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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtagcctgtgttttctgaaagatccttctgctaaattttgtcaacttggtttatagatggttaaaagtgtaacttgtcctcttatttctttttgtgatgaaattgcagCCACACCCTGATGTGAAGCCAATGGCGTATGCCAATAACTTTCTCCGGATGTTCTCTTGATTGGTGTACCGCCAGTTGTATGTCAATTTTTTCTATACAA

Basic information

species Vitis vinifera
transcript Vv12s0142g00720.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv12s0142g00720.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G126435_T01 (Zea mays), 3'ss of exon 12
gtgagtagcctgtgttttctgaaagatccttctgctaaattttgtcaacttggttt-atagatggttaaaagtgtaacttgtcctcttatttctttttgtgatgaaattgcagCCACACCCTGATGTGAAGCCAATGGCGTATGCCAATAACTTTCTCCGGATGTTCTCTTGATTGG-TGTACCGCCAGTTGTATGTCAATTTTTTCTATACAA
            | |  | | |   ||  | ||| |||| ||  |      | ||| ||       |  |  | | | |       ||    |||  ||   | |  ||||||||||| |||||||||||||| ||||| ||||| |||||||| ||| |||||||    |||  |  | || |  || |||| |  ||||||||   | |  |
-----------atatccttttatc-atgttcctgttaaacttctttgcaccgatttgattagcaactggatatctgattgagggggtttacgcttgctggtgt-atcttgcagCCACATCCTGATGTGAAGCCGATGGCATATGCAAATAACTTCCTCAGGATGTTTCAATGACGGAATATAACAACA-TTGTTTAGCAATTTTTATCAGATGA

upper sequence: Vv12s0142g00720.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G126435_T02 (Zea mays), 3'ss of exon 11
gtgagtagcctgtgttttctgaaag-atccttctgctaaattttgtcaacttggttt-atagatggttaaaagtgtaacttgtcctcttatttctttttgtgatgaaattgcagCCACACCCTGATGTGAAGCCAATGGCGTATGCCAATAACTTTCTCCGGATGTTCTCTTGATTGG-TGTACCGCCAGTTGTATGTCAATTTTTTCTATACAA
||  |     ||  | | ||   |  ||  | ||| |||| ||  |      | ||| ||       |  |  | | | |       ||    |||  ||   | |  ||||||||||| |||||||||||||| ||||| ||||| |||||||| ||| |||||||    |||  |  | || |  || |||| |  ||||             
gttggctctttgaatatccttttatcatgttcctgttaaacttctttgcaccgatttgattagcaactggatatctgattgagggggtttacgcttgctgGTGT-ATCTTGCAGCCACATCCTGATGTGAAGCCGATGGCATATGCAAATAACTTCCTCAGGATGTTTCAATGACGGAATATAACAACA-TTGTTTAGCAAT-------------

upper sequence: Vv12s0142g00720.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA18G12440.1 (Glycine max), 3'ss of exon 12
----------------------------------------------------------gtgagtagcctgtgttttctgaaa-gatccttctgctaaattttgtcaacttggtttatagatggttaaaagtg--taacttg---tcctcttatttctttt--tgtgatgaaattgcagCCACACCCTGATGTGAAGCCAATGGCGTATGCCAATAACTTTCTCCGGATGTTCTCTTGATTGGTGTACC--GCCAGTTGTATGTCAATTTTTTCTATACAA
                                                             | |  ||  | | ||||  |  |||     |  | |   |    | |||    | |  || |||| | | |  | || |    ||||  | | |  |||  | || ||||  ||||||||||||||||||| || || ||||| ||||| || ||||| |||||||||||||| | |||  |  | |   | ||  | |   ||    |  | ||    
tggttagtaccttttatgtttggagtatgctatgttatatcatgttttgtcatcctcaaaaaattaccaatatgttctttattgatttcatttatgaccgtgcatatctttcaatctgtattgttatatggggttgacatactttccttgtgtctggtttactttgttgaatatgcagcCACACCCTGATGTCAAACCTATGGCTTATGCAAACAACTTCCTCCGGATGTTCTCATAATTTATACAGCTGACTAGAAGAAGCCCAGAACTGCCAATGGC-

upper sequence: Vv12s0142g00720.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA08G42380.1 (Glycine max), 3'ss of exon 12
gtgagtagcctgtgttttctgaaagatccttctgctaaattttgtcaacttggtttatagatggttaaaagtgtaacttgtcctcttatttctttttgtgatgaaattgcagCCACACCCTGATGTGAAGCCAATGGCGTATGCCAATAACTTTCTCCGGATGTTCTCTTGATTGGTGTACCGCCAGTTGTATGTCAATTTTTTCTATACAA--
              |||||||    ||  |      | || || ||||  ||  ||||| | |||| | | | |  | |    |||  ||| ||||   | ||||  ||||||||||||||||||| || || ||||| ||||| || ||||| |||||||||||||| | |||  | ||| ||    |  | | | |    | | |       
--------aacaaattttctggtgcattatgactgcatatctt-tcaatctgtgttatatagggttgacattctttccttgtgtctggtttatttt---gttgaatatgcagCCACACCCTGATGTCAAACCTATGGCATATGCAAACAACTTCCTCCGGATGTTCTCATAATT--TATACAGCTGACTAGAAGCCTAGAACTGCCAATTGTTA

upper sequence: Vv12s0142g00720.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT2G42810.2 (Arabidopsis thaliana), 3'ss of exon 13
gtgagtagcctgtgttttctgaaagatccttctgctaaattttgt---caacttggtttatagat-ggttaaaa---gtgtaacttgtcctcttatttctttttgtgatgaaattgcagCCACACCCTGATGTGAAGCCAATGGCGTATGCCAATAACTTTCTCCGGATGTTCTCTTGATTGGTGTACCGCCAGTTGTATGTCAATTTTTTCTATACAA
||||||    |   | ||    |  ||  ||||  | ||| ||      ||  | ||| |  | | | || | |    |  ||    || ||| ||||  |  | |  | |  |  ||||| || || ||||||||||| ||||| ||||| || ||||||||| ||||||||   | |   |   |  ||   || ||    || |  |  | || | 
gtgagtgtagtcc-tcttacatagcattgttcttatgaatgtttcacagaagatagttcacggtttgatttagactcattcaaacactcttctaattttctgatattgttatttcccagCCTCATCCGGATGTGAAGCCTATGGCATATGCAAACAACTTTCTCAGGATGTTCAACTAACCAGCAAAAAGCTTCTTCTACTCAAAATGCTATTCTAAAG

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|110380672|gb|EC945956.1|EC945956
EST:     GTTTTGAAGCCCCAGATCTGAAGCCAAACATTGTCACATTTTCAGCAGTG                         CCACACCCTGATGTGAAGCCAATGGCGTATGCCAATAACTTTCTCCGGATG
genomic: GTTTTGAAGCCCCAGATCTGAAGCCAAACATTGTCACATTTTCAGCAGTGgtgagtagcc ... gaaattgcagCCACACCCTGATGTGAAGCCAATGGCGTATGCCAATAACTTTCTCCGGATG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagatggttaaaagtgtaacttgtcctcttatttctttttgtgatgaaattgcagCCACACCCTGATGTGAAGCCAATGGCGTATGCCAATAACTTTCTCCGGATGTTCTCTTGATTGGTGTACCGCCAGTTGTATGTCAATTTTTTCTATACAA
             gtgtaac  putative branch site (score: 3)
                          tcttatttcttttt  TA-rich tract