Sequence
atgc intronic sequence ATGC exonic sequence...ctcattgttgggcttgctttgcccaactactagagatgttagccctggcattattcttcaaatagtgtgctaacattctactgaaaaatttcccatatagGTTGCGAGGTTTCTCATGAAGACTGTTTCTCAGCTTGGGTCTGGAAAACAGCCTGTTGGCACCACAGCTTATATGGGGCGAGTTGCGGATTTGATGCAAT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv00s0389g00020.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: LOC_Os06g01390.1 (Oryza sativa), 3'ss of exon 9
--------------------------------------------------------ctcattgttgggcttgctttgcccaactactagagatgttagccctggcatta----ttcttcaaa--tagtgtgctaacattc-tactgaaaaatttcccatatagGTTGCGAGGTTTCTCATGAAGACTGTTTCTCAGCTTGGGTCTGGAAAACAGCCTGTTGGCACCACAGCTTATATGGGGCGAGTTGCGGATTTGATGCAAT
| |||| || | || | || || | | || | | || ||| ||| | || | ||| || || | | | ||||||| |||||||| ||||||||||| || ||| | | |||||||||||||||||||| || || ||||| ||||| | | | ||||||||||
gttagtatgctattgttgttttgttctgtggatactaataactctcctacctgcttgtggttgtgtggatggcctagcttgttgggccgaatcataggtccagtccttcaagtttcctcagttttggtcaatttacagtcataacctttggtgctctctgcagGTTGCAAGGTTTCTAATGAAGACTGTATCCCAGTTAGCTTCTGGAAAACAGCCTGTTGGTACAACGGCTTACATGGGCAACATACAGTACTTGATGCAAT
upper sequence: Vv00s0389g00020.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA01G41600.1 (Glycine max), 3'ss of exon 9
ctcattgttgggct-tgctttgcccaactactagagatgttagccctggcattattctt-caaatag--tgtgctaacattctactgaaaaatttcccatatagGTTGCGAGGTTTCTCATGAAGACTGTTTCTCAGCTTGGGTCTGGAAAACAGCCTGTTGGCACCACAGCTTATATGGGGCGAGTTGCGGATTTGATGCAAT
| | | | | || |||| || | | | || || | || ||| ||| | ||| | ||||| ||| || ||||| || |||| |||||||||||||||||||||||| || |||||||| |||||||||| || ||||||||||||| ||||| | | |||||||||
-aagtaagaaagttctaaaaggatgaaatacttgaaaattgtgattcggttttttaggaataattaggttgttttgacaacttctagaaaa---tccgatgtagGTGGCAAGGTATCTCATGAAGACTGTTTCTCAGCTGGGCTCTGGAAATAAGCCTGTTGGTACTACAGCTTATATGGCTCGAGTGGAACAACTGATGCAAT
upper sequence: Vv00s0389g00020.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA11G03800.1 (Glycine max), 3'ss of exon 9
ctcattgttgggcttgctttgcccaactactagagatgttagccctggcattattctt---caaatag--tgtgctaacattctactgaaaaatttcccatatagGTTGCGAGGTTTCTCATGAAGACTGTTTCTCAGCTTGGGTCTGGAAAACAGCCTGTTGGCACCACAGCTTATATGGGGCGAGTTGCGGATTTGATGCAAT
|| | | || || | || | || | ||| || || || ||| ||| | ||| || |||||| | || ||||| || ||| |||||||||||||||||||||||| || |||||||| |||| ||||| || ||||||||||||| ||||| | | |||||||||
--ttttatgtgtctcatattacatccctgtgaattctgctttaggaggccttttttaggaataattaggttgttttgacaacttagagaaaaactg---atgtagGTGGCAAGGCATCTCATGAAGACTGTTTCTCAGCTGGGCTCTGGAAATAAGCCCGTTGGTACTACAGCTTATATGGCTCGAGTGGAACAACTGATGCAAT
upper sequence: Vv00s0389g00020.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA14G14990.1 (Glycine max), 3'ss of exon 8
ctcattgttgggcttgctttgcccaactactagagatgttagccctggcattattcttcaaatag------tgtgctaacattctactgaaaaatttcccatatagGTTGCGAGGTTTCTCATGAAGACTGTTTCTCAGCTTGGGTCTGGAAAACAGCCTGTTGGCACCACAGCTTATATGGGGCGAGTTGCGGATTTGATGCAAT
|| | | || || | || | || | ||| || || | |||| ||| | ||| || |||||| | || ||||| || ||| |||| ||||||||||||||||||| | |||||||| |||||||||| || ||||||||||||| ||||| | | |||||||||
--ttttatgtgtctcatattacatccctgtgaattctgctttaggaggcttt-ttataggaataattaggttgttttgacaacttagagaaaaactg---atgtagGTGGCAAGGCATCTCGTGAAGACTGTTTCTCAGCTGGACTCTGGAAATAAGCCTGTTGGTACTACAGCTTATATGGCTCGAGTGGAACAACTGATGCAAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tggcattattcttcaaatagtgtgctaacattctactgaaaaatttcccatatagGTTGCGAGGTTTCTCATGAAGACTGTTTCTCAGCTTGGGTCTGGAAAACAGCCTGTTGGCACCACAGCTTATATGGGGCGAGTTGCGGATTTGATGCAAT
tgctaac putative branch site (score: 1)
tttcccat putative PPT
ttattcttcaaata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctcattgttgggcttgctttgcccaactactagagatgttagccctggcattattcttcaaatagtgtgctaacattctactgaaaaatttcccatatagGTTGCGAGGTTTCTCATGAAGACTGTTTCTCAGCTTGGGTCTGGAAAACAGCCTGTTGGCACCACAGCTTATATGGGGCGAGTTGCGGATTTGATGCAAT
- - ttgttgg
- - - - - -gcttgct
- - - - - - - - - - - ccaacta
- - - - - - - - - - - - - - - - - - - - - ccctggc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgctaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgaaaaa