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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaggacttgatggatcaaaatgaagtgatagcactttttagtgagtaaaggaataccaattttagatggcaatttattatgtcctgggagattttttaatgtttcggcttcattttcagTGGATTCCAGAATTGAAGCATTATGCACCTGGTGTTCCGATAGTTCTTGTTGGCACTAAGCTTG

Basic information

species Vitis vinifera
transcript Vv04s0023g03860.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0023g03860.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os02g02840.1 (Oryza sativa), 3'ss of exon 3
gtgaggacttgatggatcaaaatgaagtgatagcactttttagtgagtaaaggaataccaattttagatggcaatttattatgtcctgggagattttttaatgtttcggcttcattttcagTGGATTCCAGAATTGAAGCATTATGCACCTGGTGTTCCGATAGTTCTTGTTGGCACTAAGCTTG
         | |||     |  |||  ||||    | |||| |||  |  |    | |   ||||   |  | | ||||  |       |    || | ||  ||   | |  |||| |||||||| || ||  |||||||||||||||||||||| || ||  | ||||| || || |||||||
---------ttatgttgatacttgatttgat----catttttgtggctcga----ttcacttttttagtctccacttatggtacttcttgttgattctaaacttt---gttatattt-cagTGGATACCTGAGCTGAAGCATTATGCACCTGGTGTGCCTATCATCCTTGTGGGAACAAAGCTTG

upper sequence: Vv04s0023g03860.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM5G803949_T02 (Zea mays), 3'ss of exon 3
gtgaggacttgatggatcaaaatgaagtgatagcactttttagtgagtaaaggaataccaattttagatggcaatttattatgtcctgggagattttttaatgtttcggcttcattttcagTGGATTCCAGAATTGAAGCATTATGCACCTGGTGTTCCGATAGTTCTTGTTGGCACTAAGCTTG
              |   ||| ||| ||   |   |   ||  ||| ||     |  |||    ||||||||     |   | |  |  |     | | ||    |    || ||||||||||||| || ||| |||||||||||||||||||||| || ||| |||| || || || |||||||
-------------agtggaaactgatgtccaaaatcaaatttttgaataggattaatcca----tagatggcttccaaacttcttgtttgctgactctgaacccct----tttattttcagTGGATACCTGAACTGAAGCATTATGCACCTGGTGTGCCAATAATTCTCGTAGGGACAAAGCTTG

upper sequence: Vv04s0023g03860.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM5G846811_T01 (Zea mays), 3'ss of exon 3
gtgaggacttgatggatcaaaatgaagtgatagcactttttagtgagtaaaggaataccaattttagatggcaatttattatgtcctgggagattttttaatgtttcggcttcattttcagTGGATTCCAGAATTGAAGCATTATGCACCTGGTGTTCCGATAGTTCTTGTTGGCACTAAGCTTG
            || |   |||         |  |    ||  ||| ||  ||| ||  |    ||||||||     |   | |  |  |     | | ||    |    |  ||||||||||||| || ||| |||||||||||||||||||||| || ||  |||| || || || |||||||
-----------gtgtactgaaacagttctccaaaatccatttttgaata--ggattaata----tagatggctcccaaactttttgtttgctgactctgaacccct----tctattttcagTGGATACCTGAACTGAAGCATTATGCACCTGGTGTGCCAATTATTCTCGTAGGGACAAAGCTTG

upper sequence: Vv04s0023g03860.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA11G08380.1 (Glycine max), 3'ss of exon 4
-------------------------------------------------------gtgagga-cttgatggatcaaaatgaagtgatagcactttttagtgagtaaaggaataccaattttagatggcaatttatt-atgtc----ctgggagattttttaatgtttcggcttcattttcagTGGATTCCAGAATTGAAGCATTATGCACCTGGTGTTCCGATAGTTCTTGTTGGCACTAAGCTTG
                                                        |||| | | ||| |  ||   |||   ||  |  |    |   ||  | | |  |||    ||| |||    |||| ||| || |      | |  |||   ||     |  || ||| |||||||||||||||||| ||||||||||||||||||||||| || ||  |||| |||||||| |||||||
gtacttcgttgcaatttattgtggtcagagtgttttgggagaattcttatttcttttgagaatcatgaggtttctgtatggcctgtaacgaaggatgtatggatcatgttatat---tttaagaaaataattcatttatataaaaagtcgatgataaattgcatgtctggtttctttttcagTGGATTCCAGAGTTGAAGCATTATGCACCTGGTGTCCCCATTATTCTGGTTGGCACAAAGCTTG

upper sequence: Vv04s0023g03860.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA01G36880.1 (Glycine max), 3'ss of exon 4
----------------------------------------------gtgaggacttgatg-gatcaaaatgaagtgatagcac--tttttagtgagtaaaggaataccaattttagatg----gcaatttatt-atgtcctgggagattttttaatgtttc--------ggcttcattttcagTGGATTCCAGAATTGAAGCATTATGCACCTGGTGTTCCGATAGTTCTTGTTGGCACTAAGCTTG
                                               |    | ||  |  ||| |  || | ||    | |     | || |||   | | |      || ||| |||    | || | ||| || |      | | |   | ||   |         || ||||||||||||||||||| || |||||||||||||| |||||||| || ||  |||| |||||||| |||||||
gtacttcgtggcaatttattgtggtcatagtgttttgggtgtatttcttcttatttattttgataattataaggtttctgtatggcctgtaatgaaggatgtatggatcatgttatatgttaagaaaataattcatttataaaaaaagtcgatgataaattgcatgtgtggtttcattttcagTGGATTCCGGAGTTGAAGCATTATGCTCCTGGTGTCCCCATTATTCTGGTTGGCACAAAGCTTG

upper sequence: Vv04s0023g03860.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA02G05160.1 (Glycine max), 3'ss of exon 3
-----------------------------------------------------------gtgaggacttgatggatcaaaatgaagtgatagcactttttagtga--gtaaaggaataccaattttagatggcaatttattatgtcctgggagattttttaatgtttcggcttcattttcagTGGATTCCAGAATTGAAGCATTATGCACCTGGTGTTCCGATAGTTCTTGTTGGCACTAAGCTTG
                                                                 || || |   |  ||   || ||  |    |   || | |  |||||| | ||     | |  ||   |||| |  | || ||   | ||| | |  | |||     ||||||||||||||||||||| ||||| ||||||||||||| |||||| ||  || | ||||| || |||||||
gtactttttccactatagtccaaagtttaagttcctagtgttgctcaaatttagaatgcacttctacatgttacctttaatgtaaatgtgatgtttccataataattgtaaagaactatatcctatttatattaattaaaaa-gtgctaataaattgtgtgttattt-----tcattttcagTGGATTCCAGAGTTGAAACATTATGCACCTGATGTTCCCATTATTTTGGTTGGGACAAAGCTTG

upper sequence: Vv04s0023g03860.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA16G23340.1 (Glycine max), 3'ss of exon 3
-----------------------------------------------------gtgaggacttgatggatcaaaatgaagtgatagcactttt----tagtga--gtaaaggaataccaattttagatggcaatttattatgtcctgggagattttttaatgtttcggcttcattttcagTGGATTCCAGAATTGAAGCATTATGCACCTGGTGTTCCGATAGTTCTTGTTGGCACTAAGCTTG
                                                      ||     ||   || |  |   || || |  | | | ||    ||   |  |||||| |  |    || |  ||   ||||||  | ||  |   | |   | || ||| |    |||| ||||||||||||||||| ||||| ||||||||||||| |||||| ||  || | |||||||| |||||||
gtacttttcccactatttcaaggtttatgttcctagtattcctcaaatttaaaatgcacttttacaggttacattcgatgtaaatgtaatgtttccataacaattgtaaagaaccatatcttatttatattaatttaaaa-gtgttaataaacggtgta-tgtgttattttcactttcagTGGATTCCAGAGTTGAAACATTATGCACCTGATGTTCCCATTATTTTGGTTGGCACAAAGCTTG

upper sequence: Vv04s0023g03860.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT2G17800.2 (Arabidopsis thaliana), 3'ss of exon 4
gtgaggacttgatggatcaaaatgaagtgatagcactttttagtgagtaaaggaataccaattttagatggcaatttattatgtcctgggagattttttaatgtttcggcttcatttt-cagTGGATTCCAGAATTGAAGCATTATGCACCTGGTGTTCCGATAGTTCTTGTTGGCACTAAGCTTG
             | |      |||| |||  |   |||      |||   |  ||    | | |  |  | || |  ||  ||  ||      |||||  || ||   |||| |||| |||||||| |||||  ||||||||||||| |||||||| || |||||||||||||| || || || |
-------------gtacgtttttgaaatgaatg---tttgctacaagttttgatatgaatactctgaa--gaaagtcttttggttgtga-----tttttgctgctttatcttcgttttgcagTGGATCCCAGAGCTGAAGCATTATGCCCCTGGTGTCCCTATAGTTCTTGTTGGAACCAAACTAG

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|110376013|gb|EC941052.1|EC941052
EST:     TGGCATTCTCTCTCATCAGCAAGGCCAGCTATGAAAATGTTTCCAAGAAG                         TGGATTCCAGAATTGAAGCATTATGCACCTGGTGTTCCGATAGTTCTTGTT
genomic: TGGCATTCTCTCTCATCAGCAAGGCCAGCTATGAAAATGTTTCCAAGAAGgtgaggactt ... tcattttcagTGGATTCCAGAATTGAAGCATTATGCACCTGGTGTTCCGATAGTTCTTGTT
EST: gi|110713128|gb|EE088780.1|EE088780
EST:     TGGCATTCTCTCTCATCAGCAAGGCCAGCTATGAAAATGTTTCCAAGAAG                         TGGATTCCAGAATTGAAGCATTATGCACCTGGTGTTCCGATAGTTCTTGTT
genomic: TGGCATTCTCTCTCATCAGCAAGGCCAGCTATGAAAATGTTTCCAAGAAGgtgaggactt ... tcattttcagTGGATTCCAGAATTGAAGCATTATGCACCTGGTGTTCCGATAGTTCTTGTT
EST: gi|110390015|gb|EC954898.1|EC954898
EST:     TGGCATTCTCTCTCATCAGCAAGGCCAGCTATGAAAATGTTTCCAAGAAG                         TGGATTCCAGAATTGAAGCATTATGCACCTGGTGTTCCGATAGTTCTTGTT
genomic: TGGCATTCTCTCTCATCAGCAAGGCCAGCTATGAAAATGTTTCCAAGAAGgtgaggactt ... tcattttcagTGGATTCCAGAATTGAAGCATTATGCACCTGGTGTTCCGATAGTTCTTGTT
EST: gi|110396036|gb|EC961711.1|EC961711
EST:     TGGCATTCTCTCTCATCAGCAAGGCCAGCTATGAAAATGTTTCCAAGAAG                         TGGATTCCAGAATTGAAGCATTATGCACCTGGTGTTCCGATAGTTCTTGTT
genomic: TGGCATTCTCTCTCATCAGCAAGGCCAGCTATGAAAATGTTTCCAAGAAGgtgaggactt ... tcattttcagTGGATTCCAGAATTGAAGCATTATGCACCTGGTGTTCCGATAGTTCTTGTT
EST: gi|87586594|gb|DY474807.1|DY474807
EST:     TGGCATTCTCTCTCATCAGCAAGGCCAGCTATGAAAATGTTTCCAAGAAG                         TGGATTCCAGAATTGAAGCATTATGCACCTGGTGTTCCGATAGTTCTTGTT
genomic: TGGCATTCTCTCTCATCAGCAAGGCCAGCTATGAAAATGTTTCCAAGAAGgtgaggactt ... tcattttcagTGGATTCCAGAATTGAAGCATTATGCACCTGGTGTTCCGATAGTTCTTGTT
EST: gi|110404309|gb|EC969170.1|EC969170
EST:     TGGCATTCTCTCTCATCAGCAAGGCCAGCTATGAAAATGTTTCCAAGAAG                         TGGATTCCAGAATTGAAGCATTATGCACCTGGTGTTCCGATAGTTCTTGTT
genomic: TGGCATTCTCTCTCATCAGCAAGGCCAGCTATGAAAATGTTTCCAAGAAGgtgaggactt ... tcattttcagTGGATTCCAGAATTGAAGCATTATGCACCTGGTGTTCCGATAGTTCTTGTT
EST: gi|33410493|gb|CF216120.1|CF216120
EST:     TGGCATTCTCTCTCATCAGCAAGGCCAGCTATGAAAATGTTTCGATGAAG                         TGGATTCCAGAATTGAAGCATTATGCACCTGGTGTTCCGATAGTTCTTGTT
genomic: TGGCATTCTCTCTCATCAGCAAGGCCAGCTATGAAAATGTTTCCAAGAAGgtgaggactt ... tcattttcagTGGATTCCAGAATTGAAGCATTATGCACCTGGTGTTCCGATAGTTCTTGTT
EST: gi|110366542|gb|EC930452.1|EC930452
EST:     TGGCATTCTCTCTCATCAGCAAGGCCAGCTATGAAAATGTTTCCAAGAAG                         TGGATTCCAGAATTGAAGCATTATGCACCTGGTGTTCCGATAGTTCTTGTT
genomic: TGGCATTCTCTCTCATCAGCAAGGCCAGCTATGAAAATGTTTCCAAGAAGgtgaggactt ... tcattttcagTGGATTCCAGAATTGAAGCATTATGCACCTGGTGTTCCGATAGTTCTTGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatggcaatttattatgtcctgggagattttttaatgtttcggcttcattttcagTGGATTCCAGAATTGAAGCATTATGCACCTGGTGTTCCGATAGTTCTTGTTGGCACTAAGCTTG
                             ttttaat  putative branch site (score: 3)
                                           cttcattttc  putative PPT
                        agattttttaatgttt  TA-rich tract