Sequence
atgc intronic sequence ATGC exonic sequencegttggttgttctcagttctcattagcataaattaattcatgggaaacttttgctctttatcttttatttttaattgaagagtagtagatgttgataattttctttctgaattgactttggtgctatatgccttcagACTGTTCAGACAACTGTAATAAAGAGTAATTTGAATCCAGTCTGGAATGAGGAACTTATGCTGTCTGTTCCTCAGCAATTTGGAATATTGAATTTG
Basic information
species | Glycine max |
transcript | GLYMA05G29940.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA05G29940.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G138349_T02 (Zea mays), 3'ss of exon 6
gttggttgttctcagttctcattagcataaattaattcatgggaaacttttgctctttatcttttatttttaattgaagagtagtagatgttgataattttctttctgaattgactttggtgctatatgccttcagACTGTTCAGACAACTGTAATAAAGAGTAATTTGAATCCAGTCTGGAATGAGGAACTTATGCTGTCTGTTCCTCAGCAATTTGGAATATTGAATTTG----
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-------------------------------------------------gtaattttggtcgttttgttagaatcacaacaaaataaacat--atactttgttatcaaattacagcgccctcttgt-tgattgcagAAAGCACAAACTTCAGTAATCAATGGCAACCTGAATCCTGTCTGGAATGAAGAACTGAAGCTCTCTGTTCCCCAGCAATATGGACCTCTGAAGCTGGTAA
upper sequence: GLYMA05G29940.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G138349_T04 (Zea mays), 3'ss of exon 3
gttggttgttctcagttctcattagcataaattaattcatgggaaacttttgctctttatcttttatttttaattgaagagtagtagatgttgataattttctttctgaattgactttggtgctatatgccttcagACTGTTCAGACAACTGTAATAAAGAGTAATTTGAATCCAGTCTGGAATGAGGAACTTATGCTGTCTGTTCCTCAGCAATTTGGAATATTGAATTTG
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-------------------------------------------------gtaattttggtcgttttgttagaatcacaacaaaataaacat--atactttgttatcaaattacagcgccctcttgt-tgattgcagAAAGCACAAACTTCAGTAATCAATGGCAACCTGAATCCTGTCTGGAATGAAGAACTGAAGCTCTCTGTTCCCCAGCAATATGGACCTCTGAAGCTG
upper sequence: GLYMA05G29940.1 (Glycine max), 3'ss of exon 5
lower sequence: AT4G21160.4 (Arabidopsis thaliana), 3'ss of exon 6
gttggttgttctcagttctcattagcataaattaattcatgggaaacttttgctctttatcttttatttttaattgaagagtagtagatgttgataattttctttctgaattgactttggtgctatatgccttcagACTGTTCAGACAACTGTAATAAAGAGTAATTTGAATCCAGTCTGGAATGAGGAACTTATGCTGTCTGTTCCTCAGCAATTTGGAATATTGAATTTG
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-----------gtaattatagtgaatacttttgaaatcttgaaaggtttt--ctctttatatgttcttaccattgtttaagtgatcattattgtcatctctttttctga-tcgttatcatcgttttac-----cagAAGGCTCAATCTACTGTAGTGAAGAGCAACTTAAACCCTGTCTGGAATGAGGAACTCATGCTCTCTGTTCCTCATAACTATGGCTCAGTGAAATTG
upper sequence: GLYMA05G29940.1 (Glycine max), 3'ss of exon 5
lower sequence: AT4G05330.1 (Arabidopsis thaliana), 3'ss of exon 7
gttggttgttctcagttctcattagcataaattaattcatgggaaacttttgctctttatcttttatttttaattgaagagtagtagatgttgataattttctttctgaattgactttggtgctatatgccttcagACTGTTCAGACAACTGTAATAAAGAGTAATTTGAATCCAGTCTGGAATGAGGAACTTATGCTGTCTGTTCCTCAGCAATTTGGAATATTGAATTTG
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----------------------------------------gtaagtgatttgctttgcatctttt--tattagctt-----tacttcttgttgatgctgtgaatcttgagtaaaatt----gtcttgtttattcagAAACTTCAGACAACTGTTATGAATAGTAATTTGAACCCGGTATGGAATCAAGAACTCATGCTGTCTGTTCCTGAGAGCTATGGCCCTGTGAAATTG
upper sequence: GLYMA05G29940.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv10s0003g04900.t01 (Vitis vinifera), 3'ss of exon 7
gttggttgttctcagttctcattagcataaattaattcatgggaaacttttgctctttatcttttatttttaattgaagagtagtagatgttgataattttctttctga--attgactttggtgctatatgccttcagACTGTTCAGACAACTGTAATAAAGAGTAATTTGAATCCAGTCTGGAATGAGGAACTTATGCTGTCTGTTCCTCAGCAATTTGGAATATTGAATTTG
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-------------------------------------cattgtctagattagat-tttagtcaaagtggtgaattgcttttagttagacagtgatcattcttttactgataatgaagattggctgttgctgttactagACTGTCCAGACACAGGTAATAACGAGCAACTTGAATCCAGTCTGGAATGAGGAACTCATGCTTTCTGTGCCCATGGATTATGGGCCCATAAAAGTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tagtagatgttgataattttctttctgaattgactttggtgctatatgccttcagACTGTTCAGACAACTGTAATAAAGAGTAATTTGAATCCAGTCTGGAATGAGGAACTTATGCTGTCTGTTCCTCAGCAATTTGGAATATTGAATTTG
aattgac putative branch site (score: 3)
tgccttc putative PPT
ttgataattttcttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttggttgttctcagttctcattagcataaattaattcatgggaaacttttgctctttatcttttatttttaattgaagagtagtagatgttgataattttctttctgaattgactttggtgctatatgccttcagACTGTTCAGACAACTGTAATAAAGAGTAATTTGAATCCAGTCTGGAATGAGGAACTTATGCTGTCTGTTCCTCAGCAATTTGGAATATTGAATTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG