Sequence
atgc intronic sequence ATGC exonic sequencegtaagtgttacctactctctcctcttaatctttggttcccttaatctatgaacttcgtttcatgaatggctcaatgtgtgtttctttctactacagAGGAAAATTACCAATCGCCCCCTTGCTGGAACTGTCAGAAGAGGGAAGACACCCAAAGAAGATCTAATGCTGGAAAAAGAGCTCTTAAGCGATGAAAAAC
Basic information
species | Arabidopsis thaliana |
transcript | AT2G29690.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G29690.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA20G23680.2 (Glycine max), 3'ss of exon 7
gtaagtgttacctactctctcctcttaatctttggttcccttaatc---tatgaacttcgtttcatgaatggc-----tcaatgtgtgtttctt----tctactacagAGGAAAATTACCAATCGCCCCCTTGCTGGAACTGTCAGAAGAGGGAAGACACCCAAAGAAGATCTAATGCTGGAAAAAGAGCTCTTAAGCGATGAAAAAC
||| || || | | | | |||| || || | |||||||||| || || | | | | ||| | |||| | | | ||||||| || || |||||||| ||||||||||| ||||| |||||||| || ||||| ||||||||| | ||| |||| ||| | || || | |||||||| |
-------ttattaaccctttt-tatgattcttaaattttaatagaccattatgaacttcattacaggtctaacaagtattaataggcatttcatatccttttttacagAGAAAGATCACCAATCGGCCCCTTGCTGGTACTGTTAGAAGAGGAAAAACACCAAAAGAAGATATCATGTTGGAGAAACAACTTTTGAATGATGAAAAGC
upper sequence: AT2G29690.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA10G43210.1 (Glycine max), 3'ss of exon 4
gtaagtgttacctactctctcctcttaatcttt--ggttcccttaatctatgaacttcgtttcatgaatggc-----tcaatgtgtgtttctt----tctactacagAGGAAAATTACCAATCGCCCCCTTGCTGGAACTGTCAGAAGAGGGAAGACACCCAAAGAAGATCTAATGCTGGAAAAAGAGCTCTTAAGCGATGAAAAAC
| | | | | | | ||| || | | | || |||||||||| || || | | | | ||| | |||| | | | |||||| || || |||||||| ||||||||||| ||||| ||||||| || ||||| ||||||||| | ||| |||| ||||| || |||| |||||||| |
-------accctttttatgttttttaaattttatagacttgttaaaattatgaacttcattacaggtctaacaagtattaataggcatttcatatcctttttgacagAGAAAGATCACCAATCGGCCCCTTGCTGGTACTGTTAGAAGAGAAAAAACACCGAAAGAAGATATCATGTTGGAGAAAGAACTTTTAAATGATGAAAAGC
upper sequence: AT2G29690.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv06s0004g06320.t01 (Vitis vinifera), 3'ss of exon 7
------gtaagtgttacctactctctcctcttaatctttggttcccttaatctatgaacttcgtttcatgaatggctcaatgtgtgtttctttctactacagAGGAAAATTACCAATCGCCCCCTTGCTGGAACTGTCAGAAGAGGGAAGACACCCAAAGAAGATCTAATGCTGGAAAAAGAGCTCTTAAGCGATGAAAAAC
| ||| || | | | || | || | ||| | | | || | | | || || | | | | | | |||| | |||| ||||| || ||||| || ||||| ||||||||||||||||| ||||||||| | ||| ||||||| |||| | |||||||| |
tttcctgcaag-gtaatgaggtttttcatatttttatttagattttcattttcatcggcactgact-atcaaggattggcccccttccattcttatttgcagAACAGGATTATTAATCGACCTCTTGCCGGGACTGTTAGAAGAGGGAAGACACCTAAAGAAGATATCATGTTGGAAAACCAGCTTCGGAATGATGAAAAGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taatctatgaacttcgtttcatgaatggctcaatgtgtgtttctttctactacagAGGAAAATTACCAATCGCCCCCTTGCTGGAACTGTCAGAAGAGGGAAGACACCCAAAGAAGATCTAATGCTGGAAAAAGAGCTCTTAAGCGATGAAAAAC
ccttaat putative branch site (score: 4)
tgtttctttctact putative PPT
tttcttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtgttacctactctctcctcttaatctttggttcccttaatctatgaacttcgtttcatgaatggctcaatgtgtgtttctttctactacagAGGAAAATTACCAATCGCCCCCTTGCTGGAACTGTCAGAAGAGGGAAGACACCCAAAGAAGATCTAATGCTGGAAAAAGAGCTCTTAAGCGATGAAAAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT