Sequence
atgc intronic sequence ATGC exonic sequence...tactgttaatagttactgaagtgttcatgttcataggttgatgcaaaaccttttttacttttcacataactgataaatttttgttaataatgttctacagGCAGATTTGGTGGGATGTCCAATAATTAGACCTGCTGACATAGAGACAACAGCACTTGGAGCAGCCTATGCTGCAGGATTAGCTATTGGGATTTGGAAAG
Basic information
species | Glycine max |
transcript | GLYMA08G22870.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G22870.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os04g55410.1 (Oryza sativa), 3'ss of exon 3
--------tactgttaatagttactgaagtgttcatgttcataggttgatgcaaaaccttttttacttttcacataactgataaatttttgttaataatgttctacagGCAGATTTGGTGGGATGTCCAATAATTAGACCTGCTGACATAGAGACAACAGCACTTGGAGCAGCCTATGCTGCAGGATTAGCTATTGGGATTTGGAAAG
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ggtgtaattgtagctgtagcttagtgaaacgtttctctttgcaatt----gtaaaatctctccaaattcccataagatcactgattttgcatgcaca----cctgcagGCTGATTTATTGGGTAGCCCTGTTGTCAGACCTGCTGACATCGAGACAACTGCCCTTGGAGCTGCGTATGCAGCTGGATTAGCTGTTGGAGTCTGGTCGA
upper sequence: GLYMA08G22870.1 (Glycine max), 3'ss of exon 3
lower sequence: AT1G80460.2 (Arabidopsis thaliana), 3'ss of exon 3
tactgttaatagttactgaagtgttcatgttcataggttgatgcaaaaccttttttacttttcacataactgataaatttttgttaataatgttctacagGCAGATTTGGTGGGATGTCCAATAATTAGACCTGCTGACATAGAGACAACAGCACTTGGAGCAGCCTATGCTGCAGGATTAGCTATTGGGATTTGGAAAG----------------------------------------------------------------------------------
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--------------------------------------------------------------------------------tccttgaaaatgtt--gcaggctgatctgatgggaagtccggtggtgaggccagtggacatagagacaacagcattaggagcagcctatgcagctggattagCTGTGGGATTCTGGAAGGAAGCAGACATATTCGAGTCGGGAGAGAAGGCGAAGAACTCCAAAGTTTTCAGACCCGCTATGGAAGAAGGAATCAGGAAGAA
upper sequence: GLYMA08G22870.1 (Glycine max), 3'ss of exon 3
lower sequence: AT1G80460.1 (Arabidopsis thaliana), 3'ss of exon 3
---tactgttaatagttactgaagtgttcatgt-tcataggttgatgcaaaaccttttttacttttcacataactgataaatttttgttaataatgttctacagGCAGATTTGGTGGGATGTCCAATAATTAGACCTGCTGACATAGAGACAACAGCACTTGGAGCAGCCTATGCTGCAGGATTAGCTATTGGGATTTGGAAAG
| || | | || | | ||| ||| | ||||| | || | || | | | | || | || | |||||| ||||| ||| || ||||| |||| | | || || | |||||||||||||||||| | |||||||||||||| || ||||||||| | || | ||||| |
gtatgatgatgctctcctctcttctctgtatgaatcagattctgatgattgtgttgttcgaacattaatctcattctcttatctcc-ttgaaaatgtt--gcagGCTGATCTGATGGGAAGTCCGGTGGTGAGGCCAGTGGACATAGAGACAACAGCATTAGGAGCAGCCTATGCAGCTGGATTAGCTGTGGGATTCTGGAAGG
upper sequence: GLYMA08G22870.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv09s0002g07860.t01 (Vitis vinifera), 3'ss of exon 3
----tactgttaatagttactgaagtgttcatgttcataggttgatgcaaaaccttttttacttttcacataactgataaatttttgttaataatgttctacagGCAGATTTGGTGGGATGTCCAATAATTAGACCTGCTGACATAGAGACAACAGCACTTGGAGCAGCCTATGCTGCAGGATTAGCTATTGGGATTTGGAAAG
| || | | || || | | || |||| || | | | ||| | | | || ||| || || ||| ||||| | | ||||| ||| || |||| || | ||||||| ||||| |||||||||||||| |||||||| || ||||| || |||||||| | |||||||||| ||
gtcttcatgcttgtggtatcttatatcagactgcccataatcccatactgtccttgtttgaactgtttaat--ttgacaatttgctgtc--taatgatttgcagGCTGATCTGTTGGGGAACCCGGTGGTTAGACCAGCTGATATAGAGACAACAGCTCTTGGAGCCGCTTATGCAGCTGGATTAGCAGTGGGGATTTGGACAG
upper sequence: GLYMA08G22870.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv09s0002g07640.t01 (Vitis vinifera), 3'ss of exon 2
----tactgttaatagttactgaagtgttcatgttcataggttgatgcaaaaccttttttacttttcacataactgataaatttttgttaataatgttctacagGCAGATTTGGTGGGATGTCCAATAATTAGACCTGCTGACATAGAGACAACAGCACTTGGAGCAGCCTATGCTGCAGGATTAGCTATTGGGATTTGGAAAG
| || | | || || | | || |||| || | | | ||| | | | || ||| || || ||| ||||| | | ||||| ||| || |||| || | ||||||| ||||| |||||||||||||| |||||||| || ||||| || |||||||| | |||||||||| ||
gtcttcatgcttgtggtatcttatatcagactgcccataatcccatactgtccttgtttgaactgttttat--ttgacaatttgctgtc--taatgatttgcagGCTGATCTGCTGGGGAACCCGGTGGTTAGACCAGCTGATATAGAGACAACAGCTCTTGGAGCCGCTTATGCAGCTGGATTAGCAGTGGGGATTTGGACAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaaccttttttacttttcacataactgataaatttttgttaataatgttctacagGCAGATTTGGTGGGATGTCCAATAATTAGACCTGCTGACATAGAGACAACAGCACTTGGAGCAGCCTATGCTGCAGGATTAGCTATTGGGATTTGGAAAG
tgttaat putative branch site (score: 3)
ataactgataaatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tactgttaatagttactgaagtgttcatgttcataggttgatgcaaaaccttttttacttttcacataactgataaatttttgttaataatgttctacagGCAGATTTGGTGGGATGTCCAATAATTAGACCTGCTGACATAGAGACAACAGCACTTGGAGCAGCCTATGCTGCAGGATTAGCTATTGGGATTTGGAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - -gttactg
- - - - - - - - - - - - -catgttc
- - - - - - - - - - - - - - - - - - - tgatgca