Sequence
atgc intronic sequence ATGC exonic sequence...cataatgtggattgacaagaagttggtgtaaaatttctctggaaaaatttgtttcttggctttagcttggaaagaaaaatactaattgcatttgttgcagGCGTGATATGCTGGAAAATAAGTTAGCTGCTGCAGAAGTCTCTGAGGAAGAGCAAAAGAATCTGCTTAAGGATCTAGAGAAGAAGGAAACTGAATACATG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G23310.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G23310.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA10G32480.1 (Glycine max), 3'ss of exon 1
--------cataatgtggattgacaagaagttggtgtaaaatttctctgga-aaaatttgtttcttggctttagcttggaaagaaaaatactaattgcatttgttgcagGCGTGATATGCTGGAAAATAAGTTAGCTGCTGCAGAAGTCTCTGAGGAAGAGCAAAAGAATCTGCTTAAGGATCTAGAGAAGAAGGAAACTGAATACATG
| ||||| | | | | | ||| |||| | || ||| | | |||| || | ||| || ||| || |||||| ||| ||||||| ||||| ||||| |||| ||| |||||||||||||||||||| || ||| |||| || || | ||||| ||||| | |||||||||
atattgtctctgatgtgctgttatagattatgtgcaagaaacttctgcaaatggaaattgctgtaagtttttaat----aaggttaaacac--atta---ttcttgcagACGTAATATGCTAGAAAAAAAGTTGGCTGATGCTGAAGTCTCTGAGGAAGAGCAGAACAATTTGCTAAAATATTTTGAGAAAAAGGAGAGGGAATACATG
upper sequence: AT3G23310.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA20G35110.1 (Glycine max), 3'ss of exon 1
--------cataatgtggattgacaagaagttggtgtaaaatttctctgga-aaaatttgtttcttggctttagcttggaaagaaaaatactaattgcatttgttgcagGCGTGATATGCTGGAAAATAAGTTAGCTGCTGCAGAAGTCTCTGAGGAAGAGCAAAAGAATCTGCTTAAGGATCTAGAGAAGAAGGAAACTGAATACATG
| ||||| | | | | | ||| ||||| || || ||| | | |||| || | ||| || ||| || |||||| ||| ||||||| ||||| ||||| |||| ||| ||||| |||||||||||||| || ||| ||||||| || | ||||| ||||| | |||||||||
atgttgtctctgatgtgctgttatagattatgtgcaagaaacttctccagatggaaattgctgtaagtttttaat----aaggctaaacac--atta---ttcttgcagACGTAATATGCTAGAAAAAAAGTTGGCTGATGCTGAAGTTTCTGAGGAAGAGCAGAACAATTTGCTTAAATATTTTGAGAAAAAGGAGAGGGAATACATG
upper sequence: AT3G23310.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA10G00830.1 (Glycine max), 3'ss of exon 1
-cataatgtggattgacaagaagttggtgtaaaatttctctggaaa---aatttgtttcttggctttagcttggaaagaaaaatactaattgcatttgttgcagGCGTGATATGCTGGAAAATAAGTTAGCTGCTGCAGAAGTCTCTGAGGAAGAGCAAAAGAATCTGCTTAAGGATCTAGAGAAGAAGGAAACTGAATACATG
| | | || | | | ||| ||| |||||| || |||||| | ||||| || || | || ||| |||||| ||| ||||||| ||||| ||||| |||| ||| ||||||||||||||||| ||| | || ||||| || || | ||||| ||||| | ||| ||||
ctgttgtctctgatgtgatatattgtgtgcaaatacctaatggaaacagaaattgttttaagtctttaat----aagacctaaagtcatttcttttttttgcagACGTAATATGCTAGAAAAGAAGTTGGCTGATGCTGAAGTCTCTGAGGAAGAACAACACAACTTGCTTCAGCATTTGGAGAAAAAGGAGAGGGAAATCATG
upper sequence: AT3G23310.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA02G00580.2 (Glycine max), 3'ss of exon 2
---cataatgtggattgacaagaagttggtgtaaaatttctctggaaa---aatttgtttcttggctttagcttggaaagaaaaatactaattgcatttgttgcagGCGTGATATGCTGGAAAATAAGTTAGCTGCTGCAGAAGTCTCTGAGGAAGAGCAAAAGAATCTGCTTAAGGATCTAGAGAAGAAGGAAACTGAATACATG
| || | || | | | ||| ||| |||||| || ||||||| | ||||| |||| | | | ||| | ||| | |||| ||| ||||||| || || ||||| |||| ||| ||||||||||||||||||||| | || ||||| || || | ||||| ||||| | ||| ||||
ttctgttatctcagatgtgatatattatgtgcaaatacctaatggaaacagaaattgtttcaagtctttaat-----aagacctaaagtcatttctttt-tggcagACGTAATATGCTAGAGAAGAAGTTGGCTGATGCCGAAGTCTCTGAGGAAGAGCAACACAACTTGCTTCAGCATTTGGAGAAAAAGGAGAGGGAAATCATG
upper sequence: AT3G23310.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv05s0049g01220.t01 (Vitis vinifera), 3'ss of exon 1
----cataatgtggattgacaagaagttggtgtaaaatttctctggaa-aaatttgtttcttggctttagcttggaaagaaaaatactaattgcat-ttgttgcagGCGTGATATGCTGGAAAATAAGTTAGCTGCTGCAGAAGTCTCTGAGGAAGAGCAAAAGAATCTGCTTAAGGATCTAGAGAAGAAGGAAACTGAATACATG
| | ||| || |||| | || | || | |||||||| ||| || | || | | || || | || | ||| ||| |||| || || || || ||||||| ||| ||||||||||||||||||||||| || || || ||| || | |||||||||||||| ||||| |||
agaactcatcaaagatattcataccattgggtgattgttgatttgttatgaatttgttactt----ctaaat--gatggtcttttcttacatgtgtgttcatacagACGTAATATACTAGAGAAGAAATTAGCTGATGCTGAAGTCTCTGAGGAAGAGCAAAATAACCTACTGAAGCATTTGGAGAAGAAGGAAACAGAATATATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aatttgtttcttggctttagcttggaaagaaaaatactaattgcatttgttgcagGCGTGATATGCTGGAAAATAAGTTAGCTGCTGCAGAAGTCTCTGAGGAAGAGCAAAAGAATCTGCTTAAGGATCTAGAGAAGAAGGAAACTGAATACATG
tactaat putative branch site (score: 1)
aaagaaaaatactaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cataatgtggattgacaagaagttggtgtaaaatttctctggaaaaatttgtttcttggctttagcttggaaagaaaaatactaattgcatttgttgcagGCGTGATATGCTGGAAAATAAGTTAGCTGCTGCAGAAGTCTCTGAGGAAGAGCAAAAGAATCTGCTTAAGGATCTAGAGAAGAAGGAAACTGAATACATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - acaagaa
- - - - - - - - - - - - - - - - - - - - ggaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaata