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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttcctacattttctcggcgagtcaacgagcttcaagttttagttttgaggttgaaatacgttttgtgcttgtgcttacaagactctgtgttgttcttagGGAGGAGACTTGTGGTTAGGGCTGCTGAGACTGATGCAAATGAAG

Basic information

species Vitis vinifera
transcript Vv08s0105g00590.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|34547700|gb|CF515932.1|CF515932
EST:     CGCCAGGACCACTCCGCGTTTCCTTCCCCCGATCCCTCTTTCTCTCCACA                         GGAGGAGACTTGTGGTTAGGGCTGCTGAGACTGATGCAAATGAAG
genomic: CGCCAGGACCACTCCGCGTTTCCTTCCCCCAATTTCTCTTTCTCTCCACAgtcagtttgc ... ttgttcttagGGAGGAGACTTGTGGTTAGGGCTGCTGAGACTGATGCAAATGAAG
EST: gi|351018952|gb|FQ426451.1|FQ426451
EST:     CGCCAGGACCTTTCCGCGTTTCCTTCCCCCAATTTCTCTTTCTCTCCACA                         GGAGGAGACTTGTGGTTAGGGCTGCTGAGACTGATGCAAATGAAG
genomic: CGCCAGGACCACTCCGCGTTTCCTTCCCCCAATTTCTCTTTCTCTCCACAgtcagtttgc ... ttgttcttagGGAGGAGACTTGTGGTTAGGGCTGCTGAGACTGATGCAAATGAAG
EST: gi|37190125|gb|CF609474.1|CF609474
EST:     CGCCAGGACCACTCCGCGTTTCCTTCCCCCGATTTCTCTTTCTCTCCACA                         GGAGGAGACTTGTGGTTAGGGCTGCTGAGACTGATGCAAATGAAG
genomic: CGCCAGGACCACTCCGCGTTTCCTTCCCCCAATTTCTCTTTCTCTCCACAgtcagtttgc ... ttgttcttagGGAGGAGACTTGTGGTTAGGGCTGCTGAGACTGATGCAAATGAAG
EST: gi|161709684|gb|FC060175.1|FC060175
EST:     CGCCAGGACCACTCCGCGTTTCCTTCCCCCGATTTCTCTTTCTCTCCACA                         GGAGGAGACTTGTGGTTAGGGCTGCTGAGACTGATGCAAATGAAG
genomic: CGCCAGGACCACTCCGCGTTTCCTTCCCCCAATTTCTCTTTCTCTCCACAgtcagtttgc ... ttgttcttagGGAGGAGACTTGTGGTTAGGGCTGCTGAGACTGATGCAAATGAAG
EST: gi|352785482|gb|FQ477696.1|FQ477696
EST:     CGCCAGGACCACTCCGCGTTTCCTTCCCCCAATTTCTCTTTCTCTCCACA                         GGAGGAGACTTGTGGTTAGGGCTGCTGAGACTGATGCAAATGAAG
genomic: CGCCAGGACCACTCCGCGTTTCCTTCCCCCAATTTCTCTTTCTCTCCACAgtcagtttgc ... ttgttcttagGGAGGAGACTTGTGGTTAGGGCTGCTGAGACTGATGCAAATGAAG
EST: gi|349830671|gb|FQ416969.1|FQ416969
EST:     CGCCAGGACCACTCCGCGTTTCCTTCCCCCAATTTCTCTTTCTCTCCACA                         GGAGGAGACTTGTGGTTAGGGCTGCTGAGACTGATGCAAATGAAG
genomic: CGCCAGGACCACTCCGCGTTTCCTTCCCCCAATTTCTCTTTCTCTCCACAgtcagtttgc ... ttgttcttagGGAGGAGACTTGTGGTTAGGGCTGCTGAGACTGATGCAAATGAAG
EST: gi|161716004|gb|FC065529.1|FC065529
EST:     CGCCAGGACCACTCCGCGTTTCCTTCCCCCGATTTCTCTTTCTCTCCACA                         GGAGGAGACTTGTGGTTAGGGCTGCTGAGACTGATGCAAATGAAG
genomic: CGCCAGGACCACTCCGCGTTTCCTTCCCCCAATTTCTCTTTCTCTCCACAgtcagtttgc ... ttgttcttagGGAGGAGACTTGTGGTTAGGGCTGCTGAGACTGATGCAAATGAAG
EST: gi|351033623|gb|FQ447782.1|FQ447782
EST:     CGCCAGGACCACTCCGCGTTTCCTTCCCCCAATTTCTCTTTCTCTCCACA                         GGAGGAGACTTGTGGTTAGGGCTGCTGAGACTGATGCAAATGAAG
genomic: CGCCAGGACCACTCCGCGTTTCCTTCCCCCAATTTCTCTTTCTCTCCACAgtcagtttgc ... ttgttcttagGGAGGAGACTTGTGGTTAGGGCTGCTGAGACTGATGCAAATGAAG
EST: gi|351041270|gb|FQ447397.1|FQ447397
EST:     CGCCAGGACCACTCCGCGTTTCCTTCCCCCAATTTCTCTTTCTCTCCACA                         GGAGGAGACTTGTGGTTAGGGCTGCTGAGACTGATGCAAATGAAG
genomic: CGCCAGGACCACTCCGCGTTTCCTTCCCCCAATTTCTCTTTCTCTCCACAgtcagtttgc ... ttgttcttagGGAGGAGACTTGTGGTTAGGGCTGCTGAGACTGATGCAAATGAAG
EST: gi|352791138|gb|FQ477465.1|FQ477465
EST:     CGCCAGGACCACTCCGCGTTTCCTTCCCCCAATTTCTCTTTCTCTCCACA                         GGAGGAGACTTGTGGTTAGGGCTGCTGAGACTGATGCAAATGAAG
genomic: CGCCAGGACCACTCCGCGTTTCCTTCCCCCAATTTCTCTTTCTCTCCACAgtcagtttgc ... ttgttcttagGGAGGAGACTTGTGGTTAGGGCTGCTGAGACTGATGCAAATGAAG
EST: gi|351028530|gb|FQ444811.1|FQ444811
EST:     CGCCAGGACCACTCCGCGTTTCCTTCCCCCAATTTCTCTTTCTCTCCACA                         GGAGGAGACTTGTGGTTAGGGCTGCTGAGACTGATGCAAATGAAG
genomic: CGCCAGGACCACTCCGCGTTTCCTTCCCCCAATTTCTCTTTCTCTCCACAgtcagtttgc ... ttgttcttagGGAGGAGACTTGTGGTTAGGGCTGCTGAGACTGATGCAAATGAAG
EST: gi|351014975|gb|FQ444264.1|FQ444264
EST:     CGCCAGGACCACTCCGCGTTTCCTTCCCCCAATTTCTCTTTCTCTCCACA                         GGAGGAGACTTGTGGTTAGGGCTGCTGAGACTGATGCAAATGAAG
genomic: CGCCAGGACCACTCCGCGTTTCCTTCCCCCAATTTCTCTTTCTCTCCACAgtcagtttgc ... ttgttcttagGGAGGAGACTTGTGGTTAGGGCTGCTGAGACTGATGCAAATGAAG
EST: gi|351017844|gb|FQ436197.1|FQ436197
EST:     CGCCAGGACCACTCCGCGTTTCCTTCCCCCAATTTCTCTTTCTCTCCACA                         GGAGGAGACTTGTGGTTAGGGCTGCTGAGACTGATGCAAATGAAG
genomic: CGCCAGGACCACTCCGCGTTTCCTTCCCCCAATTTCTCTTTCTCTCCACAgtcagtttgc ... ttgttcttagGGAGGAGACTTGTGGTTAGGGCTGCTGAGACTGATGCAAATGAAG
EST: gi|110712697|gb|EE087971.1|EE087971
EST:     CGCCAGGACCACTCCGCGTTTCCTTCCCCCGATTTCTCTTTCTCTCCACA                         GGAGGAGACTTGTGGTTAGGGCTGCTGAGACTGATGCAAATGAAG
genomic: CGCCAGGACCACTCCGCGTTTCCTTCCCCCAATTTCTCTTTCTCTCCACAgtcagtttgc ... ttgttcttagGGAGGAGACTTGTGGTTAGGGCTGCTGAGACTGATGCAAATGAAG
EST: gi|110698374|gb|EE075807.1|EE075807
EST:     CGCCAGGACCACTCCGCGTTTCCTTCCCCCGATTTCTCTTTCTCTCCACA                         GGAGGAGACTTGTGGTTAGGGCTGCTGAGACTGATGCAAATGAAG
genomic: CGCCAGGACCACTCCGCGTTTCCTTCCCCCAATTTCTCTTTCTCTCCACAgtcagtttgc ... ttgttcttagGGAGGAGACTTGTGGTTAGGGCTGCTGAGACTGATGCAAATGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgaggttgaaatacgttttgtgcttgtgcttacaagactctgtgttgttcttagGGAGGAGACTTGTGGTTAGGGCTGCTGAGACTGATGCAAATGAAG
                           tgcttac  putative branch site (score: 2)
                                             ttgttctt  putative PPT
      ttgaaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttcctacattttctcggcgagtcaacgagcttcaagttttagttttgaggttgaaatacgttttgtgcttgtgcttacaagactctgtgttgttcttagGGAGGAGACTTGTGGTTAGGGCTGCTGAGACTGATGCAAATGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- -cctacat
- - - - - - - - - - - - - - - - - - - - - - - - - - -gaaatac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cttgtgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acaagac