Sequence
atgc intronic sequence ATGC exonic sequence...tagcagcagccatttttcccctgtttctgtatgtgatactatatatgctaagagcttgtattacaatggaatcgattgtttaaactaatttcttgtatagGGATTCTTCAATTTCACAGCACGGAGGCCGCAACATCTCTTGGAAATTTTGGAGTTAGGTTACAATGTTATGTACAACGATGTTGATATGGTTTGGTTGC
Basic information
species | Arabidopsis thaliana |
transcript | AT4G01220.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G01220.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA08G09360.1 (Glycine max), 3'ss of exon 1
--tagcagcagccattttt-cccctgtttctgtatgtgatactatatatgctaagagcttgtattacaatggaatcgattgtttaaactaatttcttgtatagGGATTCTTCAATTTCACAGCACGGAGGCCGCAACATCTCTTGGAAATTTTGGAGTTAGGTTACAATGTTATGTACAACGATGTTGATATGGTTTGGTTGC
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cttgtctgccgtggtgttgattattggaactgtctcttaatttctttctcgtgtgtggtgctga-gttttaaaatccattctt--gtttatttcactgtctagGGTTTCTTCAACTTTACAGCAAGGCGGCCAAGCCATCTGCTGAAGATTTTGGAGCTTGGATATAGTGTGATGTACAATGATGTTGATATGGTTTGGTTGG
upper sequence: AT4G01220.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv15s0046g01630.t01 (Vitis vinifera), 3'ss of exon 1
--tagcagcagccatttttcccctgtttctgtatgtga-tactatatatgctaagagcttgtattacaatggaatcgattgtttaaactaatttc-ttgtatagGGATTCTTCAATTTCACAGCACGGAGGCCGCAACATCTCTTGGAAATTTTGGAGTTAGGTTACAATGTTATGTACAACGATGTTGATATGGTTTGGTTGC
| ||| | |||| | | ||| | ||| || | |||| || ||||||| | | || ||| | | ||||| ||||| |||| ||||||||||| || | || ||||| | ||||| || | ||||||||| | || || |||||||||||||| |||||||||||||| ||||||
ctttgcatttcctatttcttctttgtcgatagtgatgaatattttata----gagtttttgtattggattatttaaaatgtttttgattgatttcattgtacagGGGTTCTTCAATTTTACTTCCCGAAGGCCTCGCCATCTGCTGAATATTTTGGAGCTTGGATATAATGTTATGTACAATGATGTTGATATGGTGTGGTTGG
upper sequence: AT4G01220.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv13s0019g04760.t01 (Vitis vinifera), 3'ss of exon 1
tagcagcagccatttttcccctgtttctgtatgtgatactatatatgctaagagcttgtattacaatggaatcgattgtttaaac---taatttc-ttgtatagGGATTCTTCAATTTCACAGCACGGAGGCCGCAACATCTCTTGGAAATTTTGGAGTTAGGTTACAATGTTATGTACAACGATGTTGATATGGTTTGGTTGC
|| | | | || | | |||| | || | |||| || | | | | | | |||| | | ||||| || || |||| ||||| ||||| || | || ||||| | || || || | ||||||||| | || |||||||||||||| || |||||||| ||||| ||||||
--gctatacactgtctttctcattttcatttcttgctg--atattgatcaatcatcaatgtgggattagtttttgaagtttgattgcttgatttcattatacagGGTTTCTTTAATTTTACTTCTCGAAGGCCTCGCCACCTACTGTACATTTTGGAGCTTGGATACAATGTTATGTATAATGATGTTGACATGGTATGGTTGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgctaagagcttgtattacaatggaatcgattgtttaaactaatttcttgtatagGGATTCTTCAATTTCACAGCACGGAGGCCGCAACATCTCTTGGAAATTTTGGAGTTAGGTTACAATGTTATGTACAACGATGTTGATATGGTTTGGTTGC
aactaat putative branch site (score: 2)
tttcttgt CT-rich tract
tttaaactaatttctt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tagcagcagccatttttcccctgtttctgtatgtgatactatatatgctaagagcttgtattacaatggaatcgattgtttaaactaatttcttgtatagGGATTCTTCAATTTCACAGCACGGAGGCCGCAACATCTCTTGGAAATTTTGGAGTTAGGTTACAATGTTATGTACAACGATGTTGATATGGTTTGGTTGC
- - - - - - - - - - ctgtttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaactaa