Sequence
atgc intronic sequence ATGC exonic sequencegtaccttcaatctcacctccatgctctattgatcagtgtaggctttaagtcaactttttaccttatcatacgaattcgagctaatatcggtagatttttatagGTATAACATTCCTGAATTGGCTAAGAAATACAAGGTTTACGCCTTGGACTTACTCGGTTTCGGATGGAGTGACAAAGCTCTCATAGAGTATGATGCCATG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G36530.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G36530.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA16G25200.2 (Glycine max), 3'ss of exon 3
gtaccttcaatctcacctccatgctctattgatcagtgtaggctttaagtcaactttttaccttatcatacgaattcgagctaatatcggtag--atttttatagGTATAACATTCCTGAATTGGCTAAGAAATACAAGGTTTACGCCTTGGACTTACTCGGTTTCGGATGGAGTGACAAAGCTCTCATAGAGTATGATGCCATG
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----ttatgattagaattcaatctgttagtggctgcaattgtctgtacgattatatcattttttatt-tatggagatagttatatatctttatttatatctccagGTACAACATTCCAGAATTGGCTAAGAAACACAAGGTATATGCCTTAGACTTGCTCGGTTTTGGGTGGAGTGACAAAGCACTTATAGATTATGATGCTATG
upper sequence: AT4G36530.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv04s0023g02010.t01 (Vitis vinifera), 3'ss of exon 3
------------gtaccttcaatctcacctccatgctctattgatcagtgtaggctttaagtcaactttttaccttatcatacgaattcgagctaatatcggtagatttttatagGTATAACATTCCTGAATTGGCTAAGAAATACAAGGTTTACGCCTTGGACTTACTCGGTTTCGGATGGAGTGACAAAGCTCTCATAGAGTATGATGCCATG
| ||| | | | || | || | ||||| | || | || | ||| ||| | || || | || || || || | |||||||||||||||||||||||||||| | |||||||||||| || | ||||| || || ||||| |||||||| ||||| | || |||||||||||||||
atggtagtgagagaggctttaggtttatcttcctg-ttgattgaatgatatatggatt-------ttatttgcctcaaagtatga-------caaagttctttattttctcatagGTATAACATTCCTGAATTGGCTAAAAGATACAAGGTTTATGCGATCGACTTGCTAGGGTTCGGGTGGAGTGATAAAGCGATTATTGAGTATGATGCCATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtcaactttttaccttatcatacgaattcgagctaatatcggtagatttttatagGTATAACATTCCTGAATTGGCTAAGAAATACAAGGTTTACGCCTTGGACTTACTCGGTTTCGGATGGAGTGACAAAGCTCTCATAGAGTATGATGCCATG
agctaat putative branch site (score: 3)
tttttat putative PPT
tagatttttata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaccttcaatctcacctccatgctctattgatcagtgtaggctttaagtcaactttttaccttatcatacgaattcgagctaatatcggtagatttttatagGTATAACATTCCTGAATTGGCTAAGAAATACAAGGTTTACGCCTTGGACTTACTCGGTTTCGGATGGAGTGACAAAGCTCTCATAGAGTATGATGCCATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA