Sequence
atgc intronic sequence ATGC exonic sequencegtaaagttaacaatatcagagtcttcatagtaatcttaccgcattatttccaattcattcagtaactgtcgccttttaaaaaaattatttgttttttgcagCACAATGAAAGAGAATTCATTCTGAAGTTCTCAGCCATGGAGATCTATAATGAGTCTGTAAGAGACCTCTTGAGTACAGACATTAGTCCACTCAGAGTTC
Basic information
species | Arabidopsis thaliana |
transcript | AT3G51150.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G51150.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA01G37340.1 (Glycine max), 3'ss of exon 3
gtaaagttaacaatatcagagtcttcatagtaatcttaccgcattatttccaattcattcagtaactgtcgccttttaaaaaaattatttgttttttgcagCACAATGAAAGAGAATTCATTCTGAAGTTCTCAGCCATGGAGATCTATAATGAGTCTGTAAGAGACCTCTTGAGTACAGACATTAGTCCACTCAGAGTTC
|| | || | | ||||| | || ||| ||| | |||| | || || |||| ||||||| |||||||||||||| ||||||| || || || ||||| |||||||| ||||| || |||||| | ||| ||||| || ||| |||||| |||
---------------gtaggtgaaatacgaacatgtcaatacattaccttgtcttt-ctcaaaaaccttt---ttttgatttggtt-ttaccttttcatagCACAAGGAAAGAGAATTCATGTTGAAGTTTTCGGCAATTGAGATTTATAATGAATCTGTCAGGGACCTCCTTAGTCCAGACTGTACTCCTCTCAGACTTC
upper sequence: AT3G51150.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA11G07950.1 (Glycine max), 3'ss of exon 3
gtaaagttaacaatatcagagtcttcatagtaatcttaccgcattatttccaattcattcagtaactgtcgccttttaaaaaaattatttgttttttgcagCACAATGAAAGAGAATTCATTCTGAAGTTCTCAGCCATGGAGATCTATAATGAGTCTGTAAGAGACCTCTTGAGTACAGACATTAGTCCACTCAGAGTTC
||| || || | | |||||| | || ||| ||| | |||| | |||| | ||| |||||| |||||||||||||| ||||||| || || || ||||| |||||||| |||||||| |||||| | ||| ||||| || || |||||| |||
---------------gtagatgaaatatgaacatgtcaatgcattaccttgtcttt-ctcaaaaaccatt--tttttgatttggttatac-ctctttatagCACACGGAAAGAGAATTCATGTTGAAGTTTTCGGCAATTGAGATTTATAATGAATCTGTAAGGGACCTCCTTAGTCCAGACTGTACCCCTCTCAGACTTC
upper sequence: AT3G51150.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv04s0023g03060.t01 (Vitis vinifera), 3'ss of exon 3
gtaaagttaacaatatcagagtcttcatagtaatcttaccgcattatttccaattcattcagtaactgtcgcctttta---aaaaaattatttgttttttgcagCACAATGAAAGAGAATTCATTCTGAAGTTCTCAGCCATGGAGATCTATAATGAGTCTGTAAGAGACCTCTTGAGTACAGACATTAGTCCACTCAGAGTTC
||| | | ||| | ||| | | || || ||| | | | | | ||||| | |||||||| || |||| ||||||| ||||||||||| || |||||||||| || |||||||| || ||||| ||||| |||||||| | || |||| | | ||| || || |||
---------gtaatcaaaacaccactata-tcatcccctttcctctctttcagttccataatttcccatttcctttgatgaaaaaaattgttatacatttgtagCACAAGGAAAGAGAATTTCTTTTGAAGTTCTCTGCTATGGAGATTTACAATGAATCTGTCAGAGACCTTCTCAGCTCAGATACTGCTCCGCTTCGACTTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttccaattcattcagtaactgtcgccttttaaaaaaattatttgttttttgcagCACAATGAAAGAGAATTCATTCTGAAGTTCTCAGCCATGGAGATCTATAATGAGTCTGTAAGAGACCTCTTGAGTACAGACATTAGTCCACTCAGAGTTC
cagtaac putative branch site (score: 2)
tttgtttttt putative PPT
ttttaaaaaaattatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaagttaacaatatcagagtcttcatagtaatcttaccgcattatttccaattcattcagtaactgtcgccttttaaaaaaattatttgttttttgcagCACAATGAAAGAGAATTCATTCTGAAGTTCTCAGCCATGGAGATCTATAATGAGTCTGTAAGAGACCTCTTGAGTACAGACATTAGTCCACTCAGAGTTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA