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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctgtaatatttttttcgtccaaatattctttttccacatgatatctatagtatttcataactaagttgacgtgtgttacctggcctattctttcagGACAAGGAATCTTGGGATATGAACACTGAAGAGAAGATTGAGGCTGCTGGCAAGAAGAAGGAAGAAGGCAATGTGCTATTCAAGGCTGGTAAATATGCAA

Basic information

species Vitis vinifera
transcript Vv00s0769g00010.t01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv00s0769g00010.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GRMZM2G349810_T01 (Zea mays), 3'ss of exon 2
------gtctgtaatatttttttcgtccaaatattctttttccacatgatatctatagtatttcataactaagttgacgtgtgttacctggcctattctttcagGACAAGGAATCTTGGGATATGAACACTGAAGAGAAGATTGAGGCTGCTGGCAAGAAGAAGGAAGAAGGCAATGTGCTATTCAAGGCTGGTAAATATGCAA
      || |     |||| | | ||  |||     | |      |    || |||| |    ||  |||   |  |    | ||   |   ||  ||   ||||||||||| ||| ||||| |||||| ||||||||||||||||| |||||| ||| ||||  | ||| | ||||   | |||||    |  |||||||| |
aagaatgtttaggtcatttgtattgttgaaaagcaatctcatgttagtggatttata-tgacacaggactggatgaattcatatt---taatcttgtcacacagGACAAGGAGTCTCGGGATTTGAACAATGAAGAGAAGATTGAGGTTGCTGGTAAGGAGAAACAGGAATGGAATGCATTGTTCAAATTGGACAAATATGCTA

upper sequence: Vv00s0769g00010.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GRMZM2G007488_T01 (Zea mays), 3'ss of exon 5
gtctgtaatatttttttcgtccaaatattctttttccacatgatatctatagtatttcataactaagttgacgtgtgttacctggcctattctttcagGACAAGGAATCTTGGGATATGAACACTGAAGAGAAGATTGAGGCTGCTGGCAAGAAGAAGGAAGAAGGCAATGTGCTATTCAAGGCTGGTAAATATGCAA
   || ||  |  | ||| ||    | |  | |       |||  | | |    || ||     || ||||   || | | || |     ||   || |||||||| ||||||||  |||||| |||||| |||||||||||||||||   ||||||  | ||||| ||||   | ||||                  
--gtgcaac-tgatattcatctgtgtgtgttctaagtcgttgacctgtgtgcagttgca-----aaattgattagTATAATCTTG-----TCACACAAGACAAGGAGTCTTGGGACGTGAACAATGAAGATAAGATTGAGGCTGCTGGTTTGAAGAAACAGGAAGGGAATGCATTGTTCA------------------

upper sequence: Vv00s0769g00010.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA08G46090.2 (Glycine max), 3'ss of exon 8
gtctgtaatatttttttcgtccaaata-ttctttttccacatgatatctatagta--tttcataactaagt---tgacgtgtgttacctggcctattctttcagGACAAGGAATCTTGGGATATGAACACTGAAGAGAAGATTGAGGCTGCTGGCAAGAAGAAGGAAGAAGGCAATGTGCTATTCAAGGCTGGTAAATATGCAA
           |||||||||    | | || |   |   |||| |||  ||  |   |||   |  |   |   |        | | |||   | | | ||||||| ||||| || |||||| ||||||||||||||||  |||| |||||||| |||||||| |||||||| |||||| | || || ||||||||  ||||||
----acttcccttttttcgtttgcacacttgtccattttcatgctatggatgattattttggcagttttatctctagtaatcttaatctgttttctgccttcagGAGAAGGAGTCCTGGGATTTGAACACTGAAGAGAAACTTGAAGCTGCTGGTAAGAAGAAAGAAGAAGGAAATGTGTTGTTTAAAGCTGGTAAGCATGCAA

upper sequence: Vv00s0769g00010.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA03G21690.1 (Glycine max), 3'ss of exon 8
------gtctgtaatatttttttcgtccaaatattcttt-ttccacatgatatctatagtatttcataactaagttgacgtgtgttacctggcctattctttcagGACAAGGAATCTTGGGATATGAACACTGAAGAGAAGATTGAGGCTGCTGGCAAGAAGAAGGAAGAAGGCAATGTGCTATTCAAGGCTGGTAAATATGCAA
        ||| |||  |      | ||||  | | ||  || || | |||   |  | |  |  ||    || || |    |  |   || |    ||||| |||| |||||||| ||||| ||| ||||   |||||||||||| |||||||| |||||||| |||||||| ||||   |||| || ||||||||||||||||
tattttaactg-aatcatcacccggcccaatcaattttagtttcaaaagatcattgaatttctctatccaaaaattaattaataatttttgcc----tcttttagGAGAAGGAATCCTGGGACATGGACACGCCAGAGAAGATTGAAGCTGCTGGTAAGAAGAAAGAAGAAGGAAATGCATTATTTAAAGCTGGTAAATATGCAA

upper sequence: Vv00s0769g00010.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA18G32830.1 (Glycine max), 3'ss of exon 8
-gtctgtaatattt-ttttcgtccaaatattctttttccacatgatatctatagtatttcataactaagttgacgtgtgtta-cctggcctattctttcagGACAAGGAATCTTGGGATATGAACACTGAAGAGAAGATTGAGGCTGCTGGCAAGAAGAAGGAAGAAGGCAATGTGCTATTCAAGGCTGGTAAATATGCAA-
    | | | |||| |  || |    || ||| |  ||   || |||| |||  | |  ||    ||     ||   | ||| |||    | |    |||||| ||||| || |||||| ||||||||||||||||  |||| |||||||| |||||||| ||||| || |||||  | || || ||| |||||||||||| 
tactttttacatttgtactcttgtccattttcatactctggattatatatat--tttggcagttttatccctactaatcttatcctcttttctcacctcaggAGAAGGAGTCCTGGGATCTGAACACTGAAGAGAAACTTGAAGCTGCTGGTAAGAAGAAAGAAGAGGGAAATGTCTTGTTTAAAGCTAGTAAATATGCAAG

upper sequence: Vv00s0769g00010.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA16G10730.1 (Glycine max), 3'ss of exon 8
-----gtctgtaatatttttttcgtccaaatattctttttccacatgatatctatagtatttcataactaagttgacgtgtgttacctggcctattctttcagGACAAGGAATCTTGGGATATGAACACTGAAGAGAAGATTGAGGCTGCTGGCAAGAAGAAGGAAGAAGGCAATGTGCTATTCAAGGCTGGTAAATATGCAA
       ||| |  ||     | | | ||  | | |||     |   |  |  || | ||| |   ||  | |  |    |  ||  |       ||||| |||| ||||| || ||||| ||| ||||   |||||||||||| |||||||| |||||||| |||||||| ||||   |||| || ||||||||||||||||
tatttaactgaatcatcaccct-gccgaatcaatttttgagttccaaaagttcattgaattcctctaccta-taaataattaataatttttgc-ctcttttagGAGAAGGAGTCCTGGGACATGGACACACCAGAGAAGATTGAAGCTGCTGGTAAGAAGAAAGAAGAAGGAAATGCATTATTTAAAGCTGGTAAATATGCAA

upper sequence: Vv00s0769g00010.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: AT3G25230.1 (Arabidopsis thaliana), 3'ss of exon 8
gtctgtaatatttttttcgtccaaatattctttttccacatgatatctatagtatttcataactaagttgacgtgtgttacctggcctattctttcagGACAAGGAATCTTGGGATATGAACACTGAAGAGAAGATTGAGGCTGCTGGCAAGAAGAAGGAAGAAGGCAATGTGCTATTCAAGGCTGGTAAATATGCAA
||  || |  | ||||   | |  ||   |  |  | |     |   ||| | | |  |  | |      ||   ||||        |    ||| |||| | |||||| ||||| ||||||||||| ||||||||||| |||||| | ||||||||||||||||| |||      || || |  || |||||| |  
gttagtgaagtattttggatgcttatgc-cgctcacaattcagtcaatatggaagtataagagt---ccaacacttgtttgtca--ttggctttttagGAAAGGGAATCGTGGGACATGAACACTGAGGAGAAGATTGAAGCTGCTAGTAAGAAGAAGGAAGAAGGAAATTCCAAGTTTAAAGGAGGCAAATATTCCC

upper sequence: Vv00s0769g00010.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: AT5G48570.1 (Arabidopsis thaliana), 3'ss of exon 8
gtctgtaatatttttttcgtccaaatattctttttccacatgatatctatagtatttcataactaagttgacgtgtgtt----acctggcctattct--ttcagGACAAGGAATCTTGGGATATGAACACTGAAGAGAAGATTGAGGCTGCTGGCAAGAAGAAGGAAGAAGGCAATGTGCTATTCAAGGCTGGTAAATATGCAA
                  ||   |  ||||  ||||    || | | | |  |  || || |  ||  | | ||||| |    |  | | || |  |  | ||||| || || |||||||||||||||||  | || | ||| || ||||| ||||||||||| ||||||||||||||| | ||||| ||||| ||||| ||||
------------------gtgagaggattcactttctgagtgttgtttct--ttctttatgaagaaacttaagtgtgctaatgatatcgtctctcttgatgcagGAGAAAGAGTCTTGGGATATGAACACACAGGAAAGGATAGAAGCTGCAGGCAAGAAGAAAGAAGAAGGCAATGTGTTGTTCAAAGCTGGAAAATACGCAA

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|351052096|gb|FQ455389.1|FQ455389
EST:     CAACAGTCTACTATGAAGTGGAGCTTGAGTCCTTCGTTAAG                         GACAAGGAATCTTGGGATATGAACACTGAAGAGAAGATTGAGGCTGCTGGC
genomic: CAACAGTCTACTATGAAGTGGAGCTTGAGTCCTTTGTTAAGgtctgtaata ... attctttcagGACAAGGAATCTTGGGATATGAACACTGAAGAGAAGATTGAGGCTGCTGGC
EST: gi|351030826|gb|FQ438862.1|FQ438862
EST:     CAACAGTCTACTATGAAGTGGAGCTTGAGTCCTTCGTTAAG                         GACAAGGAATCTTGGGATATGAACACTGAAGAGAAGATTGAGGCTGCTGGC
genomic: CAACAGTCTACTATGAAGTGGAGCTTGAGTCCTTTGTTAAGgtctgtaata ... attctttcagGACAAGGAATCTTGGGATATGAACACTGAAGAGAAGATTGAGGCTGCTGGC
EST: gi|30125943|gb|CB911282.1|CB911282
EST:     CTCCCAACTCAACAGTCTACTATGAAGTGGAGCTTGAGTCCTTTGTTAAG                         GACAAGGAATCTTGGGATATGAACACTGAAGAGAAGATTGAGGCTGCTGGC
genomic: CTCCCAACTCAACAGTCTACTATGAAGTGGAGCTTGAGTCCTTTGTTAAGgtctgtaata ... attctttcagGACAAGGAATCTTGGGATATGAACACTGAAGAGAAGATTGAGGCTGCTGGC
EST: gi|33403350|gb|CF208977.1|CF208977
EST:     CTCCCAACTCAACAGTCTACTATGAAGTGGAGCTTGAGTCCTTCGTTAAG                         GACAAGGAATCTTGGGATATGAACACTGAAGAGAAGATTGAGGCTGCTGGC
genomic: CTCCCAACTCAACAGTCTACTATGAAGTGGAGCTTGAGTCCTTTGTTAAGgtctgtaata ... attctttcagGACAAGGAATCTTGGGATATGAACACTGAAGAGAAGATTGAGGCTGCTGGC
EST: gi|30253340|gb|CB970891.1|CB970891
EST:     CTCCCAACTCAACAGTCTACTATGAAGTGGAGCTTGAGTCCTTCGTTAAG                         GACAAGGAATCTTGGGATATGAACACTGAAGAGAAGATTGAGGCTGCTGGC
genomic: CTCCCAACTCAACAGTCTACTATGAAGTGGAGCTTGAGTCCTTTGTTAAGgtctgtaata ... attctttcagGACAAGGAATCTTGGGATATGAACACTGAAGAGAAGATTGAGGCTGCTGGC
EST: gi|77587533|gb|DV222932.1|DV222932
EST:     CTCCCAACTCAACAGTCTACTATGAAGTGGAGCTTGAGTCCTTCGTTAAG                         GACAAGGAATCTTGGGATATGAACACTGAAGAGAAGATTGAGGCTGCTGGC
genomic: CTCCCAACTCAACAGTCTACTATGAAGTGGAGCTTGAGTCCTTTGTTAAGgtctgtaata ... attctttcagGACAAGGAATCTTGGGATATGAACACTGAAGAGAAGATTGAGGCTGCTGGC
EST: gi|352790570|gb|FQ478209.1|FQ478209
EST:     CAACAGTCTACTATGAAGTGGAGCTTGAGTCCTTCGTTAAG                         GACAAGGAATCTTGGGATATGAACACTGAAGAGAAGATTGAGGCTGCTGGC
genomic: CAACAGTCTACTATGAAGTGGAGCTTGAGTCCTTTGTTAAGgtctgtaata ... attctttcagGACAAGGAATCTTGGGATATGAACACTGAAGAGAAGATTGAGGCTGCTGGC
EST: gi|351042032|gb|FQ456242.1|FQ456242
EST:     CTCCCAACTCAACAGTCTACTATGAAGTGGAGCTTGAGTCCTTCGTTAAG                         GACAAGGAATCTTGGGATATGAACACTGAAGAGAAGATTGAGGCTGCTGGC
genomic: CTCCCAACTCAACAGTCTACTATGAAGTGGAGCTTGAGTCCTTTGTTAAGgtctgtaata ... attctttcagGACAAGGAATCTTGGGATATGAACACTGAAGAGAAGATTGAGGCTGCTGGC
EST: gi|29783511|gb|CB349715.2|CB349715
EST:     CTCCCAACTCAACAGTCTACTATGAAGTGGAGCTTGAGTCCTTTGTTAAG                         GACAAGGAATCTTGGGATATGAACACTGAAGAGAAGATTGAGGCTGCTGGC
genomic: CTCCCAACTCAACAGTCTACTATGAAGTGGAGCTTGAGTCCTTTGTTAAGgtctgtaata ... attctttcagGACAAGGAATCTTGGGATATGAACACTGAAGAGAAGATTGAGGCTGCTGGC
EST: gi|110398522|gb|EC964942.1|EC964942
EST:     CTCCCAACTCAACAGTCTACTATGAAGTGGAGCTTGAGTCCTTTGTTAAG                         GACAAGGAATCTTGGGATATGAACACTGAAGAGAAGATTGAGGCTGCTGGC
genomic: CTCCCAACTCAACAGTCTACTATGAAGTGGAGCTTGAGTCCTTTGTTAAGgtctgtaata ... attctttcagGACAAGGAATCTTGGGATATGAACACTGAAGAGAAGATTGAGGCTGCTGGC
EST: gi|33403274|gb|CF208901.1|CF208901
EST:     CTCCCAACTCAACAGTCTACTATGAAGTGGAGCTTGAGTCCTTCGTTAAG                         GACAAGGAATCTTGGGATATGAACACTGAAGAGAAGATTGAGGCTGCTGGC
genomic: CTCCCAACTCAACAGTCTACTATGAAGTGGAGCTTGAGTCCTTTGTTAAGgtctgtaata ... attctttcagGACAAGGAATCTTGGGATATGAACACTGAAGAGAAGATTGAGGCTGCTGGC
EST: gi|349830992|gb|FQ418276.1|FQ418276
EST:     CTCCCAACTCAACAGTCTACTATGAAGTGGAGCTTGAGTCCTTTGTTAAG                         GACAAGGAATCTTGGGATATGAACACTGAAGAGAAGATTGAGGCTGCTGGC
genomic: CTCCCAACTCAACAGTCTACTATGAAGTGGAGCTTGAGTCCTTTGTTAAGgtctgtaata ... attctttcagGACAAGGAATCTTGGGATATGAACACTGAAGAGAAGATTGAGGCTGCTGGC
EST: gi|349830215|gb|FQ420475.1|FQ420475
EST:     CTCCCAACTCAACAGTCTACTATGAAGTGGAGCTTGAGTCCTTCGTTAAG                         GACAAGGAATCTTGGGATATGAACACTGAAGAGAAGATTGAGGCTGCTGGC
genomic: CTCCCAACTCAACAGTCTACTATGAAGTGGAGCTTGAGTCCTTTGTTAAGgtctgtaata ... attctttcagGACAAGGAATCTTGGGATATGAACACTGAAGAGAAGATTGAGGCTGCTGGC
EST: gi|349829935|gb|FQ422248.1|FQ422248
EST:     CTCCCAACTCAACAGTCTACTATGAAGTGGAGCTTGAGTCCTTCGTTAAG                         GACAAGGAATCTTGGGATATGAACACTGAAGAGAAGATTGAGGCTGCTGGC
genomic: CTCCCAACTCAACAGTCTACTATGAAGTGGAGCTTGAGTCCTTTGTTAAGgtctgtaata ... attctttcagGACAAGGAATCTTGGGATATGAACACTGAAGAGAAGATTGAGGCTGCTGGC
EST: gi|110400903|gb|EC967488.1|EC967488
EST:     CTCCCAACTCAACAGTCTACTATGAAGTGGAGCTTGAGTCCTTTGTTAAG                         GACAAGGAATCTTGGGATATGAACACTGAAGAGAAGATTGAGGCTGCTGGC
genomic: CTCCCAACTCAACAGTCTACTATGAAGTGGAGCTTGAGTCCTTTGTTAAGgtctgtaata ... attctttcagGACAAGGAATCTTGGGATATGAACACTGAAGAGAAGATTGAGGCTGCTGGC
EST: gi|28969463|gb|CB348496.1|CB348496
EST:     CTCCCAACTCAACAGTCTACTATGAAGTGGAGCTTGGGTCCTTTGTTAAG                         GACAAGGAATCTTGGGATATGAACACTGAAGAGAAGATTGAGGCTGCTGGC
genomic: CTCCCAACTCAACAGTCTACTATGAAGTGGAGCTTGAGTCCTTTGTTAAGgtctgtaata ... attctttcagGACAAGGAATCTTGGGATATGAACACTGAAGAGAAGATTGAGGCTGCTGGC
EST: gi|110689806|gb|EE066352.1|EE066352
EST:     CTCCCAACTCAACAGTCTACTATGAAGTGGAGCTTGAGTCCTTTGTTAAG                         GACAAGGAATCTTGGGATATGAACACTGAAGAGAAGATTGAGGCTGCTGGC
genomic: CTCCCAACTCAACAGTCTACTATGAAGTGGAGCTTGAGTCCTTTGTTAAGgtctgtaata ... attctttcagGACAAGGAATCTTGGGATATGAACACTGAAGAGAAGATTGAGGCTGCTGGC
EST: gi|56409460|gb|CX017712.1|CX017712
EST:     CTCCCAACTCAACAGTCTACTATGAAGTGGAGCTTGAGTCCTTCGTTAAG                         GACAAGGAATCTTGGGATATGAACACTGAAGAGAAGATTGAGGCTGCTGGC
genomic: CTCCCAACTCAACAGTCTACTATGAAGTGGAGCTTGAGTCCTTTGTTAAGgtctgtaata ... attctttcagGACAAGGAATCTTGGGATATGAACACTGAAGAGAAGATTGAGGCTGCTGGC
EST: gi|110377095|gb|EC942156.1|EC942156
EST:     CTCCCAACTCAACAGTCTACTATGAAGTGGAGCTTGAGTCCTTTGTTAAG                         GACAAGGAATCTTGGGATATGAACACTGAAGAGAAGATTGAGGCTGCTGGC
genomic: CTCCCAACTCAACAGTCTACTATGAAGTGGAGCTTGAGTCCTTTGTTAAGgtctgtaata ... attctttcagGACAAGGAATCTTGGGATATGAACACTGAAGAGAAGATTGAGGCTGCTGGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatctatagtatttcataactaagttgacgtgtgttacctggcctattctttcagGACAAGGAATCTTGGGATATGAACACTGAAGAGAAGATTGAGGCTGCTGGCAAGAAGAAGGAAGAAGGCAATGTGCTATTCAAGGCTGGTAAATATGCAA
                                          cctattctttc  CT-rich tract
     atagtatttcataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctgtaatatttttttcgtccaaatattctttttccacatgatatctatagtatttcataactaagttgacgtgtgttacctggcctattctttcagGACAAGGAATCTTGGGATATGAACACTGAAGAGAAGATTGAGGCTGCTGGCAAGAAGAAGGAAGAAGGCAATGTGCTATTCAAGGCTGGTAAATATGCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG