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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagttgttttaaggaaaatatcattttattttaaccatttctcccttgacctagatatcctactccattactgttttaagtgtctgcttcttttgttactgaacttgaggttatattgttggacgtggaactaacatttatactttatatatgtgaagGTTTTGTATGACTATGAAGACAAAATCAATCAGGCTGTCTTTCCTGGACTTCAAGGTGGCCCTCACAATCACACAATTGCTGGCTTAGCTGTTGCATTGA

Basic information

species Vitis vinifera
transcript Vv00s0211g00120.t01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv00s0211g00120.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: LOC_Os03g52840.2 (Oryza sativa), 3'ss of exon 9
gtgagttgttttaaggaaaatatcattttattttaaccatttctcccttgacctagatatcctactccattactgttttaagtgtctgcttcttttgttactgaacttgaggttatattg--ttggacgtggaactaacatttat--actttatatatgtgaagGTTTTGTATGACTATGAAGACAAAATCAATCAGGCTGTCTTTCCTGGACTTCAAGGTGGCCCTCACAATCACACAATTGCTGGCTTAGCTGTTGCATTGA
                                        |     ||||| |   | |     |   ||    |  |   ||||  |     ||| ||    | | || |  | | |    ||  |      |  ||    ||   ||  | ||   ||  ||||| ||||||||| ||| ||||| ||||||   |||||||| || || || |||||||| || || ||||| || ||| ||||||||||||||||  | |
---------------------------------------gtatatacttgagcagaacaata-gcaagatagtagcgtagggtgttggtactgtttcttctccatcctgtgactctgtgagcttcaaaaaaataaaaatgcctaatgaccctctac-cgtctagGTTATGTATGACTTTGAGGACAAGATCAATGCTGCTGTCTTCCCAGGTCTGCAAGGTGGACCACATAATCATACCATTACTGGCTTAGCTGTTGCGCTTA

upper sequence: Vv00s0211g00120.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GRMZM2G135283_T02 (Zea mays), 3'ss of exon 8
gtgagttgttttaaggaaaatatcattttattttaaccatttctcccttgacctagatatcctactccattactgttttaagtgtctgcttcttttgttactgaacttgagg-ttatattgttggacgtggaactaacatttatactttatatatgtgaagGTTTTGTATGACTATGAAGACAAAATCAATCAGGCTGTCTTTCCTGGACTTCAAGGTGGCCCTCACAATCACACAATTGCTGGCTTAGCTGTTGCATTGA
                                                         |||   |       |  | |  ||    ||         | |  ||||| ||    ||  |||      |   |   ||    | |||||| |||| | |  ||||| ||||||| | ||| ||||||||||||   |||||||||||||| || |||||||| ||||| || || || ||| ||||||| ||||||||  | |
--------------------------------------------------------gtatggcatgatgaaaacgataaaaaaaactagca-----ggtgttgaacctgcttcttgcattaaaaaccaaaggtttagtgat-atacttaatat-tctatagGTTATGTATGATTTTGAGGACAAAATCAATGCTGCTGTCTTTCCTGGTCTGCAAGGTGGGCCTCATAACCATACCATTACTGGCTTGGCTGTTGCGCTCA

upper sequence: Vv00s0211g00120.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA08G37270.1 (Glycine max), 3'ss of exon 9
gtgagttgttttaaggaaaatatcattttattttaaccatttctcccttgacctagatatcctactccattactgttttaagtgtctgcttcttttgttactgaacttgaggttatattgttggacgtggaactaacatttatactt-tatatatgtgaagGTTTTGTATGACTATGAAGACAAAATCAATCAGGCTGTCTTTCCTGGACTTCAAGGTGGCCCTCACAATCACACAATTGCTGGCTTAGCTGTTGCATTGA
        ||  ||||||||  |  ||| |  ||     ||  |    |  |     | ||  | | ||||    |    ||  |  |  | | ||||| |  | |||||  |||| |   |  |      | ||||| || | ||| | |  || ||||||| ||||||||||| |||||||||||||| || ||||| || |||||||| ||||||||||||||||| ||||| ||| |||| ||||||||||| ||||
---gtcaattccaaggaaaaagttctttgacatttttgtttattttaatttctgtactctcagatttcattctcatcaacaggata-gtatgtgttgtttccca-cttgaatttatgtaaattcataaatca-taacagttgttcttctttcaatttgaagGTATTGTATGACTACGAAGACAAAATCAACCAAGCTGTTTTCCCTGGACTGCAAGGTGGCCCTCACAACCACACTATTACTGGTTTAGCTGTTGCGTTGA

upper sequence: Vv00s0211g00120.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA18G27710.1 (Glycine max), 3'ss of exon 10
gtgagttgttttaaggaaaatatcattttattttaaccatttctcccttgacctagatatcct---actccattactgttttaagtgtctgcttcttttgttactgaacttgaggttatattgttggacgtggaactaacatttatactttatata-tgtgaagGTTTTGTATGACTATGAAGACAAAATCAATCAGGCTGTCTTTCCTGGACTTCAAGGTGGCCCTCACAATCACACAATTGCTGGCTTAGCTGTTGCATTGA
|| |||  |  |   |||||||   |   |||||     | | |   |||| ||   ||  ||   | | |||| ||| |  |   |   | || | ||||| |  | |||||| | || |   |  |      | ||||| || | |||  |  | | ||||| | |||||||||||||| ||||||||||| || ||||| || |||||||| ||||| ||||||||||| ||||| ||| |||| ||||||||||||||||
gtaagt-atcctggagaaaataatttgacatttt-----tgtttattttgatctctgtactctcggatttcatt-ctgatcaataggatagtttgtgttgtttccta-cttgagttgatgtaaattcataaatca-taacagttgttcttcttgcaatttgaagCTATTGTATGACTATGAGGACAAAATCAACCAAGCTGTTTTCCCTGGACTGCAAGGGGGCCCTCACAACCACACTATTACTGGTTTAGCTGTTGCATTGA

upper sequence: Vv00s0211g00120.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA09G33480.1 (Glycine max), 3'ss of exon 9
gtgagttgttttaaggaaaatatcattt--tattttaac---catttctcccttgacctagatatcctactccattactgt--tttaagtgtctgcttcttttgttactgaacttgaggttatattgttggacgtgg-aactaacatttatacttt-----atatatgtgaagGTTTTGTATGACTATGAAGACAAAATCAATCAGGCTGTCTTTCCTGGACTTCAAGGTGGCCCTCACAATCACACAATTGCTGGCTTAGCTGTTGCATTGA
      | ||       |||| | ||||   |||||  |   | |||  |  ||   |||  ||||    ||  ||    |  |||  |  | |  ||||  | || |  || || | || |  |  | | | | |  ||  | ||    || |||     |  ||| |||||||  ||||||||||||||||||||||||||   ||||| ||||||||||| ||| |||| ||||||   ||| | ||| |||| ||||||||||||||||
-----gtattcctgaacaaattttatttgacattttggcatacttttggcttttatactatctatcaagttctgttttcatgattttggcatgttgttctagtctt-caaaaatttatgtaaattcatggcatgagccaaacagcaaccctaatttttctaacttatttgaagGTGATGTATGACTATGAAGACAAAATCAATAGAGCTGTGTTTCCTGGACTGCAAAGTGGTCCTCACTTCCACTCTATTACTGGTTTAGCTGTTGCATTGA

upper sequence: Vv00s0211g00120.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: PP1S79_54V6.1 (Physcomitrella patens), 3'ss of exon 9
gtgagttgttttaaggaaaatatcattttattttaaccatttctcccttgacctagatatcct-actccattactgttttaagtgtctgcttcttttgttactgaacttgaggttatattgttggacgtggaactaacatttatactttatata--tgtgaagGTTTTGTATGACTATGAAGACAAAATCAATCAGGCTGTCTTTCCTGGACTTCAAGGTGGCCCTCACAATCACACAATTGCTGGCTTAGCTGTTGCATTGA
                                                         | || | ||||||         || | |   | | ||  | |  |  |    ||||||     |||  |  |      ||  ||| |  |  ||     |||| || |||| || ||||||||||||||||| |||   ||||| ||||| ||||| ||||| || |||||||| ||||| ||||| ||  | |||||||| ||||
---------------------------------------------------------tgtcttcactccaacgaaagcataggggc--gatgctggtctcgcgtatgcggaggttg----gttacatttcagctgaatgtttctgatccatcctgctgtgcagATTTTCTACGACTATGAAGACAAAATTAATGCTGCTGTTTTTCCAGGACTACAAGGGGGTCCTCACAACCACACCATTGCAGGACTTGCTGTTGCCTTGA

upper sequence: Vv00s0211g00120.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: EFJ32604 (Selaginella moellendorffii), 3'ss of exon 9
gtgagttgttttaaggaaaatatcattttattttaaccatttctcccttgacctagatatcctactccattactgttttaagtgtctgcttcttttgttactgaacttgaggttatattgttggacgtggaactaacatttatactttatatatgtgaagGTTTTGTATGACTATGAAGACAAAATCAATCAGGCTGTCTTTCCTGGACTTCAAGGTGGCCCTCACAATCACACAATTGCTGGCTTAGCTGTTGCATTGA
                                                                                                                   ||   ||        || | || |   |      |   |  | ||||| | || ||||| |  || ||||| |||   || || || ||||| ||||||||||| ||||||||||||||||||||||   | || || ||  | |
------------------------------------------------------------------------------------------------------------------gtacgtttactttcccaagttacctccttgaca-gtgcct-cgcagGTTCTATACGACTACGCTGAGAAAATAAATGCTGCAGTGTTCCCTGGGCTTCAAGGTGGTCCTCACAATCACACAATTGCTGCGCTTGCCGTGGCTCTTA

upper sequence: Vv00s0211g00120.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: EFJ16660 (Selaginella moellendorffii), 3'ss of exon 9
gtgagttgttttaaggaaaatatcattttattttaaccatttctcccttgacctagatatcctactccattactgttttaagtgtctgcttcttttgttactgaacttgaggttatattgttggacgtggaactaacatttatactttatatatgtgaagGTTTTGTATGACTATGAAGACAAAATCAATCAGGCTGTCTTTCCTGGACTTCAAGGTGGCCCTCACAATCACACAATTGCTGGCTTAGCTGTTGCATTGA
                                                                                                                   ||   ||        || | || |   |     |       | ||||| | || ||||| |  || ||||| |||   || || || ||||| ||||||||||| ||||||||||||||||||||||   | || || ||  | |
------------------------------------------------------------------------------------------------------------------gtacgtttactttcccaagttacctccttgac--agcgcctcgcagGTTCTATACGACTACGCTGAGAAAATAAATGCTGCAGTGTTCCCTGGGCTTCAAGGTGGTCCTCACAATCACACAATTGCTGCGCTTGCCGTGGCTCTTA

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|33407197|gb|CF212824.1|CF212824
EST:     TGATTTTCTTCAGGAAGGGGGTAAAAGAGGTTAATAAACAAGGGAAAGAG                         GTTTTGTATGACTATGAAGACAAAATCAATCAGGCTGTCTTTCCTGGACTT
genomic: TGATTTTCTTCAGGAAGGGGGTAAAAGAGGTTAATAAACAAGGGAAAGAGgtgagttgtt ... atatgtgaagGTTTTGTATGACTATGAAGACAAAATCAATCAGGCTGTCTTTCCTGGACTT
EST: gi|349827018|gb|FQ419109.1|FQ419109
EST:     CAGGAAGGGGGTAAAAGAGGTTAATAAACAAGGGAAAGAG                         GTTTTGTATGACTATGAAGACAAAATCAATCAGGCTGTCTTTCCTGGACTT
genomic: CAGGAAGGGGGTAAAAGAGGTTAATAAACAAGGGAAAGAGgtgagttgtt ... atatgtgaagGTTTTGTATGACTATGAAGACAAAATCAATCAGGCTGTCTTTCCTGGACTT
EST: gi|32270628|gb|CD719787.1|CD719787
EST:     TGATTTTCTTCAGGAAGGGGGTAAAAGAGGTTAATAAACAAGGGAAAGAG                         GTTTTGTATGATTATGAAGACAAAATCAACCAGGCTGTCTTTCCTGGACTT
genomic: TGATTTTCTTCAGGAAGGGGGTAAAAGAGGTTAATAAACAAGGGAAAGAGgtgagttgtt ... atatgtgaagGTTTTGTATGACTATGAAGACAAAATCAATCAGGCTGTCTTTCCTGGACTT
EST: gi|27579405|gb|CB002100.1|CB002100
EST:     TGATTTTCTTCAGGAAGGGGGTAAAAGAGGTTAATAAACAAGGGAAAGAG                         GTTTTGTATGATTATGAAGACAAAATCAACCAGGCTGTCTTTCCTGGACTT
genomic: TGATTTTCTTCAGGAAGGGGGTAAAAGAGGTTAATAAACAAGGGAAAGAGgtgagttgtt ... atatgtgaagGTTTTGTATGACTATGAAGACAAAATCAATCAGGCTGTCTTTCCTGGACTT
EST: gi|110361521|gb|EC925002.1|EC925002
EST:     TGATTTTCTTCAGGAAGGGGGTAAAAGAGGTTAATAAACAAGGGAAAGAG                         GTTTTGTATGACTATGAAGACAAAATCAATCAGGCTGTCTTTCCTGGACTT
genomic: TGATTTTCTTCAGGAAGGGGGTAAAAGAGGTTAATAAACAAGGGAAAGAGgtgagttgtt ... atatgtgaagGTTTTGTATGACTATGAAGACAAAATCAATCAGGCTGTCTTTCCTGGACTT
EST: gi|110379633|gb|EC944843.1|EC944843
EST:     AAAAGAGGTTAATAAACAAGGGAAAGAG                         GTTTTGTATGATTATGAAGACAAAATCAACCAGGCTGTCTTTCCTGGACTT
genomic: AAAAGAGGTTAATAAACAAGGGAAAGAGgtgagttgtt ... atatgtgaagGTTTTGTATGACTATGAAGACAAAATCAATCAGGCTGTCTTTCCTGGACTT
EST: gi|27755145|gb|CB035900.1|CB035900
EST:     TGATTTTCTTCAGGAAGGGGGTAAAAGAGGTTAATAAACAAGGGAAAGAG                         GTTTTGTATGACTATGAAGACAAAATCAATCAGGCTGTCTTTCCTGGACTT
genomic: TGATTTTCTTCAGGAAGGGGGTAAAAGAGGTTAATAAACAAGGGAAAGAGgtgagttgtt ... atatgtgaagGTTTTGTATGACTATGAAGACAAAATCAATCAGGCTGTCTTTCCTGGACTT
EST: gi|351030429|gb|FQ432367.1|FQ432367
EST:     CAGGAAGGGGGTAAAAGAGGTTAATAAACAAGGGAAAGAG                         GTTTTGTATGACTATGAAGACAAAATCAATCAGGCTGTCTTTCCTGGACTT
genomic: CAGGAAGGGGGTAAAAGAGGTTAATAAACAAGGGAAAGAGgtgagttgtt ... atatgtgaagGTTTTGTATGACTATGAAGACAAAATCAATCAGGCTGTCTTTCCTGGACTT
EST: gi|294966171|gb|GW839394.1|GW839394
EST:     TGATTTTCTTCAGGAAGGGGGTAAAAGAGGTTAATAAACAAGGGAAAGAG                         GTTTTGTATGACTATGAAGACAAAATCAATCAGGCTGTCTTTCCTGGACTT
genomic: TGATTTTCTTCAGGAAGGGGGTAAAAGAGGTTAATAAACAAGGGAAAGAGgtgagttgtt ... atatgtgaagGTTTTGTATGACTATGAAGACAAAATCAATCAGGCTGTCTTTCCTGGACTT
EST: gi|110361068|gb|EC924521.1|EC924521
EST:     TCAGGAAGGGGGGTAAAAGAGGTTAATAAACAAGGGAAAGAG                         GTTTTGTATGACTATGAAGACAAAATCAATCAGGCTGTCTTTCCTGGACTT
genomic: TCAGGAA-GGGGGTAAAAGAGGTTAATAAACAAGGGAAAGAGgtgagttgtt ... atatgtgaagGTTTTGTATGACTATGAAGACAAAATCAATCAGGCTGTCTTTCCTGGACTT
EST: gi|351016424|gb|FQ423851.1|FQ423851
EST:     TGATTTTCTTCAGGAAGGGGGTAAAAGAGGTTAATAAACAAGGGAAAGAG                         GTTTTGTATGACTATGAAGACAAAATCAATCAGGCTGTCTTTCCTGGACTT
genomic: TGATTTTCTTCAGGAAGGGGGTAAAAGAGGTTAATAAACAAGGGAAAGAGgtgagttgtt ... atatgtgaagGTTTTGTATGACTATGAAGACAAAATCAATCAGGCTGTCTTTCCTGGACTT
EST: gi|110373188|gb|EC937406.1|EC937406
EST:     TGATTTTCTTCAGGAAGGGGGTAAAAGAGGTTAATAAACAAGGGAAAGAG                         GTTTTGTATGACTATGAAGACAAAATCAATCAGGCTGTCTTTCCTGGACTT
genomic: TGATTTTCTTCAGGAAGGGGGTAAAAGAGGTTAATAAACAAGGGAAAGAGgtgagttgtt ... atatgtgaagGTTTTGTATGACTATGAAGACAAAATCAATCAGGCTGTCTTTCCTGGACTT
EST: gi|110363609|gb|EC927210.1|EC927210
EST:     TAAAAGAGGTTAATAAACAAGGGAAAGAG                         GTTTTGTATGACTATGAAGACAAAATCAATCAGGCTGTCTTTCCTGGACTT
genomic: TAAAAGAGGTTAATAAACAAGGGAAAGAGgtgagttgtt ... atatgtgaagGTTTTGTATGACTATGAAGACAAAATCAATCAGGCTGTCTTTCCTGGACTT
EST: gi|32250119|gb|CD715938.1|CD715938
EST:     TGATTTTCTTCAGGAAGGGGGTAAAAGAGGTTAATAAACAAGGGAAAGAG                         GTTTTGTATGATTATGAAGACAAAATCAACCAGGCTGTCTTTCCTGGAC
genomic: TGATTTTCTTCAGGAAGGGGGTAAAAGAGGTTAATAAACAAGGGAAAGAGgtgagttgtt ... atatgtgaagGTTTTGTATGACTATGAAGACAAAATCAATCAGGCTGTCTTTCCTGGAC
EST: gi|351029249|gb|FQ435449.1|FQ435449
EST:     TGATTTTCTTCAGGAAGGGGGTAAAAGAGGTTAATAAACAAGGGAAAGAG                         GTTTTGTATGACTATGAAGACAAAATCAATCAGGCTGTCTTTCCTGGACTT
genomic: TGATTTTCTTCAGGAAGGGGGTAAAAGAGGTTAATAAACAAGGGAAAGAGgtgagttgtt ... atatgtgaagGTTTTGTATGACTATGAAGACAAAATCAATCAGGCTGTCTTTCCTGGACTT
EST: gi|29785493|gb|CB342547.2|CB342547
EST:     TGATTTTCTTCAGGAAGGGGGTAAAAGAGGTTAATAAACAAGGGAAAGAG                         GTTTTGTATGACTATGAAGACAAAATCAATCAGGCTGTCTTTCCTGGACTT
genomic: TGATTTTCTTCAGGAAGGGGGTAAAAGAGGTTAATAAACAAGGGAAAGAGgtgagttgtt ... atatgtgaagGTTTTGTATGACTATGAAGACAAAATCAATCAGGCTGTCTTTCCTGGACTT
EST: gi|37184833|gb|CF604187.1|CF604187
EST:     TGATTTTCTTCAGGAAGGGGGTAAAAGAGGTTAATAAACAAGGGAAAGAG                         GTTTTGTATGACTATGAAGACAAAATCAATCAGGCTGTCTTTCCTGGACTT
genomic: TGATTTTCTTCAGGAAGGGGGTAAAAGAGGTTAATAAACAAGGGAAAGAGgtgagttgtt ... atatgtgaagGTTTTGTATGACTATGAAGACAAAATCAATCAGGCTGTCTTTCCTGGACTT
EST: gi|351053957|gb|FQ441723.1|FQ441723
EST:     TGATTTTCTTCAGGAAGGGGGTACAAGAGGTTAATAAACAAGGGAAAGAG                         GTTTTGTATGACTATGAAGACAAAATCAATCAGGCTGTCTTTCCTGGACTT
genomic: TGATTTTCTTCAGGAAGGGGGTAAAAGAGGTTAATAAACAAGGGAAAGAGgtgagttgtt ... atatgtgaagGTTTTGTATGACTATGAAGACAAAATCAATCAGGCTGTCTTTCCTGGACTT
EST: gi|30299931|gb|CB976725.1|CB976725
EST:     TGATTTTCTTCAGGAAGGGGGTAAAAGAGGTTAATAAACAAGGGAAAGAG                         GTTTTGTATGATTATGAAGACAAAATCAACCAGGCTGTCTTTCCTGGACTT
genomic: TGATTTTCTTCAGGAAGGGGGTAAAAGAGGTTAATAAACAAGGGAAAGAGgtgagttgtt ... atatgtgaagGTTTTGTATGACTATGAAGACAAAATCAATCAGGCTGTCTTTCCTGGACTT
EST: gi|351013925|gb|FQ434077.1|FQ434077
EST:     CAGGAGGGGGGTAAAAGAGGTTAATAAACAAGGGAAAGAG                         GTTTTGTATGACTATGAAGACAAAATCAATCAGGCTGTCTTTCCTGGACTT
genomic: CAGGAAGGGGGTAAAAGAGGTTAATAAACAAGGGAAAGAGgtgagttgtt ... atatgtgaagGTTTTGTATGACTATGAAGACAAAATCAATCAGGCTGTCTTTCCTGGACTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttgaggttatattgttggacgtggaactaacatttatactttatatatgtgaagGTTTTGTATGACTATGAAGACAAAATCAATCAGGCTGTCTTTCCTGGACTTCAAGGTGGCCCTCACAATCACACAATTGCTGGCTTAGCTGTTGCATTGA
                         aactaac  putative branch site (score: 1)
                         aactaacatttatact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagttgttttaaggaaaatatcattttattttaaccatttctcccttgacctagatatcctactccattactgttttaagtgtctgcttcttttgttactgaacttgaggttatattgttggacgtggaactaacatttatactttatatatgtgaagGTTTTGTATGACTATGAAGACAAAATCAATCAGGCTGTCTTTCCTGGACTTCAAGGTGGCCCTCACAATCACACAATTGCTGGCTTAGCTGTTGCATTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT