Sequence
atgc intronic sequence ATGC exonic sequencegtgaagctcttataaaacgtgaactacccacatcaaaaataccaatatttgtttatgatagcaaagcaacatgttgatgcagGGTATGCAATACATTCCGACGATAACTAATTACACGAAGCTTTGGTGGGTTCCTAATGTTGTTGTGGCTCATCAAAAGGAAGGAATTGAAGCTATTCATT
Basic information
species | Arabidopsis thaliana |
transcript | AT3G51050.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G51050.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os02g01070.1 (Oryza sativa), 3'ss of exon 7
-----------------------gtgaagctcttataaaacgtgaactacccacatcaaaaataccaatatttgtttatgatagcaaagcaaca-tgttgatgcagGGTATGCAATACATTCCGACGATAACTAATTACACGAAGCTTTGGTGGGTTCCTAATGTTGTTGTGGCTCATCAAAAGGAAGGAATTGAAGCTATTCATT
||| |||| | | ||| | ||| || | | | | | | | | || | || | | || || ||||||| || || || || || | ||||||||||||||||||||||||| || || |||| ||||| || || |||
ctttttcccccaatacaatcacagtggtctcacaccaaaattttatttacatatatcgtgttactttatcatgaaatgtaacatctttcctctactgcagTCACAAAGGACGCTTTATGTTCCGACAATCACCAACTATACTCAAGTTTGGTGGGTTCCTAATGTTGTTGTTGCCCACGAAAAAGAAGGGATAGAGGCTG------
upper sequence: AT3G51050.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA01G37580.1 (Glycine max), 3'ss of exon 9
-------------------gtgaagctcttataaaacgtgaactacccacatcaaaaataccaatatttgtttatgatagcaaagcaacatgttgatgcagGGTATGCAATACATTCCGACGATAACTAATTACACGAAGCTTTGGTGGGTTCCTAATGTTGTTGTGGCTCATCAAAAGGAAGGAATTGAAGCTATTCATT
|| | | | | || | |||| | | | | |||| || | ||| | | |||||| | | ||| |||| || ||||| || ||||| | |||||||||||||||||||||||||||||||||| ||||| || || |||||| ||||||
taacaaataaaatcaacatgttatgacactg-agaagataaactttttgaaagagatggagaaataatttgcagtcataatgtttctctcttgcaatgcagCACCTTCCTTACGTTCCCACCATAACCAACTACACTCAAGTTTGGTGGGTTCCTAATGTTGTTGTGGCTCATCAGAAGGAGGGCATAGAAGCTCTTCATT
upper sequence: AT3G51050.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA11G07720.1 (Glycine max), 3'ss of exon 9
-----------------gtgaagctcttat-aaaacgtgaactacccacatcaaaaataccaatatttgtttatgatagcaaagcaacatgttgatgcagGGTATGCAATACATTCCGACGATAACTAATTACACGAAGCTTTGGTGGGTTCCTAATGTTGTTGTGGCTCATCAAAAGGAAGGAATTGAAGCTATTCATT
|| | | ||| | || |||| | | | | || | || | ||| | || | |||||| | | || |||| || ||||| || ||||| | ||||||||||||| |||||||||||| ||||||| ||||| || || |||||| |||||
acaaaaaaaatcgccatgttatgacactatgagaaaatgaattttttgagaaagatggagaaagaatttgcagtcataatgtttctaccttggaatgcagCACCTTCCTTATGTTCCTACCATAACCAACTACACTCAAGTTTGGTGGGTTCCCAATGTTGTTGTGTCTCATCAGAAGGAGGGCATAGAAGCTCTTCATC
upper sequence: AT3G51050.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv04s0023g02750.t01 (Vitis vinifera), 3'ss of exon 9
-----------gtgaagctcttataaaacgtgaactacccacatcaaaaataccaatatttgtttatgatagcaaagc-------aacatgttgatgcagGGTATGCAATACATTCCGACGATAACTAATTACACGAAGCTTTGGTGGGTTCCTAATGTTGTTGTGGCTCATCAAAAGGAAGGAATTGAAGCTATTCATT
| ||| || | | | || | | | | | || || | | | | |||||| || ||| || |||| || ||||| || ||||| | || |||||||||||||||||||||||||||||||||| ||||||||| |||||| |||| |
taattactgtattagtaagaatatcaataaccactttcttgcactggtgagtttatcttgcataaaccatgtcataacctgttttactttcttgatgtagCCGTTGCCTTATGTTCCTACCATAACAAACTACACTCAACTCTGGTGGGTTCCTAATGTTGTTGTGGCTCATCAAAGGGAAGGAATAGAAGCTGTTCACT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ccacatcaaaaataccaatatttgtttatgatagcaaagcaacatgttgatgcagGGTATGCAATACATTCCGACGATAACTAATTACACGAAGCTTTGGTGGGTTCCTAATGTTGTTGTGGCTCATCAAAAGGAAGGAATTGAAGCTATTCATT
tgttgat putative branch site (score: 4)
aaaaataccaatattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgaagctcttataaaacgtgaactacccacatcaaaaataccaatatttgtttatgatagcaaagcaacatgttgatgcagGGTATGCAATACATTCCGACGATAACTAATTACACGAAGCTTTGGTGGGTTCCTAATGTTGTTGTGGCTCATCAAAAGGAAGGAATTGAAGCTATTCATT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC