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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttcaaatgccttctgctcagaaagcaccatctctatgcacaatacatccataaattagcacaaccttgtacttgatacgagtggcaatttcttttgcagCAACTGAAATCAGCATGAGAGGAATACGATCATGGACATGAAGGGCATCTTGGCTGTAGATTTGAATTATATCGCCTTCCAAAGAAAGAAATGACAAATC

Basic information

species Vitis vinifera
transcript Vv10s0003g00300.t01
intron # 11
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|110414740|gb|EC980591.1|EC980591
EST:     TGGCAATGTACTCTTTCATAAAGGCCAAGATGGAAGAGGAGAAACGA                         CAACTGAAATCAGCATGAGAGGAATACGATCATGGACATGAAGGGCATCTT
genomic: TGGCAATGTACTCTTTCATAAAGGCCAAGATGGAAGAGGAGAAACGAgtgagttttg ... tcttttgcagCAACTGAAATCAGCATGAGAGGAATACGATCATGGACATGAAGGGCATCTT
EST: gi|110705533|gb|EE082491.1|EE082491
EST:     GAGTGGCAATGTACTCTTTCATAAAGGCCAAGATGGAAGAGGAGAAACGA                         CAACTGAAATCAGCATGAGAGGAATACGATCATGGACATGAAGGGCATCTT
genomic: GAGTGGCAATGTACTCTTTCATAAAGGCCAAGATGGAAGAGGAGAAACGAgtgagttttg ... tcttttgcagCAACTGAAATCAGCATGAGAGGAATACGATCATGGACATGAAGGGCATCTT
EST: gi|46910969|gb|CN546344.1|CN546344
EST:     GAGTGGCAATGTACTCTTTCATAAAGGCCAAGATGGAAGAGGAGAAACGA                         CAACTGAAATCAGCATGAGAGGAATACGATCATGGACATGAAGGGCATCTT
genomic: GAGTGGCAATGTACTCTTTCATAAAGGCCAAGATGGAAGAGGAGAAACGAgtgagttttg ... tcttttgcagCAACTGAAATCAGCATGAGAGGAATACGATCATGGACATGAAGGGCATCTT
EST: gi|28965272|gb|CB344305.1|CB344305
EST:     GAGTGGCAATGTACTCTTTCATAAAGGCCAAGATGGAAGAGGAGAAACGA                         CAACTGAAATCAGCATGAGAGGAATTCGATCATGGACATGAAGGGCATCTT
genomic: GAGTGGCAATGTACTCTTTCATAAAGGCCAAGATGGAAGAGGAGAAACGAgtgagttttg ... tcttttgcagCAACTGAAATCAGCATGAGAGGAATACGATCATGGACATGAAGGGCATCTT
EST: gi|110388308|gb|EC953043.1|EC953043
EST:     GAGTGGCAATGTACTCTTTCATAAAGGCCAAGATGGAAGAGGAGAAACGA                         CAACTGAAATCAGCATGAGAGGAATACGATCATGGACATGAAGGGCATCTT
genomic: GAGTGGCAATGTACTCTTTCATAAAGGCCAAGATGGAAGAGGAGAAACGAgtgagttttg ... tcttttgcagCAACTGAAATCAGCATGAGAGGAATACGATCATGGACATGAAGGGCATCTT
EST: gi|110376459|gb|EC941524.1|EC941524
EST:     GAGTGGCAATGTACTCTTTCATAAAGGCCAAGATGGAAGAGGAGAAACGA                         CAACTGAAATCAGCATGAGAGGAATACGATCATGGACATGAAGGGCATCTT
genomic: GAGTGGCAATGTACTCTTTCATAAAGGCCAAGATGGAAGAGGAGAAACGAgtgagttttg ... tcttttgcagCAACTGAAATCAGCATGAGAGGAATACGATCATGGACATGAAGGGCATCTT
EST: gi|349829387|gb|FQ419919.1|FQ419919
EST:     GAGTGGCAATGTACTCTTTCATAAAGGCCAAGATGGAAGAGGAGAAACGA                         CAACTGAAATCAGCATGAGAGGAATACGATCATGGACATGAAGGGCATCTT
genomic: GAGTGGCAATGTACTCTTTCATAAAGGCCAAGATGGAAGAGGAGAAACGAgtgagttttg ... tcttttgcagCAACTGAAATCAGCATGAGAGGAATACGATCATGGACATGAAGGGCATCTT
EST: gi|351031379|gb|FQ445404.1|FQ445404
EST:     GAGTGGCAATGTACTCTTTCATAAAGGCCAAGATGGAAGAGGAGAAACGA                         CAACTGAAATCAGCATGAGAGGAATACGATCATGGACATGAAGGGCATCTT
genomic: GAGTGGCAATGTACTCTTTCATAAAGGCCAAGATGGAAGAGGAGAAACGAgtgagttttg ... tcttttgcagCAACTGAAATCAGCATGAGAGGAATACGATCATGGACATGAAGGGCATCTT
EST: gi|110363008|gb|EC926573.1|EC926573
EST:     GAGTGGCAATGTACTCTTTCATAAAGGCCAAGATGGAAGAGGAGAAACGA                         CAACTGAAATCAGCATGAGAGGAATACGATCATGGACATGAAGGGCATCTT
genomic: GAGTGGCAATGTACTCTTTCATAAAGGCCAAGATGGAAGAGGAGAAACGAgtgagttttg ... tcttttgcagCAACTGAAATCAGCATGAGAGGAATACGATCATGGACATGAAGGGCATCTT
EST: gi|22013243|gb|BQ798277.1|BQ798277
EST:     GAGTGGCAATGTACTCTTTCATAAAGGCCAAGATGGAAGAGGAGAAACGA                         CAACTGAAATCAGCATGAGAGGAATACGATCATGGACATGAAGGGCATCTT
genomic: GAGTGGCAATGTACTCTTTCATAAAGGCCAAGATGGAAGAGGAGAAACGAgtgagttttg ... tcttttgcagCAACTGAAATCAGCATGAGAGGAATACGATCATGGACATGAAGGGCATCTT
EST: gi|349813488|gb|FQ413722.1|FQ413722
EST:     GGGTGGCAATGTACTCTTTCATAAAGGCCAAGATGGAAGAGGAGAAACGA                         CAACTGAAATCAGCATGAGAGGAATACGATCATGGACATGAAGGGCATCTT
genomic: GAGTGGCAATGTACTCTTTCATAAAGGCCAAGATGGAAGAGGAGAAACGAgtgagttttg ... tcttttgcagCAACTGAAATCAGCATGAGAGGAATACGATCATGGACATGAAGGGCATCTT
EST: gi|110361951|gb|EC925457.1|EC925457
EST:     GAGTGGCAATGTACTCTTTCATAAAGGCCAAGATGGAAGAGGAGAAACGA                         CAACTGAAATCAGCATGAGAGGAATACGATCATGGACATGAAGGGCATCTT
genomic: GAGTGGCAATGTACTCTTTCATAAAGGCCAAGATGGAAGAGGAGAAACGAgtgagttttg ... tcttttgcagCAACTGAAATCAGCATGAGAGGAATACGATCATGGACATGAAGGGCATCTT
EST: gi|71883070|gb|DT032125.1|DT032125
EST:     GAGTGGCAATGTACTCTTTCATAAAGGCCAAGATGGAAGAGGAGAAACGA                         CAACTGAAATCAGCATGAGAGGAATACGATCATGGACATGAAGGGCATCTT
genomic: GAGTGGCAATGTACTCTTTCATAAAGGCCAAGATGGAAGAGGAGAAACGAgtgagttttg ... tcttttgcagCAACTGAAATCAGCATGAGAGGAATACGATCATGGACATGAAGGGCATCTT
EST: gi|28965323|gb|CB344356.1|CB344356
EST:     GAGTGGCAATGTACTCTTTCATAAAGGCCAAGATGGAAGAGGAGAAACGA                         CAACTGAAATCAGCATGAGAGGAATACGATCATGGACATGAAGGGCATCTT
genomic: GAGTGGCAATGTACTCTTTCATAAAGGCCAAGATGGAAGAGGAGAAACGAgtgagttttg ... tcttttgcagCAACTGAAATCAGCATGAGAGGAATACGATCATGGACATGAAGGGCATCTT
EST: gi|32244911|gb|CD710730.1|CD710730
EST:     GAGTGGCAATGTACTCTTTCATAAAGGCCAAGATGGAAGAGGAGAAACGA                         CAACTGAAATCAGCATGAGAGGAATACGATCATGGACATGAAGGGCATCTT
genomic: GAGTGGCAATGTACTCTTTCATAAAGGCCAAGATGGAAGAGGAGAAACGAgtgagttttg ... tcttttgcagCAACTGAAATCAGCATGAGAGGAATACGATCATGGACATGAAGGGCATCTT
EST: gi|30252957|gb|CB970508.1|CB970508
EST:     GAGTGGCAATGTACTCTTTCATAAAGGCCAAGATGGAAGAGGAGAAACGA                         CAACTGAAATCAGCATGAGAGGAATACGATCATGGACATGAAGGGCATCTT
genomic: GAGTGGCAATGTACTCTTTCATAAAGGCCAAGATGGAAGAGGAGAAACGAgtgagttttg ... tcttttgcagCAACTGAAATCAGCATGAGAGGAATACGATCATGGACATGAAGGGCATCTT
EST: gi|110426800|gb|EC993222.1|EC993222
EST:     GAGTGGCAATGTACTCTTTCATAAAGGCCAAGATGGAAGAGGAGAAACGA                         CAACTGAAATCAGCATGAGAGGAATACGATCATGGACATGAAGGGCATCTT
genomic: GAGTGGCAATGTACTCTTTCATAAAGGCCAAGATGGAAGAGGAGAAACGAgtgagttttg ... tcttttgcagCAACTGAAATCAGCATGAGAGGAATACGATCATGGACATGAAGGGCATCTT
EST: gi|30131378|gb|CB916717.1|CB916717
EST:     GAGTGGCAATGTACTCTTTCATAAAGGCCAAGATGGAAGAGGAGAAACGA                         CAACTGAAATCAGCATGAGAGGAATACGATCATGGACATGAAGGGCATCTT
genomic: GAGTGGCAATGTACTCTTTCATAAAGGCCAAGATGGAAGAGGAGAAACGAgtgagttttg ... tcttttgcagCAACTGAAATCAGCATGAGAGGAATACGATCATGGACATGAAGGGCATCTT
EST: gi|34542626|gb|CF510858.1|CF510858
EST:     AGTGGCAATGTACTCTTTCATAAAGGG-ATCGATGGAAGAGGAGAAACGA                         CAACTGAAATCAGCATGAGATCNATACGATCATGGACATGAAGGGC
genomic: AGTGGCAATGTACTCTTTCATAAAGGCCAA-GATGGAAGAGGAGAAACGAgtgagttttg ... tcttttgcagCAACTGAAATCAGCATGAGAGGAATACGATCATGGACATGAAGGGC
EST: gi|33401641|gb|CF207268.1|CF207268
EST:     GAGTGGCAATGTACTCTTTCATAAAGGCCAAGATGGAAGAGGAGAAACGA                         CAACTGAAATC-GATATGAGAGGAATACGATCATGGACATGAAGGGCATCT
genomic: GAGTGGCAATGTACTCTTTCATAAAGGCCAAGATGGAAGAGGAGAAACGAgtgagttttg ... tcttttgcagCAACTGAAATCAGC-ATGAGAGGAATACGATCATGGACATGAAGGGCATCT
EST: gi|110389432|gb|EC954269.1|EC954269
EST:     GAGTGGCAATGTACTCTTTCATAAAGGCCAAGATGGAAGAGGAGAAACGA                         CAACTGAAATCAGCATGAGAGGAATACGATCATGGACATGAAGGGCATCTT
genomic: GAGTGGCAATGTACTCTTTCATAAAGGCCAAGATGGAAGAGGAGAAACGAgtgagttttg ... tcttttgcagCAACTGAAATCAGCATGAGAGGAATACGATCATGGACATGAAGGGCATCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catccataaattagcacaaccttgtacttgatacgagtggcaatttcttttgcagCAACTGAAATCAGCATGAGAGGAATACGATCATGGACATGAAGGGCATCTTGGCTGTAGATTTGAATTATATCGCCTTCCAAAGAAAGAAATGACAAATC
                         acttgat  putative branch site (score: 5)
                                           tttcttttgc  putative PPT
                                         aatttctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttcaaatgccttctgctcagaaagcaccatctctatgcacaatacatccataaattagcacaaccttgtacttgatacgagtggcaatttcttttgcagCAACTGAAATCAGCATGAGAGGAATACGATCATGGACATGAAGGGCATCTTGGCTGTAGATTTGAATTATATCGCCTTCCAAAGAAAGAAATGACAAATC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - aaatgcc
- - - - - -ttctgct
- - - - - - - - - - gaaagca
- - - - - - - - - - - - - -ccatctc
- - - - - - - - - - - - - - - - - tatgcac
- - - - - - - - - - - - - - - - - - - - - - acatcca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cacaacc