Sequence
atgc intronic sequence ATGC exonic sequence...gtggcatagccatgcaacgaaagagagatcaatgtttgccgacttgaagaggttaactactgcatgtagagctggtgctaacagaattgttttgatgcagAGATATGACCCGGACCCAGCTGCAAAGGCAGCTGCCGCAACTGTCCTGGCATCCAAATTGGGTGCCGATTCAGGCTTGAAAGTATATTTAGGAGATGAAT
Basic information
species | Arabidopsis thaliana |
transcript | AT4G31080.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G31080.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA06G07930.1 (Glycine max), 3'ss of exon 4
---gtggcatagccatgcaacgaaagagagatcaatgtttgccgacttgaagaggttaactactgcatgtagagctggtgc-taacagaattgtt-ttgatgcagAGATATGACCCGGACCCAGCTGCAAAGGCAGCTGCCGCAACTGTCCTGGCATCCAAATTGGGTGCCGATTCAGGCTTGAAAGTATATTTAGGAGATGAAT
| || | | | || ||| || ||| | | | ||| | |||| | || | || | | |||| | | ||||||||||| || |||||||||||||| |||||||| |||| ||| | ||||| || |||||||| ||||| || |||||||| || | ||||||||||
tatatactttataaagtgcattactgaaagagcagctcttgatggc----aactgtttgcgactg-gtttaatattattgtgtgtttcacttgtgatctactcagAGATATGATCCAGACCCAGCTGCAAAAGCAGCTGCTGCAAGTGTTTTAGCATCTAAGTTGGGTGCAGATTCTGGTTTGAAAGTGTACCTGGGAGATGAAT
upper sequence: AT4G31080.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA04G07860.1 (Glycine max), 3'ss of exon 4
gtggcatagcc-atgcaacgaaagagagatcaatgtttgccgacttgaagaggttaactactgcatgtagagctggtgc-taacagaattgtt-ttgatgcagAGATATGACCCGGACCCAGCTGCAAAGGCAGCTGCCGCAACTGTCCTGGCATCCAAATTGGGTGCCGATTCAGGCTTGAAAGTATATTTAGGAGATGAAT
| ||| || | | | | || | | | | | | ||| |||| | || || | |||| | | ||||||||||| || ||||| || ||||| |||||||| |||| ||| | ||||| || |||||||| ||||| || |||||||| ||| | ||||||||||
--tgtatactttataaagtgcattactgaaagagctgctcttgatggcatctgtttgtgactg-gtttaatatcattgtgtgtttcgcttgtgatctactcagAGATATGATCCAGACCCGGCCGCAAAAGCAGCTGCTGCAAGTGTTTTAGCATCTAAGTTGGGTGCAGATTCTGGTTTGAAAGTGTATCTGGGAGATGAAT
upper sequence: AT4G31080.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA14G17080.1 (Glycine max), 3'ss of exon 3
gtggca-tagccatgcaacgaaagagagatca--atgtttgccgacttgaagaggttaactactgcatgtagagctggtgctaacagaattgttttgat--gcagAGATATGACCCGGACCCAGCTGCAAAGGCAGCTGCCGCAACTGTCCTGGCATCCAAATTGGGTGCCGATTCAGGCTTGAAAGTATATTTAGGAGATGAAT
|| || | ||| || | | | | | | | ||| | | | ||| || || | || || | | || |||| ||||||||||| | || || || || ||||||||||| ||||||| | |||||||| |||||||| |||||||| |||||||| ||| | || |||||||
-tgacaacaaacatctaataggacaaaaaatgtcagatctatttgtttgcaaaaat--act--tgaatattattgtgtattatacttagctcttgtgatccacagAGATATGATACAGATCCTGCAGCCAAGGCAGCTGCTGCAACTGCTTTAGCATCCAAGTTGGGTGCAGATTCAGGTTTGAAAGTGTATGTGGGGGATGAAT
upper sequence: AT4G31080.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA11G18060.1 (Glycine max), 3'ss of exon 3
---gtggcatagccatgcaacgaaagagagatcaatgtttgccgacttgaagaggttaactactgcatgtagagctg-gtgcta-acagaattgttttgat--gcagAGATATGACCCGGACCCAGCTGCAAAGGCAGCTGCCGCAACTGTCCTGGCATCCAAATTGGGTGCCGATTCAGGCTTGAAAGTATATTTAGGAGATGAAT
| || | | |||| || || | | | | ||| | | |||| | || || || || || | | || |||| ||||||||||| | || || || ||||||||||| || |||||||| | |||||||| |||||||| ||||| || |||||||| ||| | || |||||||
tcctttgctttgaagtgcattataaaagtcaacttgatatatttgtttgcaaaa------tacttta-atattattgtgtattatacttagctcttgtgatccacagAGATATGATACAGATCCTGCAGCAAAGGCAGCAGCTGCAACTGTTTTAGCATCCAAGTTGGGTGCAGATTCGGGTTTGAAAGTGTATGTGGGGGATGAAT
upper sequence: AT4G31080.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA17G29620.1 (Glycine max), 3'ss of exon 3
---gtggcatagccatgcaacgaaagagagatcaatgtttgccgacttgaagaggttaactactgcatgtagagctg-gtgcta-acagaattgttttgat--gcagAGATATGACCCGGACCCAGCTGCAAAGGCAGCTGCCGCAACTGTCCTGGCATCCAAATTGGGTGCCGATTCAGGCTTGAAAGTATATTTAGGAGATGAAT
| || | | |||| || || | | | | | ||| | | |||| | || || || || || | | || |||| ||||||||||| | || || || ||||||||||| || |||||||| | |||||||| |||||||| ||||| || |||||||| ||| | || |||||||
tcctttgctttgaagtgcattataaaagtcaacttgatatatttatttgcaaaa------tacttta-atattattgtgtattatacttagctcttgtgatccacagAGATATGATACAGATCCTGCAGCAAAGGCAGCAGCTGCAACTGTTTTAGCATCCAAGTTGGGTGCAGATTCGGGTTTGAAAGTGTATGTGGGGGATGAAT
upper sequence: AT4G31080.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv02s0033g01150.t01 (Vitis vinifera), 3'ss of exon 5
-----gtggcatagccatgcaacgaaagagagatcaatgt-ttgccgacttgaagaggttaactactgcatgtagagctggtgctaacagaattgttttgatgcagAGATATGACCCGGACCCAGCTGCAAAGGCAGCTGCCGCAACTGTCCTGGCATCCAAATTGGGTGCCGATTCAGGCTTGAAAGTATATTTAGGAGATGAAT
|| | || ||||| | | | || || || | | | | ||| ||||| | ||| | | ||| ||| ||||||||||||||| | || ||||| |||||||| ||||| ||||||||||||||||| || |||||||| || |||||||| ||||| | | | || |||||||
tgcttgtaacttacacatgcgtttccatgagggcctctgggttaatgatgttatgtacctgga-actacatgttgtactgatctt--cag---ccctttaatgcagAGATATGACACTGATCCAGCAGCAAAGGCTGCTGCTGCAACTGTCCTGGCATCAAAGTTGGGTGCAGAGTCAGGCTTAAAAGTGTTTGTCGGTGATGAAT
upper sequence: AT4G31080.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv00s0432g00020.t01 (Vitis vinifera), 3'ss of exon 1
gtggcatagccatgcaacgaaagagagatcaatgtttgccgacttgaagaggttaactactgcatgtagagctggtgctaacagaattgt------tttgatgcagAGATATGACCCGGACCCAGCTGCAAAGGCAGCTGCCGCAACTGTCCTGGCATCCAAATTGGGTGCCGATTCAGGCTTGAAAGTATATTTAGGAGATGAAT
|||| | | ||| | | || ||| | | | | | | | | | |||||| | || || |||| | ||| ||||||||||||||||| |||||||| |||||||||||||| || |||||||||||||| || || || | ||||||||||| ||||| ||| |||||||||||
----ttgagccttcctcattaagtgtgtaca-tgtat-ttgtatggggcatctgagcaaatgcatgaggctatgaattgtactgaatcatcagctctttaatgcagAGATATGACCCTGACCCAGCAGCAAAGGCAGCTGCAGCGACTGTCCTGGCATCAAAGTTAGGCTCAGATTCAGGCTTAAAAGTGTATGTAGGAGATGAAC
upper sequence: AT4G31080.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv00s0215g00090.t01 (Vitis vinifera), 3'ss of exon 4
gtggcatagccatgcaacgaaagagagatcaatgtttgccgacttgaagaggttaactactgcatgtagagctggtgctaacagaattgt------tttgatgcagAGATATGACCCGGACCCAGCTGCAAAGGCAGCTGCCGCAACTGTCCTGGCATCCAAATTGGGTGCCGATTCAGGCTTGAAAGTATATTTAGGAGATGAAT
|||| | | ||| | | || ||| | | | | | | | | | |||||| || || || |||| | ||| ||||||||||||||||| |||||||| |||||||||||||| || |||||||||||||| || || || | ||||||||||| ||||| ||| |||||||||||
----ttgagccttcctcattaagtgtgtaca-tgtat-ttgtatggggcatctgagcaaatgcatggagctatgaattgtactgaatcatcagctctttaatgcagAGATATGACCCTGACCCAGCAGCAAAGGCAGCTGCAGCGACTGTCCTGGCATCAAAGTTAGGCTCAGATTCAGGCTTAAAAGTGTATGTAGGAGATGAACMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|125092262|gb|EL150085.1|EL150085EST: CAACAACTTATTCAG AGATATGACCCGGACCCAGCTGCAAAGGCAGCTGCCGCAACTGTCCTGGCN
genomic: CAACAACTTATTCAGgtgagattac ... tttgatgcagAGATATGACCCGGACCCAGCTGCAAAGGCAGCTGCCGCAACTGTCCTGGCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gaagaggttaactactgcatgtagagctggtgctaacagaattgttttgatgcagAGATATGACCCGGACCCAGCTGCAAAGGCAGCTGCCGCAACTGTCCTGGCATCCAAATTGGGTGCCGATTCAGGCTTGAAAGTATATTTAGGAGATGAAT
ttgtttt CT-rich tract
aattgtttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtggcatagccatgcaacgaaagagagatcaatgtttgccgacttgaagaggttaactactgcatgtagagctggtgctaacagaattgttttgatgcagAGATATGACCCGGACCCAGCTGCAAAGGCAGCTGCCGCAACTGTCCTGGCATCCAAATTGGGTGCCGATTCAGGCTTGAAAGTATATTTAGGAGATGAAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - -aacgaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aacagaa