Sequence
atgc intronic sequence ATGC exonic sequencegtattcccataatttgctcccctgtattttaaaacagactttgttaattgttaatacattacattttaaatccctgattttcttgaaagagacctcttttacttccccctttattctatttctaatgttttaatatgtttattgttttagTGATCAGCTTCCAGTCAGTACGAAATTTGATATGAGAAGTGATCTGGGTGTGGTAAGGAATTATGGAAGACTCTTATTGGAAATGGCTTCAGTTGTTCCA
Basic information
species | Glycine max |
transcript | GLYMA02G09080.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G09080.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G097605_T01 (Zea mays), 3'ss of exon 4
gtattcccataatttgctcccctgtattttaaaacagactttgttaattgttaatacattacattttaaatccctgattttcttgaaagagacctcttttacttccccctttattctatttctaatgttttaatatgtttattgt-tttagTGATCAGCTTCCAGTCAGTACGAAATTTGATATGAGAAGTGATCTGGGTGTGGTAAGGAATTATGGAAGACTCTTATTGGAAATGGCTTCAGTTGTTCCA
||| |||||| ||| | | ||| | || | | || | ||||| | || | | | | ||| | || | || | || ||||||||||| || || ||||| || || |||||| | ||||||| ||||| || ||||||||||| | ||||| ||||||||||||| | |||||||
------------------------------------------ctta--tgttaagcttttata----acatctttagttgtttccaacat--ttcatattactggtagcattgtacactgtgtaaacaccaaccat-tccatcatcttcagTGATCAGCTACCTGTGAGTACAAAGTTCGATATGCGTAGTGATCCTGGTGTTGTGAGGAATTATGGCCGCCTCTTGCTGGAAATGGCTTCTGCTGTTCCA
upper sequence: GLYMA02G09080.1 (Glycine max), 3'ss of exon 5
lower sequence: AT1G03190.2 (Arabidopsis thaliana), 3'ss of exon 5
gtattcccataatttgctcccctgtattttaaaacagactttgttaattgttaatacattacattttaaatccctgattttcttgaaagagacctcttttacttccccctttattctatttctaatgttttaatatgtttattgttttagTGATCAGCTTCCAGTCAGTACGAAATTTGATATGAGAAGTGATCTGGGTGTGGTAAGGAATTATGGAAGACTCTTATTGGAAATGGCTTCAGTTGTTCCA
|| | || | ||| | || ||| | || | ||| || ||| | | | | | | || | ||||| | ||| |||||||||||||| || || || |||||||| ||||||||||||| ||||| || |||||||| |||| || || | || |||| || |||||||
-----------------------------------------------------gtatgtggtatataaaa------agaatcctga---acacttaacttattttttaattttatatgtct-tgacattattggttgttttctttttcagTGATCAGCTTCCTGTTAGCACCAAATTTGACATGAGAAGTGATCCTGGTGTTGTGAGGAATTACGGAAAGCTTTTGGTAGAGATGGTATCTATTGTTCCT
upper sequence: GLYMA02G09080.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv07s0104g00060.t01 (Vitis vinifera), 3'ss of exon 5
------------------------gtattcccataatttgctcccctg--tattttaaaacagactttgttaattgttaatac--attacattttaaatccctgattttcttgaaagagacctcttttacttccccct-ttattctatttctaatgttttaatatgtttattgttttagTGATCAGCTTCCAGTCAGTACGAAATTTGATATGAGAAGTGATCTGGGTGTGGTAAGGAATTATGGAAGACTCTTATTGGAAATGGCTTCAGTTGTTCCA
| || ||| | || | | ||| | | || || || || | || ||| | | | || | | | | |||| || | || | | | || || || | | || || ||| ||||| |||||||| || ||||| |||||||||||||||||||||| ||||| |||||||||||||| || ||| | |||| |||| || ||||||||
gtaaggggttaaattaaggtttgattcttttttctattcaataatttgggtgtcttagtttctattactacaacctttcttattaatcttagttgaaagacattacttccattaggtcatttttatttatttatttttgtttctttctccttattgaattcaatttctttttatttcagTGACCAGCTTCCTGTGAGTACAAAATTTGATATGAGAAGTGATCCTGGTGTTGTAAGGAATTATGGGAGGCTCCTGCTGGAGATGGTGTCTGTTGTTCCC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttttacttccccctttattctatttctaatgttttaatatgtttattgttttagTGATCAGCTTCCAGTCAGTACGAAATTTGATATGAGAAGTGATCTGGGTGTGGTAAGGAATTATGGAAGACTCTTATTGGAAATGGCTTCAGTTGTTCCA
ttgtttt CT-rich tract
tttattctatttctaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtattcccataatttgctcccctgtattttaaaacagactttgttaattgttaatacattacattttaaatccctgattttcttgaaagagacctcttttacttccccctttattctatttctaatgttttaatatgtttattgttttagTGATCAGCTTCCAGTCAGTACGAAATTTGATATGAGAAGTGATCTGGGTGTGGTAAGGAATTATGGAAGACTCTTATTGGAAATGGCTTCAGTTGTTCCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA