Sequence
atgc intronic sequence ATGC exonic sequencegtattgttggtgattatttttatgatatttttttctaaacgtgttgtcaaattttgtcaacagtttatgtttttatctgcactgcagGGATGCATGGGACATGGCTGCTGAGCTCTGCCTCTCTCAACTTCCGTCTTTAGTTGAGGATCCTAATGCTGAATTTCAG
Basic information
species | Glycine max |
transcript | GLYMA09G41510.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G41510.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os11g01872.1 (Oryza sativa), 3'ss of exon 7
gtattgttggtgattatttttatgatatttttttctaaacgtgttgtcaaattttgtcaacagtttatgttttt----atctgcactgcagGGATGCATGGGACATGGCTGCTGAGCTCTGCCTCTCTCAACTTCCGTCTTTAGTTGAGGATCCTAATGCTGAATTTCAG
|| ||| | | | || || | | || | | | | || || | | | | ||| || | | | ||||||||||||||||||||||| ||| ||||||| ||| | ||||| ||| ||| ||||||||||| || ||||||
---------gtaattgatggcactagccattctttttatagtttagctacctcttctccattttctttaatttcctaaatttcaattttagGGATGCATGGGACATGGCTGCAGAGATCTGCCTTTCTAAGCTTCCTCAATTAATTGCTGATCCTAATGCAGAGTTTCAG
upper sequence: GLYMA09G41510.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os12g01922.1 (Oryza sativa), 3'ss of exon 8
gta-ttgttggtgattatttttatgatatttttttctaaacgtgttgtcaaattttgtcaacagtttatgtttttatctgcactgcagGGATGCATGGGACATGGCTGCTGAGCTCTGCCTCTCTCAACTTCCGTCTTTAGTTGAGGATCCTAATGCTGAATTTCAG
||| ||| ||| | || | | | ||| || | || | | ||| | || || |||| || | ||||||||||||||||||||||| ||| ||||||| ||| | ||||| ||| ||| ||||||||||| || ||||||
gtaattgatggcactagccattctttttatagtttagctacctcttctgcattttctttaatttcctaaattttaattt------tagGGATGCATGGGACATGGCTGCAGAGATCTGCCTTTCTAAGCTTCCTCAATTAATTGCTGATCCTAATGCAGAGTTTCAG
upper sequence: GLYMA09G41510.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G048067_T02 (Zea mays), 3'ss of exon 8
gtattgttggtgattatttttatgatatttttttctaaacgtgttgtcaaattttgtcaacagtttatgtttttatctgcactgcagGGATGCATGGGACATGGCTGCTGAGCTCTGCCTCTCTCAACTTCCGTCTTTAGTTGAGGATCCTAATGCTGAATTTCAG
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---------gtaactaacctgact-tgttcttttttttgcat-taactaccttttgt--gtgatttgtaacatg--ctaaatctcagGGATGCATGGGACATGGCTGCTGAGATTTGCCTTTCCAAGCTTCCTCAGTTAATTGCTGATCCAAATGCAGAGTTTCAG
upper sequence: GLYMA09G41510.1 (Glycine max), 3'ss of exon 8
lower sequence: AT3G08850.1 (Arabidopsis thaliana), 3'ss of exon 8
gtattgttggtgattatttttatgatatttttttctaaacgtgttgt---caaattttgtcaacagtttatgtttttatctgcactgcagGGATGCATGGGACATGGCTGCTGAGCTCTGCCTCTCTCAACTTCCGTCTTTAGTTGAGGATCCTAATGCTGAATTTCAG
||||| | | | | | | || | ||| || ||| | |||||| | ||| | || || ||| | ||||||||||||||||||||||||||| |||| || ||||| ||||| | ||| ||| || | | || || |||
gtatt--caacaagaaccatattcttctgttatgtaaaatgttatgtgtctagattttgact-cagct-at-ccgttgcatgcttttcagGGATGCATGGGACATGGCTGCTGAAATCTGTCTTTCTCAGCTTCCCCAACTTGTTCTGGACCCAAGCACAGAGTTCCAG
upper sequence: GLYMA09G41510.1 (Glycine max), 3'ss of exon 8
lower sequence: AT5G01770.1 (Arabidopsis thaliana), 3'ss of exon 8
gtattgttggtgattatttttatgatatttttttctaaacgtgttgtcaaattttgtcaacagtttatgtttttatctgcactgcagGGATGCATGGGACATGGCTGCTGAGCTCTGCCTCTCTCAACTTCCGTCTTTAGTTGAGGATCCTAATGCTGAATTTCAG
| |||| |||| || | |||| | || |||| | | | | | | | | || ||| | ||||||||||||||||||||||||||| ||||||| ||||| ||||| || || ||| || ||| | || ||||||
---gtattggacgttatccctagtttgcattttgatgaattgtgtgtctgagctctttacc----tccgctaatagctgttttccagGGATGCATGGGACATGGCTGCTGAAATCTGCCTTTCTCAGCTTCCTCAATTTTTTCTGGACCCAAATACGGAGTTTCAG
upper sequence: GLYMA09G41510.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv08s0058g00890.t01 (Vitis vinifera), 3'ss of exon 8
gtat-tgttggtgattatttttatgatatttttttctaaacgtgttgtcaaattttgtcaacagtttatgtttttatctgcactgcagGGATGCATGGGACATGGCTGCTGAGCTCTGCCTCTCTCAACTTCCGTCTTTAGTTGAGGATCCTAATGCTGAATTTCAG
||| | ||| || | || | ||||| || | |||| | | | | | || || || |||||||||||||||||||||||||| ||||||| ||||| ||| ||| || ||||| ||||| ||||| || ||||||
gtacctactggaaatactagataagtaattttgttaagtgttcaataatccatttgtctcataatgtgc-catgcatgtgtgctatagGGATGCATGGGACATGGCTGCTGAAATCTGCCTTTCTCAGCTTAAGTCATTGGTTGATGATCCCAATGCAGAGTTTCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttctaaacgtgttgtcaaattttgtcaacagtttatgtttttatctgcactgcagGGATGCATGGGACATGGCTGCTGAGCTCTGCCTCTCTCAACTTCCGTCTTTAGTTGAGGATCCTAATGCTGAATTTCAG
ttctaaa putative branch site (score: 2)
tttttatct putative PPT
agtttatgtttttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtattgttggtgattatttttatgatatttttttctaaacgtgttgtcaaattttgtcaacagtttatgtttttatctgcactgcagGGATGCATGGGACATGGCTGCTGAGCTCTGCCTCTCTCAACTTCCGTCTTTAGTTGAGGATCCTAATGCTGAATTTCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG