Sequence
atgc intronic sequence ATGC exonic sequencegtgtctttcttaatgttggacttctgagaacaacaactggcaatcgtgtgtttggtgctctgaagGGAGCATTGGATGGTGGCTTGGACATTCCTCACAGTGACAAGAGATTTTTTGGATTCTCAAATGATAGCAAGCAGCTTGATGCCGAGGTTCACCGAAAGT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv04s0008g00050.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os01g67134.1 (Oryza sativa), 3'ss of exon 6
-----------------------------------------------------------------------------------------------------gtgtctttcttaatgttggact-tctgagaacaacaactggcaatcgtgtgtttggtgctctgaagGGAGCATTGGATGGTGGCTTGGACATTCCTCACAGTGACAAGAGATTTTTTGGATTCTCAAATGATAGCAAGCAGCTTGATGCCGAGGTTCACCGAAAGT
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gtgtgttgtgctttgatcgcaactgttggctgctgtaataatagttgatttatcacttgaacatcaaattcctcagctcttttagaaacacaaccgttacgataacctttggattgttgatctgtattagtagctcatgtggatatact-tctcttttcttctgcagGGAGCTTTGGATGGTGGTCTTGACATTCCTCACAGTGACAAGAGGTTTGCTGGGTTCAAGAAGGACGAGAAGCAGCTTGATTCTGATATTCACCGCAAGT
upper sequence: Vv04s0008g00050.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os01g67126.1 (Oryza sativa), 3'ss of exon 6
---------------------------------------------------------------------------------------------gtgtctttcttaatgttggacttctgag----aacaacaactg--gcaatcgtgtgtttggtgctctgaagGGAGCATTGGATGGTGGCTTGGACATTCCTCACAGTGACAAGAGATTTTTTGGATTCTCAAATGATAGCAAGCAGCTTGATGCCGAGGTTCACCGAAAGT
||| | | | ||||| | ||| | | | || | | | | | |||| ||||||| ||||||||||| | ||||||||||||||||||||||| ||| ||| ||| || || |||||||||||| | || ||||||| ||||
gtgtgttgtgctttgatctcaactgttggctgctgtaataatagttgatttgtcacttgaacatcaaattcatcagctcttttagaaacacaaccgtcaatataacctttggattgttgatctgtattagtagctcatgtggatatacttctcttcttctgcagGGAGCTTTGGATGGTGGTCTTGACATTCCTCACAGTGACAAGAGGTTTGCTGGGTTCAAGAAGGACGAGAAGCAGCTTGATTCTGATATTCACCGCAAGT
upper sequence: Vv04s0008g00050.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G163081_T02 (Zea mays), 3'ss of exon 6
---------------------------------------------------------------------------------------------------gtgtctttcttaatgttggacttctgagaacaacaactggcaatcgtgtgtttggtgctctgaagGGAGCATTGGATGGTGGCTTGGACATTCCTCACAGTGACAAGAGATTTTTTGGATTCTCAAATGATAGCAAGCAGCTTGATGCCGAGGTTCACCGAAAGT
||| | | || || || | | | | | | ||||| ||| | |||||||||||||||| ||| |||| ||||||||||| || ||||| ||| ||||||| ||
gtatatatcttctgtttgttaccatgatattatattggtgtcattgtttgtatttagcccatcaagaataatcattttttcatgtgcttgctgtaagagtcatctcttgttgtggtgaacgatttcccatctctctagcccctttaacgtttgttgcc--gcagGGAGCATTGGATGGAGGCCTGGATATTCCTCACAGCGAGAAGAGGTTTGCTGGATTCAAGAAG-------------------------------------
upper sequence: Vv04s0008g00050.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G163081_T03 (Zea mays), 3'ss of exon 6
---------------------------------------------------------------------------------------------------gtgtctttcttaatgttggacttctgagaacaacaactggcaatcgtgtgtttggtgctctgaagGGAGCATTGGATGGTGGCTTGGACATTCCTCACAGTGACAAGAGATTTTTTGGATTCTCAAATGATAGCAAGCAGCTTGATGCCGAGGTTCACCGAAAGT
||| | | || || || | | | | | | ||||| ||| | |||||||||||||||| ||| |||| ||||||||||| || ||||| ||| ||||||| || || ||||||| | ||||| || ||||| |
gtatatatcttctgtttgttaccatgatattatattggtgtcattgtttgtatttagcccatcaagaataatcattttttcatgtgcttgctgtaagagtcatctcttgttgtggtgaacgatttcccatctctctagcccctttaacgtttgttgcc--gcagGGAGCATTGGATGGAGGCCTGGATATTCCTCACAGCGAGAAGAGGTTTGCTGGATTCAAGAAGGACGACAAGCAGTTGGATGCTGATACCCACCGCAG--
upper sequence: Vv04s0008g00050.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G163081_T04 (Zea mays), 3'ss of exon 6
---------------------------------------------------------------------------------------------------gtgtctttcttaatgttggacttctgagaacaacaactggcaatcgtgtgtttggtgctctgaagGGAGCATTGGATGGTGGCTTGGACATTCCTCACAGTGACAAGAGATTTTTTGGATTCTCAAATGATAGCAAGCAGCTTGATGCCGAGGTTCACCGAAAGT
||| | | || || || | | | | | | ||||| ||| | |||||||||||||||| ||| |||| ||||||||||| || ||||| ||| ||||||| || || ||||||| | ||||| || ||||| | ||
gtatatatcttctgtttgttaccatgatattatattggtgtcattgtttgtatttagcccatcaagaataatcattttttcatgtgcttgctgtaagagtcatctcttgttgtggtgaacgatttcccatctctctagcccctttaacgtttgttgcc--gcagGGAGCATTGGATGGAGGCCTGGATATTCCTCACAGCGAGAAGAGGTTTGCTGGATTCAAGAAGGACGACAAGCAGTTGGATGCTGATACCCACCGCAGGT
upper sequence: Vv04s0008g00050.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA07G06590.1 (Glycine max), 3'ss of exon 6
-----gtgtctttct-taatgttggac------ttctgagaacaacaactggc--aatcgtgtg---tttggtgctctgaagGGAGCATTGGATGGTGGCTTGGACATTCCTCACAGTGACAAGAGATTTTTTGGATTCTCAAATGATAGCAAGCAGCTTGATGCCGAGGTTCACCGAAAGT
| || | || ||||||| | | | || || ||| | | | || | | | ||||||| ||||||| || ||||| |||||||||||||||||||| ||| ||| || || || | ||| |||||||||| |||||||| || || |
gtaatctatcatactgtaatgttaatcagtgtgattttgttttaatggttgatcaaattgaataatctgtgattgtttacagGGAGCTCTGGATGGGGGGTTGGATATTCCTCACAGTGACAAGAGGTTTGCTGGGTTTGATAAGGAGAAGAAGGAGCTTGATGCAGAGGTTCATCGGAAAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taatgttggacttctgagaacaacaactggcaatcgtgtgtttggtgctctgaagGGAGCATTGGATGGTGGCTTGGACATTCCTCACAGTGACAAGAGATTTTTTGGATTCTCAAATGATAGCAAGCAGCTTGATGCCGAGGTTCACCGAAAGT
tcttaat putative branch site (score: 3)
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgtctttcttaatgttggacttctgagaacaacaactggcaatcgtgtgtttggtgctctgaagGGAGCATTGGATGGTGGCTTGGACATTCCTCACAGTGACAAGAGATTTTTTGGATTCTCAAATGATAGCAAGCAGCTTGATGCCGAGGTTCACCGAAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT