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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttacatttaaacccatcaaagaagaatgattgaaagaaaagaaggaagatgagagggaaagaagggaagaggaatgatgttattgctggttttctgatccacttttaattaacatagGTGGGCAGGTACAAGAGCCCTGATGAGCATCCTTTCTTCCCAGTTGAGTTGCCTGAACCAATGTTGCCACCTTTACAGTACCCAAAG

Basic information

species Vitis vinifera
transcript Vv14s0108g01330.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0108g01330.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os01g55870.1 (Oryza sativa), 3'ss of exon 2
gtatgttacatttaaacccatcaaagaagaatgattgaaagaaaagaaggaagatgagagggaaagaagggaagaggaatg-atgttattgctggttttctgatccacttttaattaacatagGTGGGCAGGTACAAGAGCCCTGATGAGCATCCTTTCTTCCCAGTTGAGTTGCCTGAACCAATGTTGCCACCTTTACAGTACCCAAAG
                            | |     |      ||  || || || |  |   |      |   |  | || |   | ||| |||||  |||  |  ||| |        ||||| || || |||||||||||||||||||| || ||||| || |  ||  ||||||||||| ||||||||||| | ||||| ||||||
----------------------------gtagagcagggttgtaactagcaatataattgttcattgtatgccaaaaattgcaaaatgttgatggtt--ctggccatcttgtg-------tagGTTGGGAGATACAAGAGCCCTGATGAGCACCCATTCTTTCCGGAGGATCTGCCTGAACCACTGTTGCCACCTCTCCAGTATCCAAAG

upper sequence: Vv14s0108g01330.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G116087_T02 (Zea mays), 3'ss of exon 2
gtatgttacatttaaacccatcaaagaagaatgattgaaagaaaagaaggaagatgagagggaaagaagggaagaggaatgatgttattgctggttttctgatccacttttaattaacatagGTGGGCAGGTACAAGAGCCCTGATGAGCATCCTTTCTTCCCAGTTGAGTTGCCTGAACCAATGTTGCCACCTTTACAGTACCCAAAG
            | ||  | |       || |  ||   | |||  || | |  ||| || |  |   |  |    |||| |  |                || ||  | |  || |||||||| || |||||||||||||| |||||||| ||||||||  |    ||  ||||||| ||   |||||||||| | || ||||||| |
-----------gtgaattcgtttg----gacttctttttaaaaaccaaagcaattgatagtggcatgcgaaa----gaataacat----------------atgcaaatgtttttgacatagGTTGGGAGGTACAAGAGCCCAGATGAGCACCCTTTCTTTTCCAAGGATCTGCCTGAGCCCCAGTTGCCACCTATGCAATACCCAAGG

upper sequence: Vv14s0108g01330.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G028369_T01 (Zea mays), 3'ss of exon 2
gtatgttacatttaaacccatcaaagaagaatgattgaaagaaaagaaggaagatgagagggaaagaagggaagaggaatgatgttattgctggttttctgatccacttttaattaacatagGTGGGCAGGTACAAGAGCCCTGATGAGCATCCTTTCTTCCCAGTTGAGTTGCCTGAACCAATGTTGCCACCTTTACAGTACCCAAAG
           |  ||  |||    | | | |  || | |  ||| |  |  ||| |  |      || | |  |   | | | || ||                        ||||||||||| || || ||||||||||| |||||||| |||||||| || |  ||  ||||||| ||   |||||||||| | |||||||||| |
----------gtggaattcattt--ggacattttttaagaacaaaaacagttgatcatggcatgcaaaagaataacatacgctattgttt-----------------------ttaacatagGTTGGGAGATACAAGAGCCCAGATGAGCACCCTTTCTTTCCTGAGGATCTGCCTGAGCCCCGGTTGCCACCTATGCAGTACCCAAGG

upper sequence: Vv14s0108g01330.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G124365_T02 (Zea mays), 3'ss of exon 1
gtatgttacatttaaacccatcaaagaagaatgattgaaagaaaagaaggaagatgagagggaaagaagggaagaggaatgatgttattgctggttttctgatccacttttaattaacatagGTGGGCAGGTACAAGAGCCCTGATGAGCATCCTTTCTTCCCAGTTGAGTTGCCTGAACCAATGTTGCCACCTTTACAGTACCCAAAG
       |     |     ||| |    || |  || ||| |||  ||     |  |  |   | |    |   | |||| |  |   ||||  | ||                |||||||||| || || ||||||||||| |||||||| ||||||||  |    ||  ||||||| ||   |||||||||| | || ||||||| |
-agctccatgcacaggtgaatccatttggatttctttaaaaaaacaaa-----acaattgatcatggcatgcgaaagaataacatg--tgctaatgtttg--------------taacatagGTTGGGAGATACAAGAGCCCAGATGAGCACCCTTTCTTTTCCAAGGATCTGCCTGAGCCCCGGTTGCCACCTATGCAATACCCAAGG

upper sequence: Vv14s0108g01330.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G124365_T01 (Zea mays), 3'ss of exon 2
gtatgttacatttaaacccatcaaagaagaatgattgaaagaaaagaaggaagatgagagggaaagaagggaagaggaatgatgttattgctggttttctgatccacttttaattaacatagGTGGGCAGGTACAAGAGCCCTGATGAGCATCCTTTCTTCCCAGTTGAGTTGCCTGAACCAATGTTGCCACCTTTACAGTACCCAAAG
            | || ||||       | ||   |  || |||| ||   |  |||    |  |   |  |  |  |    || || || | ||                    ||||||||| || || ||||||||||| |||||||| ||||||||  |    ||  ||||||| ||   |||||||||| | || ||||||| |
-----------gtgaatccattt-----ggatttctttaaaaaaacaaaacaattgatcatggcatgcgaaagaataacatgtgctaatgtttgt--------------------aacatagGTTGGGAGATACAAGAGCCCAGATGAGCACCCTTTCTTTTCCAAGGATCTGCCTGAGCCCCGGTTGCCACCTATGCAATACCCAAGG

upper sequence: Vv14s0108g01330.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA19G03290.1 (Glycine max), 3'ss of exon 2
--gtatgttacatttaaacccatcaaagaagaa--tgattgaaagaaaagaaggaagatgagagggaaagaaggga-agaggaatgatgtt--attgctggtttt-ctgatccacttttaatt--aacatagGTGGGCAGGTACAAGAGCCCTGATGAGCATCCTTTCTTCCCAGTTGAGTTGCCTGAACCAATGTTGCCACCTTTACAGTACCCAAAG
  || |||        ||| |   |||| |     ||| | ||||      |  || |   ||   |   |||| | | | |  |||| |   | || |  |||| ||||     |||  |||  |    ||||||| |||||||||||||||||||||||||| ||||| |||| ||   | |||||||||||||| |||||||| ||||| ||  ||
gtgtgtgtgtggacctaactctcaaaagcaattcttgactaaaagttttctataaaaaaatgataaagtaaaggcacaaatgcttgatatataaatgttacttttgctgactggatttccattccactgaagGTGGGTAGGTACAAGAGCCCTGATGAGCATCCATTCTTTCCAGATGGCCTACCTGAACCAATGTTACCACCTTTGCAGTATCCTCAG

upper sequence: Vv14s0108g01330.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA13G05830.1 (Glycine max), 3'ss of exon 2
--gtatgttacatttaaacccatcaaagaagaatgattgaaag--------aaaagaaggaagatgagagggaaagaagggaagaggaat-gatgttattgctggttttctgatccacttttaattaacatagGTGGGCAGGTACAAGAGCCCTGATGAGCATCCTTTCTTCCCAGTTGAGTTGCCTGAACCAATGTTGCCACCTTTACAGTACCCAAAG
  || |||     | |  | ||  |   |    ||| | ||||        |||| || ||  | |  | || |  || |   ||   || ||| ||| |  || |     |||   | ||  | | |   ||||||| |||||||||||||||||||||||||| ||||| |||| ||   | || |||||| |||| |||||||| ||||||||  ||
gtgtgtgtggacctaagtctcaaaagcaatttttgactaaaagttttctgtaaaaaaatgataaagtaaaggcacaaatgtttgatatatagatattacttttgctgactggatttccattccactga---agGTGGGTAGGTACAAGAGCCCTGATGAGCATCCATTCTTTCCAGATGGCCTACCCGAACCAGTGTTACCACCTTTGCAGTACCCTCAG

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|161714107|gb|FC063819.1|FC063819
EST:     GCTCTTTGGTTGAATTCATGGTCAGGGAAACCGAAAAGCTTCATGCTCAG                         GTGGGCAGGTACAAGAGCCCTGATGAGCATCCTTTCTTCCCAGTTGAGTTG
genomic: GCTCTTTGGTTGAATTCATGGTCAGGGAAACCGAAAAGCTTCATGCTCAGgtatgttaca ... attaacatagGTGGGCAGGTACAAGAGCCCTGATGAGCATCCTTTCTTCCCAGTTGAGTTG
EST: gi|351041739|gb|FQ455949.1|FQ455949
EST:     GCTCTTTGGTTGAATTCATGGTCAGGGAAACCGAAAAGCTTCATGCTCAG                         GTGGGCAGGTACAAGAGCCCTGATGAGCATCCTTTCTTCCCAGTTGAGTTG
genomic: GCTCTTTGGTTGAATTCATGGTCAGGGAAACCGAAAAGCTTCATGCTCAGgtatgttaca ... attaacatagGTGGGCAGGTACAAGAGCCCTGATGAGCATCCTTTCTTCCCAGTTGAGTTG
EST: gi|161715858|gb|FC065189.1|FC065189
EST:     GCTCTTTGGTTGAATTCATGGTCAGGGAAACCGAAAAGCTTCATGCTCAG                         GTGGGCAGGTACAAGAGCCCTGATGAGCATCCTTTCTTCCCAGTTGAGTTG
genomic: GCTCTTTGGTTGAATTCATGGTCAGGGAAACCGAAAAGCTTCATGCTCAGgtatgttaca ... attaacatagGTGGGCAGGTACAAGAGCCCTGATGAGCATCCTTTCTTCCCAGTTGAGTTG
EST: gi|351026402|gb|FQ428414.1|FQ428414
EST:     GCTCTTTGGTTGAATTCATGGTCAGGGAAACCGAAAAGCTTCATGCTCAG                         GTGGGCAGGTACAAGAGCCCTGATGAGCATCCTTTCTTCCCAGTTGAGTTG
genomic: GCTCTTTGGTTGAATTCATGGTCAGGGAAACCGAAAAGCTTCATGCTCAGgtatgttaca ... attaacatagGTGGGCAGGTACAAGAGCCCTGATGAGCATCCTTTCTTCCCAGTTGAGTTG
EST: gi|351040113|gb|FQ425199.1|FQ425199
EST:     GCTCTTTGGTTGAATTCATGGTCAGGGAAACCGAAAAGCTTCATGCTCAG                         GTGGGCAGGTACAAGAGCCCTGATGAGCATCCTTTCTTCCCAGTTGAGTTG
genomic: GCTCTTTGGTTGAATTCATGGTCAGGGAAACCGAAAAGCTTCATGCTCAGgtatgttaca ... attaacatagGTGGGCAGGTACAAGAGCCCTGATGAGCATCCTTTCTTCCCAGTTGAGTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agggaagaggaatgatgttattgctggttttctgatccacttttaattaacatagGTGGGCAGGTACAAGAGCCCTGATGAGCATCCTTTCTTCCCAGTTGAGTTGCCTGAACCAATGTTGCCACCTTTACAGTACCCAAAG
                                            aattaac  putative branch site (score: 2)
                                      acttttaattaacata  TA-rich tract