Sequence
atgc intronic sequence ATGC exonic sequence...atttgacaggagagagacttcagtagtggatatttcttcttatggcattgttttccttactgttcatttgaattatgtttgtttctgcctatggtcttagGTTCAGCTGATAAGACTGTAAAATTCTGGGACCTTGAAACATTCGAGCTTATTGGTTCTGGTGGAACTGAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G08390.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G08390.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G160702_T01 (Zea mays), 3'ss of exon 5
atttgacag--gagagagacttcagtagtggatatttcttcttatggcattgttttccttactg---ttcatttgaattatgtttgtttctgcctatggtcttagGTTCAGCTGATAAGACTGTAAAATTCTGGGACCTTGAAACATTCGAGCTTATTGGTTCTGGTGGAACTGAG
| ||| ||| | |||| || | | || | | ||| |||||| | || | |||||| | || | | ||||||||||||||| ||||| ||||||||||| | || ||||| || | ||||| ||| ||| |||||
----ggcagtgaagaatgtattcatatgtttgtgtgggagctcagaagactgtattccttttgaaactatatctctcttatgtaaaact-tgttgcttcattcagGTTCAGCTGATAAAACTGTCAAATTCTGGGATTTGGAGACATTTGAATTGATTGGATCTACAGGACCTGAG
upper sequence: AT5G08390.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA05G09360.1 (Glycine max), 3'ss of exon 6
atttga--caggagagagacttcagtagtggatatttcttcttatggcattgttttccttactgttcatttgaattatgtttgtttctgcctatggtcttagGTTCAGCTGATAAGACTGTAAAATTCTGGGACCTTGAAACATTCGAGCTTATTGGTTCTGGTGGAACTGAG
| | | | || | ||| ||||| || || | | | | | | |||| ||| ||| | ||| | ||| ||||| ||||| |||| || || |||||||||||||| ||||| || |||||||||||||| | ||| |||||
-ccgggttcttgtgttttcttttggaagtatctatttttttttttaatttgaatgaagtcaagtgtaatttttatttcatttatctctttcc-tgggtttagGCTCAGCAGATAGAACAGTTAAATTCTGGGACCTCGAAACCTTTGAGCTTATTGGTTCAGCTGGTCCTGAG
upper sequence: AT5G08390.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA19G00890.1 (Glycine max), 3'ss of exon 6
-atttgacaggagagagacttcagtagtggatatttcttcttatggcattgttttccttactgttcatttgaattatgtttgtttctgcctatggtcttagGTTCAGCTGATAAGACTGTAAAATTCTGGGACCTTGAAACATTCGAGCTTATTGGTTCTGGTGGAACTGAG
| || | | | || || | || || | | | | | | |||| ||| ||| | ||| | || ||||| || || |||| || || ||||||||||| |||||||| || |||||||||||||| | ||| |||||
tgctggattcttgggttttcttttggatgcatccatttttttttaatttgaatgaagtcaagtgtaatttttatttcatttatctctttcccacgt-ttagGCTCGGCAGATAGAACAGTTAAATTCTGGGATCTTGAAACCTTTGAGCTTATTGGTTCAGCTGGTCCTGAG
upper sequence: AT5G08390.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv10s0071g01150.t01 (Vitis vinifera), 3'ss of exon 5
--atttgacaggagagagacttcagtagtggatatttcttcttatggcattgttttccttactgttcatttgaatt-atgtttgtttctgcctatggtcttagGTTCAGCTGATAAGACTGTAAAATTCTGGGACCTTGAAACATTCGAGCTTATTGGTTCTGGTGGAACTGAG
|| | | | ||||| | || || | | ||||| || || ||| |||| | || | |||| | || | | || |||||||||||||| ||||| |||||||||||||||||||| || ||| | |||||||| | |||| |||||
ttatgttttatgctct-gacttatcacacttttgttctgtcatctaaaattgtgttttatatggtttattttactttaactttggtcttgtcctt--tcacagGTTCAGCTGATAGAACTGTTAAATTCTGGGACCTTGAAACTTTTGAGTTGATTGGTTCAGCTGGACCTGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cattgttttccttactgttcatttgaattatgtttgtttctgcctatggtcttagGTTCAGCTGATAAGACTGTAAAATTCTGGGACCTTGAAACATTCGAGCTTATTGGTTCTGGTGGAACTGAG
tccttac putative branch site (score: 2)
atttgaattatgttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atttgacaggagagagacttcagtagtggatatttcttcttatggcattgttttccttactgttcatttgaattatgtttgtttctgcctatggtcttagGTTCAGCTGATAAGACTGTAAAATTCTGGGACCTTGAAACATTCGAGCTTATTGGTTCTGGTGGAACTGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtttgt