Sequence
atgc intronic sequence ATGC exonic sequence...ttttagaaatttgacaatctactaaaatactaaatatttaagagaagatgttgatacttaagattgttttaagtgatttatggctctttataataaacagGTAGATGACAAACTTTATATATACTTGGAGTATGTCTCTGGTGGGTCAATCTATAAGTTGCTTCAACAGTATGGCCAGCTTAGTGAAATTGTTATTCGTA
Basic information
species | Glycine max |
transcript | GLYMA01G42960.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA01G42960.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os04g47240.2 (Oryza sativa), 3'ss of exon 5
ttttagaaatttgacaatctactaaaatactaaatatttaagagaagatgttgatacttaagattgttttaagtgattta--tggctctttataat---aaacagGTAGATGACAAACTTTATATATACTTGGAGTATGTCTCTGGTGGGTCAATCTATAAGTTGCTTCAACAGTATGGCCAGCTTAGTGAAATTGTTATTCGTA
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-----gaagttgcatgatagcatctaggatttcattaatgagttatttatgtaccacttttgattttcttttttggcttcacttattatttgtgccccaatacagGTTGATGATAAGCTTTATATATACTTGGAGTATGTATCTGGTGGATCTATCCATAAACTTCTACAAGAGTATGGACAGCTTGGTGAACAAGCAATACGCA
upper sequence: GLYMA01G42960.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os02g44642.1 (Oryza sativa), 3'ss of exon 5
------ttttagaaatttgacaatctactaaaatactaaatatttaagagaagatgttgatacttaagattgttttaagtgatttatggctctttataataaacagGTAGATGACAAACTTTATATATACTTGGAGTATGTCTCTGGTGGGTCAATCTATAAGTTGCTTCAACAGTATGGCCAGCTTAGTGAAATTGTTATTCGTA
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ccacattctgcagaattttacgaacttcacttttgcttgcactcctgactcctctgtttactttaaaaataactatacactatccat------ttattcaaaacagGTTGATGATAAACTTTATATATACCTGGAGTATGTTTCTGGTGGATCCATCCATAAACTACTCCAGGAGTATGGGCAATTTGGTGAACCTGCTATCCGCA
upper sequence: GLYMA01G42960.1 (Glycine max), 3'ss of exon 4
lower sequence: AT1G63700.1 (Arabidopsis thaliana), 3'ss of exon 4
------------------ttttagaaatttgacaatctactaaaatactaaatatttaagagaagatgt-tgatacttaagattgttttaagtgatttatggctctttataataaacagGTAGATGACAAACTTTATATATACTTGGAGTATGTCTCTGGTGGGTCAATCTATAAGTTGCTTCAACAGTATGGCCAGCTTAGTGAAATTGTTATTCGTA
| || || |||| ||| | | || || | ||| || | | || | | || | || | ||| | | | ||| ||||| |||||||| || |||||||| ||||||||||||| ||||| || |||||||| | |||||| ||||||| || || |||| | || |||||||
gtaagttttacagatatttcttggacatttc-tgttctctgatactatcaactgtttcagctcaaccaagtcatgcacatgactagattctttacttt----cccctcccaat--tcagGTCGATGACAAGCTGTATATATATCTGGAGTATGTCTCCGGTGGTTCGATCTATAAACTTCTTCAAGAGTATGGACAATTTGGTGAGAATGCCATTCGTA
upper sequence: GLYMA01G42960.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv02s0025g03850.t01 (Vitis vinifera), 3'ss of exon 3
--ttttagaaatttgacaatctactaaaatactaaatatttaagagaagatgttgatacttaagattgttttaagtgatttatggctctttataataaacagGTAGATGACAAACTTTATATATACTTGGAGTATGTCTCTGGTGGGTCAATCTATAAGTTGCTTCAACAGTATGGCCAGCTTAGTGAAATTGTTATTCGTA
||| | || | | | ||| || || || | || ||||| ||| || || | | || | | ||||| | | | ||||||| ||||||||||| || ||||| | ||| ||||| | |||||| || || ||||| | |||||| ||||||||||| || ||||||| | ||||| ||
tcctttgaagtttcatctgcattacattatattagatcactagatggcga--ttgattcttcagcttatgtgaaattttccttggctatattccttgaacagGTGGATGACAAACTCTACATATATTCGGAATATGTATATGGTGGTTCCATATATAAACTTCTTCAAGAGTATGGCCAGTTTGGTGAAATAGCTATTCATA
upper sequence: GLYMA01G42960.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv02s0025g03370.t01 (Vitis vinifera), 3'ss of exon 6
--ttttagaaatttgacaatctactaaaatactaaatatttaagagaagatgttgatacttaagattgttttaagtgatttatggctctttataataaacagGTAGATGACAAACTTTATATATACTTGGAGTATGTCTCTGGTGGGTCAATCTATAAGTTGCTTCAACAGTATGGCCAGCTTAGTGAAATTGTTATTCGTA
||| | || | | | ||| || | || | || ||||| ||| || || | | || | | ||||| | | | ||||||| ||||||||||| || ||||| ||||| ||||| |||||||| || || ||||| | |||||| |||||||||||||| ||||||| | ||||||||
tcctttgaagcttcatctgcattacattatattagaacactagatggcga--ttgattcttcagcttatgtgaaattttccttggctatattccttgaacagGTGGATGACAAACTCTACATATATTTGGAATATGTATCTGGTGGTTCCATATATAAACTTCTTCAAGAGTATGGCCAGCTTGGTGAAATAGCTATTCGTA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agatgttgatacttaagattgttttaagtgatttatggctctttataataaacagGTAGATGACAAACTTTATATATACTTGGAGTATGTCTCTGGTGGGTCAATCTATAAGTTGCTTCAACAGTATGGCCAGCTTAGTGAAATTGTTATTCGTA
tgttgat putative branch site (score: 4)
ctctttat putative PPT
ttaagattgttttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttttagaaatttgacaatctactaaaatactaaatatttaagagaagatgttgatacttaagattgttttaagtgatttatggctctttataataaacagGTAGATGACAAACTTTATATATACTTGGAGTATGTCTCTGGTGGGTCAATCTATAAGTTGCTTCAACAGTATGGCCAGCTTAGTGAAATTGTTATTCGTA
- - - - - - - - - - - - - - - - - - - - - - - gatgttg