Sequence
atgc intronic sequence ATGC exonic sequence...tcctttgctttgaagtgcattataaaagtcaacttgatatatttatttgcaaaatactttaatattattgtgtattatacttagctcttgtgatccacagAGATATGATACAGATCCTGCAGCAAAGGCAGCAGCTGCAACTGTTTTAGCATCCAAGTTGGGTGCAGATTCGGGTTTGAAAGTGTATGTGGGGGATGAAT
Basic information
species | Glycine max |
transcript | GLYMA17G29620.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G29620.1 (Glycine max), 3'ss of exon 3
lower sequence: AT2G24330.1 (Arabidopsis thaliana), 3'ss of exon 3
-tcctttgctttgaagtgcattataaaagtcaacttgatatatttatttgcaaaatactttaatattattgtgtattatacttagctcttgtgatccacagAGATATGATACAGATCCTGCAGCAAAGGCAGCAGCTGCAACTGTTTTAGCATCCAAGTTGGGTGCAGATTCGGGTTTGAAAGTGTATGTGGGGGATGAAT
||| ||| || | | || | ||||| ||| | || | | || | | | | ||||| | || | ||||| ||||| | || || || |||||||| || |||||||||||| | ||||||||||||||||| || || || |||||||| | ||| || |||||||
aagaattgaattgctgttatatcttaacggatacttgttattgtgggttttatcac-tattgagactggaacttgttataacatgagctattttgtatcagAGGTATGACCCTGACCCAGCTGCAAAGGCGGCTGCTGCAACTGTTCTGGCATCCAAGTTGGGTGCTGAGTCAGGCTTGAAAGTATTTGTAGGAGATGAAT
upper sequence: GLYMA17G29620.1 (Glycine max), 3'ss of exon 3
lower sequence: AT4G31080.1 (Arabidopsis thaliana), 3'ss of exon 4
tcctttgctttgaagtgcattataaaagtcaacttgatatatttatttgcaaaa------tacttta-atattattgtgtattatacttagctcttgtgatccacagAGATATGATACAGATCCTGCAGCAAAGGCAGCAGCTGCAACTGTTTTAGCATCCAAGTTGGGTGCAGATTCGGGTTTGAAAGTGTATGTGGGGGATGAAT
| || | | |||| || || | | | | | ||| | | |||| | || || || || || | | || |||| ||||||||||| | || || || ||||||||||| || |||||||| | |||||||| |||||||| ||||| || |||||||| ||| | || |||||||
---gtggcatagccatgcaacgaaagagagatcaatgtttgccgacttgaagaggttaactactgcatgtagagctg-gtgcta-acagaattgttttgat--gcagAGATATGACCCGGACCCAGCTGCAAAGGCAGCTGCCGCAACTGTCCTGGCATCCAAATTGGGTGCCGATTCAGGCTTGAAAGTATATTTAGGAGATGAAT
upper sequence: GLYMA17G29620.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv02s0033g01150.t01 (Vitis vinifera), 3'ss of exon 5
--tcctttgctttgaagtgcattataaaagtcaacttgatatatttatttgcaaaatactttaatattattgtgtattatacttagctcttgtgatccacagAGATATGATACAGATCCTGCAGCAAAGGCAGCAGCTGCAACTGTTTTAGCATCCAAGTTGGGTGCAGATTCGGGTTTGAAAGTGTATGTGGGGGATGAAT
| ||| | ||| || | || | | | | || || || |||| | ||| | | | || ||||||||||| || ||||| ||||||||||| || ||||||||||| | ||||| |||||||||||||| || || || ||||||| ||| || |||||||
tgcttgtaacttacacatgcgtttccatgagggcctctgggttaatgatgttatgtacctggaactacatgttgtactgatcttcagccctttaat--gcagAGATATGACACTGATCCAGCAGCAAAGGCTGCTGCTGCAACTGTCCTGGCATCAAAGTTGGGTGCAGAGTCAGGCTTAAAAGTGTTTGTCGGTGATGAAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttgcaaaatactttaatattattgtgtattatacttagctcttgtgatccacagAGATATGATACAGATCCTGCAGCAAAGGCAGCAGCTGCAACTGTTTTAGCATCCAAGTTGGGTGCAGATTCGGGTTTGAAAGTGTATGTGGGGGATGAAT
ctttaat putative branch site (score: 4)
ctcttgt putative PPT
aaaatactttaatatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcctttgctttgaagtgcattataaaagtcaacttgatatatttatttgcaaaatactttaatattattgtgtattatacttagctcttgtgatccacagAGATATGATACAGATCCTGCAGCAAAGGCAGCAGCTGCAACTGTTTTAGCATCCAAGTTGGGTGCAGATTCGGGTTTGAAAGTGTATGTGGGGGATGAAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
-cctttgc
- - - - - - - -tgcatta