Sequence
atgc intronic sequence ATGC exonic sequence...cccatagaatgtgctatccccatagtattaagtattcaacttcccatgacttttaaaagaaaaataatttatgcttgtgttgcatttcaatcttttacagCATTGCTGTTTACAAGGCACTATACAAAAGCTTTGGAGGATTTGCTGCAGATGTTGTTGCAGCTATTGACCAG
Basic information
species | Glycine max |
transcript | GLYMA09G09850.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G09850.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os01g56320.1 (Oryza sativa), 3'ss of exon 4
cccatagaatgtgctatccccatagtattaagtattcaacttcccatgacttttaaaagaaaaataatttatgcttgtgttgcatttcaatcttttacagCATTGCTGTTTACAAGGCACTATACAAAAGCTTTGGAGGATTTGCTGCAGATGTTGTTGCAGCTATTGACCAG
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---------------------gtaagtccattacctttttctgcggagacatataagatccactttattcccaaatgt-taatgacaaattaatttccagCATTGCTGTCTATAAAGCTCTGTACAAAAGCTTTGGAGGGTTTGCTGCTGATGTAGTAGCTGCAATAGATCAG
upper sequence: GLYMA09G09850.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G052365_T01 (Zea mays), 3'ss of exon 3
cccatagaatgtgctatccccatagtattaagtattcaacttcccatgacttttaaaagaaaaataatttatgcttgtgttgcatttcaatcttttacagCATTGCTGTTTACAAGGCACTATACAAAAGCTTTGGAGGATTTGCTGCAGATGTTGTTGCAGCTATTGACCAG
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-----gtaagatcatttccctctgctgttaggaaggtagctatg-attatttcccaaattaatataataaattattaaattgt---------ttcttcagCATTGCTGTCTATAAAGCTCTTTACAAAAGCTTTGGTGGTTTTGCTGCTGATGTTGTGGCTGCAATAGATCAG
upper sequence: GLYMA09G09850.1 (Glycine max), 3'ss of exon 4
lower sequence: AT4G20430.2 (Arabidopsis thaliana), 3'ss of exon 4
cccatagaatgtgctatccccatag-tattaagtattcaacttcccatgacttttaaaagaaaaataatttatgcttgtgttgcatttcaatcttttacagCATTGCTGTTTACAAGGCACTATACAAAAGCTTTGGAGGATTTGCTGCAGATGTTGTTGCAGCTATTGACCAG
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-------------gtaagtaaatagacattagccagatatcatctttttatcattcatattgcattgagt-gtactaatgacattttttataatgtaccagTATTTCTGTTTACAAGGCATTGTATAAGAGTTTTGGGGGATTTGCTGCAGATGTTGTTGCTGCTATAGACCAG
upper sequence: GLYMA09G09850.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G44530.1 (Arabidopsis thaliana), 3'ss of exon 4
cccatagaatgtgctatccccatagtattaagtattcaacttcccatgacttttaaaagaaaaataatttatgcttgtgttgcatttcaatctt--ttacagCATTGCTGTTTACAAGGCACTATACAAAAGCTTTGGAGGATTTGCTGCAGATGTTGTTGCAGCTATTGACCAG
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---------------gtaagtaaaataataag-acttagatcaatgtcgaaatctatacaaaactaacttaaacttttat-gtttttgaactttgttttcagTATTTCTGTTTACAAGGCATTGTATAAGAGTTTTGGAGGTTTTGCTGCAGATGTTGTAGCAGCTATAGATCAG
upper sequence: GLYMA09G09850.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv10s0092g00170.t01 (Vitis vinifera), 3'ss of exon 4
cccatagaatgtgctatccccatagtattaa-gtattcaacttcccatgacttttaaaagaaaaataat-ttatgcttgtgttgcatttcaatcttttacagCATTGCTGTTTACAAGGCACTATACAAAAGCTTTGGAGGATTTGCTGCAGATGTTGTTGCAGCTATTGACCAG
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--taaagaaaaaaatatctgtctcatgtccatgtacccgttttataggcacatacattttttttctggcattaggcactaactatattctattcttttccagCATTGCTGTTTACAAGGCACTCTACAAAAGTTTCGGAGGCTTTGCTGCAGATGTTGTTGCTGCGATAGACCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atgacttttaaaagaaaaataatttatgcttgtgttgcatttcaatcttttacagCATTGCTGTTTACAAGGCACTATACAAAAGCTTTGGAGGATTTGCTGCAGATGTTGTTGCAGCTATTGACCAG
tcttttac CT-rich tract
ttttaaaagaaaaata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cccatagaatgtgctatccccatagtattaagtattcaacttcccatgacttttaaaagaaaaataatttatgcttgtgttgcatttcaatcttttacagCATTGCTGTTTACAAGGCACTATACAAAAGCTTTGGAGGATTTGCTGCAGATGTTGTTGCAGCTATTGACCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - gaatgtg
- - - - - - - - -ccccata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcttgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcatttc