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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgatcttcaattaattaccatatacatatactaatctcgatttatttattttgttttgttaaattcttataatttagtctaaaaacagGTTTCTGATGAAGTTGAACAACGAAACCGTGTCTATCGAGCTCAAGAATGGAACCGTGGTTCATGGCACCATAACAG

Basic information

species Vitis vinifera
transcript Vv07s0104g00160.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv07s0104g00160.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os04g39444.1 (Oryza sativa), 3'ss of exon 1
-------------------------------------------------gtttgatcttcaattaattaccatatacatatactaatctcgatttatttattttgttttgttaaattcttataattta--gtctaaaaacagGTTTCTGATGAAGTTGAACAACGAAACCGTGTCTATCGAGCTCAAGAATGGAACCGTGGTTCATGGCACCATAACAG
                                                 || || |||||  ||   |      ||    | | ||| |          ||||| ||       |||       |     || |     |||||||||||||||| |||||||||| || ||  | |||||||||||||| || ||||| || || || ||||| || |
gtgaggctccggttcttctccacttcgttctgtcccgtttcgtttccctgtgtg-tcttccctttgctgatccgtatg-gtgcaaattttcccccgcgaatttttttggtgcggatttggggcgtggggggtttcgctgcagGTTTCTGATGAAGCTGAACAACGAGACGGTCACCATCGAGCTCAAGAACGGCACCGTCGTCCACGGAACCATCACCG

upper sequence: Vv07s0104g00160.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G416061_T01 (Zea mays), 3'ss of exon 1
---------------------------gtttgatcttcaattaattaccatatacatatactaatctcgatttatttattttgttttgttaaattcttataatttagtctaaa----aacagGTTTCTGATGAAGTTGAACAACGAAACCGTGTCTATCGAGCTCAAGAATGGAACCGTGGTTCATGGCACCATAACAG
                            |||   | || |||  || |  | | |  || |   |   |   | ||        |  ||     | ||           |        |||||||  |||||||| ||||||||||||| ||| | |||||||| ||||| || ||||| || || || ||||| || |
gtaagccagcatccccctgtttctcccctttccccctccattcgtttcagtctgctgattcgtttggtgcaattttcgcccgaatcggtgcggattttggcgcgggaattgcgcttttacagGTTCTTGATGAAGCTGAACAACGAAACGGTGACCATCGAGCTTAAGAACGGCACCGTCGTACACGGAACCATTACCG

upper sequence: Vv07s0104g00160.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA03G30880.1 (Glycine max), 3'ss of exon 1
gtttgatcttcaattaattaccatatacatatactaatctcgatttatttattttgttttgttaaattcttata-atttagtctaaaaacagGTTTCTGATGAAGTTGAACAACGAAACCGTGTCTATCGAGCTCAAGAATGGAACCGTGGTTCATGGCACCATAACAG
|| | |  |     |  | |         |    |  ||||  ||| ||| ||||    | | ||  |   ||   | ||       ||||||||||| |||||| |||||||||||||||| || |||||||||||||| ||||| || |||||||||||||| ||||
gtctcacatcttcattctcattccgcgtttccctttttctcactttttttttttttcaatttgaagctaaaatgtgtataaaactggaacagGTTTCTCATGAAGCTGAACAACGAAACCGTTTCAATCGAGCTCAAGAACGGAACAGTTGTTCATGGCACCATTACAG

upper sequence: Vv07s0104g00160.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA19G33700.1 (Glycine max), 3'ss of exon 1
--------gtttgatcttcaattaattaccatatacatatactaatctcgatttatttattttgttttgttaaattcttataa---tttagtctaaaaacagGTTTCTGATGAAGTTGAACAACGAAACCGTGTCTATCGAGCTCAAGAATGGAACCGTGGTTCATGGCACCATAACAG
          || ||  ||| |  |        |   | |     | |   ||| ||  | || ||   ||  |  || | ||   | ||      ||||||||||||||||||| |||||||||||||||| || |||||||||||||| || || || ||||| |||||||| ||||
gtctcacatattcattctcattccaccttttcctttttgttactctttttttttcttcttcttcttcactttgaagctaaaaagcgtctaaaactgaaacagGTTTCTGATGAAGCTGAACAACGAAACCGTATCAATCGAGCTCAAGAACGGCACAGTTGTTCACGGCACCATTACAG

upper sequence: Vv07s0104g00160.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA18G52210.1 (Glycine max), 3'ss of exon 2
--------------------------------------gtttgat-cttcaattaattaccatatacatatactaatctcgattt-atttattttgtttt-----gttaaattcttataattta------gtctaaaaacagGTTTCTGATGAAGTTGAACAACGAAACCGTGTCTATCGAGCTCAAGAATGGAACCGTGGTTCATGGCACCATAACAG-
                                       |||| | | |   | ||||    | |  || | ||  | |  |||| |||| |||| ||||      | ||| ||| ||||| ||       |  |  | ||||||| | |||||||||||||| ||||||||||| || |||||||||||||| ||  | |||||||||||||| |||| 
tttttctctgctctatctctctctttgtttttttttttttttgttgcgttggtaaattgatctgtttatgtgctgctatgtattttattttttttattttctgggatcaaagtctaataatatacgaacactgcatgagcaggTTTTTAATGAAGTTGAACAATGAAACCGTGTCAATTGAGCTCAAGAATGGCACTATTGTTCATGGCACCATTACAGG

upper sequence: Vv07s0104g00160.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA02G10640.1 (Glycine max), 3'ss of exon 2
gtttgatcttcaattaattaccatatacatatacta-atctcgatttatttattttgttttg---ttaaattcttataattta------gtctaaaaacagGTTTCTGATGAAGTTGAACAACGAAACCGTGTCTATCGAGCTCAAGAATGGAACCGTGGTTCATGGCACCATAACAG
||||     |   ||  || |  |||   |  | |   | |  |||| ||| |  | || ||   | ||| ||| ||||| ||       | ||  |  |||||| | |||||||||||||| ||||||||||| || |||||||||||||| ||  | |||||||||||||| ||||
gtttttctctttctttgttgcgttatctgttaattgcgtttttatttttttttcattttctgagatcaaagtctaataatatacgaacactgtatgagtagGTTTTTAATGAAGTTGAACAATGAAACCGTGTCAATTGAGCTCAAGAATGGCACTATTGTTCATGGCACCATTACAG

upper sequence: Vv07s0104g00160.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT4G02840.2 (Arabidopsis thaliana), 3'ss of exon 1
-----------------------------------gtttgatcttcaattaattaccatatacatatactaatctcgatttatttattttgttttgttaaattcttataatttagtctaaaaacagGTTTCTGATGAAGTTGAACAACGAAACCGTGTCTATCGAGCTCAAGAATGGAACCGTGGTTCATGGCACCATAACAG
                                   |||| || |  ||||   | | | ||    | | |  |||   |||   |  | |    ||||  ||| |  ||  |   | |     ||||||| ||||||| |||||||||||||| || || |||||||| ||||| |||||| | |||||||| ||||| || |
gtatggtttctactcggattctctttatttcttcggtttaat-tggaatttgcttcgaaattttgagatttctctttgttttcatgctcttcgatgtttgatt-tcgtatctggattttttcgcagGTTTTTGATGAAATTGAACAACGAAACAGTTTCAATCGAGCTTAAGAACGGAACCATTGTTCATGGAACCATTACTG

upper sequence: Vv07s0104g00160.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: EFJ29766 (Selaginella moellendorffii), 3'ss of exon 1
-------gtttgatcttcaattaattaccatatacatatactaatctcgatttatttattttgttttgttaaattcttataatttagtctaaaaacagGTTTCTGATGAAGTTGAACAACGAAACCGTGTCTATCGAGCTCAAGAATGGAACCGTGGTTCATGGCACCATAACAG
       |    |||| || |    |  | | |   | | | |  |  | ||||    | | |     | | | ||| ||   |   |       ||| |||||||||||| | |||||||| || || || ||||||||||||||||| ||  | ||  |||| || || ||||
gtacgtcggcgcatctcca-tcgcctctcctctttctcttcca--cagggtttagggttctcgcgcactgacagtctgatttctcgcttctcc--cagATTTCTGATGAAGCTAAACAACGAGACAGTATCCATCGAGCTCAAGAATGGGACTATTGTGAATGGAACAATCACAG

upper sequence: Vv07s0104g00160.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: EFJ08912 (Selaginella moellendorffii), 3'ss of exon 1
gtttgatcttcaattaattaccatatacatatactaatctcgatttatttatttt-gttttgttaaattcttataatttagtctaaaaa------cagGTTTCTGATGAAGTTGAACAACGAAACCGTGTCTATCGAGCTCAAGAATGGAACCGTGGTTCATGGCACCATAACAG
    |  | |||    ||  ||||   | | | ||  |     |  |     ||| |  || |      || | | | |  | |           ||| |||||||||||| | |||||||| || || || ||||||||||||||||| ||  | ||  |||| || || ||||
----gtacgtcagcgcatctccat-cgcctctcctctttctcttccacagggtttagggttctcgcgcactgacagtctgatttctcgcttctcccagATTTCTGATGAAGCTAAACAACGAGACGGTATCGATCGAGCTCAAGAATGGGACTATTGTGAATGGAACAATCACAG

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|77578860|gb|DV218230.1|DV218230
EST:     GCCGTTTTTGCTGGCTTCCGTCTTCATTCGCCAAAAATGAAGCTCGTTAG                         GTTTCTGATGAAGTTGAACAACGAAACTGTGTCTATCGAGCTCAAGAATGG
genomic: GCCGTTTTTGCTGGCTTCCGTCTTCATTCGCCAAAAATGAAGCTCGTTAGgtttgatctt ... ctaaaaacagGTTTCTGATGAAGTTGAACAACGAAACCGTGTCTATCGAGCTCAAGAATGG
EST: gi|110715316|gb|EE093229.1|EE093229
EST:     CTGGCTTCCGTCTTCATTCGCCAAAAATGAAGCTCGTTAG                         GTTTCTGATGAAGTTGAACAACGAAACTGTGTCTATCGAGCTCAAGAATGG
genomic: CTGGCTTCCGTCTTCATTCGCCAAAAATGAAGCTCGTTAGgtttgatctt ... ctaaaaacagGTTTCTGATGAAGTTGAACAACGAAACCGTGTCTATCGAGCTCAAGAATGG
EST: gi|32246247|gb|CD712066.1|CD712066
EST:     GCCGTTTTTGCTGGCTTCCGTCTTCATTCGCCAAAAATGAAGCTCGTTAG                         GTTTCTGATGAAGTTGAACAACGAAACTGTGTCTATCGAGCTCAAGAATGG
genomic: GCCGTTTTTGCTGGCTTCCGTCTTCATTCGCCAAAAATGAAGCTCGTTAGgtttgatctt ... ctaaaaacagGTTTCTGATGAAGTTGAACAACGAAACCGTGTCTATCGAGCTCAAGAATGG
EST: gi|71873275|gb|DT022330.1|DT022330
EST:     GCCGTTTTTGCTGGCTTCCGTCTTCATTCGCCAAAAATGAAGCTCGTTAG                         GTTTCTGATGAAGTTGAACAACGAAACTGTGTCTATCGAGCTCAAGAATGG
genomic: GCCGTTTTTGCTGGCTTCCGTCTTCATTCGCCAAAAATGAAGCTCGTTAGgtttgatctt ... ctaaaaacagGTTTCTGATGAAGTTGAACAACGAAACCGTGTCTATCGAGCTCAAGAATGG
EST: gi|27583587|gb|CB006282.1|CB006282
EST:     GCCGTTTTTGCTGGCTTCCGTCTTCATTCGCCAAAAATGAAGCTCGTTAG                         GTTTCTGATGAAGTTGAACAACGAAACTGTGTCTATCGAGCTCAAGAATGG
genomic: GCCGTTTTTGCTGGCTTCCGTCTTCATTCGCCAAAAATGAAGCTCGTTAGgtttgatctt ... ctaaaaacagGTTTCTGATGAAGTTGAACAACGAAACCGTGTCTATCGAGCTCAAGAATGG
EST: gi|110726188|gb|EE101761.1|EE101761
EST:     GCCGTTTTTGCTGGCTTCCGTCTTCATTCGCCAAAAATGAAGCTCGTTAG                         GTTTCTGATGAAGTTGAACAACGAAACTGTGTCTATCGAGCTCAAGAATGG
genomic: GCCGTTTTTGCTGGCTTCCGTCTTCATTCGCCAAAAATGAAGCTCGTTAGgtttgatctt ... ctaaaaacagGTTTCTGATGAAGTTGAACAACGAAACCGTGTCTATCGAGCTCAAGAATGG
EST: gi|77578278|gb|DV217913.1|DV217913
EST:     GCCGTTTTTGCTGGCTTCCGTCTTCATTCGCCAAAAATGAAGCTCGTTAG                         GTTTCTGATGAAGTTGAACAACGAAACTGTGTCTATCGAGCTCAAGAATGG
genomic: GCCGTTTTTGCTGGCTTCCGTCTTCATTCGCCAAAAATGAAGCTCGTTAGgtttgatctt ... ctaaaaacagGTTTCTGATGAAGTTGAACAACGAAACCGTGTCTATCGAGCTCAAGAATGG
EST: gi|110717228|gb|EE092911.1|EE092911
EST:     GCCGTTTTTGCTGGCTTCCGTCTTCATTCGCCAAAAATGAAGCTCGTTAG                         GTTTCTGATGAAGTTGAACAACGAAACTGTGTCTATCGAGCTCAAGAATGG
genomic: GCCGTTTTTGCTGGCTTCCGTCTTCATTCGCCAAAAATGAAGCTCGTTAGgtttgatctt ... ctaaaaacagGTTTCTGATGAAGTTGAACAACGAAACCGTGTCTATCGAGCTCAAGAATGG
EST: gi|30131461|gb|CB916800.1|CB916800
EST:     GCCGTTTTTGCTGGCTTCCGTCTTCATTCGCCAAAAATGAAGCTCGTTAG                         GTTTCTGATGAAGTTGAACAACGAAACTGTGTCTATCGAGCTCAAGAATGG
genomic: GCCGTTTTTGCTGGCTTCCGTCTTCATTCGCCAAAAATGAAGCTCGTTAGgtttgatctt ... ctaaaaacagGTTTCTGATGAAGTTGAACAACGAAACCGTGTCTATCGAGCTCAAGAATGG
EST: gi|110419993|gb|EC986253.1|EC986253
EST:     GCCGTTTTTGCTGGCTTCCGTCTTCATTCGCCAAAAATGAAGCTCGTTAG                         GTTTCTGATGAAGTTGAACAACGAAACTGTGTCTATCGAGCTCAAGAATGG
genomic: GCCGTTTTTGCTGGCTTCCGTCTTCATTCGCCAAAAATGAAGCTCGTTAGgtttgatctt ... ctaaaaacagGTTTCTGATGAAGTTGAACAACGAAACCGTGTCTATCGAGCTCAAGAATGG
EST: gi|71872888|gb|DT021943.1|DT021943
EST:     GCCGTTTTTGCTGGCTTCCGTCTTCATTCGCCAAAAATGAAGCTCGTTAG                         GTTTCTGATGAAGTTGAACAACGAAACTGTGTCTATCGAGCTCAAGAATGG
genomic: GCCGTTTTTGCTGGCTTCCGTCTTCATTCGCCAAAAATGAAGCTCGTTAGgtttgatctt ... ctaaaaacagGTTTCTGATGAAGTTGAACAACGAAACCGTGTCTATCGAGCTCAAGAATGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atctcgatttatttattttgttttgttaaattcttataatttagtctaaaaacagGTTTCTGATGAAGTTGAACAACGAAACCGTGTCTATCGAGCTCAAGAATGGAACCGTGGTTCATGGCACCATAACAG
      atttatttattttgtt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgatcttcaattaattaccatatacatatactaatctcgatttatttattttgttttgttaaattcttataatttagtctaaaaacagGTTTCTGATGAAGTTGAACAACGAAACCGTGTCTATCGAGCTCAAGAATGGAACCGTGGTTCATGGCACCATAACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA