Sequence
atgc intronic sequence ATGC exonic sequence...gtcagatgatttgtgttattagctctttccatcaacacggcaactattttggattttggtttgttatgtctatttgaatttaaatataaactgacaacagGGATATGCACCACCTAATTCAGATAGAAGGGAGGCTGTTCTGAGAAGAAAACGTCTTGAATATCTGGAATCTGTTGGCCAATTTTATGACCTTCCAGATT
Basic information
species | Arabidopsis thaliana |
transcript | AT2G30710.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G30710.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os09g34040.1 (Oryza sativa), 3'ss of exon 4
gtcagatgatttgtgttattagctctttccatcaacacggcaactattttggattttggtttgttatgtctatttgaatttaaatataaactgacaacagGGATATGCACCACCTAATTCAGATAGAAGGGAGGCTGTTCTGAGAAGAAAACGTCTTGAATATCTGGAATCTGTTGGCCAATTTTATGACCTTCCAGATT
| |||| || || ||| | || ||| | | | | || ||| | || ||| | | ||| | |||||||||||||||||||||| |||||||||| || | |||||||| || ||| | ||||| || | |||| |||| |||| ||||| |||| |||
-----------------gtgagcttatttcaa-gacatgt------ttcaatccttttaataggtgttcctgtttcgaatttaatgtcagctggctacagGGATATGCACCACCTAATGCAGATAGAAGAGAAGGTGTTCTGACGAGGAAAAGACTTGAGTACGTTGAATGTGTTTCTCAATACTATGATATTCCTGATA
upper sequence: AT2G30710.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA12G05350.1 (Glycine max), 3'ss of exon 4
gtcagatgatttgtgttattagctctttccatcaaca-cggcaactattttggattttggtttgttatgtctatttgaatttaaatataaactgacaacagGGATATGCACCACCTAATTCAGATAGAAGGGAGGCTGTTCTGAGAAGAAAACGTCTTGAATATCTGGAATCTGTTGGCCAATTTTATGACCTTCCAGATT
| | ||| | | | | | | | | | ||| || | |||| | | | || | | | |||||||| ||| ||||||||||||||||||||||||||||||||||||||||||||| ||||| ||||| ||||| ||||| ||||| || | | || || | |||||| |||| |||
attatttgagtaaggg-gtcaacattattgacccacagttacatgtgtttttatgggtagcattttgtcttcctggaaatttaaagatatactgacaacagGGATATGCACCACCTAATTCAGATAGAAGGGAGGGAGTTCTAAGAAGGAAACGCCTTGAGTATCTTGACTGTATTTCTCAGTATTATGATATTCCTGATA
upper sequence: AT2G30710.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA11G13330.2 (Glycine max), 3'ss of exon 4
gtcagatgatttgtgttattagctctttccatcaaca-cggcaactattttggattttggtttgttatgtctatttgaatttaaatataaactgacaacagGGATATGCACCACCTAATTCAGATAGAAGGGAGGCTGTTCTGAGAAGAAAACGTCTTGAATATCTGGAATCTGTTGGCCAATTTTATGACCTTCCAGATT
||| | | | | | | | | | | | ||| | | |||| | | | || | | | |||||||| ||| ||||||||||||||||||||||||||||||||||||||||||||| ||||| ||||| || || ||||| ||||| || | | || || | |||||| |||| |||
atcattttagtaaggg-gtcaacattattgacccacagtcacgtgtgtttttatggatagcattttgtcttcctggaaatttaaagatatactgacaacagGGATATGCACCACCTAATTCAGATAGAAGGGAGGGAGTTCTAAGAAGGAAGCGCCTTGAGTATCTTGACTGTATTTCTCAGTATTATGATATTCCTGATA
upper sequence: AT2G30710.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA13G42180.1 (Glycine max), 3'ss of exon 4
---gtcagatgatttgtgttattagctctttccatcaacacggcaactattttggattttggtttgttatgtctatttgaatttaaatataaactgacaacagGGATATGCACCACCTAATTCAGATAGAAGGGAGGCTGTTCTGAGAAGAAAACGTCTTGAATATCTGGAATCTGTTGGCCAATTTTATGACCTTCCAGATT
|||| || | | || ||| | || || | |||| || || | | |||| || || ||| ||||| |||||||||||||||||||||||||||||||||||||||| ||| ||| ||| || || ||||| ||||| || | |||| || | |||||| |||| |||
ccctatagataatctttttt-ttaaagtaataaataggttaatcacatgttttctatggatactttcttttcttattaaaaatttaatg--aactggcaacagGGATATGCACCACCTAATTCAGATAGAAGGGAGGGAGTTTTGAAAAGGAAGCGCCTTGAGTATCTTGACTGTGTTTCTCAGTATTATGATATTCCTGATA
upper sequence: AT2G30710.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA15G03200.1 (Glycine max), 3'ss of exon 4
----gtcagatgatttgtgttattagctctttccatcaacacggcaactattttggattttggtttgttatgtctatttgaatttaaatataaactgacaacagGGATATGCACCACCTAATTCAGATAGAAGGGAGGCTGTTCTGAGAAGAAAACGTCTTGAATATCTGGAATCTGTTGGCCAATTTTATGACCTTCCAGATT
|||| || | | || || | | || | |||| || || | | |||| || || || || || |||||||||||||||||||||||||||||||||||||||| ||| ||| ||| || || ||||| ||||| || | |||| || | |||||| |||| |||
accctatagataatctttttt--taaagtaataagtaggttaatcacatgttttctatggatactttcttttcttattaaaaatttgatgaaa--tgtcaacagGGATATGCACCACCTAATTCAGATAGAAGGGAGGGAGTTTTGAAAAGGAAGCGCCTTGAGTATCTTGACTGTGTTTCTCAGTATTATGATATTCCTGATA
upper sequence: AT2G30710.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv05s0094g00070.t01 (Vitis vinifera), 3'ss of exon 4
gtcagatgatttgtgttattagctctttccatcaaca-cggcaactattttggattttggtttgttatgtctatttgaa-tttaaatataaactgacaacagGGATATGCACCACCTAATTCAGATAGAAGGGAGGCTGTTCTGAGAAGAAAACGTCTTGAATATCTGGAATCTGTTGGCCAATTTTATGACCTTCCAGATT
|| || | | | ||| || | | | | | | | || | | | | |||| ||| | ||||| ||||||||| |||||||||||||||||||||||||||||||||||||||||||||| |||||||| ||| || || ||||| ||||| || | |||| || | ||||||| |||||||
-tctgagtacaagcatacctagtatggtctcttattaacagtgattgttattggactatatctgtt-tgtttggttgaagtttaaatatgaactgacaacagGGATATGCACCACCTAATTCAGATAGAAGGGAGGGTGTTCTGAAAAGGAAGCGCCTTGAGTATCTTGACTGTGTTTCTCAGTATTATGACATTCCAGACA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attttggattttggtttgttatgtctatttgaatttaaatataaactgacaacagGGATATGCACCACCTAATTCAGATAGAAGGGAGGCTGTTCTGAGAAGAAAACGTCTTGAATATCTGGAATCTGTTGGCCAATTTTATGACCTTCCAGATT
aactgac putative branch site (score: 2)
tttgttatgtctattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcagatgatttgtgttattagctctttccatcaacacggcaactattttggattttggtttgttatgtctatttgaatttaaatataaactgacaacagGGATATGCACCACCTAATTCAGATAGAAGGGAGGCTGTTCTGAGAAGAAAACGTCTTGAATATCTGGAATCTGTTGGCCAATTTTATGACCTTCCAGATT
- - - -gatttgt
- - - - - - - - - - - - - - -catcaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggtttgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aatataaa