Sequence
atgc intronic sequence ATGC exonic sequencegtaatatatagctcttccttatttctcttccgagacattatcaaaacatttcataatcatttgagcctttttatgatgttttgactgtaacagTTCATATCGATACCCGAAGAGCGTTACAATGAGTACAGACTAAGTTCAGATTTCATTAAAGAATACATATTCCCTGGTGGATGCCTTCCTTCTTTAGCCA
Basic information
species | Arabidopsis thaliana |
transcript | AT3G23530.1 |
intron # | 19 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G23530.1 (Arabidopsis thaliana), 3'ss of exon 19
lower sequence: LOC_Os12g16650.2 (Oryza sativa), 3'ss of exon 20
--gta-atatatagctcttccttatttctcttccgagacattatcaaaacatttcataatcatttgagcctttttatgatgttttgactgtaacagTTCATATCGATACCCGAAGAGCGTTACAATGAGTACAGACTAAGTTCAGATTTCATTAAAGAATACATATTCCCTGGTGGATGCCTTCCTTCTTTAGCCA
|| | | | | | ||| | ||| || | | | | | | || || || | ||| ||| || | | ||||| || || || || || || || || |||||||| | ||| ||||| || ||||||||||||||||||||||||||||||||||||||| | |
gtgtgtacaaacaac-ctttgtcattgtcattgacactgactgttgatatatcccac------ttaaa--tttacatgg------gattattccagTTTATCTCAATTCCGGAGGAACGGTATGATGAGTACCGGAGAAGCTCAGACTTTATTAAAGAATACATATTCCCTGGTGGATGCCTTCCTTCTCTGACTC
upper sequence: AT3G23530.1 (Arabidopsis thaliana), 3'ss of exon 19
lower sequence: Vv05s0049g01650.t01 (Vitis vinifera), 3'ss of exon 21
----gtaatatatagctcttccttatt----tctcttccgagacattatcaaaacatttcataatcatttgagcctttttatgatgttttgactgtaac-agTTCATATCGATACCCGAAGAGCGTTACAATGAGTACAGACTAAGTTCAGATTTCATTAAAGAATACATATTCCCTGGTGGATGCCTTCCTTCTTTAGCCA
| |||| | | || || | || | | | |||| | ||| | || ||| | ||| ||| ||| | | ||||||||||||| || || || | ||| |||| |||||| ||| |||||||| || || |||||||| ||||||||||||||| | ||||| ||| |
gatttgattatactgttgatcaaaataaaaatgtcattcttatgaagttcaatatttttttccaacaaccgagggtgttt--gatttttcatttttccttagTTCATATCGATCCCGGATGAAAGGTACGATGAATACAGAAGAAGCTCAGATTTTATAAAGGAATACATTTTCCCTGGTGGATGCTTGCCTTCATTAAGTA
upper sequence: AT3G23530.1 (Arabidopsis thaliana), 3'ss of exon 19
lower sequence: Vv05s0049g01620.t01 (Vitis vinifera), 3'ss of exon 17
--------gtaata-tatagctcttccttatttctcttccgagacattatcaaaacatttcataatcatttgagcctttttatgatgttttgactgtaac-agTTCATATCGATACCCGAAGAGCGTTACAATGAGTACAGACTAAGTTCAGATTTCATTAAAGAATACATATTCCCTGGTGGATGCCTTCCTTCTTTAGCCA
| ||| | | | | | |||||| | | | | | ||||| | || |||| | ||| ||| ||| | | ||||||||||||| || || || | ||| ||||||| ||| ||| |||||||| || || |||||||| ||||||||||||||| | ||||| ||| |
ggggtttaatcatactggggtttaagaatgtcattcttcctataaagttaaatgttatttcccca-caactgaggatattt--gatttttcatttttccttagTTCATATCGATCCCGGATGAAAGGTACGATGAGTATAGAAGAAGCTCAGATTTTATAAAGGAATACATTTTCCCTGGTGGATGCTTGCCTTCATTAAGTA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatcaaaacatttcataatcatttgagcctttttatgatgttttgactgtaacagTTCATATCGATACCCGAAGAGCGTTACAATGAGTACAGACTAAGTTCAGATTTCATTAAAGAATACATATTCCCTGGTGGATGCCTTCCTTCTTTAGCCA
ttttgac putative branch site (score: 3)
atttcataatcattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatatatagctcttccttatttctcttccgagacattatcaaaacatttcataatcatttgagcctttttatgatgttttgactgtaacagTTCATATCGATACCCGAAGAGCGTTACAATGAGTACAGACTAAGTTCAGATTTCATTAAAGAATACATATTCCCTGGTGGATGCCTTCCTTCTTTAGCCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA