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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctttgattttcctcatttttttcttgaatttttgttgctatatctctattcaatcggcctttgtcttatttttgatggattgtttggaaattgagaatagACACACAAATCACAAGTCCGAGGGCTGAGGTTGCTATTCGAATAGGCGGACAAGGGGAATCTGTGATCTCAATCCATGAATTCCAGAAG

Basic information

species Vitis vinifera
transcript Vv07s0005g02990.t01
intron # 1
splice site 3'
intron type U2

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|34549774|gb|CF518006.1|CF518006
EST:     TTGTGGGGA-TCTCACCTTCCCTCC-AAG                         ACACACAAATCACAAGTCCGAGGGCTGAGGTTGCTATTCGAATAGGCGGAC
genomic: TTGTGGGGATTCTCACCTTCCCTCCAAAGgtaacaattt ... ttgagaatagACACACAAATCACAAGTCCGAGGGCTGAGGTTGCTATTCGAATAGGCGGAC
EST: gi|26257147|gb|CA808210.1|CA808210
EST:     CACCTTCCCTCCAAAG                         ACACACAAATCACAAGTCCGAGGGCTGAGGTTGCTATTCGAATAGGCGGAC
genomic: CACCTTCCCTCCAAAGgtaacaattt ... ttgagaatagACACACAAATCACAAGTCCGAGGGCTGAGGTTGCTATTCGAATAGGCGGAC
EST: gi|30306129|gb|CB982923.1|CB982923
EST:     TTGTGGGGATTCTCACCTTCCCTCCAAAG                         ACACACAAATCACAAGTCCGAGGGCTGAGGTTTCTATTCGAATAGGCGGAC
genomic: TTGTGGGGATTCTCACCTTCCCTCCAAAGgtaacaattt ... ttgagaatagACACACAAATCACAAGTCCGAGGGCTGAGGTTGCTATTCGAATAGGCGGAC
EST: gi|110371595|gb|EC935706.1|EC935706
EST:     TCTCACCTTCCCTCCAAAG                         ACACACAAATCACAAGTCCGAGGGCTGAGGTTGCTATTCGAATAGGCGGAC
genomic: TCTCACCTTCCCTCCAAAGgtaacaattt ... ttgagaatagACACACAAATCACAAGTCCGAGGGCTGAGGTTGCTATTCGAATAGGCGGAC
EST: gi|294964691|gb|GW838494.1|GW838494
EST:     TTGTGGGGATTCTCACCTTCCCTCCAAAG                         ACACACAAATCACAAGTCCGAGGGCTGAGGTTGCTATTCGAATAGGCGGAC
genomic: TTGTGGGGATTCTCACCTTCCCTCCAAAGgtaacaattt ... ttgagaatagACACACAAATCACAAGTCCGAGGGCTGAGGTTGCTATTCGAATAGGCGGAC
EST: gi|29782805|gb|CB348441.2|CB348441
EST:     TCACCTTCCCTCC-AAG                         ACACACAAATCACAAGTCCGAGGGCTGAGGTTGCTATTCGAATAGGCGGAC
genomic: TCACCTTCCCTCCAAAGgtaacaattt ... ttgagaatagACACACAAATCACAAGTCCGAGGGCTGAGGTTGCTATTCGAATAGGCGGAC
EST: gi|110708420|gb|EE085941.1|EE085941
EST:     ATTCTCACCTTCCCTCCAAAG                         ACACACAAATCACAAGTCCGAGGGCTGAGGTTGCTATTCGAATAGGTGGAC
genomic: ATTCTCACCTTCCCTCCAAAGgtaacaattt ... ttgagaatagACACACAAATCACAAGTCCGAGGGCTGAGGTTGCTATTCGAATAGGCGGAC
EST: gi|110405426|gb|EC970967.1|EC970967
EST:     TCTCACCTTCCCTCCAAAG                         ACACACAAATCACAAGTCCGAGGGCTGAGGTTGCTATTCGAATAGGCGGAC
genomic: TCTCACCTTCCCTCCAAAGgtaacaattt ... ttgagaatagACACACAAATCACAAGTCCGAGGGCTGAGGTTGCTATTCGAATAGGCGGAC
EST: gi|30306203|gb|CB982997.1|CB982997
EST:     CTCACCTTCCCTCCAAAG                         ACACACAAATCACAAGTCCGATCNCTGAGGTTTCTATTCGAATAGGCGGAC
genomic: CTCACCTTCCCTCCAAAGgtaacaattt ... ttgagaatagACACACAAATCACAAGTCCGAGGGCTGAGGTTGCTATTCGAATAGGCGGAC
EST: gi|34550262|gb|CF518480.1|CF518480
EST:     TCACCTTCCCTCC-AAG                         ACACACAAATCACAAGTCCGAGGGCTGAGGTTGCTATTCGAATAGGCGGAC
genomic: TCACCTTCCCTCCAAAGgtaacaattt ... ttgagaatagACACACAAATCACAAGTCCGAGGGCTGAGGTTGCTATTCGAATAGGCGGAC
EST: gi|110724887|gb|EE101110.1|EE101110
EST:     GATTCTCACCTTCCCTCC-AAG                         ACACACAAATCACAAGTCCGAGGGCTGAGGTTGCTATTCGAATAGGCGGAC
genomic: GATTCTCACCTTCCCTCCAAAGgtaacaattt ... ttgagaatagACACACAAATCACAAGTCCGAGGGCTGAGGTTGCTATTCGAATAGGCGGAC
EST: gi|110378284|gb|EC943408.1|EC943408
EST:     TCTCACCTTCCCTCC-AAG                         ACACACAAATCACAAGTCCGAGGGCTGAGGTTGCTATTCGAATAGGCGGAC
genomic: TCTCACCTTCCCTCCAAAGgtaacaattt ... ttgagaatagACACACAAATCACAAGTCCGAGGGCTGAGGTTGCTATTCGAATAGGCGGAC
EST: gi|28969494|gb|CB348527.1|CB348527
EST:     TTGTGGGGATTCTCACCTTCCCTCCAAAG                         ACACACAAATCACAAGTCCGAGGGCTGAGGTTGCTATTCGAATAGGCGGAC
genomic: TTGTGGGGATTCTCACCTTCCCTCCAAAGgtaacaattt ... ttgagaatagACACACAAATCACAAGTCCGAGGGCTGAGGTTGCTATTCGAATAGGCGGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctattcaatcggcctttgtcttatttttgatggattgtttggaaattgagaatagACACACAAATCACAAGTCCGAGGGCTGAGGTTGCTATTCGAATAGGCGGACAAGGGGAATCTGTGATCTCAATCCATGAATTCCAGAAG
                        ttttgat  putative branch site (score: 4)
              tttgtcttattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctttgattttcctcatttttttcttgaatttttgttgctatatctctattcaatcggcctttgtcttatttttgatggattgtttggaaattgagaatagACACACAAATCACAAGTCCGAGGGCTGAGGTTGCTATTCGAATAGGCGGACAAGGGGAATCTGTGATCTCAATCCATGAATTCCAGAAG

- - - - -tcctcat
- - - - - - - - - - - - - - - - tgttgct
- - - - - - - - - - - - - - - - - - - - - - -ctattca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtttgg