Sequence
atgc intronic sequence ATGC exonic sequence...tggggagttgaaaaggataaatgggaacggttaagctgaagcttatgatagtatttggtgtgtatgtttctgtctttttgatttgctttctgtttttcagGGTGAAAAGAAGGTGGCCACCATTCAAAATGTTTTTGCTGTCATAAAGGGATCGGAAGAACCGGATCGATATGTTCTGCTTGGGAACCATAGAGATGCAT
Basic information
species | Glycine max |
transcript | GLYMA03G36430.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA03G36430.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv00s0352g00020.t01 (Vitis vinifera), 3'ss of exon 1
tggggagttgaaaaggataaatg---ggaacggttaagctgaagc----ttatgatagtatttggtgtgtatgtttctgtctttttgatttgctttctgtttttcagGGTGAAAAGAAGGTGGCCACCATTCAAAATGTTTTTGCTGTCATAAAGGGATCGGAAGAACCGGATCGATATGTTCTGCTTGGGAACCATAGAGATGCAT
|| ||||||| ||||| |||| || || |||| || || | || | | | || | | ||| |||| | || ||||| ||| || || ||| | || |||||||| |||||||||||| |||||| |||||| ||||| || ||||| ||||| |||||||| ||||| ||||||||||
-------ttaaaaaggaaaaatgagtggaagacttctactaaagcccacttgtggaaagcttattgaaatgtttctccatttattttattttttccctcttttttagGTGGAGAAAAAGATAGCTACCATTCATAATGTTTTTGCTATCATAAGGGGATCTGAAGAGCCTGATCGCTATGTCCTGCTTGGCAACCACAGAGATGCAT
upper sequence: GLYMA03G36430.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv08s0032g00670.t01 (Vitis vinifera), 3'ss of exon 1
tggggagttgaaaaggataaatg---ggaacggttaagctgaagc----ttatgatagtatttggtgtgtatgtttctgtctttttgatttgctttctgtttttcagGGTGAAAAGAAGGTGGCCACCATTCAAAATGTTTTTGCTGTCATAAAGGGATCGGAAGAACCGGATCGATATGTTCTGCTTGGGAACCATAGAGATGCAT
|| ||||||| ||||| |||| || || |||| || || | || | | | || | | ||| |||| | || ||||||||| || || ||| | || |||||||| |||||||||||| |||||| |||||| ||||| || ||||| ||||| |||||||| ||||| ||||||||||
-------ttaaaaaggaaaaatgagtggaagacttctactaaagcccacttgtggaaagcttattgaaatgtttctccatttattttattttttccctctttttcagGCGGAGAAAAAGATAGCTACCATTCATAATGTTTTTGCTATCATAAGGGGATCTGAAGAGCCTGATCGCTATGTCCTGCTTGGCAACCACAGAGATGCAT
upper sequence: GLYMA03G36430.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv00s0285g00060.t01 (Vitis vinifera), 3'ss of exon 1
tggggagttgaaaaggataaatg---ggaacggttaagctgaagctta-tgatagta--tttggtgtgt-atgtttctgtctttttgatttgctttctgtttttcagGGTGAAAAGAAGGTGGCCACCATTCAAAATGTTTTTGCTGTCATAAAGGGATCGGAAGAACCGGATCGATATGTTCTGCTTGGGAACCATAGAGATGCAT
|| ||||||| ||||| |||| || || |||| | | | | | || || | | | || | | ||| |||| | || ||||||||| || || ||| | || |||||||| ||||||||||||||||||| |||||| ||||| || ||| | ||||| ||||||| ||||| ||||||||||
-------ttaaaaaggaaaaatgagtggaaaaattctactaaagcccacttgtggaaagcttattgaattgtttctccatttattttattttttccctctttttcagGCGGAGAAAAAGATAGCTACCATTCATAATGTTTTTGCTGTCATAAGGGGATCTGAAGAGCCTGATTGCTATGTCTTGCTTGGCAACCACAGAGATGCAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgatagtatttggtgtgtatgtttctgtctttttgatttgctttctgtttttcagGGTGAAAAGAAGGTGGCCACCATTCAAAATGTTTTTGCTGTCATAAAGGGATCGGAAGAACCGGATCGATATGTTCTGCTTGGGAACCATAGAGATGCAT
ttttgat putative branch site (score: 4)
tttgctttctgttttt CT-rich tract
tttttgattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tggggagttgaaaaggataaatgggaacggttaagctgaagcttatgatagtatttggtgtgtatgtttctgtctttttgatttgctttctgtttttcagGGTGAAAAGAAGGTGGCCACCATTCAAAATGTTTTTGCTGTCATAAAGGGATCGGAAGAACCGGATCGATATGTTCTGCTTGGGAACCATAGAGATGCAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
tggggag
- - - - -gaaaagga
- - - - - - - - - - - - - - - - - gctgaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - -tggtgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgctttc