008:1800470-1801832 ## 104 transcript::Pocillopora_meandrina_HIv1___Sc0000008:3565328-3586776 ## 105 transcript::Pocillopora_meandrina_HIv1___Sc0000008:3565450-3586776 ## 106 transcript::Pocillopora_meandrina_HIv1___Sc0000008:3614527-3621648 ## 107 transcript::Pocillopora_meandrina_HIv1___Sc0000008:5381562-5389641 ## 108 transcript::Pocillopora_meandrina_HIv1___Sc0000008:5382168-5389641 ## 109 transcript::Pocillopora_meandrina_HIv1___Sc0000008:5382569-5389641 ## 110 transcript::Pocillopora_meandrina_HIv1___Sc0000008:8107759-8110602 ## 111 transcript::Pocillopora_meandrina_HIv1___Sc0000008:6398051-6398288 ## 112 transcript::Pocillopora_meandrina_HIv1___Sc0000009:349274-366723 ## 113 transcript::Pocillopora_meandrina_HIv1___Sc0000009:117318-141456 ## 114 transcript::Pocillopora_meandrina_HIv1___Sc0000009:201308-215495 ## 115 transcript::Pocillopora_meandrina_HIv1___Sc0000009:363783-364923 ## 116 transcript::Pocillopora_meandrina_HIv1___Sc0000009:38821-39831 ## 117 transcript::Pocillopora_meandrina_HIv1___Sc0000009:4942328-4943412 ## 118 transcript::Pocillopora_meandrina_HIv1___Sc0000009:4981780-4986592 ## 119 transcript::Pocillopora_meandrina_HIv1___Sc0000009:5189715-5195146 ## 120 transcript::Pocillopora_meandrina_HIv1___Sc0000009:4943735-4948260 ## 121 transcript::Pocillopora_meandrina_HIv1___Sc0000009:5073793-5076792 ## 122 transcript::Pocillopora_meandrina_HIv1___Sc0000009:5251729-5252395 ## 123 transcript::Pocillopora_meandrina_HIv1___Sc0000009:1079984-1081215 ## 124 transcript::Pocillopora_meandrina_HIv1___Sc0000010:8008539-8014109 ## 125 transcript::Pocillopora_meandrina_HIv1___Sc0000010:8010601-8014109 ## 126 transcript::Pocillopora_meandrina_HIv1___Sc0000010:8009381-8011801 ## 127 transcript::Pocillopora_meandrina_HIv1___Sc0000010:1646160-1646595 ## 128 transcript::Pocillopora_meandrina_HIv1___Sc0000010:2940968-2941837 ## 129 transcript::Pocillopora_meandrina_HIv1___Sc0000010:8008539-8012086 ## 130 transcript::Pocillopora_meandrina_HIv1___Sc0000010:8008765-8013853 ## 131 transcript::Pocillopora_meandrina_HIv1___Sc0000010:8009039-8013853 ## 132 transcript::Pocillopora_meandrina_HIv1___Sc0000010:8009189-8013853 ## 133 transcript::Pocillopora_meandrina_HIv1___Sc0000012:2166865-2182411 ## 135 transcript::Pocillopora_meandrina_HIv1___Sc0000012:2166880-2182411 ## 136 transcript::Pocillopora_meandrina_HIv1___Sc0000012:2167010-2182411 ## 137 transcript::Pocillopora_meandrina_HIv1___Sc0000012:2176350-2182411 ## 138 transcript::Pocillopora_meandrina_HIv1___Sc0000012:2176394-2182411 ## 139 transcript::Pocillopora_meandrina_HIv1___Sc0000012:3434543-3435563 ## 140 transcript::Pocillopora_meandrina_HIv1___Sc0000012:6412836-6456125 ## 141 transcript::Pocillopora_meandrina_HIv1___Sc0000012:6453048-6455906 ## 142 transcript::Pocillopora_meandrina_HIv1___Sc0000012:6715832-6717774 ## 143 transcript::Pocillopora_meandrina_HIv1___Sc0000012:4184475-4184801 ## 144 transcript::Pocillopora_meandrina_HIv1___Sc0000012:9073278-9073560 ## 145 transcript::Pocillopora_meandrina_HIv1___Sc0000013:196768-201047 ## 146 transcript::Pocillopora_meandrina_HIv1___Sc0000013:1265263-1268528 ## 147 transcript::Pocillopora_meandrina_HIv1___Sc0000013:690078-692442 ## 148 transcript::Pocillopora_meandrina_HIv1___Sc0000013:7498054-7499352 ## 149 transcript::Pocillopora_meandrina_HIv1___Sc0000013:4585798-4587258 ## 150 transcript::Pocillopora_meandrina_HIv1___Sc0000014:2590221-2602242 ## 151 transcript::Pocillopora_meandrina_HIv1___Sc0000014:2593067-2602242 ## 152 transcript::Pocillopora_meandrina_HIv1___Sc0000014:9359559-9367897 ## 153 transcript::Pocillopora_meandrina_HIv1___Sc0000015:6262498-6283369 ## 154 transcript::Pocillopora_meandrina_HIv1___Sc0000015:6262499-6283369 ## 155 transcript::Pocillopora_meandrina_HIv1___Sc0000015:6262571-6283369 ## 156 transcript::Pocillopora_meandrina_HIv1___Sc0000016:7555702-7558865 ## 157 transcript::Pocillopora_meandrina_HIv1___Sc0000016:7747686-7748696 ## 158 transcript::Pocillopora_meandrina_HIv1___Sc0000017:2350877-2384115 ## 159 transcript::Pocillopora_meandrina_HIv1___Sc0000017:2350877-2386038 ## 160 transcript::Pocillopora_meandrina_HIv1___Sc0000017:2351020-2384115 ## 161 transcript::Pocillopora_meandrina_HIv1___Sc0000017:2351885-2383746 ## 162 transcript::Pocillopora_meandrina_HIv1___Sc0000017:5040660-5060662 ## 163 transcript::Pocillopora_meandrina_HIv1___Sc0000017:4996397-4996672 ## 164 transcript::Pocillopora_meandrina_HIv1___Sc0000018:4534718-4536055 ## 165 transcript::Pocillopora_meandrina_HIv1___Sc0000018:4534771-4536218 ## 166 transcript::Pocillopora_meandrina_HIv1___Sc0000018:6845867-6863996 ## 167 transcript::Pocillopora_meandrina_HIv1___Sc0000018:6845930-6863996 ## 168 transcript::Pocillopora_meandrina_HIv1___Sc0000018:6851678-6863996 ## 169 transcript::Pocillopora_meandrina_HIv1___Sc0000018:6852954-6863996 ## 170 transcript::Pocillopora_meandrina_HIv1___Sc0000018:4932736-4938146 ## 171 transcript::Pocillopora_meandrina_HIv1___Sc0000019:2022846-2023129 ## 172 transcript::Pocillopora_meandrina_HIv1___Sc0000019:2026660-2027078 ## 173 transcript::Pocillopora_meandrina_HIv1___Sc0000019:2026660-2027078 ## 174 transcript::Pocillopora_meandrina_HIv1___Sc0000019:2051105-2053095 ## 175 transcript::Pocillopora_meandrina_HIv1___Sc0000019:2051105-2053095 ## 176 transcript::Pocillopora_meandrina_HIv1___Sc0000021:4193159-4195190 ## 177 transcript::Pocillopora_meandrina_HIv1___Sc0000021:4343937-4359207 ## 178 transcript::Pocillopora_meandrina_HIv1___Sc0000021:4343945-4359207 ## 179 transcript::Pocillopora_meandrina_HIv1___Sc0000021:4346471-4359207 ## 180 transcript::Pocillopora_meandrina_HIv1___Sc0000021:4346968-4359207 ## 181 transcript::Pocillopora_meandrina_HIv1___Sc0000021:1640083-1646308 ## 182 transcript::Pocillopora_meandrina_HIv1___Sc0000021:4633401-4650590 ## 183 transcript::Pocillopora_meandrina_HIv1___Sc0000021:5467722-5471705 ## 184 transcript::Pocillopora_meandrina_HIv1___Sc0000022:1332829-1350806 ## 185 transcript::Pocillopora_meandrina_HIv1___Sc0000022:1334250-1354008 ## 186 transcript::Pocillopora_meandrina_HIv1___Sc0000024:4797252-4815862 ## 187 transcript::Pocillopora_meandrina_HIv1___Sc0000024:4797853-4815862 ## 188 transcript::Pocillopora_meandrina_HIv1___Sc0000025:905693-906134 ## 189 transcript::Pocillopora_meandrina_HIv1___Sc0000026:1150884-1161746 ## 190 transcript::Pocillopora_meandrina_HIv1___Sc0000026:4883141-4885213 ## 192 transcript::Pocillopora_meandrina_HIv1___Sc0000028:4625257-4626015 ## 193 transcript::Pocillopora_meandrina_HIv1___Sc0000028:3342173-3358295 ## 194 transcript::Pocillopora_meandrina_HIv1___Sc0000029:2587601-2589783 ## 195 transcript::Pocillopora_meandrina_HIv1___Sc0000030:3539446-3539692 ## 196 transcript::Pocillopora_meandrina_HIv1___Sc0000031:684983-695081 ## 197 transcript::Pocillopora_meandrina_HIv1___Sc0000031:686581-695081 ## 198 transcript::Pocillopora_meandrina_HIv1___Sc0000031:709507-714670 ## 199 transcript::Pocillopora_meandrina_HIv1___Sc0000031:1903357-1903624 ## 200 transcript::Pocillopora_meandrina_HIv1___Sc0000032:3191145-3199335 ## 201 transcript::Pocillopora_meandrina_HIv1___Sc0000034:2872289-2873827 ## 202 transcript::Pocillopora_meandrina_HIv1___Sc0000034:1172949-1173195 ## 203 transcript::Pocillopora_meandrina_HIv1___Sc0000039:2419201-2438332 ## 204 transcript::Pocillopora_meandrina_HIv1___Sc0000039:2383777-2435226 ## 205 transcript::Pocillopora_meandrina_HIv1___Sc0000039:2397808-2435226 ## 206 transcript::Pocillopora_meandrina_HIv1___Sc0000041:1683190-1683468 ## 207 transcript::Pocillopora_meandrina_HIv1___Sc0000042:76196-77071 ## 208 transcript::Pocillopora_meandrina_HIv1___Sc0000043:799050-802563 ## 209 transcript::Pocillopora_meandrina_HIv1___Sc0000046:348855-349201 ## 210 transcript::Pocillopora_meandrina_HIv1___xfSc0000376:21603-21970 ## 211 transcript::Pocillopora_meandrina_HIv1___xfSc0000376:21603-21970 ## 212 transcript::Pocillopora_meandrina_HIv1___xfSc0000699:22919-26051 ## 213 transcript::Pocillopora_meandrina_HIv1___xfSc0000699:22949-24870 ## 214 transcript::Pocillopora_meandrina_HIv1___xfSc0000699:22981-24870 ## 215 transcript::Pocillopora_meandrina_HIv1___xfSc0000824:3618-30980 ## 216 transcript::Pocillopora_meandrina_HIv1___xfSc0000824:5126-31123 ## 217 transcript::Pocillopora_meandrina_HIv1___xfSc0000824:2616-3139 ## 218 transcript::Pocillopora_meandrina_HIv1___xfSc0000868:12186-13209 ## sseqid ## 1 Cluster_3392.mature::Pocillopora_meandrina_HIv1___Sc0000010:8012938-8012959(+) ## 2 Cluster_4754.mature::Pocillopora_meandrina_HIv1___Sc0000018:4564906-4564927(+) ## 3 Cluster_390.mature::Pocillopora_meandrina_HIv1___Sc0000001:1459455-1459476(+) ## 4 Cluster_2793.mature::Pocillopora_meandrina_HIv1___Sc0000008:1783824-1783844(+) ## 5 Cluster_4435.mature::Pocillopora_meandrina_HIv1___Sc0000016:7549579-7549600(+) ## 6 Cluster_360.mature::Pocillopora_meandrina_HIv1___Sc0000000:20372469-20372490(-) ## 7 Cluster_360.mature::Pocillopora_meandrina_HIv1___Sc0000000:20372469-20372490(-) ## 8 Cluster_6382.mature::Pocillopora_meandrina_HIv1___Sc0000035:1989842-1989863(+) ## 9 Cluster_2839.mature::Pocillopora_meandrina_HIv1___Sc0000008:3619363-3619384(-) ## 10 Cluster_6382.mature::Pocillopora_meandrina_HIv1___Sc0000035:1989842-1989863(+) ## 11 Cluster_6382.mature::Pocillopora_meandrina_HIv1___Sc0000035:1989842-1989863(+) ## 12 Cluster_3392.mature::Pocillopora_meandrina_HIv1___Sc0000010:8012938-8012959(+) ## 13 Cluster_3392.mature::Pocillopora_meandrina_HIv1___Sc0000010:8012938-8012959(+) ## 14 Cluster_6382.mature::Pocillopora_meandrina_HIv1___Sc0000035:1989842-1989863(+) ## 15 Cluster_6382.mature::Pocillopora_meandrina_HIv1___Sc0000035:1989842-1989863(+) ## 17 Cluster_6382.mature::Pocillopora_meandrina_HIv1___Sc0000035:1989842-1989863(+) ## 18 Cluster_6382.mature::Pocillopora_meandrina_HIv1___Sc0000035:1989842-1989863(+) ## 19 Cluster_6382.mature::Pocillopora_meandrina_HIv1___Sc0000035:1989842-1989863(+) ## 20 Cluster_3392.mature::Pocillopora_meandrina_HIv1___Sc0000010:8012938-8012959(+) ## 21 Cluster_6382.mature::Pocillopora_meandrina_HIv1___Sc0000035:1989842-1989863(+) ## 22 Cluster_6382.mature::Pocillopora_meandrina_HIv1___Sc0000035:1989842-1989863(+) ## 23 Cluster_6382.mature::Pocillopora_meandrina_HIv1___Sc0000035:1989842-1989863(+) ## 24 Cluster_2973.mature::Pocillopora_meandrina_HIv1___Sc0000009:3894922-3894943(-) ## 25 Cluster_2859.mature::Pocillopora_meandrina_HIv1___Sc0000008:5387760-5387781(-) ## 26 Cluster_2859.mature::Pocillopora_meandrina_HIv1___Sc0000008:5387760-5387781(-) ## 27 Cluster_2859.mature::Pocillopora_meandrina_HIv1___Sc0000008:5387760-5387781(-) ## 28 Cluster_2859.mature::Pocillopora_meandrina_HIv1___Sc0000008:5387760-5387781(-) ## 29 Cluster_21.mature::Pocillopora_meandrina_HIv1___Sc0000000:818049-818070(+) ## 30 Cluster_3392.mature::Pocillopora_meandrina_HIv1___Sc0000010:8012938-8012959(+) ## 31 Cluster_21.mature::Pocillopora_meandrina_HIv1___Sc0000000:818049-818070(+) ## 32 Cluster_3392.mature::Pocillopora_meandrina_HIv1___Sc0000010:8012938-8012959(+) ## 33 Cluster_6382.mature::Pocillopora_meandrina_HIv1___Sc0000035:1989842-1989863(+) ## 34 Cluster_6382.mature::Pocillopora_meandrina_HIv1___Sc0000035:1989842-1989863(+) ## 35 Cluster_6382.mature::Pocillopora_meandrina_HIv1___Sc0000035:1989842-1989863(+) ## 36 Cluster_6382.mature::Pocillopora_meandrina_HIv1___Sc0000035:1989842-1989863(+) ## 37 Cluster_3392.mature::Pocillopora_meandrina_HIv1___Sc0000010:8012938-8012959(+) ## 38 Cluster_6382.mature::Pocillopora_meandrina_HIv1___Sc0000035:1989842-1989863(+) ## 39 Cluster_3392.mature::Pocillopora_meandrina_HIv1___Sc0000010:8012938-8012959(+) ## 40 Cluster_5740.mature::Pocillopora_meandrina_HIv1___Sc0000026:1154772-1154793(-) ## 41 Cluster_5740.mature::Pocillopora_meandrina_HIv1___Sc0000026:1154772-1154793(-) ## 42 Cluster_2793.mature::Pocillopora_meandrina_HIv1___Sc0000008:1783824-1783844(+) ## 43 Cluster_2973.mature::Pocillopora_meandrina_HIv1___Sc0000009:3894922-3894943(-) ## 44 Cluster_2973.mature::Pocillopora_meandrina_HIv1___Sc0000009:3894922-3894943(-) ## 45 Cluster_4118.mature::Pocillopora_meandrina_HIv1___Sc0000014:9365481-9365502(-) ## 46 Cluster_1080.mature::Pocillopora_meandrina_HIv1___Sc0000002:16106609-16106630(+) ## 47 Cluster_1080.mature::Pocillopora_meandrina_HIv1___Sc0000002:16106609-16106630(+) ## 48 Cluster_4754.mature::Pocillopora_meandrina_HIv1___Sc0000018:4564906-4564927(+) ## 49 Cluster_4754.mature::Pocillopora_meandrina_HIv1___Sc0000018:4564906-4564927(+) ## 50 Cluster_1015.mature::Pocillopora_meandrina_HIv1___Sc0000002:10845744-10845765(-) ## 51 Cluster_1015.mature::Pocillopora_meandrina_HIv1___Sc0000002:10845744-10845765(-) ## 53 Cluster_1015.mature::Pocillopora_meandrina_HIv1___Sc0000002:10845744-10845765(-) ## 54 Cluster_1015.mature::Pocillopora_meandrina_HIv1___Sc0000002:10845744-10845765(-) ## 55 Cluster_1015.mature::Pocillopora_meandrina_HIv1___Sc0000002:10845744-10845765(-) ## 56 Cluster_1068.mature::Pocillopora_meandrina_HIv1___Sc0000002:15749310-15749331(+) ## 57 Cluster_1080.mature::Pocillopora_meandrina_HIv1___Sc0000002:16106609-16106630(+) ## 58 Cluster_4118.mature::Pocillopora_meandrina_HIv1___Sc0000014:9365481-9365502(-) ## 60 Cluster_4118.mature::Pocillopora_meandrina_HIv1___Sc0000014:9365481-9365502(-) ## 61 Cluster_4118.mature::Pocillopora_meandrina_HIv1___Sc0000014:9365481-9365502(-) ## 62 Cluster_4118.mature::Pocillopora_meandrina_HIv1___Sc0000014:9365481-9365502(-) ## 63 Cluster_4118.mature::Pocillopora_meandrina_HIv1___Sc0000014:9365481-9365502(-) ## 64 Cluster_4118.mature::Pocillopora_meandrina_HIv1___Sc0000014:9365481-9365502(-) ## 65 Cluster_4118.mature::Pocillopora_meandrina_HIv1___Sc0000014:9365481-9365502(-) ## 66 Cluster_4118.mature::Pocillopora_meandrina_HIv1___Sc0000014:9365481-9365502(-) ## 68 Cluster_4118.mature::Pocillopora_meandrina_HIv1___Sc0000014:9365481-9365502(-) ## 69 Cluster_4118.mature::Pocillopora_meandrina_HIv1___Sc0000014:9365481-9365502(-) ## 70 Cluster_4118.mature::Pocillopora_meandrina_HIv1___Sc0000014:9365481-9365502(-) ## 71 Cluster_4754.mature::Pocillopora_meandrina_HIv1___Sc0000018:4564906-4564927(+) ## 72 Cluster_757.mature::Pocillopora_meandrina_HIv1___Sc0000001:19145788-19145809(+) ## 73 Cluster_1793.mature::Pocillopora_meandrina_HIv1___Sc0000005:601626-601646(+) ## 74 Cluster_1938.mature::Pocillopora_meandrina_HIv1___Sc0000005:10385519-10385541(+) ## 75 Cluster_1953.mature::Pocillopora_meandrina_HIv1___Sc0000005:11261378-11261399(+) ## 76 Cluster_1952.mature::Pocillopora_meandrina_HIv1___Sc0000005:11260782-11260803(+) ## 79 Cluster_1953.mature::Pocillopora_meandrina_HIv1___Sc0000005:11261378-11261399(+) ## 80 Cluster_1952.mature::Pocillopora_meandrina_HIv1___Sc0000005:11260782-11260803(+) ## 81 Cluster_1953.mature::Pocillopora_meandrina_HIv1___Sc0000005:11261378-11261399(+) ## 82 Cluster_1952.mature::Pocillopora_meandrina_HIv1___Sc0000005:11260782-11260803(+) ## 83 Cluster_1953.mature::Pocillopora_meandrina_HIv1___Sc0000005:11261378-11261399(+) ## 84 Cluster_1952.mature::Pocillopora_meandrina_HIv1___Sc0000005:11260782-11260803(+) ## 85 Cluster_1793.mature::Pocillopora_meandrina_HIv1___Sc0000005:601626-601646(+) ## 86 Cluster_4754.mature::Pocillopora_meandrina_HIv1___Sc0000018:4564906-4564927(+) ## 87 Cluster_4754.mature::Pocillopora_meandrina_HIv1___Sc0000018:4564906-4564927(+) ## 88 Cluster_4754.mature::Pocillopora_meandrina_HIv1___Sc0000018:4564906-4564927(+) ## 90 Cluster_4754.mature::Pocillopora_meandrina_HIv1___Sc0000018:4564906-4564927(+) ## 92 Cluster_4754.mature::Pocillopora_meandrina_HIv1___Sc0000018:4564906-4564927(+) ## 94 Cluster_4754.mature::Pocillopora_meandrina_HIv1___Sc0000018:4564906-4564927(+) ## 95 Cluster_4754.mature::Pocillopora_meandrina_HIv1___Sc0000018:4564906-4564927(+) ## 96 Cluster_2793.mature::Pocillopora_meandrina_HIv1___Sc0000008:1783824-1783844(+) ## 97 Cluster_1793.mature::Pocillopora_meandrina_HIv1___Sc0000005:601626-601646(+) ## 98 Cluster_4118.mature::Pocillopora_meandrina_HIv1___Sc0000014:9365481-9365502(-) ## 99 Cluster_4118.mature::Pocillopora_meandrina_HIv1___Sc0000014:9365481-9365502(-) ## 100 Cluster_1080.mature::Pocillopora_meandrina_HIv1___Sc0000002:16106609-16106630(+) ## 101 Cluster_2793.mature::Pocillopora_meandrina_HIv1___Sc0000008:1783824-1783844(+) ## 102 Cluster_2793.mature::Pocillopora_meandrina_HIv1___Sc0000008:1783824-1783844(+) ## 103 Cluster_4437.mature::Pocillopora_meandrina_HIv1___Sc0000016:7550615-7550635(+) ## 104 Cluster_2837.mature::Pocillopora_meandrina_HIv1___Sc0000008:3576442-3576463(+) ## 105 Cluster_2837.mature::Pocillopora_meandrina_HIv1___Sc0000008:3576442-3576463(+) ## 106 Cluster_2839.mature::Pocillopora_meandrina_HIv1___Sc0000008:3619363-3619384(-) ## 107 Cluster_2859.mature::Pocillopora_meandrina_HIv1___Sc0000008:5387760-5387781(-) ## 108 Cluster_2859.mature::Pocillopora_meandrina_HIv1___Sc0000008:5387760-5387781(-) ## 109 Cluster_2859.mature::Pocillopora_meandrina_HIv1___Sc0000008:5387760-5387781(-) ## 110 Cluster_4118.mature::Pocillopora_meandrina_HIv1___Sc0000014:9365481-9365502(-) ## 111 Cluster_2859.mature::Pocillopora_meandrina_HIv1___Sc0000008:5387760-5387781(-) ## 112 Cluster_3392.mature::Pocillopora_meandrina_HIv1___Sc0000010:8012938-8012959(+) ## 113 Cluster_3392.mature::Pocillopora_meandrina_HIv1___Sc0000010:8012938-8012959(+) ## 114 Cluster_3392.mature::Pocillopora_meandrina_HIv1___Sc0000010:8012938-8012959(+) ## 115 Cluster_6382.mature::Pocillopora_meandrina_HIv1___Sc0000035:1989842-1989863(+) ## 116 Cluster_3392.mature::Pocillopora_meandrina_HIv1___Sc0000010:8012938-8012959(+) ## 117 Cluster_4439.mature::Pocillopora_meandrina_HIv1___Sc0000016:7555692-7555713(+) ## 118 Cluster_4439.mature::Pocillopora_meandrina_HIv1___Sc0000016:7555692-7555713(+) ## 119 Cluster_4439.mature::Pocillopora_meandrina_HIv1___Sc0000016:7555692-7555713(+) ## 120 Cluster_4439.mature::Pocillopora_meandrina_HIv1___Sc0000016:7555692-7555713(+) ## 121 Cluster_4439.mature::Pocillopora_meandrina_HIv1___Sc0000016:7555692-7555713(+) ## 122 Cluster_4439.mature::Pocillopora_meandrina_HIv1___Sc0000016:7555692-7555713(+) ## 123 Cluster_4754.mature::Pocillopora_meandrina_HIv1___Sc0000018:4564906-4564927(+) ## 124 Cluster_3392.mature::Pocillopora_meandrina_HIv1___Sc0000010:8012938-8012959(+) ## 125 Cluster_3392.mature::Pocillopora_meandrina_HIv1___Sc0000010:8012938-8012959(+) ## 126 Cluster_3392.mature::Pocillopora_meandrina_HIv1___Sc0000010:8012938-8012959(+) ## 127 Cluster_2973.mature::Pocillopora_meandrina_HIv1___Sc0000009:3894922-3894943(-) ## 128 Cluster_5612.mature::Pocillopora_meandrina_HIv1___Sc0000024:4808688-4808708(+) ## 129 Cluster_3392.mature::Pocillopora_meandrina_HIv1___Sc0000010:8012938-8012959(+) ## 130 Cluster_3392.mature::Pocillopora_meandrina_HIv1___Sc0000010:8012938-8012959(+) ## 131 Cluster_3392.mature::Pocillopora_meandrina_HIv1___Sc0000010:8012938-8012959(+) ## 132 Cluster_3392.mature::Pocillopora_meandrina_HIv1___Sc0000010:8012938-8012959(+) ## 133 Cluster_1938.mature::Pocillopora_meandrina_HIv1___Sc0000005:10385519-10385541(+) ## 135 Cluster_1938.mature::Pocillopora_meandrina_HIv1___Sc0000005:10385519-10385541(+) ## 136 Cluster_1938.mature::Pocillopora_meandrina_HIv1___Sc0000005:10385519-10385541(+) ## 137 Cluster_1938.mature::Pocillopora_meandrina_HIv1___Sc0000005:10385519-10385541(+) ## 138 Cluster_1938.mature::Pocillopora_meandrina_HIv1___Sc0000005:10385519-10385541(+) ## 139 Cluster_4118.mature::Pocillopora_meandrina_HIv1___Sc0000014:9365481-9365502(-) ## 140 Cluster_3661.mature::Pocillopora_meandrina_HIv1___Sc0000012:6455205-6455226(+) ## 141 Cluster_3661.mature::Pocillopora_meandrina_HIv1___Sc0000012:6455205-6455226(+) ## 142 Cluster_1793.mature::Pocillopora_meandrina_HIv1___Sc0000005:601626-601646(+) ## 143 Cluster_4823.mature::Pocillopora_meandrina_HIv1___Sc0000018:6855521-6855542(+) ## 144 Cluster_5612.mature::Pocillopora_meandrina_HIv1___Sc0000024:4808688-4808708(+) ## 145 Cluster_1793.mature::Pocillopora_meandrina_HIv1___Sc0000005:601626-601646(+) ## 146 Cluster_2839.mature::Pocillopora_meandrina_HIv1___Sc0000008:3619363-3619384(-) ## 147 Cluster_2839.mature::Pocillopora_meandrina_HIv1___Sc0000008:3619363-3619384(-) ## 148 Cluster_2839.mature::Pocillopora_meandrina_HIv1___Sc0000008:3619363-3619384(-) ## 149 Cluster_2859.mature::Pocillopora_meandrina_HIv1___Sc0000008:5387760-5387781(-) ## 150 Cluster_4040.mature::Pocillopora_meandrina_HIv1___Sc0000014:2594792-2594813(+) ## 151 Cluster_4040.mature::Pocillopora_meandrina_HIv1___Sc0000014:2594792-2594813(+) ## 152 Cluster_4118.mature::Pocillopora_meandrina_HIv1___Sc0000014:9365481-9365502(-) ## 153 Cluster_4754.mature::Pocillopora_meandrina_HIv1___Sc0000018:4564906-4564927(+) ## 154 Cluster_4754.mature::Pocillopora_meandrina_HIv1___Sc0000018:4564906-4564927(+) ## 155 Cluster_4754.mature::Pocillopora_meandrina_HIv1___Sc0000018:4564906-4564927(+) ## 156 Cluster_4439.mature::Pocillopora_meandrina_HIv1___Sc0000016:7555692-7555713(+) ## 157 Cluster_757.mature::Pocillopora_meandrina_HIv1___Sc0000001:19145788-19145809(+) ## 158 Cluster_4823.mature::Pocillopora_meandrina_HIv1___Sc0000018:6855521-6855542(+) ## 159 Cluster_4823.mature::Pocillopora_meandrina_HIv1___Sc0000018:6855521-6855542(+) ## 160 Cluster_4823.mature::Pocillopora_meandrina_HIv1___Sc0000018:6855521-6855542(+) ## 161 Cluster_4823.mature::Pocillopora_meandrina_HIv1___Sc0000018:6855521-6855542(+) ## 162 Cluster_4572.mature::Pocillopora_meandrina_HIv1___Sc0000017:5050959-5050980(-) ## 163 Cluster_5740.mature::Pocillopora_meandrina_HIv1___Sc0000026:1154772-1154793(-) ## 164 Cluster_2839.mature::Pocillopora_meandrina_HIv1___Sc0000008:3619363-3619384(-) ## 165 Cluster_2839.mature::Pocillopora_meandrina_HIv1___Sc0000008:3619363-3619384(-) ## 166 Cluster_4823.mature::Pocillopora_meandrina_HIv1___Sc0000018:6855521-6855542(+) ## 167 Cluster_4823.mature::Pocillopora_meandrina_HIv1___Sc0000018:6855521-6855542(+) ## 168 Cluster_4823.mature::Pocillopora_meandrina_HIv1___Sc0000018:6855521-6855542(+) ## 169 Cluster_4823.mature::Pocillopora_meandrina_HIv1___Sc0000018:6855521-6855542(+) ## 170 Cluster_3392.mature::Pocillopora_meandrina_HIv1___Sc0000010:8012938-8012959(+) ## 171 Cluster_6382.mature::Pocillopora_meandrina_HIv1___Sc0000035:1989842-1989863(+) ## 172 Cluster_21.mature::Pocillopora_meandrina_HIv1___Sc0000000:818049-818070(+) ## 173 Cluster_3392.mature::Pocillopora_meandrina_HIv1___Sc0000010:8012938-8012959(+) ## 174 Cluster_3392.mature::Pocillopora_meandrina_HIv1___Sc0000010:8012938-8012959(+) ## 175 Cluster_21.mature::Pocillopora_meandrina_HIv1___Sc0000000:818049-818070(+) ## 176 Cluster_4823.mature::Pocillopora_meandrina_HIv1___Sc0000018:6855521-6855542(+) ## 177 Cluster_5253.mature::Pocillopora_meandrina_HIv1___Sc0000021:4351839-4351860(+) ## 178 Cluster_5253.mature::Pocillopora_meandrina_HIv1___Sc0000021:4351839-4351860(+) ## 179 Cluster_5253.mature::Pocillopora_meandrina_HIv1___Sc0000021:4351839-4351860(+) ## 180 Cluster_5253.mature::Pocillopora_meandrina_HIv1___Sc0000021:4351839-4351860(+) ## 181 Cluster_2859.mature::Pocillopora_meandrina_HIv1___Sc0000008:5387760-5387781(-) ## 182 Cluster_6382.mature::Pocillopora_meandrina_HIv1___Sc0000035:1989842-1989863(+) ## 183 Cluster_6382.mature::Pocillopora_meandrina_HIv1___Sc0000035:1989842-1989863(+) ## 184 Cluster_4754.mature::Pocillopora_meandrina_HIv1___Sc0000018:4564906-4564927(+) ## 185 Cluster_4754.mature::Pocillopora_meandrina_HIv1___Sc0000018:4564906-4564927(+) ## 186 Cluster_5612.mature::Pocillopora_meandrina_HIv1___Sc0000024:4808688-4808708(+) ## 187 Cluster_5612.mature::Pocillopora_meandrina_HIv1___Sc0000024:4808688-4808708(+) ## 188 Cluster_5253.mature::Pocillopora_meandrina_HIv1___Sc0000021:4351839-4351860(+) ## 189 Cluster_5740.mature::Pocillopora_meandrina_HIv1___Sc0000026:1154772-1154793(-) ## 190 Cluster_6382.mature::Pocillopora_meandrina_HIv1___Sc0000035:1989842-1989863(+) ## 192 Cluster_2859.mature::Pocillopora_meandrina_HIv1___Sc0000008:5387760-5387781(-) ## 193 Cluster_757.mature::Pocillopora_meandrina_HIv1___Sc0000001:19145788-19145809(+) ## 194 Cluster_4754.mature::Pocillopora_meandrina_HIv1___Sc0000018:4564906-4564927(+) ## 195 Cluster_2839.mature::Pocillopora_meandrina_HIv1___Sc0000008:3619363-3619384(-) ## 196 Cluster_1793.mature::Pocillopora_meandrina_HIv1___Sc0000005:601626-601646(+) ## 197 Cluster_1793.mature::Pocillopora_meandrina_HIv1___Sc0000005:601626-601646(+) ## 198 Cluster_3661.mature::Pocillopora_meandrina_HIv1___Sc0000012:6455205-6455226(+) ## 199 Cluster_2839.mature::Pocillopora_meandrina_HIv1___Sc0000008:3619363-3619384(-) ## 200 Cluster_6382.mature::Pocillopora_meandrina_HIv1___Sc0000035:1989842-1989863(+) ## 201 Cluster_2793.mature::Pocillopora_meandrina_HIv1___Sc0000008:1783824-1783844(+) ## 202 Cluster_4118.mature::Pocillopora_meandrina_HIv1___Sc0000014:9365481-9365502(-) ## 203 Cluster_3392.mature::Pocillopora_meandrina_HIv1___Sc0000010:8012938-8012959(+) ## 204 Cluster_3392.mature::Pocillopora_meandrina_HIv1___Sc0000010:8012938-8012959(+) ## 205 Cluster_3392.mature::Pocillopora_meandrina_HIv1___Sc0000010:8012938-8012959(+) ## 206 Cluster_5253.mature::Pocillopora_meandrina_HIv1___Sc0000021:4351839-4351860(+) ## 207 Cluster_4118.mature::Pocillopora_meandrina_HIv1___Sc0000014:9365481-9365502(-) ## 208 Cluster_2793.mature::Pocillopora_meandrina_HIv1___Sc0000008:1783824-1783844(+) ## 209 Cluster_390.mature::Pocillopora_meandrina_HIv1___Sc0000001:1459455-1459476(+) ## 210 Cluster_1793.mature::Pocillopora_meandrina_HIv1___Sc0000005:601626-601646(+) ## 211 Cluster_390.mature::Pocillopora_meandrina_HIv1___Sc0000001:1459455-1459476(+) ## 212 Cluster_2839.mature::Pocillopora_meandrina_HIv1___Sc0000008:3619363-3619384(-) ## 213 Cluster_2839.mature::Pocillopora_meandrina_HIv1___Sc0000008:3619363-3619384(-) ## 214 Cluster_2839.mature::Pocillopora_meandrina_HIv1___Sc0000008:3619363-3619384(-) ## 215 Cluster_3392.mature::Pocillopora_meandrina_HIv1___Sc0000010:8012938-8012959(+) ## 216 Cluster_3392.mature::Pocillopora_meandrina_HIv1___Sc0000010:8012938-8012959(+) ## 217 Cluster_3392.mature::Pocillopora_meandrina_HIv1___Sc0000010:8012938-8012959(+) ## 218 Cluster_4118.mature::Pocillopora_meandrina_HIv1___Sc0000014:9365481-9365502(-) ## pident length mismatch gapopen qstart qend sstart send evalue bitscore ## 1 95.000 20 1 0 1606 1625 20 1 4.94e-04 32.8 ## 2 90.476 21 2 0 2794 2814 21 1 1.00e-03 30.1 ## 3 100.000 17 0 0 6096 6112 20 4 5.89e-04 31.9 ## 4 94.737 19 1 0 195 213 2 20 3.82e-04 31.0 ## 5 100.000 15 0 0 103 117 6 20 8.38e-04 28.3 ## 6 100.000 22 0 0 3141 3162 22 1 8.48e-07 41.0 ## 7 100.000 22 0 0 2873 2894 22 1 8.16e-07 41.0 ## 8 86.364 22 3 0 158 179 1 22 1.00e-03 27.4 ## 9 90.476 21 1 1 101 121 3 22 8.90e-04 26.5 ## 10 95.238 21 1 0 72355 72375 2 22 1.00e-03 34.6 ## 11 95.238 21 1 0 72351 72371 2 22 1.00e-03 34.6 ## 12 90.909 22 2 0 18795 18816 1 22 1.00e-03 31.9 ## 13 90.909 22 2 0 611 632 1 22 1.96e-04 31.9 ## 14 95.238 21 1 0 11097 11117 2 22 5.51e-04 34.6 ## 15 95.238 21 1 0 29755 29775 2 22 4.98e-04 34.6 ## 17 95.238 21 1 0 5353 5373 2 22 4.09e-04 34.6 ## 18 95.238 21 1 0 4774 4794 2 22 3.93e-04 34.6 ## 19 95.238 21 1 0 13596 13616 2 22 3.98e-04 34.6 ## 20 90.909 22 2 0 12464 12485 1 22 1.00e-03 31.9 ## 21 95.238 21 1 0 106 126 2 22 2.26e-04 34.6 ## 22 90.000 20 2 0 1109 1128 3 22 1.00e-03 28.3 ## 23 90.000 20 2 0 1096 1115 3 22 1.00e-03 28.3 ## 24 90.000 20 2 0 128 147 21 2 1.00e-03 28.3 ## 25 89.474 19 2 0 43 61 21 3 1.00e-03 26.5 ## 26 94.737 19 1 0 2711 2729 22 4 8.84e-04 31.0 ## 27 94.737 19 1 0 1704 1722 22 4 6.35e-04 31.0 ## 28 94.737 19 1 0 1586 1604 22 4 6.05e-04 31.0 ## 29 100.000 16 0 0 71 86 5 20 1.38e-04 30.1 ## 30 86.364 22 3 0 268 289 22 1 1.00e-03 27.4 ## 31 89.474 19 2 0 300 318 19 1 1.00e-03 26.5 ## 32 90.909 22 2 0 2932 2953 1 22 1.00e-03 31.9 ## 33 95.238 21 1 0 31607 31627 2 22 5.12e-04 34.6 ## 34 95.238 21 1 0 11123 11143 2 22 5.51e-04 34.6 ## 35 95.238 21 1 0 3176 3196 2 22 3.69e-04 34.6 ## 36 95.238 21 1 0 15433 15453 2 22 3.59e-04 34.6 ## 37 90.909 22 2 0 14301 14322 1 22 1.00e-03 31.9 ## 38 95.238 21 1 0 1682 1702 2 22 6.75e-05 34.6 ## 39 90.909 22 2 0 550 571 1 22 2.36e-04 31.9 ## 40 90.476 21 2 0 4943 4963 21 1 1.00e-03 30.1 ## 41 90.476 21 2 0 3814 3834 21 1 1.00e-03 30.1 ## 42 94.737 19 1 0 2487 2505 2 20 6.33e-04 31.0 ## 43 100.000 15 0 0 82 96 15 1 1.00e-03 28.3 ## 44 100.000 15 0 0 82 96 15 1 4.84e-04 28.3 ## 45 90.000 20 2 0 285 304 1 20 3.84e-04 28.3 ## 46 100.000 22 0 0 7663 7684 1 22 1.32e-06 41.0 ## 47 100.000 22 0 0 7640 7661 1 22 1.31e-06 41.0 ## 48 95.238 21 1 0 26385 26405 1 21 4.39e-04 34.6 ## 49 95.238 21 1 0 21898 21918 1 21 3.71e-04 34.6 ## 50 100.000 22 0 0 2520 2541 22 1 7.29e-07 41.0 ## 51 100.000 22 0 0 2520 2541 22 1 8.34e-07 41.0 ## 53 100.000 22 0 0 2514 2535 22 1 8.33e-07 41.0 ## 54 100.000 22 0 0 2495 2516 22 1 8.31e-07 41.0 ## 55 100.000 22 0 0 1832 1853 22 1 7.52e-07 41.0 ## 56 100.000 22 0 0 3740 3761 1 22 5.16e-07 41.0 ## 57 100.000 22 0 0 3286 3307 1 22 5.45e-07 41.0 ## 58 90.476 21 2 0 646 666 22 2 1.00e-03 30.1 ## 60 90.476 21 2 0 165 185 22 2 1.00e-03 30.1 ## 61 90.476 21 2 0 110 130 22 2 1.00e-03 30.1 ## 62 90.476 21 2 0 109 129 22 2 1.00e-03 30.1 ## 63 100.000 18 0 0 59344 59361 20 3 1.00e-03 33.7 ## 64 100.000 18 0 0 43756 43773 20 3 1.00e-03 33.7 ## 65 100.000 18 0 0 40977 40994 20 3 8.81e-04 33.7 ## 66 100.000 18 0 0 40943 40960 20 3 8.80e-04 33.7 ## 68 90.000 20 2 0 46 65 20 1 1.00e-03 28.3 ## 69 100.000 18 0 0 14602 14619 20 3 3.61e-04 33.7 ## 70 100.000 18 0 0 37880 37897 20 3 8.41e-04 33.7 ## 71 94.118 17 1 0 134 150 5 21 1.00e-03 27.4 ## 72 100.000 16 0 0 5886 5901 21 6 1.00e-03 30.1 ## 73 100.000 15 0 0 709 723 1 15 1.00e-03 28.3 ## 74 100.000 23 0 0 3779 3801 1 23 1.83e-07 42.8 ## 75 100.000 22 0 0 7153 7174 1 22 1.26e-06 41.0 ## 76 100.000 22 0 0 6557 6578 1 22 1.26e-06 41.0 ## 79 100.000 22 0 0 7144 7165 1 22 1.26e-06 41.0 ## 80 100.000 22 0 0 6548 6569 1 22 1.26e-06 41.0 ## 81 100.000 22 0 0 5767 5788 1 22 1.10e-06 41.0 ## 82 100.000 22 0 0 5171 5192 1 22 1.10e-06 41.0 ## 83 100.000 22 0 0 3372 3393 1 22 8.09e-07 41.0 ## 84 100.000 22 0 0 2776 2797 1 22 8.09e-07 41.0 ## 85 100.000 15 0 0 442 456 1 15 1.00e-03 28.3 ## 86 90.476 21 2 0 3469 3489 1 21 1.00e-03 30.1 ## 87 100.000 16 0 0 5591 5606 18 3 1.00e-03 30.1 ## 88 100.000 17 0 0 7492 7508 5 21 5.67e-04 31.9 ## 90 100.000 17 0 0 7410 7426 5 21 5.62e-04 31.9 ## 92 100.000 17 0 0 7409 7425 5 21 5.62e-04 31.9 ## 94 100.000 17 0 0 7319 7335 5 21 5.56e-04 31.9 ## 95 100.000 17 0 0 6618 6634 5 21 5.13e-04 31.9 ## 96 100.000 16 0 0 2054 2069 16 1 1.00e-03 30.1 ## 97 90.000 20 2 0 985 1004 2 21 1.00e-03 28.3 ## 98 100.000 17 0 0 5630 5646 6 22 3.66e-04 31.9 ## 99 100.000 17 0 0 5624 5640 6 22 3.65e-04 31.9 ## 100 89.474 19 2 0 97 115 22 4 1.00e-03 26.5 ## 101 100.000 21 0 0 2971 2991 1 21 2.17e-06 39.2 ## 102 100.000 21 0 0 580 600 1 21 1.16e-06 39.2 ## 103 100.000 15 0 0 1071 1085 1 15 1.00e-03 28.3 ## 104 100.000 22 0 0 11114 11135 1 22 2.19e-06 41.0 ## 105 100.000 22 0 0 10992 11013 1 22 2.18e-06 41.0 ## 106 100.000 22 0 0 4836 4857 22 1 8.50e-07 41.0 ## 107 100.000 22 0 0 6198 6219 22 1 9.65e-07 41.0 ## 108 100.000 22 0 0 5592 5613 22 1 8.92e-07 41.0 ## 109 100.000 22 0 0 5191 5212 22 1 8.44e-07 41.0 ## 110 100.000 16 0 0 982 997 22 7 7.00e-04 30.1 ## 111 100.000 14 0 0 170 183 4 17 1.00e-03 26.5 ## 112 90.909 22 2 0 14178 14199 1 22 1.00e-03 31.9 ## 113 95.455 22 1 0 23095 23116 1 22 1.05e-04 36.5 ## 114 90.909 22 2 0 13691 13712 1 22 8.78e-04 31.9 ## 115 90.476 21 2 0 328 348 2 22 3.14e-04 30.1 ## 116 95.455 22 1 0 661 682 1 22 6.54e-06 36.5 ## 117 90.476 21 2 0 1027 1047 2 22 2.99e-04 30.1 ## 118 90.476 21 2 0 4459 4479 2 22 1.00e-03 30.1 ## 119 90.476 21 2 0 5282 5302 2 22 1.00e-03 30.1 ## 120 90.476 21 2 0 34 54 2 22 1.00e-03 30.1 ## 121 90.476 21 2 0 2598 2618 2 22 7.39e-04 30.1 ## 122 90.476 21 2 0 106 126 2 22 2.03e-04 30.1 ## 123 100.000 15 0 0 366 380 19 5 1.00e-03 28.3 ## 124 100.000 22 0 0 4399 4420 1 22 7.61e-07 41.0 ## 125 100.000 22 0 0 2337 2358 1 22 4.78e-07 41.0 ## 126 95.238 21 1 0 1583 1603 22 2 4.89e-05 34.6 ## 127 100.000 15 0 0 82 96 15 1 4.58e-04 28.3 ## 128 94.444 18 1 0 481 498 20 3 1.00e-03 29.2 ## 129 95.238 21 1 0 2425 2445 22 2 7.18e-05 34.6 ## 130 100.000 22 0 0 4173 4194 1 22 6.95e-07 41.0 ## 131 100.000 22 0 0 3899 3920 1 22 6.57e-07 41.0 ## 132 100.000 22 0 0 3749 3770 1 22 6.37e-07 41.0 ## 133 95.238 21 1 0 10411 10431 3 23 2.36e-04 34.6 ## 135 95.238 21 1 0 10396 10416 3 23 2.36e-04 34.6 ## 136 95.238 21 1 0 10266 10286 3 23 2.34e-04 34.6 ## 137 95.238 21 1 0 926 946 3 23 1.07e-04 34.6 ## 138 95.238 21 1 0 882 902 3 23 1.07e-04 34.6 ## 139 90.000 20 2 0 29 48 3 22 1.00e-03 28.3 ## 140 100.000 22 0 0 42369 42390 1 22 3.68e-06 41.0 ## 141 100.000 22 0 0 2157 2178 1 22 3.89e-07 41.0 ## 142 100.000 16 0 0 246 261 2 17 5.38e-04 30.1 ## 143 89.474 19 2 0 62 80 22 4 1.00e-03 26.5 ## 144 100.000 14 0 0 72 85 14 1 1.00e-03 26.5 ## 145 94.737 19 1 0 3069 3087 1 19 1.00e-03 31.0 ## 146 94.737 19 1 0 281 299 1 19 8.05e-04 31.0 ## 147 94.737 19 1 0 1469 1487 19 1 5.82e-04 31.0 ## 148 90.909 22 1 1 779 800 21 1 1.00e-03 28.3 ## 149 100.000 15 0 0 435 449 3 17 1.00e-03 28.3 ## 150 100.000 22 0 0 4571 4592 1 22 1.44e-06 41.0 ## 151 100.000 22 0 0 1725 1746 1 22 1.10e-06 41.0 ## 152 100.000 22 0 0 5922 5943 22 1 9.96e-07 41.0 ## 153 95.000 20 1 0 5435 5454 1 20 1.00e-03 32.8 ## 154 95.000 20 1 0 5434 5453 1 20 1.00e-03 32.8 ## 155 95.000 20 1 0 5362 5381 1 20 1.00e-03 32.8 ## 156 95.455 22 1 0 678 699 1 22 1.83e-05 36.5 ## 157 100.000 15 0 0 846 860 2 16 1.00e-03 28.3 ## 158 95.238 21 1 0 26191 26211 21 1 5.05e-04 34.6 ## 159 95.238 21 1 0 26191 26211 21 1 5.34e-04 34.6 ## 160 95.238 21 1 0 26048 26068 21 1 5.03e-04 34.6 ## 161 95.238 21 1 0 25183 25203 21 1 4.84e-04 34.6 ## 162 100.000 22 0 0 10299 10320 22 1 2.05e-06 41.0 ## 163 89.474 19 2 0 143 161 1 19 1.00e-03 26.5 ## 164 94.444 18 1 0 1092 1109 5 22 1.00e-03 29.2 ## 165 94.444 18 1 0 1039 1056 5 22 1.00e-03 29.2 ## 166 100.000 22 0 0 9654 9675 1 22 1.85e-06 41.0 ## 167 100.000 22 0 0 9591 9612 1 22 1.85e-06 41.0 ## 168 100.000 22 0 0 3843 3864 1 22 1.47e-06 41.0 ## 169 100.000 22 0 0 2567 2588 1 22 1.32e-06 41.0 ## 170 100.000 16 0 0 4802 4817 6 21 1.00e-03 30.1 ## 171 89.474 19 2 0 153 171 22 4 1.00e-03 26.5 ## 172 100.000 19 0 0 127 145 19 1 2.96e-06 35.6 ## 173 90.909 22 2 0 95 116 22 1 3.61e-05 31.9 ## 174 90.909 22 2 0 1352 1373 22 1 1.58e-04 31.9 ## 175 100.000 16 0 0 1384 1399 19 4 5.51e-04 30.1 ## 176 100.000 16 0 0 214 229 17 2 5.63e-04 30.1 ## 177 100.000 22 0 0 7902 7923 1 22 1.56e-06 41.0 ## 178 100.000 22 0 0 7894 7915 1 22 1.56e-06 41.0 ## 179 100.000 22 0 0 5368 5389 1 22 1.52e-06 41.0 ## 180 100.000 22 0 0 4871 4892 1 22 1.46e-06 41.0 ## 181 95.238 21 0 1 5103 5122 2 22 1.00e-03 31.0 ## 182 100.000 17 0 0 4642 4658 5 21 1.00e-03 31.9 ## 183 100.000 16 0 0 3365 3380 4 19 1.00e-03 30.1 ## 184 100.000 17 0 0 13123 13139 21 5 1.00e-03 31.9 ## 185 100.000 17 0 0 11702 11718 21 5 1.00e-03 31.9 ## 186 100.000 21 0 0 11436 11456 1 21 6.64e-06 39.2 ## 187 100.000 21 0 0 10835 10855 1 21 6.43e-06 39.2 ## 188 94.444 18 1 0 40 57 2 19 4.64e-04 29.2 ## 189 100.000 22 0 0 3888 3909 22 1 1.30e-06 41.0 ## 190 95.238 21 1 0 66 86 22 2 4.71e-05 34.6 ## 192 100.000 16 0 0 122 137 5 20 2.31e-04 30.1 ## 193 100.000 17 0 0 6063 6079 6 22 8.54e-04 31.9 ## 194 100.000 16 0 0 19 34 18 3 6.05e-04 30.1 ## 195 89.474 19 2 0 27 45 19 1 1.00e-03 26.5 ## 196 100.000 17 0 0 2513 2529 1 17 6.25e-04 31.9 ## 197 100.000 17 0 0 915 931 1 17 5.26e-04 31.9 ## 198 94.737 19 1 0 3588 3606 4 22 1.00e-03 31.0 ## 199 94.118 17 1 0 243 259 20 4 1.00e-03 27.4 ## 200 95.000 20 1 0 2474 2493 21 2 5.07e-04 32.8 ## 201 94.737 19 1 0 249 267 2 20 4.25e-04 31.0 ## 202 100.000 15 0 0 83 97 6 20 2.80e-04 28.3 ## 203 95.455 22 1 0 15552 15573 1 22 8.32e-05 36.5 ## 204 95.455 22 1 0 50976 50997 1 22 1.86e-04 36.5 ## 205 95.455 22 1 0 36945 36966 1 22 1.63e-04 36.5 ## 206 94.737 19 1 0 41 59 21 3 9.12e-05 31.0 ## 207 100.000 15 0 0 194 208 6 20 1.00e-03 28.3 ## 208 100.000 17 0 0 2278 2294 1 17 2.48e-04 31.9 ## 209 100.000 14 0 0 308 321 15 2 1.00e-03 26.5 ## 210 94.737 19 1 0 4 22 1 19 1.22e-04 31.0 ## 211 89.474 19 2 0 4 22 1 19 1.00e-03 26.5 ## 212 94.737 19 1 0 383 401 1 19 7.72e-04 31.0 ## 213 94.737 19 1 0 353 371 1 19 5.32e-04 31.0 ## 214 94.737 19 1 0 321 339 1 19 5.23e-04 31.0 ## 215 90.909 22 2 0 25202 25223 1 22 1.00e-03 31.9 ## 216 90.909 22 2 0 23694 23715 1 22 1.00e-03 31.9 ## 217 95.455 22 1 0 361 382 1 22 3.73e-06 36.5 ## 218 90.000 20 2 0 29 48 3 22 1.00e-03 28.3 207 putative lncRNA sponges with these parameters. Ultimately though these results are insufficient to determine lncRNA sponging. We need to evaluate miRNA-lncRNA binding. # 4 miRanda miRanda is a target prediction software, used to identify likely miRNA-mRNA interactions. Inputs: - FASTA of A.pulchra lncRNAs - FASTA of A.pulchra mature miRNAs ## 4.1 Run miRanda ``` bash # score cutoff >100 # energy cutoff <-20 # strict binding /home/shared/miRanda-3.3a/src/miranda \ ../output/14-Ptuh-miRNA-lncRNA-BLASTs-miRanda/Ptuh_ShortStack_4.1.0_mature.fasta \ ../output/14-Ptuh-miRNA-lncRNA-BLASTs-miRanda/Ptuh_lncRNA.fasta \ -sc 100 \ -en -20 \ -strict \ -out ../output/14-Ptuh-miRNA-lncRNA-BLASTs-miRanda/Ptuh-miRanda-lncRNA-strict_all.tab ``` # 5 Summarize results Let’s look at the output ``` bash echo "miranda run finished!" echo "Counting number of interacting miRNA-lncRNA pairs" zgrep -c "Performing Scan" ../output/14-Ptuh-miRNA-lncRNA-BLASTs-miRanda/Ptuh-miRanda-lncRNA-strict_all.tab echo "Parsing output" grep -A 1 "Scores for this hit:" ../output/14-Ptuh-miRNA-lncRNA-BLASTs-miRanda/Ptuh-miRanda-lncRNA-strict_all.tab | sort | grep '>' > ../output/14-Ptuh-miRNA-lncRNA-BLASTs-miRanda/Ptuh-miRanda-lncRNA-strict-parsed.txt echo "counting number of putative interactions predicted (can include multiple interactions between single miRNA-lncRNA pair)" wc -l ../output/14-Ptuh-miRNA-lncRNA-BLASTs-miRanda/Ptuh-miRanda-lncRNA-strict_all.tab ``` ## miranda run finished! ## Counting number of interacting miRNA-lncRNA pairs ## 2088465 ## Parsing output ## counting number of putative interactions predicted (can include multiple interactions between single miRNA-lncRNA pair) ## 17400791 ../output/14-Ptuh-miRNA-lncRNA-BLASTs-miRanda/Ptuh-miRanda-lncRNA-strict_all.tab This is a lot of putative interactions! We can probably narrow it down though. In vertebrates, miRNA-mRNA binding only requires complementarity of an miRNA seed region of \~8 nucleotides. This requirement is built in to miRanda target prediction. In cnidarians, however, miRNA-mRNA binding is believed to require near-complete complementarity of the full mature miRNA, similarly to plants ( Admoni et al. ([2023](#ref-admoni_target_2023)) , Admoni et al. ([2025](#ref-admoni_mirna-target_2025)) ). While I couldn’t find any information on expected requirements for miRNA-lncRNA sponges, its possible the binding will function similarly to miRNA-mRNA binding. Let’s look at how many putative interactions are predicted for a binding length of at least 21 nucleotides (the length of our smallest mature miRNA). ``` bash echo "number of putative interactions of at least 21 nucleotides" awk -F'\t' '$7 >= 21' ../output/14-Ptuh-miRNA-lncRNA-BLASTs-miRanda/Ptuh-miRanda-lncRNA-strict-parsed.txt | wc -l echo "" echo "check some:" awk -F'\t' '$7 >= 21' ../output/14-Ptuh-miRNA-lncRNA-BLASTs-miRanda/Ptuh-miRanda-lncRNA-strict-parsed.txt | head -5 ``` ## number of putative interactions of at least 21 nucleotides ## 11992 ## ## check some: ## >Cluster_1015.mature::Pocillopora_meandrina_HIv1___Sc0000002:10845744-10845765(-) transcript::Pocillopora_meandrina_HIv1___Sc0000000:12879605-12913594 149.00 -20.34 2 21 14424 14450 24 70.83% 70.83% ## >Cluster_1015.mature::Pocillopora_meandrina_HIv1___Sc0000002:10845744-10845765(-) transcript::Pocillopora_meandrina_HIv1___Sc0000000:12883388-12903706 149.00 -20.34 2 21 10641 10667 24 70.83% 70.83% ## >Cluster_1015.mature::Pocillopora_meandrina_HIv1___Sc0000002:10845744-10845765(-) transcript::Pocillopora_meandrina_HIv1___Sc0000000:12889831-12913594 149.00 -20.34 2 21 4198 4224 24 70.83% 70.83% ## >Cluster_1015.mature::Pocillopora_meandrina_HIv1___Sc0000002:10845744-10845765(-) transcript::Pocillopora_meandrina_HIv1___Sc0000000:13480158-13493628 145.00 -21.67 2 20 13018 13042 21 61.90% 76.19% ## >Cluster_1015.mature::Pocillopora_meandrina_HIv1___Sc0000002:10845744-10845765(-) transcript::Pocillopora_meandrina_HIv1___Sc0000000:13585121-13601084 145.00 -21.67 2 20 15372 15396 21 61.90% 76.19% The header for this output is formatted as: mirna Target Score Energy-Kcal/Mol Query-Aln(start-end) Subject-Al(Start-End) Al-Len Subject-Identity Query-Identity We can see from the percent identities (last 2 entries) that this number includes alignments with multiple mismatches. Let’s filter again to reduce the number of permissible mismatches. Let’s say we want no more than 3 mismatches (a gap is counted as a mismatch). For an alignment of 21 nucleotides, this would be an percent identity of (21-3)/21 = 85.7%. The miRNA is our “subject”, so we will filter by column 8. ``` bash echo "number of putative interactions of at least 21 nucleotides, with at most 3 mismatches" awk -F'\t' '$7 >= 21' ../output/14-Ptuh-miRNA-lncRNA-BLASTs-miRanda/Ptuh-miRanda-lncRNA-strict-parsed.txt | awk -F'\t' '$8 >= 85' | wc -l echo "" echo "check some:" awk -F'\t' '$7 >= 21' ../output/14-Ptuh-miRNA-lncRNA-BLASTs-miRanda/Ptuh-miRanda-lncRNA-strict-parsed.txt | awk -F'\t' '$8 >= 85' | head -5 ``` ## number of putative interactions of at least 21 nucleotides, with at most 3 mismatches ## 115 ## ## check some: ## >Cluster_1116.mature::Pocillopora_meandrina_HIv1___Sc0000003:495117-495138(+) transcript::Pocillopora_meandrina_HIv1___Sc0000002:19443263-19445715 183.00 -32.26 2 21 424 447 21 85.71% 90.48% ## >Cluster_1116.mature::Pocillopora_meandrina_HIv1___Sc0000003:495117-495138(+) transcript::Pocillopora_meandrina_HIv1___Sc0000002:19443289-19445715 183.00 -32.26 2 21 398 421 21 85.71% 90.48% ## >Cluster_1116.mature::Pocillopora_meandrina_HIv1___Sc0000003:495117-495138(+) transcript::Pocillopora_meandrina_HIv1___Sc0000016:8887476-8889667 168.00 -20.58 2 20 757 781 21 85.71% 85.71% ## >Cluster_1116.mature::Pocillopora_meandrina_HIv1___Sc0000003:495117-495138(+) transcript::Pocillopora_meandrina_HIv1___Sc0000029:1950203-1961939 174.00 -21.65 2 21 9437 9460 21 85.71% 85.71% ## >Cluster_1116.mature::Pocillopora_meandrina_HIv1___Sc0000003:495117-495138(+) transcript::Pocillopora_meandrina_HIv1___Sc0000029:1950754-1962391 174.00 -21.65 2 21 8886 8909 21 85.71% 85.71% This is a dramatically smaller number – only interactions are at least 115 nucleotides with \<=3 mismatches
Admoni, Yael, Arie Fridrich, Talya Razin, Miguel Salinas-Saavedra, Michal Rabani, Uri Frank, and Yehu Moran. 2023. “Target Complementarity in Cnidarians Supports a Common Origin for Animal and Plant microRNAs.” bioRxiv. .
Admoni, Yael, Arie Fridrich, Paris K Weavers, Reuven Aharoni, Talya Razin, Miguel Salinas-Saavedra, Michal Rabani, Uri Frank, and Yehu Moran. 2025. “miRNA-Target Complementarity in Cnidarians Resembles Its Counterpart in Plants.” *EMBO Reports*, January, 1–24. .
Moran, Yehu, David Fredman, Daniela Praher, Xin Li, Liang Wee, Fabian Rentzsch, Phillip Zamore, Ulrich Technau, and Hervé Seitz. 2014. “Cnidarian microRNAs Frequently Regulate Targets by Cleavage.” *Genome Research* 24 (March). .