Sequence
atgc intronic sequence ATGC exonic sequencegtattttataatcaagcaaactctattgtgaaattaatatagccataaatctctctaagatttgtatgtgatttatgattgtcttgtgttaaccaaccttcagtctcaaatacttgaagcccttggggcaactgttgaaagAGTGAGACCGGTGTCCATTACCCACAAAGACCATTTTGTCAAATCGCAAGAAGACGGGCATCTGAAGCAAATGAGTTTGCATTGAAGCGTACAAATTCAC
Basic information
species | Glycine max |
transcript | GLYMA02G46950.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G46950.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G128744_T01 (Zea mays), 3'ss of exon 1
gtattttataatcaagcaaactctattgtgaaattaatatagccataaatctctctaagatttgtatgtgatttatg--attgtcttgtgttaac-caaccttcagtctcaaatacttgaagcccttggggcaactgttgaaagAGTGAGACCGGTGTCCATTACCCACAAAGACCATTTTGTCAA-ATCGCAAGAAGACGGGCATCTGAAGCAAATGAGTTTGCATTGAAGCGTACAAATTCAC
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-----gttccatttaatgtattcaacttagcagccagaact-ccttttgtctgtctgttgcctttctcctgtatatgcaatttacttgaaataatattgtttccagTCTCAAATAATTGAGGCGCTTGGAGCTACTGTTGAACGAGTGCGCCCTGTTTCAATAACTCACAGAGACCATTTTGTCAACATTGCCAGAAGAAGGGCTT---------------------------------------
upper sequence: GLYMA02G46950.1 (Glycine max), 3'ss of exon 5
lower sequence: AT1G55880.1 (Arabidopsis thaliana), 3'ss of exon 3
gtattttataatcaagcaaactctattgtgaaattaatatagccataaatctctctaagatttgtatgtg-atttatgattgtcttgtgttaaccaaccttcagtctcaaatacttgaagcccttggggcaactgttgaaagAGTGAGACCGGTGTCCATTACCCACAAAGACCATTTTGTCAA-ATCGCAAGAAGACGGGCATCTGAAGCAAATGAGTTTGCATTGAAGCGTACAAATTCAC
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--gttatatcttttaaataccttgatgatga--ttcaaattcccttgtatgcatt-----attgtacatacactcaaatttgtatcgtgttggacttattttagTCTCAAATAATTGAAGCCCTTGGAGCTTCTGTTGAGAGAGTGAGGCCAGTGTCAATAACTCACAAGGATCACTATGTCAACATTGCGAGGCGACGGGCTG---------------------------------------
upper sequence: GLYMA02G46950.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv19s0015g00380.t01 (Vitis vinifera), 3'ss of exon 4
-gtattttataatcaagcaaactctattgtgaaattaatatagccataaatctctctaagatttgtatgtgatttatgattgtcttgt-gttaaccaaccttcagtctcaaatacttgaagcccttggggcaactgttgaaagAGTGAGACCGGTGTCCATTACCCACAAAGACCATTTTGTCAA-ATCGCAAGAAGACGGGCATCTGAAGCAAATGAGTTTGCATTGAAGCGTACAAATTCAC
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ggtactcttaaggttttttg--tttccttttaatttcccacttttctttatttattta---tttttatttcatttaaaaaaaaattcttgtgcaacttttctcagTCTCAAATTCTCGAAGCCCTTGGAGCTACAGTTGAAAGAGTTAGACCAGTTTCAATTACACATAAAGACCACTATGTCAATGTTGCAAGGAGAAGAGCTT--------------------------------------- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgttaaccaaccttcagtctcaaatacttgaagcccttggggcaactgttgaaagAGTGAGACCGGTGTCCATTACCCACAAAGACCATTTTGTCAAATCGCAAGAAGACGGGCATCTGAAGCAAATGAGTTTGCATTGAAGCGTACAAATTCAC
tgttaac putative branch site (score: 2)
aaatactt TA-rich tract
Putative cis-regulatory sequences
atgc | intron | ATGC | exonic elements by Pertea et al. |
ATGC | exon | atgc | putative intronic elements |
| | ATGC | putative exonic elements identified for retained introns |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtattttataatcaagcaaactctattgtgaaattaatatagccataaatctctctaagatttgtatgtgatttatgattgtcttgtgttaaccaaccttcagtctcaaatacttgaagcccttggggcaactgttgaaagAGTGAGACCGGTGTCCATTACCCACAAAGACCATTTTGTCAAATCGCAAGAAGACGGGCATCTGAAGCAAATGAGTTTGCATTGAAGCGTACAAATTCAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC