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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttttgggtgggtgtggtggttggttgtggtttctagatctctctacattagccttttttcatggatatctctctcagtttatccttaagtacattatagGAGTCCCACAGAAGATACAAAACCTCGTAGAGTTGCTGCACTTCCATCCTACAATTTCAGCTTTAGGTGTGATGAACGAGCTGAGAAAAGAAGAGAG

Basic information

species Vitis vinifera
transcript Vv04s0008g05480.t01
intron # 5
splice site 3'
intron type U12 (go to U12 genes for details)

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|110711956|gb|EE089029.1|EE089029
EST:     CCTGTGAAACTGGGAGCCCCTACTGTGTCTGATGTGAACACAAAATCTCC                         GAGTCCCACAGAAGATACAAAACCTCGTAGAGTTGCTGCACTTCCATCCTA
genomic: CCTGTGAAACTGGGAGCCCCTACTGTGTCTGATGTGAACACAAAATCTCCgtatcctcat ... tacattatagGAGTCCCACAGAAGATACAAAACCTCGTAGAGTTGCTGCACTTCCATCCTA
EST: gi|110732118|gb|EE107126.1|EE107126
EST:     GAACACAAAATCTCC                         GAGTCCCACAGAAGATACAAAACCTCGTAGAGTTGCTGCACTTCCATCCTA
genomic: GAACACAAAATCTCCgtatcctcat ... tacattatagGAGTCCCACAGAAGATACAAAACCTCGTAGAGTTGCTGCACTTCCATCCTA
EST: gi|110713754|gb|EE089952.1|EE089952
EST:     CCTGTGAAACTGGGAGCCCCTACTGTGTCTGATGTGAACACAAAATCTCC                         GAGTCCCACAGAAGATACAAAACCTCGTAGAGTTGCTGCACTTCCATCCTA
genomic: CCTGTGAAACTGGGAGCCCCTACTGTGTCTGATGTGAACACAAAATCTCCgtatcctcat ... tacattatagGAGTCCCACAGAAGATACAAAACCTCGTAGAGTTGCTGCACTTCCATCCTA
EST: gi|294964234|gb|GW838037.1|GW838037
EST:     CCTGTGAAACTGGGAGCCCCTACTGTGTCTGATGTGAACACAAAATCTCC                         GAGTCCCACAGAAGATACAAAACCTCGTAGAGTTGCTGCACTTCCATCCTA
genomic: CCTGTGAAACTGGGAGCCCCTACTGTGTCTGATGTGAACACAAAATCTCCgtatcctcat ... tacattatagGAGTCCCACAGAAGATACAAAACCTCGTAGAGTTGCTGCACTTCCATCCTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acattagccttttttcatggatatctctctcagtttatccttaagtacattatagGAGTCCCACAGAAGATACAAAACCTCGTAGAGTTGCTGCACTTCCATCCTACAATTTCAGCTTTAGGTGTGATGAACGAGCTGAGAAAAGAAGAGAG
                                    atccttaag  putative branch site 
                                        ttaagtacattata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttttgggtgggtgtggtggttggttgtggtttctagatctctctacattagccttttttcatggatatctctctcagtttatccttaagtacattatagGAGTCCCACAGAAGATACAAAACCTCGTAGAGTTGCTGCACTTCCATCCTACAATTTCAGCTTTAGGTGTGATGAACGAGCTGAGAAAAGAAGAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - -gggtggg
- - - - - - -gtggtgg
- - - - - - - - - - - ggttgtg
- - - - - - - - - - - - - - - - - - - - -ctctaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctctctc