Sequence
atgc intronic sequence ATGC exonic sequencegtatgttctttagacctttctttgtctgcatttcactgagagatatcatatctttctgactttttcatttctgcagTATTCCAAAAACAATTGGTGTCTCGATTCCAATGAAAGCGACCTTCTTTATAACATACATAATGGTGGATGGATGGGCTGGTGTTGCTGGTGAGATATTG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G15430.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G15430.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os01g35050.3 (Oryza sativa), 3'ss of exon 9
----------gtatgttctttagacctttctt----tgtctgcatttcactgagaga-tatcatat--ctttctgact-------ttttcatttctgcagTATTCCAAAAACAATTGGTGTCTCGATTCCAATGAAAGCGACCTTCTTTATAACATACATAATGGTGGATGGATGGGCTGGTGTTGCTGGTGAGATATTG
| ||| || | | || | || ||| | ||| | | | ||| |||| ||| ||| | | | ||||| || |||| |||||||||| | |||||||||||||| ||||| ||||||||||| ||||||| ||||| |||||||| || |||||||| || ||
catgctcttcatttgtgctacaatttcctattgtatttcctttctttttcgaagaaactcttatactccttttcaactgtacttatttgcctctttgcagAATACCAAGGACAATTGGTGAAGCAATTCCAATGAAAGCAACCTTTTTTATAACATATGTAATGGTTGATGGTTGGGCTGGGGTAGCTGGTGAAATTTTA
upper sequence: AT4G15430.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G021194_T01 (Zea mays), 3'ss of exon 9
----------------------gtatgttctttagacctttctttgtctgcatttcactgagagatatcat--atctttctgactttttcatttctgcagTATTCCAAAAACAATTGGTGTCTCGATTCCAATGAAAGCGACCTTCTTTATAACATACATAATGGTGGATGGATGGGCTGGTGTTGCTGGTGAGATATTG
| | |||| || || | ||| | ||| || || | || || || | |||| | | | ||| || |||| || ||||||| | ||||||||||| || ||||| ||||||||||| | |||||| ||||| |||||||| || |||||||||||||||
atttgaaggtcctgctattaccatggcatatttaagccctttcgtttctccttttgcgtgtatgaatttatttatattgtctatttttcctcgtttacagAATACCAAGGACGATTGGTGAAGCAATTCCAATGAAGGCAACCTTTTTTATAACATATACAATGGTTGATGGTTGGGCTGGGGTAGCTGGTGAGATATTG
upper sequence: AT4G15430.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G064189_T01 (Zea mays), 3'ss of exon 2
---------------------gtatgt-tctttagacctttctttgtctgcatttcactgagagatatcat--atctttctgactttttcatttctgcagTATTCCAAAAACAATTGGTGTCTCGATTCCAATGAAAGCGACCTTCTTTATAACATACATAATGGTGGATGGATGGGCTGGTGTTGCTGGTGAGATATTG
| | || | |||| || || | ||| | ||| || || | || || || | |||| | | | ||| || |||| || ||||||| | ||||||||||| || ||||| ||||||||||| | |||||| ||||| |||||||| || |||||||||||||||
tttctggtatgtcactaatttgaaggtatatttaagccctttcgtttctccttttgcgtgtatgaatttatttatattgtctatttttcctcgtttacagAATACCAAGGACGATTGGTGAAGCAATTCCAATGAAGGCAACCTTTTTTATAACATATACAATGGTTGATGGTTGGGCTGGGGTAGCTGGTGAGATATTG
upper sequence: AT4G15430.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA02G43910.2 (Glycine max), 3'ss of exon 9
-------------------gtatgttctttagacctttctttgtctgcatttcactgagagatatca-tatctt----tctgactttttcatttctgcagTATTCCAAAAACAATTGGTGTCTCGATTCCAATGAAAGCGACCTTCTTTATAACATACATAATGGTGGATGGATGGGCTGGTGTTGCTGGTGAGATATTG
|| | || ||| | | || |||| | || | ||| || | | | | | ||| | ||||| ||||||||||||||||||||||| ||||||||||| || || ||||| ||||| ||||||||||||||||| |||||||| |||||||||||| ||
caacttgcctcttctgacgataaagttttatagtcttgagggttatagatgtcacaaatagctttcaataacctaaagtaaacatatgccatgtatgcagAATTCCAAAAACAATTGGTGTCTCAATTCCAATGAAGGCAACTTTCTTCATAACTTACATAATGGTGGATGGGTGGGCTGGATGTGCTGGTGAGATTTTA
upper sequence: AT4G15430.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv12s0059g01090.t01 (Vitis vinifera), 3'ss of exon 8
----------------gtatgttctttagacctttctttgtc---------tgcatttcactgagagatatcatatctttctgactttttcatttctgcagTATTCCAAAAACAATTGGTGTCTCGATTCCAATGAAAGCGACCTTCTTTATAACATACATAATGGTGGATGGATGGGCTGGTGTTGCTGGTGAGATATTG
| || ||||| || | || | | | || |||| | | | |||| | | || |||| |||||||| ||||| | || || ||| ||||||||||| || || ||||| ||||| ||||||||||| |||||||||||||| ||| |||| ||||| |
aataccatttttgttactggattaattagatctggatgtgacatcaagtgctactttgatctgatatgtttaatataaagtcaagtggttgattt-tgcagTATCCCAAAGATCATCGGAACCTCAATTCCAATGAAGGCAACTTTCTTCATAACTTACATAATGGTTGATGGATGGGCTGGAGTTTCTGGGGAGATTCTA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgtctgcatttcactgagagatatcatatctttctgactttttcatttctgcagTATTCCAAAAACAATTGGTGTCTCGATTCCAATGAAAGCGACCTTCTTTATAACATACATAATGGTGGATGGATGGGCTGGTGTTGCTGGTGAGATATTG
ttctgac putative branch site (score: 2)
tctttctgactttttc CT-rich tract
tttttcattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgttctttagacctttctttgtctgcatttcactgagagatatcatatctttctgactttttcatttctgcagTATTCCAAAAACAATTGGTGTCTCGATTCCAATGAAAGCGACCTTCTTTATAACATACATAATGGTGGATGGATGGGCTGGTGTTGCTGGTGAGATATTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA