Sequence
atgc intronic sequence ATGC exonic sequence...ctggtggtgtgcatgtctggatcttgacttggaaatatagaattgctggtccttgacacaaatctcaacaattctatttgtttatttcttctttcttcagAATGCTGCTCGTTTGGACAGTGAAATCATTTATGACCGGGACTTTGATTATGATTACTTTGGTTTCAAAACCCTTGAGAGGTCCTACCTCCTGAAGATTC
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv07s0031g01990.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os06g07210.1 (Oryza sativa), 3'ss of exon 3
-------------------------------------------------------ctggtggtgtgcatgtctggatcttgac--ttggaaatatagaattgctggtccttgacacaaatctcaacaattctatttgtttatttcttctttcttcagAATGCTGCTCGTTTGGACAGTGAAATCATTTATGACCGGGACTTTGATTATGATTACTTTGGTTTCAAAACCCTTGAGAGGTCCTACCTCCTGAAGATTC
| || | | | || |||| || ||| ||| || | || | ||| | |||| | | | | ||| ||| |||||||||| |||| |||||||| || || |||||||| ||||||| ||||||||||| ||||||||||| || || |||||||| ||||||||||| ||
gtgagatatcaaattaaactttagggacttgcactgatagctgttcttgttctgatttgtaaaatttactgttccattcaatttattggtcat-taggattattgatgtatgttatgcttcttacggtttctgatgttctgatccttattt--tcagAATGCTTCTCGCTTGGACAGCGAGATAATTTATGATAGGGACTTCGATTATGATTATTTTGGTTTCAAGACTCTGGAGAGGTCTTACCTCCTGAAACTTG
upper sequence: Vv07s0031g01990.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os02g56100.1 (Oryza sativa), 3'ss of exon 3
-ctggtggtgtgcatgtctggatcttgacttggaaatatagaattgctggtccttgacacaaatctcaacaattctatttgtttatttcttctttcttcagAATGCTGCTCGTTTGGACAGTGAAATCATTTATGACCGGGACTTTGATTATGATTACTTTGGTTTCAAAACCCTTGAGAGGTCCTACCTCCTGAAGATTC
| | ||||| || | | | | ||| | ||| || | | ||| | | | |||| | ||| |||||||| | | || ||||||||||| || ||||||||| | || ||||| ||||| ||||||||||| || ||||||||||| || || || | || ||
atttcttgtgtggatatatttcttcaggtgcttcaattttttattatatgtatattgtgccaatgtgacttgata-atttctatatgatgcaccatttcagAATACCACCCGCTTGGACAGTGAGATAATTTATGACAGAGATTTTGACTATGACTACTTTGGTTTTAAGACCCTTGAGAGATCTTATCTGTTAAAAGTTG
upper sequence: Vv07s0031g01990.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G340527_T01 (Zea mays), 3'ss of exon 3
------------------------------------------------------------------------------------------------ctggtggtgtgcatgtctggatcttgacttggaaatatagaattgctggt---ccttgacacaaatctcaacaattctatttgtttatttcttctttc--ttcagAATGCTGCTCGTTTGGACAGTGAAATCATTTATGACCGGGACTTTGATTATGATTACTTTGGTTTCAAAACCCTTGAGAGGTCCTACCTCCTGAAGATTC
| | | | ||| | || | | | | | | | |||||| |||| | | ||| | | | | || | |||||||||||||||| |||||||||||||| |||||||| |||| || || ||||| |||||||| |||||||| || |||||||| |||||| ||||| ||
gtgagattctagttgctcctggcacatttctgacagagcatctgtgtagataatgccgatgtgtttctggcagttgaatttactgttgcattcctttttttattaaggttgtttatctcatacagtaaatctgttgtgcccttcactcaccttgatgtaaatt--ggccctcatatcgctccaaatgctgttacatttcagAATGCTGCTCGCTTGGACAGTGAAATAATTTATGATAGGGATTTCGACTATGACTACTTTGGCTTCAAAACTCTGGAGAGGTCTTACCTCTTGAAGCTTG
upper sequence: Vv07s0031g01990.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G304362_T01 (Zea mays), 3'ss of exon 3
ctggtggtgtgcatgtctggatcttgacttggaaatatagaattgctggtccttgacacaaatctcaacaattctatttgtttatttcttctttcttcagAATGCTGCTCGTTTGGACAGTGAAATCATTTATGACCGGGACTTTGATTATGATTACTTTGGTTTCAAAACCCTTGAGAGGTCCTACCTCCTGAAGATTC
| ||| || || | | || ||||| |||| | | | || | |||||||||||||||| ||||||||||| || |||||||| |||| || || || || |||||||| |||||||| || |||||||| ||||| ||||| ||
acaaggctgtttatctcatacagtaaatctgttgtgccccgcacaacacaccttgttggaaattggccctcacatgactccaaatgatgttacatttcagAATGCTGCTCGCTTGGACAGTGAGATAATTTATGATAGGGATTTCGACTACGACTACTTTGGCTTCAAAACTCTGGAGAGGTCTTACCTGTTGAAGCTTG
upper sequence: Vv07s0031g01990.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA05G32070.1 (Glycine max), 3'ss of exon 3
ctggtg-gtgtgcatg-tctggatcttgacttggaaatatagaattgctggtccttgacacaa-atctcaacaattctatttgtttatttcttctttcttcagAATGCTGCTCGTTTGGACAGTGAAATCATTTATGACCGGGACTTTGATTATGATTACTTTGGTTTCAAAACCCTTGAGAGGTCCTACCTCCTGAAGATTC
||| ||| | || | | ||| ||| || | | | | |||| || | | | | | | | | | | || | || || ||||||||||||| ||||||||||| || || ||||| |||||||||| ||||||||||||||||||||||| ||||||||||| |||||| ||||| |||
---gtgtgtgagtgtggtgtaattctatgcttttaagttttgtttggctgtgttttagtatgatgtgaaattcactttggtattgttttctattttgttttagAATGCTGCTCGATTGGACAGTGAGATAATCTATGATAGGGACTTTGACTATGATTACTTTGGTTTCAAAACTCTTGAGAGGTCATACCTCTTGAAGGTTC
upper sequence: Vv07s0031g01990.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA08G15360.1 (Glycine max), 3'ss of exon 2
ctggtggtgtgcatgtctggatcttgacttggaaatatagaattgctggt-ccttgacacaaatctcaacaattctatttgtttatttct---tctttcttcagAATGCTGCTCGTTTGGACAGTGAAATCATTTATGACCGGGACTTTGATTATGATTACTTTGGTTTCAAAACCCTTGAGAGGTCCTACCTCCTGAAGATTC
|| ||||| || | | ||| | | || | | | ||| | ||| | | | | | | ||||||| || | | || || |||||| |||||| ||||||||||| || || ||||| | |||||||| ||||||||||||||||||||||||||||||||||| ||| |||||||| |||
-tgtgtgtgtgtg-gtgtatttgttggttgtgtgattttgtttgactgttgttttggtatga--tttgaaattcacgtttgttttgttttctgttttgttttagAATGTTGCTCGATTGGACAGTGAGATAATCTATGATAGAGACTTTGACTATGATTACTTTGGTTTCAAAACCCTTGAGAGGTCATACATCCTGAAGGTTC
upper sequence: Vv07s0031g01990.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA06G15350.1 (Glycine max), 3'ss of exon 3
ctggtggtgtgcatg-tctggatcttgacttggaaatatagaattgctggtccttgacacaaatctcaacaattctatttgtttatttcttcttt--cttcagAATGCTGCTCGTTTGGACAGTGAAATCATTTATGACCGGGACTTTGATTATGATTACTTTGGTTTCAAAACCCTTGAGAGGTCCTACCTCCTGAAGATTC
| | | ||| | || | | | | | || || || || || ||| | | | |||||| | ||| || |||||||||||||| | ||||| || || || |||||| |||||||||| |||||||| ||||| |||||||||||||||||||| |||||| ||||| |||
---gatttatttatggtttgaaattctttaagttgttgtttggctgttgttcttttgtgtgtgaagaaataatcttttattattattttgtgtttggctgtagAATGCTGCTCGTCTAGACAGCGAGATAATCTATGACAGGGACTTTGACTATGATTATTTTGGATTCAAAACCCTTGAGAGGTCTTACCTCTTGAAGGTTC
upper sequence: Vv07s0031g01990.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA04G39500.1 (Glycine max), 3'ss of exon 3
ctggtggtgtgcatgtctggat-cttgacttggaaatatagaattgctggtccttgacacaaatctcaacaattctatttgtttatttcttctttctt-----cagAATGCTGCTCGTTTGGACAGTGAAATCATTTATGACCGGGACTTTGATTATGATTACTTTGGTTTCAAAACCCTTGAGAGGTCCTACCTCCTGAAGATTC
| | | | || ||||| | | | | || || | || | || ||| | | | ||||| || || || |||||||||||||| | |||||||| || || |||||| | |||||||| |||||||| ||||| |||||||||||||||||||| |||||| ||||| |||
----ttatttatgctttcaaatgcttgaagtttttgtttgg--ctgttgttttttcgtatgtgatgaaataatcttttattattattattttttgtttggttgtagAATGCTGCTCGTCTAGACAGTGAGATAATCTATGACAGAGACTTTGACTATGATTATTTTGGATTCAAAACCCTTGAGAGGTCTTACCTCTTGAAGGTTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctggtccttgacacaaatctcaacaattctatttgtttatttcttctttcttcagAATGCTGCTCGTTTGGACAGTGAAATCATTTATGACCGGGACTTTGATTATGATTACTTTGGTTTCAAAACCCTTGAGAGGTCCTACCTCCTGAAGATTC
ccttgac putative branch site (score: 4)
ttctatttgtttattt putative PPT
aacaattctatttgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctggtggtgtgcatgtctggatcttgacttggaaatatagaattgctggtccttgacacaaatctcaacaattctatttgtttatttcttctttcttcagAATGCTGCTCGTTTGGACAGTGAAATCATTTATGACCGGGACTTTGATTATGATTACTTTGGTTTCAAAACCCTTGAGAGGTCCTACCTCCTGAAGATTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- ggtggtg
- - - - - gcatgtc
- - - - - - - - - - - - - - - ggaaata
- - - - - - - - - - - - - - - - - - - - - ttgctgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - cacaaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctcaaca
