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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atggaaaatgtaaagttgtaactttgatcattcttattcttccaaggggaatccctttcttctagtaaatttaatgaaatcttattgtttaccactgtagGTTTTTGGTGAGGTTGCAGAAGGGCTTGAGACACTAACGAGGATAAATGAAGCTTATGTGGATGATAAAGGGAGACCATATAAAAATATCCG

Basic information

species Vitis vinifera
transcript Vv19s0027g01660.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv19s0027g01660.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G146190_T01 (Zea mays), 3'ss of exon 4
--atggaaaatgtaaagttgtaactttgatcattcttattcttccaaggggaatccctttcttctagtaaatttaatgaaatcttattgtttaccactgtagGTTTTTGGTGAGGTTGCAGAAGGGCTTGAGACACTAACGAGGATAAATGAAGCTTATGTGGATGATAAAGGGAGACCATATAAAAATATCCG
    | |  |  | |   ||| |  | | |  ||||| |||||        ||| || || ||  |  || | |  ||   |  |  |||| ||||   ||||| |||||   |||||| |||||  |||| || || || |  ||||||||||||||||| |||||||| || |||||||  ||  | ||  |
gtgagcagcacttgattctgttaactggttttttcttcttcttatgtacaaaattcccttatttgaacaattcttgtgt--ttgttctgttgacca---tagGTGTTTGGGATGGTTGCCGAAGGTTTTGATACGCTGACAAAAATAAATGAAGCTTATGTTGATGATAATGGAAGACCATTCAAGGACATAAG

upper sequence: Vv19s0027g01660.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA19G00460.1 (Glycine max), 3'ss of exon 4
---------atggaaaatgtaaagttgtaactttgatcattctta---ttcttccaaggggaatccctttcttctagtaaatttaatgaaatcttattgtttaccactgtagGTTTTTGGTGAGGTTGCAGAAGGGCTTGAGACACTAACGAGGATAAATGAAGCTTATGTGGATGATAAAGGGAGACCATATAAAAATATCCG
         ||||||| ||  |  ||  |  |||  |||   ||    ||  | | | || | |  |||  ||        ||| |||| ||||    |||      |  |||||||||| ||||| || |||||  |||||||  ||||||| |||||||| |||||||||||||| || || ||||| |||||||||||  |
gacattgatatggaaa-tgctactttaaatatttactcacatttgacttttataccatggaagttacttcgtt-------gttttatgagatct----gttccttgttacagGTTTTTGGCGAGGTAGCTGAAGGATTTGAGACTTTAACGAGAATAAATGAGGCTTATGTGGATGAGAAGGGAAGACCCTATAAAAATATAAG

upper sequence: Vv19s0027g01660.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA15G28380.1 (Glycine max), 3'ss of exon 4
atggaaaatgtaaagttgtaactttgatcattcttattcttccaaggggaatccctttcttctagtaaatttaatgaaatctta---ttgtttaccactgtagGTTTTTGGTGAGGTTGCAGAAGGGCTTGAGACACTAACGAGGATAAATGAAGCTTATGTGGATGATAAAGGGAGACCATATAAAAATATCCG
       || |  |  ||  ||| | |  |||      | |   |     || || |      | | | ||   ||   ||| |   |||||      |  |||||||||||||| | || |||||  | |||||  |||| || |||||||| |||||||||||||| ||||| ||||| |||||||||||  |
gacattgatatggaaatgctactataaatatttactcacatttgacttttataccgtgga---aattacttcgttgttttctgagatttgttccttgttacagGTTTTTGGTGAGCTAGCTGAAGGATTCGAGACTTTAACTAGAATAAATGAGGCTTATGTGGATGAGAAAGGAAGACCCTATAAAAATATAAG

upper sequence: Vv19s0027g01660.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: EFJ33268 (Selaginella moellendorffii), 3'ss of exon 4
atggaaaatgtaaagttgtaactttgatcattcttattcttccaaggggaatccctttcttctagtaaatttaatgaaatcttattgtttaccactgtagGTTTTTGGTGAGGTTGCAGAAGGGCTTGAGACACTAACGAGGATAAATGAAGCTTATGTGGATGATAAAGGGAGACCATATAAAAATATCCG
                                               | || |   ||||  |    | ||   |||   ||||||  ||   |    || ||||||| ||||| || |||||  |||| || || ||||||||||||||||||||||| ||||| ||     | || || ||||| || ||
-----------------------------------------------gtaagcgtcttctagtttcgagttcgttgatg-cttattactttgaatc--agATTTTTGGGGAGGTCGCGGAAGGTTTTGAAACTCTGACGAGGATAAATGAAGCTTATGTCGATGACAACCATCGGCCTTACAAAAACATACG

upper sequence: Vv19s0027g01660.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: EFJ15908 (Selaginella moellendorffii), 3'ss of exon 4
atggaaaatgtaaagttgtaactttgatcattcttattcttccaaggggaatccctttcttctagtaaatttaatgaaatcttattgtttaccactgtagGTTTTTGGTGAGGTTGCAGAAGGGCTTGAGACACTAACGAGGATAAATGAAGCTTATGTGGATGATAAAGGGAGACCATATAAAAATATCCG
                                               | || |   ||||  |    | ||   |||   ||||||  ||   |    || ||||||| |||||||| |||||  |||| || || ||||||||||||||||||||||| ||||| ||     | || || ||||| || ||
-----------------------------------------------gtaagcgtcttctagtttcgagttcgttgatg-cttattactttgaatc--agATTTTTGGGGAGGTTGCGGAAGGTTTTGAAACTCTGACGAGGATAAATGAAGCTTATGTCGATGACAACCATCGGCCTTACAAAAACATACG

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|351013338|gb|FQ425043.1|FQ425043
EST:     TCTATTTCACGCTGCGTGATGATCTAGACTACCTGGATGGAAAGCATACT                         GTTTTTGGTGAGGTTGCAGAAGGGCTTGAGACACTAACGAGGATAAATGAA
genomic: TCTATTTCACGCTGCGTGATGATCTAGACTACCTGGATGGAAAGCATACTgtaagtctcc ... accactgtagGTTTTTGGTGAGGTTGCAGAAGGGCTTGAGACACTAACGAGGATAAATGAA
EST: gi|351056299|gb|FQ454160.1|FQ454160
EST:     TCTATTTCACGCTGCGTGATGATCTAGACTACCTGGATGGAAGGCATACT                         GTTTTTGGTGAGGTTGCAGAAGGGCTTGAGACACTAACGAGGATAAATGAA
genomic: TCTATTTCACGCTGCGTGATGATCTAGACTACCTGGATGGAAAGCATACTgtaagtctcc ... accactgtagGTTTTTGGTGAGGTTGCAGAAGGGCTTGAGACACTAACGAGGATAAATGAA
EST: gi|351019880|gb|FQ439697.1|FQ439697
EST:     TCTATTTCACGCTGCGTGATGATCTAGACTACCTGGATGGAAAGCATACT                         GTTTTTGGTGAGGTTGCAGAAGGGCTTGAGACACTAACGAGGATAAATGAA
genomic: TCTATTTCACGCTGCGTGATGATCTAGACTACCTGGATGGAAAGCATACTgtaagtctcc ... accactgtagGTTTTTGGTGAGGTTGCAGAAGGGCTTGAGACACTAACGAGGATAAATGAA
EST: gi|349829098|gb|FQ419630.1|FQ419630
EST:     TCTATTTCACGCTGCGTGATGATCTAGACTACCTGGATGGAAAGCATACT                         GTTTTTGGTGAGGTTGCAGAAGGGCTTGAGACACTAACGAGGATAAATGAA
genomic: TCTATTTCACGCTGCGTGATGATCTAGACTACCTGGATGGAAAGCATACTgtaagtctcc ... accactgtagGTTTTTGGTGAGGTTGCAGAAGGGCTTGAGACACTAACGAGGATAAATGAA
EST: gi|351021566|gb|FQ429670.1|FQ429670
EST:     TCTATTTCACGCTGCGTGATGATCTAGACTACCTGGATGGAAAGCATACT                         GTTTTTGGTGAGGTTGCAGAAGGGCTTGAGACACTAACGAGGATAAATGAA
genomic: TCTATTTCACGCTGCGTGATGATCTAGACTACCTGGATGGAAAGCATACTgtaagtctcc ... accactgtagGTTTTTGGTGAGGTTGCAGAAGGGCTTGAGACACTAACGAGGATAAATGAA
EST: gi|349828467|gb|FQ417209.1|FQ417209
EST:     TCTATTTCACGCTGCGTGATGATCTAGACTACCTGGATGGAAAGCATACT                         GTTTTTGGTGAGGTTGCAGAAGGGCTTGAGACACTAACGAGGATAAATGAA
genomic: TCTATTTCACGCTGCGTGATGATCTAGACTACCTGGATGGAAAGCATACTgtaagtctcc ... accactgtagGTTTTTGGTGAGGTTGCAGAAGGGCTTGAGACACTAACGAGGATAAATGAA
EST: gi|351029259|gb|FQ436653.1|FQ436653
EST:     TCTATTTCACGCTGCGTGATGATCTAGACCACCTGGATGGAAAGCATACT                         GTTTTTGGTGAGGTTGCAGAAGGGCTTGAGACACTAACGAGGATAAATGAA
genomic: TCTATTTCACGCTGCGTGATGATCTAGACTACCTGGATGGAAAGCATACTgtaagtctcc ... accactgtagGTTTTTGGTGAGGTTGCAGAAGGGCTTGAGACACTAACGAGGATAAATGAA
EST: gi|351015245|gb|FQ445529.1|FQ445529
EST:     TCTATTTCACGCTGCGTGATGATCTAGACTACCTGGATGGAAAGCATACT                         GTTTTTGGTGAGGTTGCAGAAGGGCTTGAGACACTAACGAGGATAAATGAA
genomic: TCTATTTCACGCTGCGTGATGATCTAGACTACCTGGATGGAAAGCATACTgtaagtctcc ... accactgtagGTTTTTGGTGAGGTTGCAGAAGGGCTTGAGACACTAACGAGGATAAATGAA
EST: gi|352786284|gb|FQ478895.1|FQ478895
EST:     TCTATTTCACGCTGCGTGATGATCTAGACTACCTGGATGGAAGGCATACT                         GTTTTTGGTGAGGTTGCAGAAGGGCTTGAGACACTAACGAGGATAAATGAA
genomic: TCTATTTCACGCTGCGTGATGATCTAGACTACCTGGATGGAAAGCATACTgtaagtctcc ... accactgtagGTTTTTGGTGAGGTTGCAGAAGGGCTTGAGACACTAACGAGGATAAATGAA
EST: gi|351014040|gb|FQ434192.1|FQ434192
EST:     TCTATTTCACGCTGCGTGATGATCTAGACTACCTGGATGGAAAGCATACT                         GTTTTTGGTGAGGTTGCAGAAGGGCTTGAGACACTAACGAGGATAAATGAA
genomic: TCTATTTCACGCTGCGTGATGATCTAGACTACCTGGATGGAAAGCATACTgtaagtctcc ... accactgtagGTTTTTGGTGAGGTTGCAGAAGGGCTTGAGACACTAACGAGGATAAATGAA
EST: gi|349824097|gb|FQ417484.1|FQ417484
EST:     TCTATTTCACGCTGCGTGATGATCTAGACTACCTGGATGGAAAGCATACT                         GTTTTTGGTGAGGTTGCAGAAGGGCTTGAGACACTAACGAGGATAAATGAA
genomic: TCTATTTCACGCTGCGTGATGATCTAGACTACCTGGATGGAAAGCATACTgtaagtctcc ... accactgtagGTTTTTGGTGAGGTTGCAGAAGGGCTTGAGACACTAACGAGGATAAATGAA
EST: gi|351014258|gb|FQ434847.1|FQ434847
EST:     TCTATTTCACGCTGCGTGATGATCTAGACTACCTGGATGGAAAGCATACT                         GTTTTTGGTGAGGTTGCAGAAGGGCTTGAGACACTAACGAGGATAAATGAA
genomic: TCTATTTCACGCTGCGTGATGATCTAGACTACCTGGATGGAAAGCATACTgtaagtctcc ... accactgtagGTTTTTGGTGAGGTTGCAGAAGGGCTTGAGACACTAACGAGGATAAATGAA
EST: gi|351019573|gb|FQ439390.1|FQ439390
EST:     TCTATTTCACGCTGCGTGATGATCTAGACTACCTGGATGGAAAGCATACT                         GTTTTTGGTGAGGTTGCAGAAGGGCTTGAGACACTAACGAGGATAAATGAA
genomic: TCTATTTCACGCTGCGTGATGATCTAGACTACCTGGATGGAAAGCATACTgtaagtctcc ... accactgtagGTTTTTGGTGAGGTTGCAGAAGGGCTTGAGACACTAACGAGGATAAATGAA
EST: gi|351030963|gb|FQ438999.1|FQ438999
EST:     TCTATTTCACGCTGCGTGATGATCTAGACTACCTGGATGGAAAGCATACT                         GTTTTTGGTGAGGTTGCAGAAGGGCTTGAGACACTAACGAGGATAAATGAA
genomic: TCTATTTCACGCTGCGTGATGATCTAGACTACCTGGATGGAAAGCATACTgtaagtctcc ... accactgtagGTTTTTGGTGAGGTTGCAGAAGGGCTTGAGACACTAACGAGGATAAATGAA
EST: gi|351030959|gb|FQ438995.1|FQ438995
EST:     TCTATTTCACGCTGCGTGATGATCTAGACTACCTGGATGGAAAGCATACT                         GTTTTTGGTGAGGTTGCAGAAGGGCTTGAGACACTAACGAGGATAAATGAA
genomic: TCTATTTCACGCTGCGTGATGATCTAGACTACCTGGATGGAAAGCATACTgtaagtctcc ... accactgtagGTTTTTGGTGAGGTTGCAGAAGGGCTTGAGACACTAACGAGGATAAATGAA
EST: gi|351015056|gb|FQ444345.1|FQ444345
EST:     TCTATTTCACGCTGCGTGATGATCTAGACTACCTGGATGGAAAGCATACT                         GTTTTTGGTGAGGTTGCAGAAGGGCTTGAGACACTAACGAGGATAAATGAA
genomic: TCTATTTCACGCTGCGTGATGATCTAGACTACCTGGATGGAAAGCATACTgtaagtctcc ... accactgtagGTTTTTGGTGAGGTTGCAGAAGGGCTTGAGACACTAACGAGGATAAATGAA
EST: gi|351052152|gb|FQ450722.1|FQ450722
EST:     TCTATTTCACGCTGCGTGATGATCTAGACTACCTGGATGGAAGGCATACT                         GTTTTTGGTGAGGTTGCAGAAGGGCTTGAGCCACTAACGAGGATAAATGAA
genomic: TCTATTTCACGCTGCGTGATGATCTAGACTACCTGGATGGAAAGCATACTgtaagtctcc ... accactgtagGTTTTTGGTGAGGTTGCAGAAGGGCTTGAGACACTAACGAGGATAAATGAA
EST: gi|351036687|gb|FQ457400.1|FQ457400
EST:     TCTATTTCACGCTGCGTGATGATCTAGACTACCTGGATGGAAGGCATACT                         GTTTTTGGTGAGGTTGCAGAAGGGCTTGAGACACTAACGAGGATAAATGAA
genomic: TCTATTTCACGCTGCGTGATGATCTAGACTACCTGGATGGAAAGCATACTgtaagtctcc ... accactgtagGTTTTTGGTGAGGTTGCAGAAGGGCTTGAGACACTAACGAGGATAAATGAA
EST: gi|349832490|gb|FQ421051.1|FQ421051
EST:     TCTATTTCACGCTGCGTGATGATCTAGACTACCTGGATGGAAAGCATACT                         GTTTTTGGTGAGGTTGCAGAAGGGCTTGAGACACTAACGAGGATAAATGAA
genomic: TCTATTTCACGCTGCGTGATGATCTAGACTACCTGGATGGAAAGCATACTgtaagtctcc ... accactgtagGTTTTTGGTGAGGTTGCAGAAGGGCTTGAGACACTAACGAGGATAAATGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggggaatccctttcttctagtaaatttaatgaaatcttattgtttaccactgtagGTTTTTGGTGAGGTTGCAGAAGGGCTTGAGACACTAACGAGGATAAATGAAGCTTATGTGGATGATAAAGGGAGACCATATAAAAATATCCG
                       atttaat  putative branch site (score: 4)
                 tagtaaatttaatgaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atggaaaatgtaaagttgtaactttgatcattcttattcttccaaggggaatccctttcttctagtaaatttaatgaaatcttattgtttaccactgtagGTTTTTGGTGAGGTTGCAGAAGGGCTTGAGACACTAACGAGGATAAATGAAGCTTATGTGGATGATAAAGGGAGACCATATAAAAATATCCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- ggaaaat
- - - - - - - - - - - - - - - - - - - cttccaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aatgaaa