Sequence
atgc intronic sequence ATGC exonic sequence...tccgactttgtgtcttagtatagtaaaccatctaattctgtgtaggtcgactgagatcattctttattaaatggaaagtgtttaatatcttgtgctttagGATTCAGATGCTTCAATTCAGAAAAGGGCACTTGAGCTTATTTACCTTCTAGTGAATGAGAATAACGTGAAGCCACTAGCAAAGGAGCTTATAGAATATT
Basic information
species | Arabidopsis thaliana |
transcript | AT1G60070.2 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G60070.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA02G03800.1 (Glycine max), 3'ss of exon 6
tccgactttgtgtcttagtatagtaaaccatctaattctgtgtaggtcgactgagatca-ttctttatta-aatggaaagtgtttaatatcttgt-----gctttagGATTCAGATGCTTCAATTCAGAAAAGGGCACTTGAGCTTATTTACCTTCTAGTGAATGAGAATAACGTGAAGCCACTAGCAAAGGAGCTTATAGAATATT
|||| | | ||| | || ||| |||| | ||| | ||| ||| || | ||| | || | ||| |||||||||||||||| |||| |||||| || ||||| ||| |||| || | |||||||||| ||| |||||||| | ||||| ||||||||||| |||
-----------------gtatt-tgatttgtcttccctcattcag--tgacaaagatgagctctgttttacaatccaaggggttgatcatttgactcttaacttcagGATTCAGATGCTTCGATTCGGAAAAGAGCCCTTGAACTTGTTTATGTTTTGGTGAATGAGACTAATGTGAAGCCCTTGGCAAAAGAGCTTATAGATTATC
upper sequence: AT1G60070.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA01G03890.1 (Glycine max), 3'ss of exon 7
tccgactttgtgtcttagtatagtaaaccatctaattctgtgtaggtcgactgagatcattctttattaaatggaaagtgtttaatatcttgtg-ctttagGATTCAGATGCTTCAATTCAGAAAAGGGCACTTGAGCTTATTTACCTTCTAGTGAATGAGAATAACGTGAAGCCACTAGCAAAGGAGCTTATAGAATATT
|| || | | || || || |||| ||| | || | || | | | | ||| | | || | ||| |||||||||||||||| ||||||||||| || ||||| ||| |||| || | |||||||| | ||| |||||||| | ||||| ||||||||||| |||
-----------gtatttgatttgtcttccctc--attcagtg-acaaagatgagctttgttttacaatccaaggagttgatcatttgactcttaacttcagGATTCAGATGCTTCGATTCAGAAAAGAGCCCTTGAACTTGTTTATGTTTTGGTGAATGAAACTAATGTGAAGCCCTTGGCAAAAGAGCTTATAGATTATC
upper sequence: AT1G60070.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA08G39930.1 (Glycine max), 3'ss of exon 7
tccgactttgtgtcttagtatagtaaac---catctaattctgtgta---ggtcgactgagatcattctttattaaatggaaagtgtttaat---atcttgtgctttagGATTCAGATGCTTCAATTCAGAAAAGGGCACTTGAGCTTATTTACCTTCTAGTGAATGAGAATAACGTGAAGCCACTAGCAAAGGAGCTTATAGAATATT
|| ||| | || | | | || ||| | || | |||| || | | |||| | || ||||| | | | || || |||||||||| ||||||||||||| |||||| || ||||| ||| ||| |||| |||||||| | ||| |||||| | || |||| ||||| ||||||||
-----------gtattaattgagcagtctttcttcctatttcttataatggagagactcagctt-tgttttacaatgtgaaaagttagtgacttaactttttggtttagGATTCTGATGCTTCAATTCGGAAAAGAGCTCTTGAACTTGTTTGTATTCTGGTGAATGAAACTAATGTGAAGGCCTTAACAAAAGAGCTAGTAGAATATC
upper sequence: AT1G60070.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv01s0026g00310.t01 (Vitis vinifera), 3'ss of exon 7
tccgactttgtgtcttagtatagtaa-accatctaattctgtgtaggtcgactgagatcattctt-tat-taaatggaaagtgtttaat----atcttgtgctttagGATTCAGATGCTTCAATTCAGAAAAGGGCACTTGAGCTTATTTACCTTCTAGTGAATGAGAATAACGTGAAGCCACTAGCAAAGGAGCTTATAGAATATT
| |||| | | |||| ||| ||| ||| | | | | || |||| ||| | || ||||| | ||| || || | || ||||||||||||||||||||| ||||||||| ||||| |||||||| ||||||||||||| | || |||||||| | ||||| ||||| || || |||
-------tcgtgtagttttttagttgtgttatcggattgtgtcaaaattgccacagccacttctaatatacatatagaaagcttgtaactttaatattctctttcagGATTCAGATGCTTCAATTCGGAAAAGGGCCCTTGAACTTATTTATGTTCTAGTGAATGACAGCAATGTGAAGCCTTTGGCAAAAGAGCTAATTGATTATC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtcgactgagatcattctttattaaatggaaagtgtttaatatcttgtgctttagGATTCAGATGCTTCAATTCAGAAAAGGGCACTTGAGCTTATTTACCTTCTAGTGAATGAGAATAACGTGAAGCCACTAGCAAAGGAGCTTATAGAATATT
gtttaat putative branch site (score: 4)
atcattctttattaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tccgactttgtgtcttagtatagtaaaccatctaattctgtgtaggtcgactgagatcattctttattaaatggaaagtgtttaatatcttgtgctttagGATTCAGATGCTTCAATTCAGAAAAGGGCACTTGAGCTTATTTACCTTCTAGTGAATGAGAATAACGTGAAGCCACTAGCAAAGGAGCTTATAGAATATT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT