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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agaatatttctatacttgccatatattgattttttttatttatatgtaaagtactttttgagagctccagtttgatccttcctcaatgtttttaatgcagCGCATTTTGGAAATCTGAGGATGACGCAGGAGGGATGGCTGGTCTAGGAGGTGACGCTGATGCCCACCCATATGTCTGCTTCACAATTAATCTTGTTTGA

Basic information

species Vitis vinifera
transcript Vv14s0068g01280.t01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0068g01280.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA02G07260.1 (Glycine max), 3'ss of exon 10
agaatatttctatacttgccatatattgattttttttatttatatgtaaagtactttttgagagctccagtttgatccttcctcaatgtttttaatgcagCGCATTTTGGAAATCTGAGGATGACGCAGGAGGGATGGCTGGTCTAGGAGGTGACGCTGATGCCCACCCATATGTCTGCTTCACAATTAATCTTGTTTGA
  | ||||  | |  ||      | |  | |||||| ||   | | |  | | |    || |  |      ||  |  | | |  || ||||   ||||| || |  |||||  | ||||| || | ||  ||||||||||| |||| |||||| |||||||||||||| ||||||| |||||| || ||||||||||||
ttattattattttttttttttcttctcaacttttttcataattctctttaatgccacatgtgctcatattgttattgttcctttcatattttcgctgcagTGCTTACTGGAAGACCGAGGACGAAGGAGTTGGGATGGCTGGCCTAGCAGGTGATGCTGATGCCCACCCTTATGTCTCCTTCACTATCAATCTTGTTTGA
















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|83276100|gb|DV940108.1|DV940108
EST:     GAGAAGAAAGTGCAATCAATTCTTGAAGGGCTATGTGACAGCACAAACAG                         TGCATTTTGGAAATCTGAGGATGACGCAGGAGGGATGGCTGGTCTAGGAGG
genomic: GAGAAGAAAGTGCGATCAATTCTTGAAGGGCTATGTGACAGCACAAACAGgcaagtcaat ... tttaatgcagCGCATTTTGGAAATCTGAGGATGACGCAGGAGGGATGGCTGGTCTAGGAGG
EST: gi|110364030|gb|EC927670.1|EC927670
EST:     GAGAAGAAAGTGCGATCAATTCTTGAAGGGCTATGTGACAGCACAAACAG                         CGCATTTTGGAAATCTGAGGATGACGCAGGAGGGATGGCTGGTCTAGGAGG
genomic: GAGAAGAAAGTGCGATCAATTCTTGAAGGGCTATGTGACAGCACAAACAGgcaagtcaat ... tttaatgcagCGCATTTTGGAAATCTGAGGATGACGCAGGAGGGATGGCTGGTCTAGGAGG
EST: gi|45770351|gb|CN006203.1|CN006203
EST:     GAGAAGAAAGTGCAATCAATTCTTGAAGGGCTATGTGACAGCACAAACAG                         TGCATTTTGGAAATCTGAGGATGACGCAGGAGGGATGGCTGGTCTAGGAGG
genomic: GAGAAGAAAGTGCGATCAATTCTTGAAGGGCTATGTGACAGCACAAACAGgcaagtcaat ... tttaatgcagCGCATTTTGGAAATCTGAGGATGACGCAGGAGGGATGGCTGGTCTAGGAGG
EST: gi|349827680|gb|FQ422548.1|FQ422548
EST:     GAGAAGAAAGTGCGATCAATTCTTGAAGGGCTATGTGACAGCACAAACAG                         CGCATTTTGGAAATCTGAGGATGACGCAGGAGGGATGGCTGGTCTAGGAGG
genomic: GAGAAGAAAGTGCGATCAATTCTTGAAGGGCTATGTGACAGCACAAACAGgcaagtcaat ... tttaatgcagCGCATTTTGGAAATCTGAGGATGACGCAGGAGGGATGGCTGGTCTAGGAGG
EST: gi|110694446|gb|EE071558.1|EE071558
EST:     GACAGCACAAACAG                         CGCATTTTGGAAATCTGAGGATGACGCAGGAGGGATGGCTGGTCTAGGAGG
genomic: GACAGCACAAACAGgcaagtcaat ... tttaatgcagCGCATTTTGGAAATCTGAGGATGACGCAGGAGGGATGGCTGGTCTAGGAGG
EST: gi|110688297|gb|EE066689.1|EE066689
EST:     GAGAAGAAAGTGCGATCAATTCTTGAAGGGCTATGTGACAGCACAAACAG                         CGCATTTTGGAAATCTGAGGATGACGCANGAGGGATGGCTGGTCTAGGAGG
genomic: GAGAAGAAAGTGCGATCAATTCTTGAAGGGCTATGTGACAGCACAAACAGgcaagtcaat ... tttaatgcagCGCATTTTGGAAATCTGAGGATGACGCAGGAGGGATGGCTGGTCTAGGAGG
EST: gi|351022393|gb|FQ445168.1|FQ445168
EST:     GAGAAGAAAGTGTGATCAATTCTTGAAGGGCTATGTGACAGCACAAACAG                         CGCATTTTGGAAATCTGAGGATGACGCAGGAGGGATGGCTGGTCTAGGAGG
genomic: GAGAAGAAAGTGCGATCAATTCTTGAAGGGCTATGTGACAGCACAAACAGgcaagtcaat ... tttaatgcagCGCATTTTGGAAATCTGAGGATGACGCAGGAGGGATGGCTGGTCTAGGAGG
EST: gi|34362548|gb|CF404133.1|CF404133
EST:     GAGAAGAAAGTGCAATCAATTCTTGAAGGGCTATGTGACAGCACAAACAG                         TGCATTTTGGAAATCTGAGGATNACGCAGGAGGGATGGCTGGTCTAGGAGG
genomic: GAGAAGAAAGTGCGATCAATTCTTGAAGGGCTATGTGACAGCACAAACAGgcaagtcaat ... tttaatgcagCGCATTTTGGAAATCTGAGGATGACGCAGGAGGGATGGCTGGTCTAGGAGG
EST: gi|351013608|gb|FQ429749.1|FQ429749
EST:     GAGAAGAAAGTGCGATCAATTCTTGAAGGGCTATGTGACAGCACAAACAG                         CGCATTTTGGAAATCTGAGGATGACGCAGGAGGGATGGCTGGTCTAGGAGG
genomic: GAGAAGAAAGTGCGATCAATTCTTGAAGGGCTATGTGACAGCACAAACAGgcaagtcaat ... tttaatgcagCGCATTTTGGAAATCTGAGGATGACGCAGGAGGGATGGCTGGTCTAGGAGG
EST: gi|110400248|gb|EC966803.1|EC966803
EST:     CAATTCTTGAAGGGCTATGTGACAGCACAAACAG                         TGCATTTTGGAAATCTGAGGATGACGCAGGAGGGATGGCTGGTCTAGGAGG
genomic: CAATTCTTGAAGGGCTATGTGACAGCACAAACAGgcaagtcaat ... tttaatgcagCGCATTTTGGAAATCTGAGGATGACGCAGGAGGGATGGCTGGTCTAGGAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaaagtactttttgagagctccagtttgatccttcctcaatgtttttaatgcagCGCATTTTGGAAATCTGAGGATGACGCAGGAGGGATGGCTGGTCTAGGAGGTGACGCTGATGCCCACCCATATGTCTGCTTCACAATTAATCTTGTTTGA
                                            ttttaat  putative branch site (score: 3)
                                         tgttttt  CT-rich tract
                                     tcaatgtttttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agaatatttctatacttgccatatattgattttttttatttatatgtaaagtactttttgagagctccagtttgatccttcctcaatgtttttaatgcagCGCATTTTGGAAATCTGAGGATGACGCAGGAGGGATGGCTGGTCTAGGAGGTGACGCTGATGCCCACCCATATGTCTGCTTCACAATTAATCTTGTTTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - cttgcca