Sequence
atgc intronic sequence ATGC exonic sequence...aatgaggtggggagttgaaaaggagaaatgggaacggttaaactgaagcttatagatagtgtttggtgtgtatgtttctgatttgctttctgtttttcagGGTGAAAAGAAGGTGGCCACCATTCAAAATGTTTTTGCCGTCATAAAGGGATCGGAAGAACCTGATCGATATGTTCTGCTTGGGAACCATAGAGATGCAT
Basic information
species | Glycine max |
transcript | GLYMA19G39080.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA19G39080.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv00s0352g00020.t01 (Vitis vinifera), 3'ss of exon 1
----aatgaggtggggagttgaaaaggagaaatgggaacggttaaactgaagcttatagatagtgtttggtgtgtatgtttctgatttgctttctgtttttcagGGTGAAAAGAAGGTGGCCACCATTCAAAATGTTTTTGCCGTCATAAAGGGATCGGAAGAACCTGATCGATATGTTCTGCTTGGGAACCATAGAGATGCAT
|| | |||| ||| | | | | | |||||||| || | ||||| | || | | | |||| | || ||||| ||| || || ||| | || |||||||| ||||||||||| |||||| |||||| ||||| |||||||| ||||| |||||||| ||||| ||||||||||
ttaaaaaggaaaaatgagtggaagacttctactaaagcccacttgtggaaagcttattga-aatgtttc---tccatttattttattttttccctcttttttagGTGGAGAAAAAGATAGCTACCATTCATAATGTTTTTGCTATCATAAGGGGATCTGAAGAGCCTGATCGCTATGTCCTGCTTGGCAACCACAGAGATGCAT
upper sequence: GLYMA19G39080.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv08s0032g00670.t01 (Vitis vinifera), 3'ss of exon 1
----aatgaggtggggagttgaaaaggagaaatgggaacggttaaactgaagcttatagatagtgtttggtgtgtatgtttctgatttgctttctgtttttcagGGTGAAAAGAAGGTGGCCACCATTCAAAATGTTTTTGCCGTCATAAAGGGATCGGAAGAACCTGATCGATATGTTCTGCTTGGGAACCATAGAGATGCAT
|| | |||| ||| | | | | | |||||||| || | ||||| | || | | | |||| | || ||||||||| || || ||| | || |||||||| ||||||||||| |||||| |||||| ||||| |||||||| ||||| |||||||| ||||| ||||||||||
ttaaaaaggaaaaatgagtggaagacttctactaaagcccacttgtggaaagcttattga-aatgtttc---tccatttattttattttttccctctttttcagGCGGAGAAAAAGATAGCTACCATTCATAATGTTTTTGCTATCATAAGGGGATCTGAAGAGCCTGATCGCTATGTCCTGCTTGGCAACCACAGAGATGCAT
upper sequence: GLYMA19G39080.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv00s0285g00060.t01 (Vitis vinifera), 3'ss of exon 1
----aatgaggtggggagttgaaaaggagaaatgggaacggttaaactgaagcttatagatagtgtttggtgtgtatgtttctgatttgctttctgtttttcagGGTGAAAAGAAGGTGGCCACCATTCAAAATGTTTTTGCCGTCATAAAGGGATCGGAAGAACCTGATCGATATGTTCTGCTTGGGAACCATAGAGATGCAT
|| | |||| ||||| | | | | |||||||| || | ||||| | || | | | |||| | || ||||||||| || || ||| | || |||||||| ||||||||||| ||||||| |||||| ||||| |||||| | ||||| ||||||| ||||| ||||||||||
ttaaaaaggaaaaatgagtggaaaaattctactaaagcccacttgtggaaagcttattga-attgtttc---tccatttattttattttttccctctttttcagGCGGAGAAAAAGATAGCTACCATTCATAATGTTTTTGCTGTCATAAGGGGATCTGAAGAGCCTGATTGCTATGTCTTGCTTGGCAACCACAGAGATGCAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aagcttatagatagtgtttggtgtgtatgtttctgatttgctttctgtttttcagGGTGAAAAGAAGGTGGCCACCATTCAAAATGTTTTTGCCGTCATAAAGGGATCGGAAGAACCTGATCGATATGTTCTGCTTGGGAACCATAGAGATGCAT
ttctgat putative branch site (score: 3)
tttgctttctgttttt CT-rich tract
tatagata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aatgaggtggggagttgaaaaggagaaatgggaacggttaaactgaagcttatagatagtgtttggtgtgtatgtttctgatttgctttctgtttttcagGGTGAAAAGAAGGTGGCCACCATTCAAAATGTTTTTGCCGTCATAAAGGGATCGGAAGAACCTGATCGATATGTTCTGCTTGGGAACCATAGAGATGCAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - aggtggg
- - - - - - - - gaaaagga
- - - - - - - - - - - - - - - - - - - - - ctgaagc
- - - - - - - - - - - - - - - - - - - - - - - - - - - gatagtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tggtgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtttctg