Sequence
atgc intronic sequence ATGC exonic sequence...aaaaaatatatgaagctgacttggattttccatcttaatctctatttttttgcttttgtgttttggattttgtgctgaaatttgttggctgtgggtatagCTTACTGGGGATCTAGACAAGATGGTTGCACTGCAAAGGTTATTGGAGCCCTATGGTATATGTGAG
Basic information
species | Arabidopsis thaliana |
transcript | AT2G31810.2 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G31810.2 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: LOC_Os02g39570.1 (Oryza sativa), 3'ss of exon 10
--aaaaaatatatgaagc-tgacttggattttccatcttaatctctattttt-ttgcttttgtgttttggattttgtgctgaaatttgttggctgtgggtatagCTTACTGGGGATCTAGACAAGATGGTTGCACTGCAAAGGTTATTGGAGCCCTATGGTATATGTGAG
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tgaatgtttagctgaaccacaactgtcatttactcatttaatgcccattcaaattattgtgggacttctgcatacttgat--aacttgccg--cgattgtgcagCTTACTGGGGATCTCGACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCTTATGGCATCTGTGAG
upper sequence: AT2G31810.2 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: LOC_Os02g39570.5 (Oryza sativa), 3'ss of exon 10
--aaaaaatatatgaagc-tgacttggattttccatcttaatctctattttt-ttgcttttgtgttttggattttgtgctgaaatttgttggctgtgggtatagCTTACTGGGGATCTAGACAAGATGGTTGCACTGCAAAGGTTATTGGAGCCCTATGGTATATGTGAG----------------------------------
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tgaatgtttagctgaaccacaactgtcatttactcatttaatgcccattcaaattattgtgggacttctgcatacttgat--aacttgccg--cgattgtgcagCTTACTGGGGATCTCGACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCTTATGGCATCTGTGAGGTATATTGAATTCTTTTTGTACTTTTCTTTCACC
upper sequence: AT2G31810.2 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GRMZM2G407044_T01 (Zea mays), 3'ss of exon 10
aaaaaatatatgaagctgacttggattttccatcttaatc--tctattttttt---gcttttg--tgttttggattttgtgctgaa---atttgttggctgtgggtatagCTTACTGGGGATCTAGACAAGATGGTTGCACTGCAAAGGTTATTGGAGCCCTATGGTATATGTGAG
||| || | ||| ||| | | |||| | | ||| || |||| | | ||| || | | || | |||||||||| ||||| ||||||||||||||||| ||||||||||||||||| ||||| || ||||||
----------tgatgccggtaccattttctcatgctgttttatctaactgctccaagctattagctgttgcaaaactcttgcataatggagggatcattgatgattgcagCTTACTGGAGATCTTGACAAGATGGTTGCACTACAAAGGTTATTGGAGCCATATGGCATCTGTGAG
upper sequence: AT2G31810.2 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GRMZM2G007647_T01 (Zea mays), 3'ss of exon 10
-aaaaaatatatgaagctgacttggattttccatcttaat--ctctatttttttgcttttgtgttttggattttgtgctg-aaatttgttggctgtgggtatagCTTACTGGGGATCTAGACAAGATGGTTGCACTGCAAAGGTTATTGGAGCCCTATGGTATATGTGAG
| | | | | | || | | |||| | | | | || ||| ||| | ||| || || || | |||||||||| ||||| ||||||||||||||||| ||||||||||| ||||| ||||| || || |||
tgacggcagcactatgttttcatgc-tgctttatctaactgctccaagcgattagctattgcaa---aactcttgcataatggatcccttattgatgattgcagCTTACTGGAGATCTTGACAAGATGGTTGCACTACAAAGGTTATTAGAGCCATATGGCATCTGCGAG
upper sequence: AT2G31810.2 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv05s0094g01110.t01 (Vitis vinifera), 3'ss of exon 10
aaaaaatatatgaagctgacttggattttccatcttaatctctatttttttgcttttgtgttttggattttgtgctgaaatttgttggctgtgggtat-agCTTACTGGGGATCTAGACAAGATGGTTGCACTGCAAAGGTTATTGGAGCCCTATGGTATATGTGAG
| | | | ||| | | || | | ||||||| | | | | ||| ||| | | | | | | || | || ||| ||||||| || | | ||||||| |||||||| ||||||||| | || ||||||||||| || ||||||
gctatctttctttggctttatgttttctttggcttcttccactattttctctcctcttagttggtgatact-tacggtattgcttttgatgcttgtaccagCTTACAGGAGCTTTAGACAAAATGGTTGCTCTGCAAAGGCTGTTAGAGCCCTATGGCATTTGTGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttttgcttttgtgttttggattttgtgctgaaatttgttggctgtgggtatagCTTACTGGGGATCTAGACAAGATGGTTGCACTGCAAAGGTTATTGGAGCCCTATGGTATATGTGAG
aaatttgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aaaaaatatatgaagctgacttggattttccatcttaatctctatttttttgcttttgtgttttggattttgtgctgaaatttgttggctgtgggtatagCTTACTGGGGATCTAGACAAGATGGTTGCACTGCAAAGGTTATTGGAGCCCTATGGTATATGTGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
-aaaaata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gttttgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgaaat