Sequence
atgc intronic sequence ATGC exonic sequencegtaagtaggttatgaatatgtgtgagacttaatttcttgtgtgatagagttatccttattgtgatacaaagcatgctgattacttctaaatattatagGTTATAAACATGGAGTGGGGTAATTTCCGATCATCACATCTTCCTCTAACAGAATATGATCTAGCTCTGGATGCTCAGAGCTTAAACCCTGGAGAACAG
Basic information
species | Glycine max |
transcript | GLYMA08G03730.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G03730.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv11s0016g03070.t01 (Vitis vinifera), 3'ss of exon 5
------------------------------------------------------------------------------------------------------gtaagtaggttatgaatatgtgtgagacttaatttcttgtgtgatagagttatccttattgtgatacaaagcatgctgattacttctaaatatt---atagGTTATAAACATGGAGTGGGGTAATTTCCGATCATCACATCTTCCTCTAACAGAATATGATCTAGCTCTGGATGCTCAGAGCTTAAACCCTGGAGAACAG
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gttagcagttctcttataatttccatctattgatatgtgattaggaatgtactatccatcttctattaaaaacaaaaaatcttgacttttttttaatgtctctttcctgatatagaaatgtttctgtggtttggaacctagtata--caagttatgct-attatgtcggaagataaataattttcttaataaaatttctgtagGTTATCAACATGGAGTGGGGTAACTTTCGATCATCTCACCTTCCACTAACAGAATATGATCAGGTGCTGGATGCTGAGAGTTTAAACCCTGGAGAACAG
upper sequence: GLYMA08G03730.1 (Glycine max), 3'ss of exon 5
lower sequence: PP1S12_19V6.1 (Physcomitrella patens), 3'ss of exon 5
gtaagtaggttatgaatatgtgtgagacttaatttcttgtgt--gatagagttat---ccttattgtgatacaaagcatg-ctgattacttctaaatatt-atagGTTATAAACATGGAGTGGGGTAATTTCCGATCATCACATCTTCCTCTAACAGAATATGATCTAGCTCTGGATGCTCAGAGCTTAAACCCTGGAGAACAG
| || ||| | | | || || || | ||| ||| | ||| | || |||| ||| | | | | | | | | |||| | |||||||||||||||||||||| |||||| | ||||| || | |||| || | ||| | |||| |||| || || || |||||| |
-----aaaattttgatcacgattttgatttgatattgggtgatgaatataattagtggctttgttgtaatatagcatctaatttgtagcatatgactattgacagGTTATAAACATGGAGTGGGGGAATTTCTGGTCATCTCACTTGCCTCGGACCTATGTGGATGAGTCATTGGACAACGAGAGTTTGAATCCAGGAGAATAT
upper sequence: GLYMA08G03730.1 (Glycine max), 3'ss of exon 5
lower sequence: PP1S414_10V6.1 (Physcomitrella patens), 3'ss of exon 4
gtaagtaggtt-atg-aatatgtgtgagacttaatttcttgtgtgatagagttatcct--tattgtgatacaaagcatgctgattacttctaaatattatagGTTATAAACATGGAGTGGGGTAATTTCCGATCATCACATCTTCCTCTAACAGAATATGATCTAGCTCTGGATGCTCAGAGCTTAAACCCTGGAGAACAG
| || | || || || ||||| |||| | | || | | | || | ||| || | | | || || | | | |||| ||||||||||||||||| |||||| | ||||||||| | ||| || | ||| | | ||||| |||| || ||||| |||||| |
--acgttgtttcatatgattcccatgagatgatatttttgacgaactaaactagtgctattgttgcaatgcgtcatctaatctataggatgaattttgacagGTGATAAACATGGAGTGGGGGAATTTCTGGTCATCACATTTGCCTAGGACTTATGTGGATGAATCCTTGGATAACGAGAGTTTGAACCCAGGAGAATAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atagagttatccttattgtgatacaaagcatgctgattacttctaaatattatagGTTATAAACATGGAGTGGGGTAATTTCCGATCATCACATCTTCCTCTAACAGAATATGATCTAGCTCTGGATGCTCAGAGCTTAAACCCTGGAGAACAG
ttctaaa putative branch site (score: 2)
tgattacttctaaata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtaggttatgaatatgtgtgagacttaatttcttgtgtgatagagttatccttattgtgatacaaagcatgctgattacttctaaatattatagGTTATAAACATGGAGTGGGGTAATTTCCGATCATCACATCTTCCTCTAACAGAATATGATCTAGCTCTGGATGCTCAGAGCTTAAACCCTGGAGAACAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA