Sequence
atgc intronic sequence ATGC exonic sequencegtgagaagtaaacataacttgttataagatgatagtaatagttatgcaaaaggcattgatttgcatcatttctttgtttcagATAAGATATCGACCCAATGCTCCGTTGGTTCTCAAAGGAATCTCTTGCACATTCAGGGAAGGGACAAGAGTAGGAGTTGTCGGGAGGACGGGAAGCGGAA
Basic information
species | Arabidopsis thaliana |
transcript | AT3G21250.2 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G21250.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv09s0002g02430.t01 (Vitis vinifera), 3'ss of exon 19
-----------------------gtgagaagtaaacataacttgttataagatgatagtaatagttatgcaaaaggcattgatttgc--atcatttc--tttgtttcagATAAGATATCGACCCAATGCTCCGTTGGTTCTCAAAGGAATCTCTTGCACATTCAGGGAAGGGACAAGAGTAGGAGTTGTCGGGAGGACGGGAAGCGGAA
|| || | || | | | | | | | | || || || | | || | ||| || | |||||||||||| ||| || ||||||||||| | |||||||| |||||| |||||||||||| ||| ||||| |||||||||||||| || ||||| ||||| ||||
gtaagatagttcttctagtccatgttttaaatgaataaatgaatatgttccttagcattga-gtttgtgttttagacttaaatccgatgatccgtttgatgtgtttcagATAAAATACCGCCCCAATGCTCCTCTAGTTCTCAAGGGAATCACTTGCACATTCAAGGAGGGGACTAGAGTAGGAGTTGTTGGAAGGACTGGAAGTGGAA
upper sequence: AT3G21250.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv09s0002g02430.t01 (Vitis vinifera), 3'ss of exon 8
--------------------------------------gtgagaagtaaacataacttgttataagatgatagtaatagttatgcaaaaggcattgatttgcatcatttctttgtttcagATAAGATATCGACCCAATGCTCCGTTGGTTCTCAAAGGAATCTCTTGCACATTCAGGGAAGGGACAAGAGTAGGAGTTGTCGGGAGGACGGGAAGCGGAA
||| || | |||| | || | || | | | | ||||| | |||| | || ||||||||||| ||| || || ||| |||| ||||||| || || ||| |||||| ||||| |||||||| |||||||| || || || ||||| |||||||| |
gtaaggaagctattaatcaagttcatctcttaaatgatgtgtctcatagcaacctcttgaaagaatgctctggtgacaat-acttaaaagccgacgattctgtcttctggttggtttcagATAAAATACCGCCCAAATTCTCCACTGGTTCTGAAGGGTATCACTTGCATATTCAAAGAAGGGACTAGAGTAGGGGTCGTTGGAAGGACTGGAAGCGGCA
upper sequence: AT3G21250.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv09s0002g02440.t01 (Vitis vinifera), 3'ss of exon 7
gtgag-aagtaaacataact-tgttataagatgatagt----aatagtt-atgcaaaaggcattgatttgc--atcatttcttt-------gtttcagATAAGATATCGACCCAATGCTCCGTTGGTTCTCAAAGGAATCTCTTGCACATTCAGGGAAGGGACAAGAGTAGGAGTTGTCGGGAGGACGGGAAGCGGAA
||||| || | || | | ||| | || | | | || || || |||| | | || || || ||||||| ||||||||||| ||| || || |||||||| | |||||||||||||| ||||||| || | ||| ||||| ||||||||| |||| || ||||| ||||| || |
gtgaggaaattcttctagttcttttaaatgactgtgttccttagtacttgattgaaaatacttaaatctgatgatgctttcttttcggtgggtttcagATAAAATACCGCCCTAATGCTCCTCTAGTTCTCAAAGGAATTACTTGCACGTTTAAGGAGGGGACTAGAGTAGGAATTGTTGGAAGGACTGGAAGTGGCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gatgatagtaatagttatgcaaaaggcattgatttgcatcatttctttgtttcagATAAGATATCGACCCAATGCTCCGTTGGTTCTCAAAGGAATCTCTTGCACATTCAGGGAAGGGACAAGAGTAGGAGTTGTCGGGAGGACGGGAAGCGGAA
cattgat putative branch site (score: 4)
tcatttctttgtttc putative PPT
taatagttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagaagtaaacataacttgttataagatgatagtaatagttatgcaaaaggcattgatttgcatcatttctttgtttcagATAAGATATCGACCCAATGCTCCGTTGGTTCTCAAAGGAATCTCTTGCACATTCAGGGAAGGGACAAGAGTAGGAGTTGTCGGGAGGACGGGAAGCGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA