Sequence
atgc intronic sequence ATGC exonic sequence...aatgcatgttatatattgtttagttatagcattagcaacgtgaaacatgaaatgaaatctctatttctgactctcctttttattttatgtgtgaaatcagTTTGGCAGAAATTGGAAGAAGAAAACGCAGACTTTTTCAGGGCATATTATATAAGGCTGAAACTGAAGAAGCAAATAATTTTGTTCAATCATTTGCTTGA
Basic information
species | Arabidopsis thaliana |
transcript | AT3G61700.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G61700.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA07G06230.2 (Glycine max), 3'ss of exon 4
aatgcatgttatatattgt-ttagttatagcattagcaacgtgaaacatgaaatgaaatctctatttctgactctcctttttattttatgtgtg--aaatcagTTTGGCAGAAATTGGAAGAAGAAAACGCAGACTTTTTCAGGGCATATTATATAAGGCTGAAACTGAAGAAGCAAATAATTTTGTTCAATCATTTGCTTGA
| | | || | | | | || ||| | || || ||| | || | || || | |||||| | | |||| || || || | | || ||||| |||||||| ||||||||||| ||||| || || |||||||| || ||||| ||||| ||| |||| ||||||||| | || ||||||||||| |||||
attacttgcattcttgtatattttccataccttttataa-gtgga-tgcaaactcaagtccc-atttctttcaatgctttgtaattgatcttttttaattcagTATGGCAGAAGTTGGAAGAAGAGAACGCTGATTTCTTCAGGGCCTACTATATCAGGCTAAAATTGAAAAAGCAAATACTATTATTCAATCATTTACTTGA
upper sequence: AT3G61700.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA16G02860.2 (Glycine max), 3'ss of exon 4
aatgcatgttatatattgt-ttagttatagcattagcaacgtgaaacatgaaatgaaatctctatttctgactctcctttttattttatg--tgtgaaatcagTTTGGCAGAAATTGGAAGAAGAAAACGCAGACTTTTTCAGGGCATATTATATAAGGCTGAAACTGAAGAAGCAAATAATTTTGTTCAATCATTTGCTTGA
| | || | | | | || | || | || || ||| | || | | || | ||| || | | |||| || || || | | || ||||| |||||||| ||||||||||| || || || ||||||||||| || ||||| || || ||| |||| ||||||||| | || ||||||||||| |||||
attatttgcattcttgtatattttctgtaccttttataa-gtgga-tgcaaactcatgtccc-attgctttcaatgctttgtaattgatcctttttaattcagTATGGCAGAAGTTGGAAGAAGAGAATGCCGATTTTTTCAGGGCCTACTATATCAGACTAAAATTGAAAAAGCAAATACTATTATTCAATCATTTACTTGA
upper sequence: AT3G61700.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA19G44420.1 (Glycine max), 3'ss of exon 4
aatgcatgttatatattgtttagttatagcattagcaacgtgaa-acatgaaatgaaatctctat---ttctgactctcctttttattttatgtgtgaaatcagTTTGGCAGAAATTGGAAGAAGAAAACGCAGACTTTTTCAGGGCATATTATATAAGGCTGAAACTGAAGAAGCAAATAATTTTGTTCAATCATTTGCTTGA
||| || | || |||| || | | | | ||| | ||||||| | ||||| | |||| | || | | || ||||| |||||||| ||||||| || ||| | || || || ||||| || ||||| ||||| ||| | || | ||||||| ||||||||||||||||||||||
----aatggcctacactgcagttttatctattttcctttatacatagatgccctcaaatctcattgccttctgtttgattcttttttctttttttaaaattcagTATGGCAGAAGCTGGAAGAGGAGAACACTGATTTCTTTAGGGCCTACTATATCAGGCTAAAATTAAAAAGGCAAATACTTTTGTTCAATCATTTGCTTGA
upper sequence: AT3G61700.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv15s0046g00990.t01 (Vitis vinifera), 3'ss of exon 4
--aatgcatgttatatattgtttagttatagcattagca-acgtgaaacatgaaatgaaatctctatttctgactctcctttttattttatgtgtgaaatcagTTTGGCAGAAATTGGAAGAAGAAAACGCAGACTTTTTCAGGGCATATTATATAAGGCTGAAACTGAAGAAGCAAATAATTTTGTTCAATCATTTGCTTGA
| | ||| | || ||| ||| | | | | | || || | ||||||| | || | | || ||| || ||||| |||||||| |||||||||||||| || || ||||||||||| ||||| ||||| | ||| ||||||| ||||| |||||||| ||||||||||||||
tttgagaagcttagctgcctaataaatatgatatttgtttgtctaatgcttccaagcaagcattgttttctgatgtcctcttctttctt---tgttaactcagTATGGCAGAAGTTGGAAGAAGAAAATGCTGATTTTTTCAGGGCCTATTACATAAGATTAAAATTGAAGAAACAAATCATTTTGTTTAATCATTTGCTTGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.catgaaatgaaatctctatttctgactctcctttttattttatgtgtgaaatcagTTTGGCAGAAATTGGAAGAAGAAAACGCAGACTTTTTCAGGGCATATTATATAAGGCTGAAACTGAAGAAGCAAATAATTTTGTTCAATCATTTGCTTGA
ttctgac putative branch site (score: 2)
tttttattttatgtgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aatgcatgttatatattgtttagttatagcattagcaacgtgaaacatgaaatgaaatctctatttctgactctcctttttattttatgtgtgaaatcagTTTGGCAGAAATTGGAAGAAGAAAACGCAGACTTTTTCAGGGCATATTATATAAGGCTGAAACTGAAGAAGCAAATAATTTTGTTCAATCATTTGCTTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - tgtttag
- - - - - - - - - - - - - - - - - - - - -gaaacat
- - - - - - - - - - - - - - - - - - - - - - - - - aatgaaa