Sequence
atgc intronic sequence ATGC exonic sequence...ggtaacagattcttgccttatcatatatgtggaaattaaatctcccccctgtaactttttcaatttattgtctttaacatgttgaaattcatattatcagGCTGCAGTACTGGCTATGGATGATTCAGTGTTAGATGTTGATCAGGTGGAAAATCTCATTAAATTTTGTCCTACCAAAGAGGAAATAGAGCTTTTAAAG
Basic information
species | Glycine max |
transcript | GLYMA06G21190.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G21190.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os04g17130.1 (Oryza sativa), 3'ss of exon 8
ggtaacagattcttgccttatcatatatgtggaaattaaatctcccccctgtaactttttcaatttattgtctttaacatgttgaaattca----tattatcagGCTGCAGTACTGGCTATGGATGATTCAGTGTTAGATGTTGATCAGGTGGAAAATCTCATTAAATTTTGTCCTACCAAAGAGGAAATAGAGCTTTTAAAG
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----gtggacatttactcaaaagttactcccattttttaaatggctaccggtaaggcttaaggtgcttcatccattctatatctactttctctacttgtaacagAGTGCTGCTCTAGCTTTGGATGATTCAGTTCTAGACGCTGATCAACTGGAAAATCTCATAAAATTTTGCCCAACAAAAGAGGAGATGGAACTTCTAAAG
upper sequence: GLYMA06G21190.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os07g40510.1 (Oryza sativa), 3'ss of exon 3
ggtaacagattcttgccttatcatatatgtggaaattaaatctcccccctgtaactttttcaatttattgtctttaacatgttgaaattcatattatcagGCTGCAGTACTGGCTATGGATGATTCAGTGTTAGATGTTGATCAGGTGGAAAATCTCATTAAATTTTGTCCTACCAAAGAGGAAATAGAGCTTTTAAAG
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--------gtaattatcttataaaacaagcaaagataatg----------gtaacatgattgattttttatatcttaatggcttaaattt---tctctagAGTGCGGCTTTGGCACTGGACCAATCTACCTTGGATGTTGATCAAGTGGAGAATCTCATAAAGTTCTGTCCTACAAAAGAAGAAATGGAACTTCTCAAG
upper sequence: GLYMA06G21190.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G414002_T02 (Zea mays), 3'ss of exon 6
ggtaacagattcttgccttatcatatatgtggaaattaaatctcccccctgtaactttttcaatttattgtctttaacatgttgaaattcatattatcagGCTGCAGTACTGGCTATGGATGATTCAGTGTTAGATGTTGATCAGGTGGAAAATCTCATTAAATTTTGTCCTACCAAAGAGGAAATAGAGCTTTTAAAG
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-gtaagaa----tgaggacagtataca-----agataaggtctcactattttataatttctgacatattgccatttgccaat---gattgatttctccagAGTGCAGCTCTCACGCTAGATCAATCTACCTTGGATGTTGATCAAGTGGAGAATCTCATAAAGTTCTGTCCTACGAAAGAAGAAATGGAACTTCTCAAG
upper sequence: GLYMA06G21190.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv17s0000g06640.t01 (Vitis vinifera), 3'ss of exon 8
ggtaacagattcttgccttatcatatatgtggaaattaaatctcccccctgtaactttttcaatt---tattgtctttaacatgttgaaattcatattatcagGCTGCAGTACTGGCTATGGATGATTCAGTGTTAGATGTTGATCAGGTGGAAAATCTCATTAAATTTTGTCCTACCAAAGAGGAAATAGAGCTTTTAAAG
| ||||| | | | || || | || |||| || | | || | | || | |||||| |||||||||||| || || |||||||| ||| | |||||||||||||| |||||||||||||| || || || ||||| |||||||| || || ||| | |||
---attgctttcttttttgggtccaactatgatttatagtttgattattagttttttttattgttaggcagtagctgttgtttactgttgtacatattctcagGCTGCAGTTCTAGCAATGGATGAGTCAATTTTAGATGTTGATCAAGTGGAAAATCTCATAAAGTTCTGCCCTACTAAAGAGGAGATGGAACTTCTTAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cccctgtaactttttcaatttattgtctttaacatgttgaaattcatattatcagGCTGCAGTACTGGCTATGGATGATTCAGTGTTAGATGTTGATCAGGTGGAAAATCTCATTAAATTTTGTCCTACCAAAGAGGAAATAGAGCTTTTAAAG
ctttaac putative branch site (score: 3)
tttttcaatttattgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ggtaacagattcttgccttatcatatatgtggaaattaaatctcccccctgtaactttttcaatttattgtctttaacatgttgaaattcatattatcagGCTGCAGTACTGGCTATGGATGATTCAGTGTTAGATGTTGATCAGGTGGAAAATCTCATTAAATTTTGTCCTACCAAAGAGGAAATAGAGCTTTTAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - -ttcttgc
- - - - - - - - - - - - - - - - aaattaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catgttg