Sequence
atgc intronic sequence ATGC exonic sequence...aagaattgaattgctgttatatcttaacggatacttgttattgtgggttttatcactattgagactggaacttgttataacatgagctattttgtatcagAGGTATGACCCTGACCCAGCTGCAAAGGCGGCTGCTGCAACTGTTCTGGCATCCAAGTTGGGTGCTGAGTCAGGCTTGAAAGTATTTGTAGGAGATGAAT
Basic information
species | Arabidopsis thaliana |
transcript | AT2G24330.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G24330.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA06G07930.1 (Glycine max), 3'ss of exon 4
-aagaattgaattgctgttatatcttaacggatacttgttattgtgggttttatcactattgagactggaacttgttata-acatgagctattttgta-tcagAGGTATGACCCTGACCCAGCTGCAAAGGCGGCTGCTGCAACTGTTCTGGCATCCAAGTTGGGTGCTGAGTCAGGCTTGAAAGTATTTGTAGGAGATGAAT
| | | || || || || | | | || || | | | | | || | | || || | | | | | | || |||||| ||||| || |||||||||||||| || |||||||||| |||| | ||||| ||||||||||| || || || |||||||| | | ||||||||||
tatatactttataaagtgcattactgaaagagcagctcttgatggcaactgt-ttgcgactgg--tttaatattattgtgtgtttcacttgtgatctactcagAGATATGATCCAGACCCAGCTGCAAAAGCAGCTGCTGCAAGTGTTTTAGCATCTAAGTTGGGTGCAGATTCTGGTTTGAAAGTGTACCTGGGAGATGAAT
upper sequence: AT2G24330.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA14G17080.1 (Glycine max), 3'ss of exon 3
aagaattgaattgctgttatatcttaacggatacttgttattgtgggttttatcactattgagactggaacttgttataacatgagctattttgtatc--agAGGTATGACCCTGACCCAGCTGCAAAGGCGGCTGCTGCAACTGTTCTGGCATCCAAGTTGGGTGCTGAGTCAGGCTTGAAAGTATTTGTAGGAGATGAAT
| || || || | || || | | | | | || | | || | | | ||| || | |||| || || | |||| ||||| | || || || || ||||| ||||||||||||| | | ||||||||||||||||| || ||||| |||||||| | ||| || |||||||
tgacaacaaacatctaataggac--aaaaaatgtcagatctatttgtttgcaaaaatacttgaatattattgtgtattatacttagctcttgtgatccacagAGATATGATACAGATCCTGCAGCCAAGGCAGCTGCTGCAACTGCTTTAGCATCCAAGTTGGGTGCAGATTCAGGTTTGAAAGTGTATGTGGGGGATGAAT
upper sequence: AT2G24330.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA11G18060.1 (Glycine max), 3'ss of exon 3
aagaattgaattgctgttatatcttaacggatacttgttattgtgggttttatcac-tattgagactggaacttgttataacatgagctattttgtatcagAGGTATGACCCTGACCCAGCTGCAAAGGCGGCTGCTGCAACTGTTCTGGCATCCAAGTTGGGTGCTGAGTCAGGCTTGAAAGTATTTGTAGGAGATGAAT
||| ||| || | | || | ||||| ||| | | || | | || | | | | ||||| | || | ||||| ||||| | || || || |||||||| || |||||||||||| | ||||||||||||||||| || || || |||||||| | ||| || |||||||
-tcctttgctttgaagtgcattataaaagtcaacttgatatatttgtttgcaaaatactttaatattattgtgtattatacttagctcttgtgatccacagAGATATGATACAGATCCTGCAGCAAAGGCAGCAGCTGCAACTGTTTTAGCATCCAAGTTGGGTGCAGATTCGGGTTTGAAAGTGTATGTGGGGGATGAAT
upper sequence: AT2G24330.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA17G29620.1 (Glycine max), 3'ss of exon 3
aagaattgaattgctgttatatcttaacggatacttgttattgtgggttttatcac-tattgagactggaacttgttataacatgagctattttgtatcagAGGTATGACCCTGACCCAGCTGCAAAGGCGGCTGCTGCAACTGTTCTGGCATCCAAGTTGGGTGCTGAGTCAGGCTTGAAAGTATTTGTAGGAGATGAAT
||| ||| || | | || | ||||| ||| | || | | || | | | | ||||| | || | ||||| ||||| | || || || |||||||| || |||||||||||| | ||||||||||||||||| || || || |||||||| | ||| || |||||||
-tcctttgctttgaagtgcattataaaagtcaacttgatatatttatttgcaaaatactttaatattattgtgtattatacttagctcttgtgatccacagAGATATGATACAGATCCTGCAGCAAAGGCAGCAGCTGCAACTGTTTTAGCATCCAAGTTGGGTGCAGATTCGGGTTTGAAAGTGTATGTGGGGGATGAAT
upper sequence: AT2G24330.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA04G07860.1 (Glycine max), 3'ss of exon 4
--aagaattgaattgctgttatatcttaacggatacttgttattgtgggt-tttatcacta--ttgagactggaacttgttataacatgagctattttgtatcagAGGTATGACCCTGACCCAGCTGCAAAGGCGGCTGCTGCAACTGTTCTGGCATCCAAGTTGGGTGCTGAGTCAGGCTTGAAAGTATTTGTAGGAGATGAAT
| | || | || || || | | || | || | | ||| | ||| || | | |||| | | || | | | | ||||| ||||| || ||||| || ||||| || |||||||||| |||| | ||||| ||||||||||| || || || |||||||| | | | ||||||||||
tgtatactttataaagtgcattactgaaagagctgctcttgatggcatctgtttgtgactggtttaatatcattgtgtgtt-tcgcttgtgatctact----cagAGATATGATCCAGACCCGGCCGCAAAAGCAGCTGCTGCAAGTGTTTTAGCATCTAAGTTGGGTGCAGATTCTGGTTTGAAAGTGTATCTGGGAGATGAAT
upper sequence: AT2G24330.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv02s0033g01150.t01 (Vitis vinifera), 3'ss of exon 5
aagaattgaattgctgttatatcttaacggatacttgtta-ttgtgggttttatcactattgagactggaacttgttataa-catgagctattttgtatcagAGGTATGACCCTGACCCAGCTGCAAAGGCGGCTGCTGCAACTGTTCTGGCATCCAAGTTGGGTGCTGAGTCAGGCTTGAAAGTATTTGTAGGAGATGAAT
| | || | | | | | | | | | || | | |||| || ||| | |||| | | | | ||| ||| | ||||| |||||| |||| ||||| |||||||| |||||||||||||| |||||||| ||||||||||| ||||||||||| ||||| ||||| || |||||||
tgcttgtaacttacacatgcgtttccatgagggcctctgggttaatgatgttat-gtacctggaactacatgttgtactgatcttcagccctttaatg-cagAGATATGACACTGATCCAGCAGCAAAGGCTGCTGCTGCAACTGTCCTGGCATCAAAGTTGGGTGCAGAGTCAGGCTTAAAAGTGTTTGTCGGTGATGAAT
upper sequence: AT2G24330.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv00s0432g00020.t01 (Vitis vinifera), 3'ss of exon 1
aagaattgaa---ttgctgttatatcttaacggatacttgttattgtgggttttatca--ctattgagactggaacttgttataa--catgagctattttgtatcagAGGTATGACCCTGACCCAGCTGCAAAGGCGGCTGCTGCAACTGTTCTGGCATCCAAGTTGGGTGCTGAGTCAGGCTTGAAAGTATTTGTAGGAGATGAAT
|||| | ||| | | || || |||| || | | | | | || |||| || | |||| | | ||| |||| ||| | ||||| ||||||||||||||||| |||||||| ||||| || ||||| |||||||| ||||| || | || |||||||| ||||| | |||||||||||||
-----ttgagccttcctcattaagtgtgtacatgtatttgt-atggggcatctgagcaaatgcatgaggctatgaattgtactgaatcatcagctctttaatg-cagAGATATGACCCTGACCCAGCAGCAAAGGCAGCTGCAGCGACTGTCCTGGCATCAAAGTTAGGCTCAGATTCAGGCTTAAAAGTGTATGTAGGAGATGAAC
upper sequence: AT2G24330.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv00s0215g00090.t01 (Vitis vinifera), 3'ss of exon 4
aagaattgaa---ttgctgttatatcttaacggatacttgttattgtgggttttatcac---tattgagactggaact-tgttataacatgagctattttgtatcagAGGTATGACCCTGACCCAGCTGCAAAGGCGGCTGCTGCAACTGTTCTGGCATCCAAGTTGGGTGCTGAGTCAGGCTTGAAAGTATTTGTAGGAGATGAAT
|||| | ||| | | || || |||| || | | | | | || || ||| ||| | | | | ||| |||| ||| | ||||| ||||||||||||||||| |||||||| ||||| || ||||| |||||||| ||||| || | || |||||||| ||||| | |||||||||||||
-----ttgagccttcctcattaagtgtgtacatgtatttgt-atggggcatctgagcaaatgcatggagctatgaattgtactgaatcatcagctctttaatg-cagAGATATGACCCTGACCCAGCAGCAAAGGCAGCTGCAGCGACTGTCCTGGCATCAAAGTTAGGCTCAGATTCAGGCTTAAAAGTGTATGTAGGAGATGAAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggttttatcactattgagactggaacttgttataacatgagctattttgtatcagAGGTATGACCCTGACCCAGCTGCAAAGGCGGCTGCTGCAACTGTTCTGGCATCCAAGTTGGGTGCTGAGTCAGGCTTGAAAGTATTTGTAGGAGATGAAT
ttataac putative branch site (score: 2)
ctatttt putative PPT
tattttgtat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aagaattgaattgctgttatatcttaacggatacttgttattgtgggttttatcactattgagactggaacttgttataacatgagctattttgtatcagAGGTATGACCCTGACCCAGCTGCAAAGGCGGCTGCTGCAACTGTTCTGGCATCCAAGTTGGGTGCTGAGTCAGGCTTGAAAGTATTTGTAGGAGATGAAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aacatga