Sequence
atgc intronic sequence ATGC exonic sequence...tgtgccaaagaataatgtattggaaacaaataaaagagatacttcgttggaccttcaagaattatgagagaccataaccagattatctttcattttacagAATGCAGGGATGCGTCTCTATGGGGGTGCACAATATCACCGTGCCATGGCTGAGTTTCGTTTTCTAGTTGGTGCTATCAAATGTCCCCCAATAACGAGGG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G19720.2 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G19720.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA08G07990.2 (Glycine max), 3'ss of exon 7
-tgtgccaaagaata-atgtattggaaacaaataaaagagatacttcgttggacc-ttcaagaattatgagagaccataaccagattatctttcattttacagAATGCAGGGATGCGTCTCTATGGGGGTGCACAATATCACCGTGCCATGGCTGAGTTTCGTTTTCTAGTTGGTGCTATCAAATGTCCCCCAATAACGAGGG
|||| | | | || | | ||| | | || || | | | | ||| | || | |||| |||| | |||||||||||||||||||||| ||||| |||||||||||||| || || |||||||| ||||||||| | ||||| | ||||| ||||||||||| || |||
tcatgcccgtatacataaataatacatacatttcacagtcctatattttcagtttactttgtctctataatctgaca-agccagtctatccatg--catacagAATGCAGGGATGCGTCTTTATGGTGGTGCACAATATCATCGGGCAATGGCTGAATTTCGTTTTTTGGTTGGAGGAATCAAGTGTCCCCCAATTACTCGGG
upper sequence: AT3G19720.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA05G24890.1 (Glycine max), 3'ss of exon 5
tgtgccaaagaataatgtattggaaacaaataaaagaga-tacttcgttggaccttcaagaattatgagagaccataaccagattatctttcattttacagAATGCAGGGATGCGTCTCTATGGGGGTGCACAATATCACCGTGCCATGGCTGAGTTTCGTTTTCTAGTTGGTGCTATCAAATGTCCCCCAATAACGAGGG
||| | |||||| || | | | || | || | | || | | | || | | | | || || | ||||||||||||||||||||| ||||| |||||||||||||| || || |||| ||| ||||||||| | ||||| | ||||| ||||||||||| || |||
tgtatgcataaataataaataatacatacatttcacagtcttgtattttcagtttactttgtctctgtaatctgacatgctagtttatacacacat-acagAATGCAGGGATGCGTCTTTATGGTGGTGCACAATATCATCGGGCAATGGGTGAATTTCGTTTTGTGGTTGGAGGAATCAAGTGTCCCCCAATTACTCGGG
upper sequence: AT3G19720.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv12s0055g00490.t01 (Vitis vinifera), 3'ss of exon 9
tgtgccaaagaata-atgtattggaaacaaataaaagagatacttcgttggacct---tcaagaattatgagagaccataaccagattatctttcattttacagAATGCAGGGATGCGTCTCTATGGGGGTGCACAATATCACCGTGCCATGGCTGAGTTTCGTTTTCTAGTTGGTGCTATCAAATGTCCCCCAATAACGAGGG
| | | | | | | | || | | | || || | | | || | || | | ||| ||| ||||| ||||||| ||||||||||| |||||||||||||||||||| ||||| |||||||| || |||||| | ||||| | ||||||||||| ||||| || ||||
----tctaggcacatactaactctaagctttcctattcattgtttgtttacatttaaatagagtagcatacagaaagagtgtggttttactttttattttgtagAATGCGGGGATGCGTCTTTATGGGGGTGCACAATATCATCGTGCAATGGCTGAATTCCGTTTTGTGGTTGGAGGAATCAAATGTCCTCCAATTACAAGGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttggaccttcaagaattatgagagaccataaccagattatctttcattttacagAATGCAGGGATGCGTCTCTATGGGGGTGCACAATATCACCGTGCCATGGCTGAGTTTCGTTTTCTAGTTGGTGCTATCAAATGTCCCCCAATAACGAGGG
ccataac putative branch site (score: 3)
ttatctttcatttt putative PPT
attatctttcatttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgtgccaaagaataatgtattggaaacaaataaaagagatacttcgttggaccttcaagaattatgagagaccataaccagattatctttcattttacagAATGCAGGGATGCGTCTCTATGGGGGTGCACAATATCACCGTGCCATGGCTGAGTTTCGTTTTCTAGTTGGTGCTATCAAATGTCCCCCAATAACGAGGG
- - -caaagaa
- - - - - - - - - - - -aaacaaa
- - - - - - - - - - - - - - - - aaagaga
- - - - - - - - - - - - - - - - - - - - - - - - - - - -caagaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gagacca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaccaga