Sequence
atgc intronic sequence ATGC exonic sequence...gaatttgcacatcacgtgtacacttttgtggtttatgcaggatttttaaaataaaaaatttaatgtatgaattggctctcatgttttttttttcacttagGTGTGGGAATATCAATTGGGCAAAGCGGACTAAATGCAATATCTGCAATACAAATAAGCCTGGGCATAATGAGGGTGGTGTAAG
Basic information
species | Glycine max |
transcript | GLYMA11G11060.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA11G11060.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os09g12800.1 (Oryza sativa), 3'ss of exon 4
------gaatttgcacatcacgtgtacacttttgtggtttatgcaggatttttaaaataaaaaatttaatgtatgaattggctctcatgttttttttttcacttagGTGTGGGAATATCAATTGGGCAAAGCGGACTAAATGCAATATCTGCAATACAAATAAGCCTGGGCATAATGAGGGTGGTGTAAG
|| ||| || || || | | | || | | | | | | || |||| || | ||| || | || | ||||| |||||||| || || |||||||||||||||| ||||| |||||||| || || | |||||| || || ||||| |||||||| ||
attgactaaattgatcaacagtaataaaagcatcatggttgtaccatgtact-atattataaaaccgcatatgtga--tgataaataatttaatgttttc---cagGTGTGGCAACATAAATTGGGCAAAGCGGATGAAATGTAATATCTGTAACACCACTAAGCCAGGTCACAATGAAGGTGGTGTGAG
upper sequence: GLYMA11G11060.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv01s0010g01410.t01 (Vitis vinifera), 3'ss of exon 3
-gaatttgcacatcacgtgtacacttttgtggtttatgcaggatttttaaaataaaaaatttaatgtatgaattggctctcatgttttttttttcacttagGTGTGGGAATATCAATTGGGCAAAGCGGACTAAATGCAATATCTGCAATACAAATAAGCCTGGGCATAATGAGGGTGGTGTAAG
| || ||| | || | | | |||| | | || |||| | ||| ||| || || ||| || | || | |||||||| || || || |||||||||||||| || |||||||| ||||| || ||||||||||| |||||||| |||||||| ||
caatttaatccatgatgttttaaaaaatatggtcaaataaacatcacataaattattgctttt-catattgcttcttccttatgattatgagttgtttcagGTGTGGCAACATTAACTGGGCAAAGCGGACAAAGTGCAATATATGCAACACCAATAAGCCTGGCCATAATGAAGGTGGTGTGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttaaaataaaaaatttaatgtatgaattggctctcatgttttttttttcacttagGTGTGGGAATATCAATTGGGCAAAGCGGACTAAATGCAATATCTGCAATACAAATAAGCCTGGGCATAATGAGGGTGGTGTAAG
atttaat putative branch site (score: 4)
ctctcatgtttttttt putative PPT
ataaaaaatttaatgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gaatttgcacatcacgtgtacacttttgtggtttatgcaggatttttaaaataaaaaatttaatgtatgaattggctctcatgttttttttttcacttagGTGTGGGAATATCAATTGGGCAAAGCGGACTAAATGCAATATCTGCAATACAAATAAGCCTGGGCATAATGAGGGTGGTGTAAG
- - - -cacatca
- - - - - - - cgtgtac
- - - - - - - - - - - -ttttgtg
- - - - - - - - - - - - - - - -tttatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - aaaaaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtatga