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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gagtaacttttttcactagtggtgcaaggaatggggtactatatgttttaattgtgtatactggtgtttatgttatttggtcattatttttattaagcagAAGAGAGCTGGAAGCTGGAAACCTCTGCTAGGGCTGGTGGGAATGAAAACGCAGAGGTAACTTTGGTTTTTGAAGTTTGTGGTGGTTTATATCTTTGGGT

Basic information

species Vitis vinifera
transcript Vv10s0003g01240.t01
intron # 5
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|351053794|gb|FQ441560.1|FQ441560
EST:     TCTGAGGGACAACCTCACCTTGTGGACTACTGACATCCCAGGGGATGATG                         AAGAGAGCTGGAAGCTGGAAACCTCTGCTAGGGCTGGTGGGAATGAAAACG
genomic: TCTGAGGGACAACCTCACCTTGTGGACTACTGACATCCCAGGGGATGATGgtaaataaca ... tattaagcagAAGAGAGCTGGAAGCTGGAAACCTCTGCTAGGGCTGGTGGGAATGAAAACG
EST: gi|349812444|gb|FQ407063.1|FQ407063
EST:     TCTGAGGGACAACCTCACCTTGTGGACTACTGGCATCCCAGGGGATGATG                         AAAAGAGCTGGAAGCTG
genomic: TCTGAGGGACAACCTCACCTTGTGGACTACTGACATCCCAGGGGATGATGgtaaataaca ... tattaagcagAAGAGAGCTGGAAGCTG
EST: gi|349808236|gb|FQ403423.1|FQ403423
EST:     TCTGAGGGACAACCTCACCTTGTGGACTACTGACATCCCAGGGGATGATG                         AAGAGAGCTGGAAGCTGGAAACCTCTGCTAGGGCTGGTGGGAATGAAAACG
genomic: TCTGAGGGACAACCTCACCTTGTGGACTACTGACATCCCAGGGGATGATGgtaaataaca ... tattaagcagAAGAGAGCTGGAAGCTGGAAACCTCTGCTAGGGCTGGTGGGAATGAAAACG
EST: gi|351024890|gb|FQ433307.1|FQ433307
EST:     TCTGAGGGACAACCTCACCTTGTGGACTACTGACATCCCAGGGGATGATG                         AAGAGAGCTGGAAGCTGGAAACCTCTGCT
genomic: TCTGAGGGACAACCTCACCTTGTGGACTACTGACATCCCAGGGGATGATGgtaaataaca ... tattaagcagAAGAGAGCTGGAAGCTGGAAACCTCTGCT
EST: gi|349828886|gb|FQ419219.1|FQ419219
EST:     TCTGAGGGACAACCTCACCTTGTGGACTACTGGCATCCCAGGGGATGATG                         AANAGAGCTGGAAGC
genomic: TCTGAGGGACAACCTCACCTTGTGGACTACTGACATCCCAGGGGATGATGgtaaataaca ... tattaagcagAAGAGAGCTGGAAGC
EST: gi|110686512|gb|EE064232.1|EE064232
EST:     CTGNAGGGACA-CCTCACCTTGTGGACTACAGACATCCCAGGGGATGATG                         AAAAGAGCTGGGAGCTGGAAACCTCTGCTAGGGCTGGTGGGAATGAAAAC
genomic: CTG-AGGGACAACCTCACCTTGTGGACTACTGACATCCCAGGGGATGATGgtaaataaca ... tattaagcagAAGAGAGCTGGAAGCTGGAAACCTCTGCTAGGGCTGGTGGGAATGAAAAC
EST: gi|349811098|gb|FQ406086.1|FQ406086
EST:     TCTGAGGGACAACCTCACCTTGTGGACTACTGACATCCCCGGGGACGACG                         AAGAGAGCTGGAAGCTGGAAACCTCTGC
genomic: TCTGAGGGACAACCTCACCTTGTGGACTACTGACATCCCAGGGGATGATGgtaaataaca ... tattaagcagAAGAGAGCTGGAAGCTGGAAACCTCTGC
EST: gi|30299169|gb|CB975963.1|CB975963
EST:     TCTGAGGGATAACCTCACCTTGTGGACTACTGACATCCCAGGGGATGATG                         AAGAGAGCTGGAAGCTGGAAACCTCTGCTAGGGCTGGTGGGAATGAAAACG
genomic: TCTGAGGGACAACCTCACCTTGTGGACTACTGACATCCCAGGGGATGATGgtaaataaca ... tattaagcagAAGAGAGCTGGAAGCTGGAAACCTCTGCTAGGGCTGGTGGGAATGAAAACG
EST: gi|351036840|gb|FQ459362.1|FQ459362
EST:     TCTGAGGGACAACCTCACCTTGTGGACTACTGACATCCCAAGGGATGATG                         AAGAGAGCTGGAAGCTGGGAAAC-TCTGCTAGGGCTGGTGGGAATGGAAAC
genomic: TCTGAGGGACAACCTCACCTTGTGGACTACTGACATCCCAGGGGATGATGgtaaataaca ... tattaagcagAAGAGAGCTGGAAGCTGG-AAACCTCTGCTAGGGCTGGTGGGAATGAAAAC
EST: gi|349823307|gb|FQ402506.1|FQ402506
EST:     TCTGAGGGACAACCTCACCTTGTGGACTACTGACATCCCANGGGACGATG                         AAGAGAGCTGGAAGCTGGAAACCTCTGCTAG
genomic: TCTGAGGGACAACCTCACCTTGTGGACTACTGACATCCCAGGGGATGATGgtaaataaca ... tattaagcagAAGAGAGCTGGAAGCTGGAAACCTCTGCTAG
EST: gi|349824616|gb|FQ413283.1|FQ413283
EST:     TCTGAGGGGCAACCTCACCTTGTGGACTACTGACATCCCAGGGGATGATG                         AAGAGAGCTGGAAGCTGGAAACCTCTGCTAAGGCTGGTGGGAATGAAAACG
genomic: TCTGAGGGACAACCTCACCTTGTGGACTACTGACATCCCAGGGGATGATGgtaaataaca ... tattaagcagAAGAGAGCTGGAAGCTGGAAACCTCTGCTAGGGCTGGTGGGAATGAAAACG
EST: gi|351030304|gb|FQ432242.1|FQ432242
EST:     TCTGAGGGACAACCTCACCTTGTGGACTACTGACATCCCAGGGGATGATG                         AAGAGAGCTGGAAGCTGGGAACCTCTGCTAGGGCTGGGTGGGAATGAAAAC
genomic: TCTGAGGGACAACCTCACCTTGTGGACTACTGACATCCCAGGGGATGATGgtaaataaca ... tattaagcagAAGAGAGCTGGAAGCTGGAAACCTCTGCTAGGGCTGG-TGGGAATGAAAAC
EST: gi|349826263|gb|FQ416068.1|FQ416068
EST:     TCTGAGGGACAACCTCACCTTGTGGACTACTGACATCCCAGGGGATGATG                         AAGAGAGCTGGAAGCTGGAAACCTCTGCTAGGGCTGGTGGG
genomic: TCTGAGGGACAACCTCACCTTGTGGACTACTGACATCCCAGGGGATGATGgtaaataaca ... tattaagcagAAGAGAGCTGGAAGCTGGAAACCTCTGCTAGGGCTGGTGGG
EST: gi|351029922|gb|FQ427762.1|FQ427762
EST:     TCTGAGGGACAACCTCACCTTGTGGACTACTGGCATCCCAGGGGATGATG                         AAGAGAGCTGGAAGCTGGAAACCTCTGCTAGGGC
genomic: TCTGAGGGACAACCTCACCTTGTGGACTACTGACATCCCAGGGGATGATGgtaaataaca ... tattaagcagAAGAGAGCTGGAAGCTGGAAACCTCTGCTAGGGC
EST: gi|351018819|gb|FQ425721.1|FQ425721
EST:     TCTGAGGGACAACCTCACCTTGTGGACTACTGACATCCCAGGGGATGATG                         AAGAGAGCTGGGAAGCTGGAA-CCTCTGC
genomic: TCTGAGGGACAACCTCACCTTGTGGACTACTGACATCCCAGGGGATGATGgtaaataaca ... tattaagcagAAGAGAGCTGG-AAGCTGGAAACCTCTGC
EST: gi|110685470|gb|EE062216.1|EE062216
EST:     TCTGAGGGACAACCTCACCTTGTGGACTACAGACATCCCAGGGGATGATG                         AAGAGAGCTGGAAGCTGGAAACC
genomic: TCTGAGGGACAACCTCACCTTGTGGACTACTGACATCCCAGGGGATGATGgtaaataaca ... tattaagcagAAGAGAGCTGGAAGCTGGAAACC
EST: gi|349827590|gb|FQ422458.1|FQ422458
EST:     TCTGAGGGACAACCTCACCTTGTGGACTACTGACATCCCGGGGGATGATG                         AAGAGAGCTGGAAGCTGGAAACCTCTGCTAGGGCTGGTGGGAATGAAA
genomic: TCTGAGGGACAACCTCACCTTGTGGACTACTGACATCCCAGGGGATGATGgtaaataaca ... tattaagcagAAGAGAGCTGGAAGCTGGAAACCTCTGCTAGGGCTGGTGGGAATGAAA
EST: gi|351016120|gb|FQ432075.1|FQ432075
EST:     TCTGAGGGACAACCTCACCTTGTGGACTACTGGCATCCCAGGGGATGATG                         AAGAGAGCTGGAAGCTGGAAACCTCTGCTAGGGCTGG
genomic: TCTGAGGGACAACCTCACCTTGTGGACTACTGACATCCCAGGGGATGATGgtaaataaca ... tattaagcagAAGAGAGCTGGAAGCTGGAAACCTCTGCTAGGGCTGG
EST: gi|349827588|gb|FQ422456.1|FQ422456
EST:     CTGAGGGGACA-CCTCACCTTGTGGACTACTGACATCCCAGGGGATGATG                         GAGAGAGCTGGAAGCTGG
genomic: CTGAGGG-ACAACCTCACCTTGTGGACTACTGACATCCCAGGGGATGATGgtaaataaca ... tattaagcagAAGAGAGCTGGAAGCTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttaattgtgtatactggtgtttatgttatttggtcattatttttattaagcagAAGAGAGCTGGAAGCTGGAAACCTCTGCTAGGGCTGGTGGGAATGAAAACGCAGAGGTAACTTTGGTTTTTGAAGTTTGTGGTGGTTTATATCTTTGGGT
 ttttaat  putative branch site (score: 3)
                                      ttattttt  putative PPT
                     tttatgttatttggtc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gagtaacttttttcactagtggtgcaaggaatggggtactatatgttttaattgtgtatactggtgtttatgttatttggtcattatttttattaagcagAAGAGAGCTGGAAGCTGGAAACCTCTGCTAGGGCTGGTGGGAATGAAAACGCAGAGGTAACTTTGGTTTTTGAAGTTTGTGGTGGTTTATATCTTTGGGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - -gcaagga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctggtgt