Sequence
atgc intronic sequence ATGC exonic sequence...gttgttgctcactgtaacttaaatttgtcaatatacatatggctgtcatttcctttaccgctattccgctaattgtaaatatcgtttgaacattttgtagGGCAATGGGGGATGTTTCTGATCGTATAGGCCGACCGACAGACAATGGTCAG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G21100.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G21100.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA08G13680.1 (Glycine max), 3'ss of exon 4
----gttgttgctcactgtaacttaaatttgtcaatatacatatggctg-tcatttcctttaccgctattccgctaattgtaaatatcgtttgaacattttgtagGGCAATGGGGGATGTTTCTGATCGTATAGGCCGACCGACAGACAATGGTCAG
||| || ||| ||| || || || | || ||| || | | | ||||| | | || | | || | | | | | ||||||||||||||||||||||| || ||||| || || ||||| |||||||||
gatttctgtatcttactataaattgaaattcctagtaagggcatgaatgattgtcttctttatc--tgtttaattctctt---atgttatgttattgccatccagGGCAATGGGGGATGTTTCTGACCGGATAGGACGTCCCACAGATAATGGTCAG
upper sequence: AT4G21100.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA05G30530.1 (Glycine max), 3'ss of exon 4
---gttgttgctcactgtaactta-aatttgtcaatatacatatggctgtcatttcctttaccgct-attccgctaattgtaaatatcgtttgaacattttgtagGGCAATGGGGGATGTTTCTGATCGTATAGGCCGACCGACAGACAATGGTCAG
|| || | | || ||| || ||| | | || || | | | | | | ||| ||||| | || | || || | ||||||||||||||||||||||| || ||||| || || ||||| ||||| |||
ccaatttctgtatattatatattataaattgaaattccttgtaagggcatgaatggttggctcatttatttgtttaattctctatgttattgtaa-----tccagGGCAATGGGGGATGTTTCTGACCGGATAGGACGTCCCACAGATAATGGCCAG
upper sequence: AT4G21100.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv10s0003g04360.t01 (Vitis vinifera), 3'ss of exon 4
gttgttgctcactgtaacttaaatttgtcaatatacatatggct---gtcatttcctttaccgctattccgctaattgtaaatatcgtttgaacattttgtagGGCAATGGGGGATGTTTCTGATCGTATAGGCCGACCGACAGACAATGGTCAG
||| ||| | | ||||| ||| | | | || ||| | | | || || ||| | | | |||||| |||||||| ||||| || ||||||||||| || || ||||||||||| |||
-ttggcttgattgaaaaccttgacactctaatatgtctatactttatgagaatttatttgtcacattcttgc--atcaacaattccatgctcttttcttgtagAGCAATGGGAGATGTCTCAGATCGTATAGGTCGTCCTACAGACAATGGACAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcatttcctttaccgctattccgctaattgtaaatatcgtttgaacattttgtagGGCAATGGGGGATGTTTCTGATCGTATAGGCCGACCGACAGACAATGGTCAG
cgctaat putative branch site (score: 3)
taattgtaaatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttgttgctcactgtaacttaaatttgtcaatatacatatggctgtcatttcctttaccgctattccgctaattgtaaatatcgtttgaacattttgtagGGCAATGGGGGATGTTTCTGATCGTATAGGCCGACCGACAGACAATGGTCAG
- - - -ctcactg
- - - - - - - - acttaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccgctaa