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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcttgatcagtactactccccatttcttctctcctaccactgttccatctttttgatccatttcccacatggggttctcacactttcatgtgttttcttgtcaaaagTGGTTTGAAGTTCTTGATGGGCTGCTTGGCAAACACTGGAGGAACGTGGGGTTGGCTTTCAACTGCACTTTTCTTCTGTTTGGATCCGTGATTCAACTCA

Basic information

species Vitis vinifera
transcript Vv03s0038g02140.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv03s0038g02140.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G045057_T02 (Zea mays), 3'ss of exon 2
---------------gtcttgat-cagtactactccccatttcttctc-tcctaccactgttccatctttttgatccatttcccac------------atggggttctcacactttcatgtgttttcttgt---------caaaagTGGTTTGAAGTTCTTGATGGGCTGCTTGGCAAACACTGGAGGAACGTGGGGTTGGCTTTCAACTGCACTTTTCTTCTGTTTGGATCCGTGATTCAACTCA
               || |  ||  |  |||| |  | |  | | ||  |  |     |||||||  |||| | |  | ||  |||             |||   |   ||||    |  ||| || || |         |   |||||||||| ||||| |||||||| || || || |||||||||||||| ||  |    |||||||||||||| || || || || ||||| || || ||||
gtgcgtgtgtcatgtgtatatatatatgactatttgctagctatacttgtattttgtttgttccaaattttggtttgaattaacaccatcagaagtttgtggaaattctacaccaataattgtcttttttttctggggagccgcagTGGTTTGAGGTTCTGGATGGGCTACTGGGGAAGCACTGGAGGAACGTCGGCCTCTTCTTCAACTGCACTTTCCTCCTCTTCGGCTCCGTCATCCAGCTCA

upper sequence: Vv03s0038g02140.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA04G00640.1 (Glycine max), 3'ss of exon 2
---------------gtcttgatcagtactactccccatttcttctctcctaccactgttccatctttttgatccatttcccacatggggttct-cacactttcatgtgttttcttgtcaaaagTGGTTTGAAGTTCTTGATGGGCTGCTTGGCAAACACTGGAGGAACGTGGGGTTGGCTTTCAACTGCACTTTTCTTCTGTTTGGATCCGTGATTCAACTCA
                |    ||    | || | |    ||||| | |     | |||| | |  ||| | ||  | ||| || ||| |  | |    | ||| |      ||||       |||||||||| |||||||||||||| || || ||||||||||| |||||||| ||||| ||||||||||| |||||||| |||||||| || || |||||||
gttccactatcccactttcaaattctaaatattgcatgcttcttatattg-gtctctgtgcaacttttat-atatacttctca-atgtgtctgtgtttaatttaacacaagttctctattgcagTGGTTTGAGGTTCTTGATGGGCTCCTCGGGAAACACTGGAGAAACGTGGGCTTGGCCTTCAACTGCACATTTCTTCTATTTGGATCTGTTATCCAACTCA

upper sequence: Vv03s0038g02140.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA06G00690.1 (Glycine max), 3'ss of exon 2
gtcttgatcagtactactccccatttctt----ctctcctaccactgttccatctttttgatccatttc-----ccacatggggttctcacactttcatgtgttttcttgtcaaa------agTGGTTTGAAGTTCTTGATGGGCTGCTTGGCAAACACTGGAGGAACGTGGGGTTGGCTTTCAACTGCACTTTTCTTCTGTTTGGATCCGTGATTCAACTCA
||     ||  | | | || | | ||||      | |  |  | || | | |  ||||  ||  | |||     | |  |  |  |||  |  |||       || |   | ||       |||||||||| |||||||||||||| || || || |||||||| |||||||| ||||| ||||||||||| |||||||| |||||||| || || |||||||
gttccactc--tcccattctcaaattctaaatattatattgtctctctgcaactttttatatatacttcgatctcaatgtatgtatctatctgtttttaacacttacaacttaactattgcagTGGTTTGAGGTTCTTGATGGGCTCCTCGGGAAGCACTGGAGAAACGTGGGCTTGGCCTTCAACTGCACATTTCTTCTATTTGGATCTGTTATCCAACTCA

upper sequence: Vv03s0038g02140.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA11G11310.1 (Glycine max), 3'ss of exon 2
gtcttgatcagtactactccccatttcttctctcctaccactgttccatctttttgatccatttcccacatggg--gttctcacactttcatgtgttttcttgtca-aaagTGGTTTGAAGTTCTTGATGGGCTGCTTGGCAAACACTGGAGGAACGTGGGGTTGGCTTTCAACTGCACTTTTCTTCTGTTTGGATCCGTGATTCAACTCA
||     |||  |  | |    |  |  | |      | |   | |  ||    | ||  | ||   || | ||  ||  |   | |   ||   |       | |   |||||||||||||||||||||| || || || || |||||||| |||||||| ||||| || |||||||| ||||||||||||||||| || || ||| | |
gttcaactcaccaacatta---agataatttaattagctaacatacgttcaaagtaattaaattttaactttggttgtcgttttattcaaataaataaataaattatgcagTGGTTTGAAGTTCTTGATGGACTCCTCGGGAAGCACTGGAGAAACGTGGGTTTGGCCTTTAACTGCACATTTCTTCTGTTTGGATCTGTTATACAATTGA

upper sequence: Vv03s0038g02140.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA12G03490.1 (Glycine max), 3'ss of exon 2
gtcttgatcagtactact--ccccatttcttctctcctaccact----gttccatctttttgatccatttcccacatggggttctcacactttcatgtgttttcttgtcaaaagTGGTTTGAAGTTCTTGATGGGCTGCTTGGCAAACACTGGAGGAACGTGGGGTTGGCTTTCAACTGCACTTTTCTTCTGTTTGGATCCGTGATTCAACTCA
||     |||  |  | |  |   |||| || | |  ||  | |         | | | || ||  | | |  | ||  | || ||    ||| ||    |   || |    |||||||||| ||||||||||| || || || || |||||||| |||||||| ||||| || |||||||| ||||||||||||||||| || || ||||| |
gttcaactcaccaacattaacataattttttatttaatataagtccaaacaataacctcttaattaaat-cttaaatttgattgtcgt--tttaatcaaataaattttatgcagTGGTTTGAGGTTCTTGATGGACTCCTCGGGAAGCACTGGAGAAACGTGGGTTTGGCCTTTAACTGCACATTTCTTCTGTTTGGATCTGTTATACAACTGA

upper sequence: Vv03s0038g02140.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT2G21050.1 (Arabidopsis thaliana), 3'ss of exon 2
gtcttgatcagtactactccccatttcttctctcctaccactgttccatctttttgatccatttcccacatggggttctcacactttcatgtgttttcttgtcaaaagTGGTTTGAAGTTCTTGATGGGCTGCTTGGCAAACACTGGAGGAACGTGGGGTTGGCTTTCAACTGCACTTTTCTTCTGTTTGGATCCGTGATTCAACTCA
              | ||   |   |||| |||  ||       |  || | |   ||   |||   |||      | | |||  ||     |||   |  |   ||||||||||| |||||||||||  ||||||| || || |||||||| || || || || || |||||||| || ||||| |||||||| || ||||||||||
------------gtttctttactgatcttttctattattcaaagtatatatctgacatgttttttgtacaaaaacatttgacatgtt-----gttggttaatgtgaagTGGTTTGAGGTTCTTGATGGATTGCTTGGGAAGCATTGGAGGAATGTTGGTTTAGCCTTTAACTGCACCTTCCTTCTCTTTGGATCTGTCATTCAACTCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgatccatttcccacatggggttctcacactttcatgtgttttcttgtcaaaagTGGTTTGAAGTTCTTGATGGGCTGCTTGGCAAACACTGGAGGAACGTGGGGTTGGCTTTCAACTGCACTTTTCTTCTGTTTGGATCCGTGATTCAACTCA
                      ttctcac  putative branch site (score: 2)
                                        ttttcttgtc  putative PPT
                                        ttttctt  TA-rich tract