Sequence
atgc intronic sequence ATGC exonic sequencegtctcttttttctcgcatgtctccattcttctgatggcctgtttcgcagaataagtaaagtcatattactaaattcttgaaatttcagGAATATTGCTCCCTAGCCCACTGCTTAGCTGGTGGTTCTGCAAGCATTGCAACTTCTTTTATCTTCACGCCTAGTGAGCGCATAAAACAGCAGATGCAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G11440.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G11440.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os02g44570.1 (Oryza sativa), 3'ss of exon 3
----------------------gtctcttttttctcgcatgtctccattcttctgatggcctgtttcgcagaataagtaaa-gtcatattactaaattcttgaaatttcagGAATATTGCTCCCTAGCCCACTGCTTAGCTGGTGGTTCTGCAAGCATTGCAACTTCTTTTATCTTCACGCCTAGTGAGCGCATAAAACAGCAGATGCAAG
| | |||| | || | || || | | | | | | ||| | || || || | | ||||||| ||| || | || || ||| |||||||||| | | |||||||||||||| || | || || || ||||| |||||||||||||||||||||
gtgacaatatgttcattcattcattttaattttttggctcatgtctatctagttttttgtttaccacagattttaattttgtactatgttgttacaatgccatttcttcagGAGTATCATTCAATTGCTCATTGCACTGCTGGTGGTTGTTCTAGCATTGCAACTTCCTTCGTTTTTACACCCAGTGAATGCATAAAACAGCAGATGCAAG
upper sequence: AT4G11440.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA05G37810.1 (Glycine max), 3'ss of exon 3
-----------------gtctcttttttctcgcatgtctccatt-cttctgatggcctgtttcgcagaataagtaaagtcatattactaaattcttgaaatttcagGAATATTGCTCCCTAGCCCACTGCTTAGCTGGTGGTTCTGCAAGCATTGCAACTTCTTTTATCTTCACGCCTAGTGAGCGCATAAAACAGCAGATGCAAG
| | | ||| | || | || || | | ||||| | |||| | | || | | | || | | | ||||| |||| || | ||||| ||| | | ||||||| |||||||||||| || ||||| || || || || |||||||| ||||| |||||||||||||
aaacatcgctgtaaatattatagtgtttgacatcagtaactcttactattattttagtgtttattggcataaatgaggtttca--atcatcttttcg----tgcagGAGTATTATTCTTTTGCCCATTGCATGGGAGGTGGTTGTGCAAGCATTGCCACCTCTTTCATTTTTACTCCCAGTGAGCGAATAAAGCAGCAGATGCAAG
upper sequence: AT4G11440.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA08G01790.1 (Glycine max), 3'ss of exon 8
-------------------gtctcttttttctcgcatgtctccattcttctgatggcctgtttcgcagaataagtaaagtcatattactaaattcttgaaatttcagGAATATTGCTCCCTAGCCCACTGCTTAGCTGGTGGTTCTGCAAGCATTGCAACTTCTTTTATCTTCACGCCTAGTGAGCGCATAAAACAGCAGATGCAAG
| ||| | || ||| | || | | ||||| | |||| | | || | | | || | | | ||||| ||||| || | ||||| ||| | | ||||||| |||||||||||| || ||||| || || || || |||||||| ||||| |||||||||||||
aaacatcgctgtaaatattatggtgtttgacatcagtgactct-tactattattttagtgtttattggcataaatgaggtttca--atcatcttttcg----tgcagGAGTATTGTTCTTTTGCCCATTGCGTGGGAGGTGGTTGTGCAAGCATTGCCACCTCTTTCATTTTTACTCCCAGTGAGCGAATAAAGCAGCAGATGCAAG
upper sequence: AT4G11440.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv02s0025g03490.t01 (Vitis vinifera), 3'ss of exon 2
----------gtctc----ttttttctcgcatgtctccattcttctgatggcctgtttcgcagaataagtaaagtcatattactaaattcttgaaatttcagGAATATTGCTCCCTAGCCCACTGCTTAGCTGGTGGTTCTGCAAGCATTGCAACTTCTTTTATCTTCACGCCTAGTGAGCGCATAAAACAGCAGATGCAAG
| || ||| |||| |||| | | | | | | || | | || | | | | || | | || || | | ||||||| | ||| | || |||||| | || ||||||| |||||||||||| |||||||| || || || || ||||||| ||||| || |||||||||
caagtgtgaagcctagaagtttattctggcatttgttcttagtataacagatgtgatgcttagtgtcattgtggagcacttgatcatttttttta--tgcagGAATGTCACTCTATTGCACACTGCATGGCAGGTGGTTGTGCAAGCATTGCTACTTCTTTCATTTTTACTCCCAGTGAGCATATAAAGCAACAGATGCAAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atggcctgtttcgcagaataagtaaagtcatattactaaattcttgaaatttcagGAATATTGCTCCCTAGCCCACTGCTTAGCTGGTGGTTCTGCAAGCATTGCAACTTCTTTTATCTTCACGCCTAGTGAGCGCATAAAACAGCAGATGCAAG
tactaaa putative branch site (score: 1)
atattactaaattctt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtctcttttttctcgcatgtctccattcttctgatggcctgtttcgcagaataagtaaagtcatattactaaattcttgaaatttcagGAATATTGCTCCCTAGCCCACTGCTTAGCTGGTGGTTCTGCAAGCATTGCAACTTCTTTTATCTTCACGCCTAGTGAGCGCATAAAACAGCAGATGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG