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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaggttgaaatgattggtgcttttcctttagttttataattattataactattgctgctgctactgctactgctactattatttatccatcttataggccctttgcgattcatgaaaattttctgataccttcagGTCTGAGGTTAACAGGAAGCCTGCTGGCCAGACAGACTTAATCCGGATTGAGACACTCCACCATGCAGATAAGGAGAAAACTGAAGCTTATATTCTTGAA

Basic information

species Vitis vinifera
transcript Vv18s0076g00260.t01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0076g00260.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA20G31400.1 (Glycine max), 3'ss of exon 14
gtaaggttgaaatgattggtgcttttcctttagttttataattattataactattgctgctgctactgctactgctac-tattatttatccat-cttataggccctttgcgattcatgaaaattttctgataccttcagGTCTGAGGTTAACAGGAAGCCTGCTGGCCAGACAGACTTAATCCGGATTGAGACACTCCACCATGCAGATAAGGAGAAAACTGAAGCTTATATTCTTGAA
                                                          |     || |  | |||||  | || ||  |  || ||| || |  ||      ||    ||    | |   |   |  ||||||||||| ||| | || ||||| |||||||| |||||  |  | ||||| ||||| |||||||| ||||| || ||||| ||||||||||| ||||||
----------------------------------------------------------gtgaggacag--aatgctagattttcttcctgtatgcttctatgttctacctagttttctaa----tgcaagtttgtatagGTCTGAGGTCAACCGAAAACCTGCCGGCCAGACCGACTTGTTGAGAATTGAAACACTACACCATGCTGATAAAGACAAAACAGAAGCTTATATACTTGAA
















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|110719053|gb|EE096590.1|EE096590
EST:     AGCTCATCATGGCTTTGGTTGGGTTGGCGAATGGGCCAATACCGG                         GTCTGAGGTTAACAGGAAGCCTGCTGGCCAGACAGACTTAATCCGGATTGA
genomic: AGCTCATCATGGCTTTGGTTGGGTTGGCGAATGGGCCAATACCGGgtaaggttga ... ataccttcagGTCTGAGGTTAACAGGAAGCCTGCTGGCCAGACAGACTTAATCCGGATTGA
EST: gi|110720867|gb|EE097166.1|EE097166
EST:     AGCTCATCATGGCTTTGGTTGGGTTGGCGAATGGGCCAATACCGG                         GTCTGAGGTTAACAGGAAGCCTGCTGGCCAGACAGACTTAATCCGGATTGA
genomic: AGCTCATCATGGCTTTGGTTGGGTTGGCGAATGGGCCAATACCGGgtaaggttga ... ataccttcagGTCTGAGGTTAACAGGAAGCCTGCTGGCCAGACAGACTTAATCCGGATTGA
EST: gi|110720638|gb|EE096734.1|EE096734
EST:     AGCTCATCATGGCTTTGGTTGGGTTGGCGAATGGGCCAATACCGG                         GTCTGAGGTTAACAGGAAGCCTGCTGGCCAGACAGACTTAATCCGGATTGA
genomic: AGCTCATCATGGCTTTGGTTGGGTTGGCGAATGGGCCAATACCGGgtaaggttga ... ataccttcagGTCTGAGGTTAACAGGAAGCCTGCTGGCCAGACAGACTTAATCCGGATTGA
EST: gi|351022377|gb|FQ445152.1|FQ445152
EST:     AAAGCTCATCATGGCTTTGGTTGGGTTGGCGAATGGGCCAATACCGG                         GTCTGAGGTTAACAGGAAGCCTGCTGGCCAGACAGACTTAATCCGGATTGA
genomic: AAAGCTCATCATGGCTTTGGTTGGGTTGGCGAATGGGCCAATACCGGgtaaggttga ... ataccttcagGTCTGAGGTTAACAGGAAGCCTGCTGGCCAGACAGACTTAATCCGGATTGA
EST: gi|351025753|gb|FQ426767.1|FQ426767
EST:     AAAGCTCATCATGGCTTTGGTTGGGTTGGCGAATGGGCCAATACCGG                         GTCTGAGGTTAACAGGAAGCCTGCTGGCCAGACAGACTTAATCCGGATTGA
genomic: AAAGCTCATCATGGCTTTGGTTGGGTTGGCGAATGGGCCAATACCGGgtaaggttga ... ataccttcagGTCTGAGGTTAACAGGAAGCCTGCTGGCCAGACAGACTTAATCCGGATTGA
EST: gi|110718519|gb|EE095448.1|EE095448
EST:     AGCTCATCATGGCTTTGGTTGGGTTGGCGAATGGGCCAATACCGG                         GTCTGAGGTTAACAGGAAGCCTGCTGGCCAGACAGACTTAATCCGGATTGA
genomic: AGCTCATCATGGCTTTGGTTGGGTTGGCGAATGGGCCAATACCGGgtaaggttga ... ataccttcagGTCTGAGGTTAACAGGAAGCCTGCTGGCCAGACAGACTTAATCCGGATTGA
EST: gi|110696366|gb|EE072430.1|EE072430
EST:     AGCTCATCATGGCTTTGGTTGGGTTGGCGAATGGGCCAATACCGG                         GTCTGAGGTTAACAGGAAGCCTGCTGGCCAGACAGACTTAATCCGGATTGA
genomic: AGCTCATCATGGCTTTGGTTGGGTTGGCGAATGGGCCAATACCGGgtaaggttga ... ataccttcagGTCTGAGGTTAACAGGAAGCCTGCTGGCCAGACAGACTTAATCCGGATTGA
EST: gi|351013632|gb|FQ429773.1|FQ429773
EST:     AAAGCTCATCATGGCTTTGGTTGGGTTGGCGAATGGGCCAATACCGG                         GTCTGAGGTTAACAGGAAGCCTGCTGGCCAGACAGACTTAATCCGGATTGA
genomic: AAAGCTCATCATGGCTTTGGTTGGGTTGGCGAATGGGCCAATACCGGgtaaggttga ... ataccttcagGTCTGAGGTTAACAGGAAGCCTGCTGGCCAGACAGACTTAATCCGGATTGA
EST: gi|110720216|gb|EE095942.1|EE095942
EST:     AGCTCATCATGGCTTTGGTTGGGTTGGCGAATGGGCCAATACCGG                         GTCTGAGGTTAACAGGAAGCCTGCTGGCCAGACAGACTTAATCCGGATTGA
genomic: AGCTCATCATGGCTTTGGTTGGGTTGGCGAATGGGCCAATACCGGgtaaggttga ... ataccttcagGTCTGAGGTTAACAGGAAGCCTGCTGGCCAGACAGACTTAATCCGGATTGA
EST: gi|110720676|gb|EE096807.1|EE096807
EST:     AGCTCATCATGGCTTTGGTTGGGTTGGCGAATGGGCCAATACCGG                         GTCTGAGGTTAACAGGAAGCCTGCTGGCCAGACAGACTTAATCCGGATTGA
genomic: AGCTCATCATGGCTTTGGTTGGGTTGGCGAATGGGCCAATACCGGgtaaggttga ... ataccttcagGTCTGAGGTTAACAGGAAGCCTGCTGGCCAGACAGACTTAATCCGGATTGA
EST: gi|110720592|gb|EE096647.1|EE096647
EST:     AGCTCATCATGGCTTTGGTTGGGTTGGCGAATGGGCCAATACCGG                         GTCTGAGGTTAACAGGAAGCCTGCTGGCCAGACAGACTTAATCCGGATTGA
genomic: AGCTCATCATGGCTTTGGTTGGGTTGGCGAATGGGCCAATACCGGgtaaggttga ... ataccttcagGTCTGAGGTTAACAGGAAGCCTGCTGGCCAGACAGACTTAATCCGGATTGA
EST: gi|110719214|gb|EE096935.1|EE096935
EST:     AGCTCATCATGGCTTTGGTTGGGTTGGCGAATGGGCCAATACCGG                         GTCTGAGGTTAACAGGAAGCCTGCTGGCCAGACAGACTTAATCCGGATTGA
genomic: AGCTCATCATGGCTTTGGTTGGGTTGGCGAATGGGCCAATACCGGgtaaggttga ... ataccttcagGTCTGAGGTTAACAGGAAGCCTGCTGGCCAGACAGACTTAATCCGGATTGA
EST: gi|110713860|gb|EE090149.1|EE090149
EST:     AGCTCATCATGGCTTTGGTTGGGTTGGCGAATGGGCCAATACCGG                         GTCTGAGGTTAACAGGAAGCCTGCTGGCCAGACAGACTTAATCCGGATTGA
genomic: AGCTCATCATGGCTTTGGTTGGGTTGGCGAATGGGCCAATACCGGgtaaggttga ... ataccttcagGTCTGAGGTTAACAGGAAGCCTGCTGGCCAGACAGACTTAATCCGGATTGA
EST: gi|110718805|gb|EE096054.1|EE096054
EST:     AGCTCATCATGGCTTTGGTTGGGTTGGCGAATGGGCCAATACCGG                         GTCTGAGGTTAACAGGAAGCCTGCTGGCCAGACAGACTTAATCCGGATTGA
genomic: AGCTCATCATGGCTTTGGTTGGGTTGGCGAATGGGCCAATACCGGgtaaggttga ... ataccttcagGTCTGAGGTTAACAGGAAGCCTGCTGGCCAGACAGACTTAATCCGGATTGA
EST: gi|110719766|gb|EE095191.1|EE095191
EST:     AGCTCATCATGGCTTTGGTTGGGTTGGCGAATGGGCCAATACCGG                         GTCTGAGGTTAACAGGAAGCCTGCTGGCCAGACAGACTTAATCCGGATTGA
genomic: AGCTCATCATGGCTTTGGTTGGGTTGGCGAATGGGCCAATACCGGgtaaggttga ... ataccttcagGTCTGAGGTTAACAGGAAGCCTGCTGGCCAGACAGACTTAATCCGGATTGA
EST: gi|30302844|gb|CB979638.1|CB979638
EST:     AGCTCATCATGGCTTTGATTGGGTTGGCGAATGGGCCAATACCGG                         GTCTGAGGTTAACAGGAAGCCTGCTGGCCAGACAGACTTAATCCGGATTGA
genomic: AGCTCATCATGGCTTTGGTTGGGTTGGCGAATGGGCCAATACCGGgtaaggttga ... ataccttcagGTCTGAGGTTAACAGGAAGCCTGCTGGCCAGACAGACTTAATCCGGATTGA
EST: gi|110720643|gb|EE096746.1|EE096746
EST:     AGCTCATCATGGCTTTGGTTGGGTTGGCGAATGGGCCAATACCGG                         GTCTGAGGTTAACAGGAAGCCTGCTGGCCAGACAGACTTAATCCGGATTGA
genomic: AGCTCATCATGGCTTTGGTTGGGTTGGCGAATGGGCCAATACCGGgtaaggttga ... ataccttcagGTCTGAGGTTAACAGGAAGCCTGCTGGCCAGACAGACTTAATCCGGATTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttatccatcttataggccctttgcgattcatgaaaattttctgataccttcagGTCTGAGGTTAACAGGAAGCCTGCTGGCCAGACAGACTTAATCCGGATTGAGACACTCCACCATGCAGATAAGGAGAAAACTGAAGCTTATATTCTTGAA
                                        ttctgat  putative branch site (score: 3)
                                              taccttc  CT-rich tract
                           attcatgaaaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaggttgaaatgattggtgcttttcctttagttttataattattataactattgctgctgctactgctactgctactattatttatccatcttataggccctttgcgattcatgaaaattttctgataccttcagGTCTGAGGTTAACAGGAAGCCTGCTGGCCAGACAGACTTAATCCGGATTGAGACACTCCACCATGCAGATAAGGAGAAAACTGAAGCTTATATTCTTGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC