Sequence
atgc intronic sequence ATGC exonic sequence...caaagattttgttaagaactaagattattttcttcctgaactctgcaaaaaaaatattggtctgaagctattcttgtttctttcctttttttattgtcagCCTCGGACAAAAGATGGCACTGATAGCTTTGGTGGCCTTGGAGCAACTATGGTAGATTCTTTAGATACACTCTATATAATGGGTCTAGATGAGCAGTTTC
Basic information
species | Arabidopsis thaliana |
transcript | AT1G51590.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G51590.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA08G23730.1 (Glycine max), 3'ss of exon 3
----caaagatt---ttgttaagaactaagattattttcttcctgaactctgcaaaaaaaatattggtctgaagctattcttgtttctttcctttttttattgtcagCCTCGGACAAAAGATGGCACTGATAGCTTTGGTGGCCTTGGAGCAACTATGGTAGATTCTTTAGATACACTCTATATAATGGGTCTAGATGAGCAGTTTC
||| ||| ||||| || || ||| | || | | ||| | ||| | || || || | || |||| | | ||||| | |||| |||| |||||||||| || |||||||||||| | |||||||| | |||||||| ||||| |||||||| | || |||||||
atgataaaaattggtttgtttttcgtaaaaataattattttatttgttcttt--aaatttacattttttaaaaatta-----attgttatctttttggtgctaccagCCACAATCAAAGAATGGTGTCAATAGCTTTGGAGGTCTTGGAGCAACTTTAATAGATTCTCTTGATACACTATATATTATGGGTCTCAACGAACAGTTTC
upper sequence: AT1G51590.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA07G02290.1 (Glycine max), 3'ss of exon 2
caaagattttgttaagaact---aagattattttcttcctgaactctgcaaaaaaaatattggtctgaagctattcttgtttctttcctttttttattgtcagCCTCGGACAAAAGATGGCACTGATAGCTTTGGTGGCCTTGGAGCAACTATGGTAGATTCTTTAGATACACTCTATATAATGGGTCTAGATGAGCAGTTTC
||| || ||| || || | || || || | ||| ||| | ||| | || || || ||| ||| |||| | | ||||| | |||| |||| |||||||||| || |||||||||||| | |||||||| | ||||| || ||||| |||||||| |||| |||||||
taaaatattggtttctttctcgtaaaaataattattttatttgttctttaaattta-cattttttaaaaattaatc--gttattttttttttggtgctaccagCCACAATCAAAGAATGGTGTCAATAGCTTTGGAGGTCTTGGAGCAACTTTAATAGATTCTCTTGATACGCTATATATTATGGGTCTCAATGAACAGTTTC
upper sequence: AT1G51590.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv11s0052g00140.t01 (Vitis vinifera), 3'ss of exon 3
--------caaagattttgttaagaactaagattattttcttcctgaactctgcaaaaaaaatattggtctgaagctattcttgtttctttcctttttttattgtcagCCTCGGACAAAAGATGGCACTGATAGCTTTGGTGGCCTTGGAGCAACTATGGTAGATTCTTTAGATACACTCTATATAATGGGTCTAGATGAGCAGTTTC
|| || ||||||| | | | ||| || | | | ||| | | ||| || ||| | | | || ||| | ||||| | |||||| |||| | ||||| ||||||||| |||||||||||||| ||||||| | | ||||| | | ||||||||||| ||||| |||||||
tatttactcagaggttttgtttgtg--tgtgtgtgctttttttttttttttttcaat-----tgtgcatcttctgcaatttatatattcaattttcatttgaag-cagCCACAAACAAAAAATGGTATTGATACCTTTGGTGGTCTTGGAGCAACTATAGTAGATTGTCTTGATACCTTATTCATAATGGGTCTTGATGAACAGTTTC
upper sequence: AT1G51590.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv09s0054g00370.t01 (Vitis vinifera), 3'ss of exon 3
caaagattttgttaagaactaagattattttcttcctgaactctgcaaaaaaaatattggtctgaagctattcttgtttctt--------tcctttttttattgtcagCCTCGGACAAAAGATGGCACTGATAGCTTTGGTGGCCTTGGAGCAACTATGGTAGATTCTTTAGATACACTCTATATAATGGGTCTAGATGAGCAGTTTC
| ||| | | || | || | | | | | | || | | | | | | | || | |||||| || ||||| | | || |||| |||| ||||| || ||||||||||| | |||||||| | |||||| | ||||||||||| |||||||||||||| |
--------attcctagatttgtggcatttgtatttccatagtgtttatgatgttgtttcattttatccaagttctacaactaacatgcaattgttttttccttaacagCCACAATCCAAGAATGGTGTCAATAGTTTTGGAGGTCTTGGAGCAACATTAATAGATTCTCTTGATACATTATATATAATGGGACTAGATGAGCAGTTCC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.caaaaaaaatattggtctgaagctattcttgtttctttcctttttttattgtcagCCTCGGACAAAAGATGGCACTGATAGCTTTGGTGGCCTTGGAGCAACTATGGTAGATTCTTTAGATACACTCTATATAATGGGTCTAGATGAGCAGTTTC
ctattcttgtttcttt CT-rich tract
tttcctttttttatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
caaagattttgttaagaactaagattattttcttcctgaactctgcaaaaaaaatattggtctgaagctattcttgtttctttcctttttttattgtcagCCTCGGACAAAAGATGGCACTGATAGCTTTGGTGGCCTTGGAGCAACTATGGTAGATTCTTTAGATACACTCTATATAATGGGTCTAGATGAGCAGTTTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG