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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtaagagttgaatcatttcagttgtgaagtcatctataaccctaaacttacaacttatctgacaagttcttttgattggaatttggcagTAAAATTGATAGGAAAATTGCAAGATGGAACAGTGTTTCTGAAGAAGGGTCATGGTGAAGGAGAGGATCTCTTCGAGTTCAAGACTGATGATG

Basic information

species Vitis vinifera
transcript Vv00s0769g00010.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv00s0769g00010.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT3G25230.1 (Arabidopsis thaliana), 3'ss of exon 6
gttagtaagagttgaatcatttcagttgtgaagtcatctataacc---ctaaacttacaacttatctgacaagttcttttgattggaatttggcagTAAAATTGATAGGAAAATTGCAAGATGGAACAGTGTTTCTGAAGAAGGGTCATGGTGAAGGAGAGGATCTCTTCGAGTTCAAGACTGATGATG
          |||    |||||| | | | |   ||   ||  |    | | |  ||    ||   |     |||   ||  ||    | ||||||| ||||||||||| ||| | |||||||| || || ||| ||||||| |||||||||||    ||||| |  || |||||||| || ||||| |
----------gtttg--catttcggattttagtacactcatgtcttcaccagatataacggtttcttacggggtttcatttgtttctttctggcagTGAAATTGATAGGGAAACTTCAAGATGGTACTGTATTTTTGAAGAAAGGTCATGGTGAGAATGAGGAACCGTTTGAGTTCAAAACAGATGAAG
















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|161709131|gb|FC058397.1|FC058397
EST:     AAAGGAAGGAGAGGGATACGAACGTCCAAATGAAGGAGCTGTTGTCAAAT                         TAAAATTGATTGGAAAATTGCAAGGTGGAACAGTGTTTCTGAAGAAGGGTC
genomic: AAAGGAAGGAGAGGGATACGAACGTCCAAATGAAGGAGCTGTTGTCAAATgttagtaaga ... aatttggcagTAAAATTGATAGGAAAATTGCAAGATGGAACAGTGTTTCTGAAGAAGGGTC
EST: gi|33403350|gb|CF208977.1|CF208977
EST:     GTCCAAATGAAGGAGCTGTTGTCAAAT                         TAAAATTGATTGGAAAATTGCAAGGTGGAACAGTGTTTCTGAAGAAGGGTC
genomic: GTCCAAATGAAGGAGCTGTTGTCAAATgttagtaaga ... aatttggcagTAAAATTGATAGGAAAATTGCAAGATGGAACAGTGTTTCTGAAGAAGGGTC
EST: gi|30253340|gb|CB970891.1|CB970891
EST:     AAAGGAAGGAGAGGGATACGAACGTCCAAATGAAGGAGCTGTTGTCAAAT                         TAAAATTGATTGGAAAATTGCAAGGTGGAACAGTGTTTCTGAAGAAGGGTC
genomic: AAAGGAAGGAGAGGGATACGAACGTCCAAATGAAGGAGCTGTTGTCAAATgttagtaaga ... aatttggcagTAAAATTGATAGGAAAATTGCAAGATGGAACAGTGTTTCTGAAGAAGGGTC
EST: gi|77587533|gb|DV222932.1|DV222932
EST:     AAAGGAAGGAGAGGGATACGAACGTCCAAATGAAGGAGCTGTTGTCAAAT                         TAAAATTGATTGGAAAATTGCAAGGTGGAACAGTGTTTCTGAAGAAGGGTC
genomic: AAAGGAAGGAGAGGGATACGAACGTCCAAATGAAGGAGCTGTTGTCAAATgttagtaaga ... aatttggcagTAAAATTGATAGGAAAATTGCAAGATGGAACAGTGTTTCTGAAGAAGGGTC
EST: gi|29783511|gb|CB349715.2|CB349715
EST:     AAAGGAAGGAGAGGGATACGAACGTCCAAATGAAGGAGCTGTTGTCAAAT                         TAAAATTGATAGGAAAATTGCAAGATGGAACAGTGTTTCTGAAGAAGGGTC
genomic: AAAGGAAGGAGAGGGATACGAACGTCCAAATGAAGGAGCTGTTGTCAAATgttagtaaga ... aatttggcagTAAAATTGATAGGAAAATTGCAAGATGGAACAGTGTTTCTGAAGAAGGGTC
EST: gi|110398522|gb|EC964942.1|EC964942
EST:     AAAGGAAGGAGAGGGATACGAACGTCCAAATGAAGGAGCTGTTGTCAAAT                         TAAAATTGATAGGAAAATTGCAAGATGGAACAGTGTTTCTGAAGAAGGGTC
genomic: AAAGGAAGGAGAGGGATACGAACGTCCAAATGAAGGAGCTGTTGTCAAATgttagtaaga ... aatttggcagTAAAATTGATAGGAAAATTGCAAGATGGAACAGTGTTTCTGAAGAAGGGTC
EST: gi|33403274|gb|CF208901.1|CF208901
EST:     AAAGGAAGGAGAGGGATACGAACGTCCAAATGAAGGAGCTGTTGTCAAAT                         TAAAATTGATTGGAAAATTGCAAGGTGGAACAGTGTTTCTGAAGAAGGGTC
genomic: AAAGGAAGGAGAGGGATACGAACGTCCAAATGAAGGAGCTGTTGTCAAATgttagtaaga ... aatttggcagTAAAATTGATAGGAAAATTGCAAGATGGAACAGTGTTTCTGAAGAAGGGTC
EST: gi|110690423|gb|EE067508.1|EE067508
EST:     NAAGGAAGGAGAGGGATACGAACGTCCAAATGAANGAGCTGTTGTCAAAT                         TAAAATTGATTGGAAAATTGCAAGGTGGAACAGTGTTTCTGAAGAAAGGTC
genomic: AAAGGAAGGAGAGGGATACGAACGTCCAAATGAAGGAGCTGTTGTCAAATgttagtaaga ... aatttggcagTAAAATTGATAGGAAAATTGCAAGATGGAACAGTGTTTCTGAAGAAGGGTC
EST: gi|110400903|gb|EC967488.1|EC967488
EST:     CGAACGTCCAAATGAAGGAGCTGTTGTCAAAT                         TAAAATTGATAGGAAAATTGCAAGATGGAACAGTGTTTCTGAAGAAGGGTC
genomic: CGAACGTCCAAATGAAGGAGCTGTTGTCAAATgttagtaaga ... aatttggcagTAAAATTGATAGGAAAATTGCAAGATGGAACAGTGTTTCTGAAGAAGGGTC
EST: gi|28969463|gb|CB348496.1|CB348496
EST:     AAAGGAAGGAGAGGGATACGAACGTCCAAATGAAGGAGCTGTTGTCAAAT                         TAAAATTGATAGGAAAATTGCAAGATGGAACAGTGTTTCTGAAGAAGGGTC
genomic: AAAGGAAGGAGAGGGATACGAACGTCCAAATGAAGGAGCTGTTGTCAAATgttagtaaga ... aatttggcagTAAAATTGATAGGAAAATTGCAAGATGGAACAGTGTTTCTGAAGAAGGGTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tataaccctaaacttacaacttatctgacaagttcttttgattggaatttggcagTAAAATTGATAGGAAAATTGCAAGATGGAACAGTGTTTCTGAAGAAGGGTCATGGTGAAGGAGAGGATCTCTTCGAGTTCAAGACTGATGATG
        taaactta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagtaagagttgaatcatttcagttgtgaagtcatctataaccctaaacttacaacttatctgacaagttcttttgattggaatttggcagTAAAATTGATAGGAAAATTGCAAGATGGAACAGTGTTTCTGAAGAAGGGTCATGGTGAAGGAGAGGATCTCTTCGAGTTCAAGACTGATGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT