Sequence
atgc intronic sequence ATGC exonic sequence...ttttaaaaccttgatttttactttaacataacacaaaattggacatgggtttgatgattgacaattgacaattgacaatttttttttttttgtttttcagGTTTGTATCGTTACAGAGTTGGTGATGTGCTGAGGGTGGCTGGATTCAAGAACAAGGCACCCCAATTCAACTTTGTGTGCAGAAAGAACGTGGTGTTGAG
Basic information
species | Glycine max |
transcript | GLYMA06G40860.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G40860.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os01g57610.1 (Oryza sativa), 3'ss of exon 2
---------ttttaaaaccttgatttttactttaacataacacaaaattggacatgggtttgatgattgacaattgacaattgacaatttttttttttttgttttt--cagGTTTGTATCGTTACAGAGTTGGTGATGTGCTGAGGGTGGCTGGATTCAAGAACAAGGCACCCCAATTCAACTTTGTGTGCAGAAAGAACGTGGTGTTGAG
||| | | || || | | | | | || || || || | | | | | | | |||| |||| | || | |||| ||||||||||| | || || || |||||||||||||| || |||||||||||||| || |||| ||| ||| | | ||||||||| | ||||
gtaaatctgccttacctcttcgacacataacgtggccgcgcgcgatggatgatatatattcttatatgcagtagtaatatat-ataattaacagttttgcgattgtgacagGGTTGTATCGTTATCGCGTGGGCGACGTGCTGAGGGTGGCGGGGTTCAAGAACAAGGCCCCGATGTTCAGCTTCGTGCGGCGGCAGAACGTGGCGCTGAG
upper sequence: GLYMA06G40860.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv19s0014g04690.t01 (Vitis vinifera), 3'ss of exon 2
ttttaaaaccttgatttttactttaacataacacaaaattggacatgggtttgatgattgacaattgacaattgacaatttttttttttttgtttttcagGTTTGTATCGTTACAGAGTTGGTGATGTGCTGAGGGTGGCTGGATTCAAGAACAAGGCACCCCAATTCAACTTTGTGTGCAGAAAGAACGTGGTGTTGAG
| | ||| | || || || ||| || | | || ||| | | || | | || | | |||| ||||| | || ||||| || |||||||| | ||||| ||||||||||||||||||||||| |||||||| || ||| | ||||| |||||||||||
--------gtcagttgcccgacataat-tgacttaatttttttcatttgtctttcaaatgtatgctgatatat----atgtcatgaacttgatgctgcagGGCTGTATAGGTATAGAGTAGGAGATGTGCTCCGTGTGGCCGGATTCAAGAACAAGGCACCCCAGTTCAACTTCGTATGCCGGAAGAATGTGGTGTTGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgggtttgatgattgacaattgacaattgacaatttttttttttttgtttttcagGTTTGTATCGTTACAGAGTTGGTGATGTGCTGAGGGTGGCTGGATTCAAGAACAAGGCACCCCAATTCAACTTTGTGTGCAGAAAGAACGTGGTGTTGAG
aattgac putative branch site (score: 3)
caattttttttttttt CT-rich tract
aattgacaattgacaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttttaaaaccttgatttttactttaacataacacaaaattggacatgggtttgatgattgacaattgacaattgacaatttttttttttttgtttttcagGTTTGTATCGTTACAGAGTTGGTGATGTGCTGAGGGTGGCTGGATTCAAGAACAAGGCACCCCAATTCAACTTTGTGTGCAGAAAGAACGTGGTGTTGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - acacaaa
- - - - - - - - - - - - - - - - - - - - - - - gggtttg