Sequence
atgc intronic sequence ATGC exonic sequence...tatgctatgtgtcatcgagtagcttaactaagaggctgcactgtgtgaatgtgagttcttatgcataatgcactttttctttttgcgctaattctttcagGTGTGGCAATGTCAACTGGGCGAAACGTCTAAAATGTAATATCTGCAACACCAATAAACCTGGTCAGAATGAAGGTGGTGTGAG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G50300.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G50300.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os09g12800.1 (Oryza sativa), 3'ss of exon 4
-tatgctatgtgtcatcga--gtagcttaactaaga-ggctgcactgtgtg----aatgtgagttcttatgcataatgcactttttctttttgcgctaattctttcagGTGTGGCAATGTCAACTGGGCGAAACGTCTAAAATGTAATATCTGCAACACCAATAAACCTGGTCAGAATGAAGGTGGTGTGAG
| ||| | | ||| | ||| || | | || || || ||| | | | | | || | ||| | || || | || |||||||||||| | || ||||| || || | |||||||||||||| ||||||| ||| || ||||| |||||||||||||||||
attgactaaat-tgatcaacagtaataaaagcatcatggttgtaccatgtactatattataaaaccgcatatgtgatgataaataatttaatg-------ttttccagGTGTGGCAACATAAATTGGGCAAAGCGGATGAAATGTAATATCTGTAACACCACTAAGCCAGGTCACAATGAAGGTGGTGTGAG
upper sequence: AT1G50300.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os07g19560.2 (Oryza sativa), 3'ss of exon 4
tatgct-atgtgtcatcg-agtagcttaactaaga-ggctgcactgtgtg-aatgtgagttcttatgcataatgcactttttctttttgcgctaattctttcagGTGTGGCAATGTCAACTGGGCGAAACGTCTAAAATGTAATATCTGCAACACCAATAAACCTGGTCAGAATGAAGGTGGTGTGAG
|| | || || | | ||| || | || || || ||| ||||| | | | | ||| | | ||| | | | || |||||||||||| | || ||||| || || | |||||||||||||| ||||||| || || ||||| |||||||||||||| ||
taaattgatctgcagtaataaaagcacaatggttatggttgtaccttgtacaatgtta--taaaaccgcttatgtgatgatacttcatttaatg--ttttccagGTGTGGCAACATAAATTGGGCAAAGCGGATGAAATGTAATATCTGTAACACCACCAAGCCAGGTCACAATGAAGGTGGTGTTAG
upper sequence: AT1G50300.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA12G03260.1 (Glycine max), 3'ss of exon 3
tatgctatgtgtcat-cgagtagcttaactaag-aggctgcactgtgtgaatgtgagttcttatgcat-aatgcactttttctt-tttgcgctaattctttcagGTGTGGCAATGTCAACTGGGCGAAACGTCTAAAATGTAATATCTGCAACACCAATAAACCTGGTCAGAATGAAGGTGGTGTGAG
| |||| | | || | | || | | | | ||| | || | ||| || ||| ||||| || | ||| | || | |||||||| ||| |||| ||||| || || ||||| |||||||||||||| ||||| ||||| || ||||| |||||||| ||
---tttgcacatcatgtgtacacttttgttgtttatgcaggatttttaaaataaaaatt-taatgtatgaattgactttctcatgtttttttttttttgcttagGTGTGGGAATATCAATTGGGCAAAGCGGACTAAATGCAATATCTGCAACACAAATAAGCCTGGGCATAATGAGGGTGGTGTAAG
upper sequence: AT1G50300.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv01s0010g01410.t01 (Vitis vinifera), 3'ss of exon 3
-----tatgctatgtgtcatcgagtagcttaactaagaggctgcactgtgtgaatgtgagttcttatgcataatgcactttttctttttgcgctaattctttcagGTGTGGCAATGTCAACTGGGCGAAACGTCTAAAATGTAATATCTGCAACACCAATAAACCTGGTCAGAATGAAGGTGGTGTGAG
|| | ||| | | | | || || | ||| || | | |||| ||| || | | | || ||||||||||||||| | |||||||| || || ||| || ||||| |||||||||||||| ||||| || |||||||||||||||||
caatttaatccatgatgttttaaaaaatatggtcaaataa--acatcacataaatt---attgcttttcatattgcttcttccttatgattatgagttgtttcagGTGTGGCAACATTAACTGGGCAAAGCGGACAAAGTGCAATATATGCAACACCAATAAGCCTGGCCATAATGAAGGTGGTGTGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgaatgtgagttcttatgcataatgcactttttctttttgcgctaattctttcagGTGTGGCAATGTCAACTGGGCGAAACGTCTAAAATGTAATATCTGCAACACCAATAAACCTGGTCAGAATGAAGGTGGTGTGAG
cgctaat putative branch site (score: 3)
ttctttc CT-rich tract
tttttcttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tatgctatgtgtcatcgagtagcttaactaagaggctgcactgtgtgaatgtgagttcttatgcataatgcactttttctttttgcgctaattctttcagGTGTGGCAATGTCAACTGGGCGAAACGTCTAAAATGTAATATCTGCAACACCAATAAACCTGGTCAGAATGAAGGTGGTGTGAG
- - - - - - - - - - - - taactaa