Sequence
atgc intronic sequence ATGC exonic sequencegtaaaccgtaaactgctggtttgtttgtttcaagacttcacatttcagctcttggctattttcgctgattcaatttccaatgtagGCATGCAAAATTGTCGAGGGACAACGGTACACGAAAAGGTTGAATGAGAAGCAGATTACTGCTCTCTTGAAAGTTACATGCCAAAGGCCGAGGGACAGAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G43810.2 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G43810.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA02G00510.1 (Glycine max), 3'ss of exon 7
gtaaaccgtaaactgctggtttgtttgtttcaagacttcacatttcagctcttggctattttcgctgattcaatttccaatgt--agGCATGCAAAATTGTCGAGGGACAACGGTACACGAAAAGGTTGAATGAGAAGCAGATTACTGCTCTCTTGAAAGTTACATGCCAAAGGCCGAGGGACAGAG
||| | ||| | ||||| || | ||| | || | || | ||| || | || | |||| ||||||||||| ||||||||||| || || |||||||||||||||||||| || ||||||||| |||||||||| || ||||| || | || |||
gtagg--ggaaattcctggta-attgacataggtgcttttctttcttgtaattatttgatttttcttacatgcttctggttcctcagGCCTGCAAAATTGTTGAGGGACAACGATATACAAAAAGGTTGAATGAGAAGCAAATCACTGCTCTCCTGAAAGTTACTTGTCAAAGACCTCGTGATCGAG
upper sequence: AT5G43810.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA20G28970.1 (Glycine max), 3'ss of exon 8
-----gtaaaccgtaaactgctggtttgtttgtttcaagacttcacatttcagctcttggctattttcgct-gattcaatttccaatgtagGCATGCAAAATTGTCGAGGGACAACGGTACACGAAAAGGTTGAATGAGAAGCAGATTACTGCTCTCTTGAAAGTTACATGCCAAAGGCCGAGGGACAGAG
| || | | ||| | | | | |||| | | | | ||| || | ||| | | || |||| |||| ||||||||||| ||||| ||||| || || ||||| |||||||||||||| ||||| ||||| ||||||||||| ||||| ||||| | || | |
gtagggaaagttcttggcaattggagtagtcactcaacattttcataat---gattttgtgtaatgtcgtttgcttttggttccc---cagGCCTGCAAAATTGTTGAGGGGCAACGTTATACAAAAAGATTGAATGAGAAGCAAATTACGGCTCTATTGAAAGTTACTTGCCAGAGGCCTCGCGATCGGG
upper sequence: AT5G43810.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA10G38770.1 (Glycine max), 3'ss of exon 8
-----gtaaaccgtaaactgctggtttgtttgtttcaagacttcacatttcagctcttggctattttcgctgattcaatttccaatgtagGCATGCAAAATTGTCGAGGGACAACGGTACACGAAAAGGTTGAATGAGAAGCAGATTACTGCTCTCTTGAAAGTTACATGCCAAAGGCCGAGGGACAGAG
| | | | || | | | | |||| | | | | ||| ||| | || | || | |||| ||||||||||| ||||| ||||| || || ||||| |||||||||||||| ||||| ||||| ||||||||||| ||||| || || | || | |
gtaaggacagttcttggcaattgaagtagtcactcaacattttcataat---gattttgtctaatgtcatttgcct--ttggctccccagGCCTGCAAAATTGTTGAGGGGCAACGTTATACAAAAAGATTGAATGAGAAGCAAATTACAGCTCTGTTGAAAGTTACTTGCCAGAGACCTCGCGATCGGG
upper sequence: AT5G43810.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv05s0020g04190.t01 (Vitis vinifera), 3'ss of exon 7
--gtaaaccgtaaactgctggtttgtttgtttcaa--gact--tcacatttcag---ctcttggctattttcgct---gattcaatttccaatg------tagGCATGCAAAATTGTCGAGGGACAACGGTACACGAAAAGGTTGAATGAGAAGCAGATTACTGCTCTCTTGAAAGTTACATGCCAAAGGCCGAGGGACAGAG
| | || | ||| | ||| | | || | || | | || ||| |||| | ||| || ||| | | | || |||| ||||||||||| ||||| || ||||| || |||||||||||||||| ||| ||||||||||| || ||||||||||||||||| || ||||| |
gtacagagtgttagctgataatttttcttttcttactgattgatttggttacaggttctctctgtaattctcatctggaatttacatgcttgtggtttgccagGCCTGCAAAATTGTAGAGGGGCAGCGGTATACCAAAAGGTTGAATGAGAGGCAAATTACTGCTCTATTAAAAGTTACATGCCAAAGACCCAGGGATCAGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.caagacttcacatttcagctcttggctattttcgctgattcaatttccaatgtagGCATGCAAAATTGTCGAGGGACAACGGTACACGAAAAGGTTGAATGAGAAGCAGATTACTGCTCTCTTGAAAGTTACATGCCAAAGGCCGAGGGACAGAG
cgctgat putative branch site (score: 4)
tttcc putative PPT
attcaattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaaccgtaaactgctggtttgtttgtttcaagacttcacatttcagctcttggctattttcgctgattcaatttccaatgtagGCATGCAAAATTGTCGAGGGACAACGGTACACGAAAAGGTTGAATGAGAAGCAGATTACTGCTCTCTTGAAAGTTACATGCCAAAGGCCGAGGGACAGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT