Sequence
atgc intronic sequence ATGC exonic sequencegtgaaaccatgtttgacatacattttgcagctttaattgggtaaatctttcgtatctttagcagGGTAGTGCCAGGCAATTGTTTCAACGTTTGCAGGGGCCAATGGAGGAGGATACACTGAAGTCTCATTTTGAGAAAATTATAAAGATTGGGCAGAAGCAGC
Basic information
species | Glycine max |
transcript | GLYMA03G18730.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA03G18730.1 (Glycine max), 3'ss of exon 9
lower sequence: AT3G24880.1 (Arabidopsis thaliana), 3'ss of exon 16
--------------gtgaaaccatgtttgacatacattttgcagctttaattgggt-aaatctttcg----tatctttag----cagGGTAGTGCCAGGCAATTGTTTCAACGTTTGCAGGGGCCAATGGAGGAGGATACACTGAAGTCTCATTTTGAGAAAATTATAAAGATTGGGCAGAAGCAGC
||| | || | | || | |||| || | | |||| || | ||| | ||||| ||||| || || ||||||||||| |||| |||||||||||||| ||||| |||||||||||||||||||| ||| ||||||| |||| |
gtttttctatagctctgagatggtgaacaaagtgtcttctat-gcttaaactaatttaaatgccccggatatgtctgtgatattcagGGAAGTGCGAGACAGTTGTTTCAACGACTGCAAGGGCCAATGGAGGAAGATACCCTGAAGTCTCATTTTGAGAAGATTTGTTTGATTGGGAAGAAATTAC
upper sequence: GLYMA03G18730.1 (Glycine max), 3'ss of exon 9
lower sequence: AT3G24870.1 (Arabidopsis thaliana), 3'ss of exon 17
--------------gtgaaaccatgtttgacatacattttgcagctttaattgggtaaatctttcg----tatctttag----cagGGTAGTGCCAGGCAATTGTTTCAACGTTTGCAGGGGCCAATGGAGGAGGATACACTGAAGTCTCATTTTGAGAAAATTATAAAGATTGGGCAGAAGCAGC
||| | || | | || | |||| | | ||||| | | ||| | ||||| ||||| || || ||||||||||| |||| |||||||||||||| ||||| |||||||||||||||||||| ||| ||||||| |||| |
gtttttctatagctctgagatggtgaacaaagtgtcttctat-gcttagactaattaaatgccctggatatgtctgtgatattcagGGAAGTGCGAGACAGTTGTTTCAACGACTGCAAGGGCCAATGGAGGAAGATACCCTGAAGTCTCATTTTGAGAAGATTTGTTTGATTGGGAAGAAATTAC
upper sequence: GLYMA03G18730.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv07s0005g06680.t01 (Vitis vinifera), 3'ss of exon 17
-------------------------------------------------------------------gtgaaaccatgtttgacatacattttgc-agctttaattgggtaaatctttcg-tatctttag-------cagGGTAGTGCCAGGCAATTGTTTCAACGTTTGCAGGGGCCAATGGAGGAGGATACACTGAAGTCTCATTTTGAGAAAATTATAAAGATTGGGCAGAAGCAGC
|| || | ||||| || | |||| || | ||| | || | | | || ||||| |||||||| || |||||||||| |||||||||||| ||| ||||| || || |||||||| ||||||||||| || |||||||||| |||| |
gtaagaattttgattttccctttttgacaagttagaaatagttccttttttatttttttgtattgatgtaaacttgtagactgttgacattgagctaattttagctgtttgaatttatctctgtttctacacttgctcagGGCAGTGCCAGACAGTTGTTTCAACATTTGCAGGGGCCGATGCTAGAGGAAACCCTCAAGTCTCACTTTGAGAAAATCATTTTGATTGGGCAGCAGCATC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtttgacatacattttgcagctttaattgggtaaatctttcgtatctttagcagGGTAGTGCCAGGCAATTGTTTCAACGTTTGCAGGGGCCAATGGAGGAGGATACACTGAAGTCTCATTTTGAGAAAATTATAAAGATTGGGCAGAAGCAGC
ctttaat putative branch site (score: 4)
tctttcgtatcttt putative PPT
atacatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgaaaccatgtttgacatacattttgcagctttaattgggtaaatctttcgtatctttagcagGGTAGTGCCAGGCAATTGTTTCAACGTTTGCAGGGGCCAATGGAGGAGGATACACTGAAGTCTCATTTTGAGAAAATTATAAAGATTGGGCAGAAGCAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC