Sequence
atgc intronic sequence ATGC exonic sequence...tataatatgacattggtaccatatcattaccattgcatttatttcataaatgtgcagttactggttgtggaagttaattgatttaaatatttgtgtgcagGTGGTAGGAACTCCCAACTATATGTGTCCTGAACTGCTTGCTGATATTCCTTATGGATTCAAATCTGATATTTGGTCACTAG
Basic information
species | Glycine max |
transcript | GLYMA13G38980.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G38980.1 (Glycine max), 3'ss of exon 8
lower sequence: AT3G44200.1 (Arabidopsis thaliana), 3'ss of exon 8
tataatatgacattggtaccatatcattaccattgcatttatttcataaatgtgcagt-tactggttgtggaagttaattgatt-taaatatttgtgtgcagGTGGTAGGAACTCCCAACTATATGTGTCCTGAACTGCTTGCTGATATTCCTTATGGATTCAAATCTGATATTTGGTCACTAG
| | |||| | | | || ||| | | || | | ||| ||| | | | | ||| || | | | ||| | | |||| || |||||||| ||||| ||||| || ||||||||||||||||| |||||||| || || || ||||| ||||| |||
tccataatgattattat-tcttaggattgctctcaagctt-ctgaactaatacttagtgtgatagaaaatggtgtttatgactcatggaattttatatttagGTTGTTGGAACTCCAAACTACATGTGCCCGGAACTGCTTGCTGATATCCCTTATGGTTTTAAGTCAGATATCTGGTCCTTAG
upper sequence: GLYMA13G38980.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv06s0009g00690.t01 (Vitis vinifera), 3'ss of exon 8
--tataatatgacattggtaccatatcattaccattgcatttatttcataaatgtgcagttactggttgtggaagttaattgatttaa-atatttgtgtgcagGTGGTAGGAACTCCCAACTATATGTGTCCTGAACTGCTTGCTGATATTCCTTATGGATTCAAATCTGATATTTGGTCACTAG
| ||| | | || | || ||| || | || ||||| || || | || | ||| |||| | | |||| ||||| || ||||||||||| || |||||||||||||| ||||| |||||||||||||| |||||||||||||| ||||| ||||
gttgaaatcttgc-ctgtgcttgtcctgttgatatt-cacggacttggtaaatttg-agcaatgggacacgctcacctattcatttcctacttatgtgcacagGTAGTTGGAACTCCCAATTACATGTGTCCTGAACTTCTTGCAGATATTCCTTATGGCTTCAAATCTGATATCTGGTCTCTAG
upper sequence: GLYMA13G38980.1 (Glycine max), 3'ss of exon 8
lower sequence: PP1S22_216V6.1 (Physcomitrella patens), 3'ss of exon 8
------------------------tataatatgacattggtaccat-atcattaccattgcatttatttcataaatgtgcagt--tactggttgt--ggaagttaattgattta--aata---------------tttgtg----tgcagGTGGTAGGAACTCCCAACTATATGTGTCCTGAACTGCTTGCTGATATTCCTTATGGATTCAAATCTGATATTTGGTCACTAG
||| || || |||||| | || ||| | | | | || ||| | | || || ||||| | || |||||||||| || | ||| || || ||||||| ||||| ||||| || || |||||||| || || ||||| || || || |||||||||||||| || ||||||||| |||
gtaagtaatccgttgtgaacctcgtatcatttg-cattggaatgatgatcgctgctgt-gaatagtttttaccatctcgcggtcgtactgttcgtttggaagttaatcaatccactaatggccggaacgtgctgcttcttgctattgcagGTAGTAGGCACTCCAAATTACATGTGTCCAGAGCTACTTGCAGACATCCCATATGGATTCAAATCAGACATTTGGTCATTAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ataaatgtgcagttactggttgtggaagttaattgatttaaatatttgtgtgcagGTGGTAGGAACTCCCAACTATATGTGTCCTGAACTGCTTGCTGATATTCCTTATGGATTCAAATCTGATATTTGGTCACTAG
aattgat putative branch site (score: 4)
aagttaattgatttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tataatatgacattggtaccatatcattaccattgcatttatttcataaatgtgcagttactggttgtggaagttaattgatttaaatatttgtgtgcagGTGGTAGGAACTCCCAACTATATGTGTCCTGAACTGCTTGCTGATATTCCTTATGGATTCAAATCTGATATTTGGTCACTAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - -catatca
- - - - - - - - - - - - - - -ccattgc
- - - - - - - - - - - - - - - - - - - - - - - - - - tgcagtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggttgtg