Sequence
atgc intronic sequence ATGC exonic sequence...catgttgtgatttctctacacctatgtctattacataggcctatgccttttatctctatgatgttcccgttcatctatatattctttttttcttttgcagCTGCGAAGGTTTAATCATTAAAACATTGGACTCAGATGCTACCTATGAGCCTGCAAAGCGATCAAATAATTGGCTAAAACTGAAGAAAGACTATATGGAC
Basic information
species | Arabidopsis thaliana |
transcript | AT1G08130.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G08130.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os10g34750.2 (Oryza sativa), 3'ss of exon 9
--------catgttgtgatttctctacacctatgtctattacataggcctatgccttttatctctatgatgttcccgttcatctatatattctttttttcttttgcagCTGCGAAGGTTTAATCATTAAAACATTGGACTCAGATGCTACCTATGAGCCTGCAAAGCGATCAAATAATTGGCTAAAACTGAAGAAAGACTATATGGAC
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aaacattttaggcagggatttttaatgatttttgggtgttgcaag----tttgcaattagactat-tggagttttgtcctgccactaagatcaatcgctgt---gcagTTGTGAAGGGTTGATTATCAAGACATTGGATAAGGATGCTACATATGAGCCAGCAAAACGATCGAACAATTGGTTGAAATTGAAGAAAGACTACATGGAC
upper sequence: AT1G08130.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA12G08600.1 (Glycine max), 3'ss of exon 9
catgttgtgatttctctacacctatgtctattacataggcctatgccttttatctctatgatgttcccgttcatctatat---attctttttttcttttgcagCTGCGAAGGTTTAATCATTAAAACATTGGACTCAGATGCTACCTATGAGCCTGCAAAGCGATCAAATAATTGGCTAAAACTGAAGAAAGACTATATGGAC
|| | | ||| || | || | | | | | | | || | |||| || | |||| |||| | || | || || || || || ||||| ||||||||||| | |||||||| ||||| ||| | ||||||||| || |||||||||||||||||||| |||||||||
--gtttatctaacattcacatctgtttccaactt-tggttttcttgcaataatttgaatgagaaattttgtcgttgatatttggctcttctcttgatatgtagTTGTGAGGGATTAATTATTAAAACATTAAATGAGGATGCTACATATGAACCTTCCAAGCGATCACTCAACTGGCTAAAACTGAAGAAAGATTATATGGAC
upper sequence: AT1G08130.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA11G19880.1 (Glycine max), 3'ss of exon 9
catgttgtgatttctcta--cacctatgtctattacataggcctatgccttttatctctatgatg--ttcccgttcatctatatattctttttttcttttgcagCTGCGAAGGTTTAATCATTAAAACATTGGACTCAGATGCTACCTATGAGCCTGCAAAGCGATCAAATAATTGGCTAAAACTGAAGAAAGACTATATGGAC
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---ttaattatttatctaagcattcacagcccaactttggttttcttgcaataatatgaacgagaaattgtcattgatatttg-gcttgtctcttgatatgtagTTGTGAGGGGTTAATTATTAAAACATTAAATGAGGATGCTACATATGAACCTTTGAAGCGATCACTCAACTGGCTAAAACTGAAGAAAGATTATATGGAC
upper sequence: AT1G08130.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv06s0061g00690.t01 (Vitis vinifera), 3'ss of exon 9
catgttgtgatttctctacacctatgtctattacataggcc-tatgccttttatctctatgatgttcccgttcatctat-atattctttttttcttttgcagCTGCGAAGGTTTAATCATTAAAACATTGGACTCAGATGCTACCTATGAGCCTGCAAAGCGATCAAATAATTGGCTAAAACTGAAGAAAGACTATATGGAC
|| | | | | | | ||||| | | |||| || | |||| | | || | ||| | | | || | |||| | |||| || ||||| || ||||||||||||||| | ||||||||| ||||||||| ||||||| ||| |||| ||||||||| |||||||||| || |||||
caagcgattaaaattgttc--tgatgtcattaagatagttaacttgtcatttactgcattaattgttgtgttgttgtgtcatcaattcattttaactggcagTTGTGAAGGCTTGATCATTAAAACATTGAATGGAGATGCTACATATGAGCCTTCAAAGCGGTCACATAACTGGCTAAAATTGAAGAAAGATTACATGGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ccttttatctctatgatgttcccgttcatctatatattctttttttcttttgcagCTGCGAAGGTTTAATCATTAAAACATTGGACTCAGATGCTACCTATGAGCCTGCAAAGCGATCAAATAATTGGCTAAAACTGAAGAAAGACTATATGGAC
ttcatctatatattct CT-rich tract
ttcatctatatattct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
catgttgtgatttctctacacctatgtctattacataggcctatgccttttatctctatgatgttcccgttcatctatatattctttttttcttttgcagCTGCGAAGGTTTAATCATTAAAACATTGGACTCAGATGCTACCTATGAGCCTGCAAAGCGATCAAATAATTGGCTAAAACTGAAGAAAGACTATATGGAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - -ctacacc