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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gatcaaatataatcggacacccaccaattattgaataattcaatagagcagattcatgatcactacccaaaattaatcatgtcatgctataccatttcagGAACGTTTCTCTACAGGACAACAGAGTTCAAAGAAACTACCAGCTTTGGGAGGAGTTTAGCAAAGTATAGGTATAGCGGATGATAATTTAACTATGTAAG

Basic information

species Vitis vinifera
transcript Vv10s0003g01640.t01
intron # 16
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|30329616|gb|CD012878.1|CD012878
EST:     TACCACTATGATGTTGAAAACTAACAGGACCACCTTCATTATTATGCCTT                         GAACGTTTCTCTACAGGACAACAGAGTTCAAAGAAACTACCAGCTTTGGGA
genomic: TACCACTATGATGTTGAAAACTAACAGGACCACCTTCATTATTATGCCTTgtaagtacaa ... accatttcagGAACGTTTCTCTACAGGACAACAGAGTTCAAAGAAACTACCAGCTTTGGGA
EST: gi|351013609|gb|FQ429750.1|FQ429750
EST:     TACCACTATGATGTTGAAAACTAACAGGACCACCTTCATTATTATGCCTT                         GAACGTTTCTCTACAGGACAACAGAGTTCAAAGAAACTACCAGCTTTGGGA
genomic: TACCACTATGATGTTGAAAACTAACAGGACCACCTTCATTATTATGCCTTgtaagtacaa ... accatttcagGAACGTTTCTCTACAGGACAACAGAGTTCAAAGAAACTACCAGCTTTGGGA
EST: gi|110724595|gb|EE100559.1|EE100559
EST:     TACCACTATGATGTTGAAAACTAACAGGACCACCTTCATTATTATGCCTT                         GAACGTTTCTCTACAGGACAACAGAGTTCAAAGAAACTACCAGCTTAGGGA
genomic: TACCACTATGATGTTGAAAACTAACAGGACCACCTTCATTATTATGCCTTgtaagtacaa ... accatttcagGAACGTTTCTCTACAGGACAACAGAGTTCAAAGAAACTACCAGCTTTGGGA
EST: gi|351019257|gb|FQ429417.1|FQ429417
EST:     TACCACTATGATGTTGAAAACTAACAGGACCACCTTCATTATTATGCCTT                         GAACGTTTCTCTACAGGACAACAGAGTTCAAAGAAACTACCAGCTTTGGGA
genomic: TACCACTATGATGTTGAAAACTAACAGGACCACCTTCATTATTATGCCTTgtaagtacaa ... accatttcagGAACGTTTCTCTACAGGACAACAGAGTTCAAAGAAACTACCAGCTTTGGGA
EST: gi|30131130|gb|CB916469.1|CB916469
EST:     TACCACTATGATGTTGAAAACTAACAGGACCACCTTCATTATTATGCCTT                         GAACGTTTCTCTACAGGACAACAGAGTTCAAAGAAACTACCAGCTTTGGGA
genomic: TACCACTATGATGTTGAAAACTAACAGGACCACCTTCATTATTATGCCTTgtaagtacaa ... accatttcagGAACGTTTCTCTACAGGACAACAGAGTTCAAAGAAACTACCAGCTTTGGGA
EST: gi|30330265|gb|CD013527.1|CD013527
EST:     TACCACTATGATGTTGAAAACTAACAGGACCACCTTCATTATTATGCCTT                         GAACGTTTCTCTACAGGACAACAGAGTTCAAAGAAACTACCAGCTTTGGGA
genomic: TACCACTATGATGTTGAAAACTAACAGGACCACCTTCATTATTATGCCTTgtaagtacaa ... accatttcagGAACGTTTCTCTACAGGACAACAGAGTTCAAAGAAACTACCAGCTTTGGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagcagattcatgatcactacccaaaattaatcatgtcatgctataccatttcagGAACGTTTCTCTACAGGACAACAGAGTTCAAAGAAACTACCAGCTTTGGGAGGAGTTTAGCAAAGTATAGGTATAGCGGATGATAATTTAACTATGTAAG
                         aattaat  putative branch site (score: 3)
                                              ccatttc  putative PPT
                       aaaattaatcatgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gatcaaatataatcggacacccaccaattattgaataattcaatagagcagattcatgatcactacccaaaattaatcatgtcatgctataccatttcagGAACGTTTCTCTACAGGACAACAGAGTTCAAAGAAACTACCAGCTTTGGGAGGAGTTTAGCAAAGTATAGGTATAGCGGATGATAATTTAACTATGTAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
-atcaaat
- - - - - - - - - -cccacca
- - - - - - - - - - - - - - - - - - - - -aatagag
- - - - - - - - - - - - - - - - - - - - - - - - - - - catgatc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctaccca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaattaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tcatgct