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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtcttggcatatgtgaatagaaaaatatgaaatttaagattgcaattgtgtaagggtttggattttaggtatgaaaattgtgatttgaattggtttgcagAGTAAAGCAGATGCCTTTGAATATGCTGACCAAGTTTTGGAGAGGTGGTATCCCACAATTGAAGAAGGCAGCAATAAGGGTATTGTTGTGCTTGTCACCA

Basic information

species Vitis vinifera
transcript Vv14s0128g00050.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0128g00050.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA20G37520.1 (Glycine max), 3'ss of exon 1
-----gtcttggcatatgtgaatagaaaaatatgaaatttaagattgcaattgtgtaagggtttggattttaggtatgaaaattgtgatttgaattggtttgcagAGTAAAGCAGATGCCTTTGAATATGCTGACCAAGTTTTGGAGAGGTGGTATCCCACAATTGAAGAAGGCAGCAATAAGGGTATTGTTGTGCTTGTCACCA
         || |||      | ||  ||  ||||||      |    |||  |  | |    |  ||   | || |  | | | | || ||  |   |  |||||| ||||| ||||| ||||| |||||||||||||| |||||| | ||||| ||  |  | |||||||| | ||| ||||||||||| ||||||||||| |
catgttctctgccatgcaactaaagtgaagcatgaaaggaccaaacaaaatgctaaatg---ctaaatgaaatgttttgatagtataatgtggttgaat--gcagAGCAAAGCTGATGCATTTGAGTATGCTGACCAAGTCTTGGAGCGTTGGTACCCTTCTGTAGAAGAAGGGAACAAGAAGGGTATTGTGGTGCTTGTCACGA

upper sequence: Vv14s0128g00050.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA10G29810.1 (Glycine max), 3'ss of exon 1
gtcttggcatatgtgaatagaaaaatatgaaatttaagattgcaattgtgtaagggtttgg-attttaggtatgaaaattgtgatttgaattggtttgcagAGTAAAGCAGATGCCTTTGAATATGCTGACCAAGTTTTGGAGAGGTGGTATCCCACAATTGAAGAAGGCAGCAATAAGGGTATTGTTGTGCTTGTCACCA
  |||| |   | |   |   |    |  ||| |   |  || ||      ||     ||  |  | |  | |    ||||||    |   | | |||||||| ||||| ||||| ||||| |||||||||||||| |||||| | ||||| ||  |  | |||||||| | ||| ||||| ||||| ||||||||||| |
-acttgtccattttctctgccatggaactaaaatggtgcatgaaaggaccaaacaaaatgctaaatgaaatgttttgattgtgtaacgtggttggttgcagAGCAAAGCTGATGCATTTGAGTATGCTGACCAAGTCTTGGAGCGTTGGTACCCTTCTGTAGAAGAAGGGAACAACAAGGGCATTGTGGTGCTTGTCACGA

upper sequence: Vv14s0128g00050.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT1G54780.1 (Arabidopsis thaliana), 3'ss of exon 1
gtcttggcatatgtgaatagaaaaatatgaaatttaagattgcaattgtgtaagggtttggattttaggtatgaaaattgtgatttgaattggtttgcagAGTAAAGCAGATGCCTTTGAATATGCTGACCAAGTTTTGGAGAGGTGGTATCCCACAATTGAAGAAGGCAGCAATAAGGGTATTGTTGTGCTTGTCACCA
    ||   | | ||  |       |||||||||   |||||   |||| |||      |||  || | |  | ||   ||    | || |  || |||||||||||||||||| ||||| ||||| ||||| |||||||| |  ||||||||  | ||||||||||| | ||||||||||||||||||  |  | || |
---gtgagttttttgttttct----tatgaaatt---gattgtttttgtttaa----ccggaaatt-gatccggaaccggtttggtaaaat--ttggcagAGTAAAGCAGATGCGTTTGAGTATGCAGACCAGGTTTTGGAAAAATGGTATCCTTCTATTGAAGAAGGTAACAATAAGGGTATTGTTGTTTTGATAACAA

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|351040205|gb|FQ425291.1|FQ425291
EST:     AGTCCAGGAAGAACTTGCGCATCAATTTCATCACTGTTCGGAAGCTCACT                         AGTAAAGCAGATGCCTTTGAATATGCTGACCAAGTTTTGGAGAGGTGGTAT
genomic: AGTCCAGGAAGAACTTGCGCATCAATTTCATCACTGTTCGGAAGCTCACTgtaagtttag ... tggtttgcagAGTAAAGCAGATGCCTTTGAATATGCTGACCAAGTTTTGGAGAGGTGGTAT
EST: gi|351040023|gb|FQ425109.1|FQ425109
EST:     AGTCCAGGAAGAACTTGCGCATCAATTTCATCACTGTTCGGAAGCTCACT                         AGTAAAGCAGATGCCTTTGAATATGCTGACCAAGTTTTGGAGAGGTGGTAT
genomic: AGTCCAGGAAGAACTTGCGCATCAATTTCATCACTGTTCGGAAGCTCACTgtaagtttag ... tggtttgcagAGTAAAGCAGATGCCTTTGAATATGCTGACCAAGTTTTGGAGAGGTGGTAT
EST: gi|349808323|gb|FQ405467.1|FQ405467
EST:     AGTCCAGGAAGAACTTGCGCATCAATTTCATCACTGTTCGGAAGCTCACT                         AGTAAAGCAGATGCCTTTGAATATGCTGACCAAGTTTTGGAGAGGTGGTAT
genomic: AGTCCAGGAAGAACTTGCGCATCAATTTCATCACTGTTCGGAAGCTCACTgtaagtttag ... tggtttgcagAGTAAAGCAGATGCCTTTGAATATGCTGACCAAGTTTTGGAGAGGTGGTAT
EST: gi|351019285|gb|FQ429445.1|FQ429445
EST:     AGTCCAGGAAGAACTTGCGCATCAATTTCATCACTGTTCGGAAGCTCACT                         AGTAAAGCAGATGCCTTTGAATATGCTGACCAAGTTTTGGAGAGGTGGTAT
genomic: AGTCCAGGAAGAACTTGCGCATCAATTTCATCACTGTTCGGAAGCTCACTgtaagtttag ... tggtttgcagAGTAAAGCAGATGCCTTTGAATATGCTGACCAAGTTTTGGAGAGGTGGTAT
EST: gi|33408060|gb|CF213687.1|CF213687
EST:     AGTCCAGGAAGAACTTGCGCATCGATTTCGTCACTGTTCGGAAGCTCACT                         AGTAAAGCAGATGCCTTTGAATATGCTGACCAAGTTTTGGAGAGGTGGTAT
genomic: AGTCCAGGAAGAACTTGCGCATCAATTTCATCACTGTTCGGAAGCTCACTgtaagtttag ... tggtttgcagAGTAAAGCAGATGCCTTTGAATATGCTGACCAAGTTTTGGAGAGGTGGTAT
EST: gi|110384796|gb|EC949258.1|EC949258
EST:     AGTCCAGGAAGAACTTGCGCATCAATTTCATCACTGTTCGGAAGCTCACT                         AGTAAAGCAGATGCCTTTGAATATGCTGACCAAGTTTTGGAGAGGTGGTAT
genomic: AGTCCAGGAAGAACTTGCGCATCAATTTCATCACTGTTCGGAAGCTCACTgtaagtttag ... tggtttgcagAGTAAAGCAGATGCCTTTGAATATGCTGACCAAGTTTTGGAGAGGTGGTAT
EST: gi|110388378|gb|EC953120.1|EC953120
EST:     AGTCCAGGAAGAACTTGCGCATCGATTTCATCACTGTTCGGAAGCTCACT                         AGTAAAGCAGATGCCTTTGAATATGCTGACCAAGTTTTGGAGAGGTGGTAT
genomic: AGTCCAGGAAGAACTTGCGCATCAATTTCATCACTGTTCGGAAGCTCACTgtaagtttag ... tggtttgcagAGTAAAGCAGATGCCTTTGAATATGCTGACCAAGTTTTGGAGAGGTGGTAT
EST: gi|32268811|gb|CD717970.1|CD717970
EST:     AGTCCAGGAAGAACTTGCGCATCAATTTCATCACTGTTCGGAAGCTCACT                         AGTAAAGCAGATGCCTTTGAATATGCTGACCAAGTTTTGGAGAGGTGGTAT
genomic: AGTCCAGGAAGAACTTGCGCATCAATTTCATCACTGTTCGGAAGCTCACTgtaagtttag ... tggtttgcagAGTAAAGCAGATGCCTTTGAATATGCTGACCAAGTTTTGGAGAGGTGGTAT
EST: gi|110383081|gb|EC947430.1|EC947430
EST:     AGTCCAGGAAGAACTTGCGCATCGATTTCATCACTGTTCGGAAGCTCACT                         AGTAAAGCAGATGCCTTTGAATATGCTGACCAAGTTTTGGAGAGGTGGTAT
genomic: AGTCCAGGAAGAACTTGCGCATCAATTTCATCACTGTTCGGAAGCTCACTgtaagtttag ... tggtttgcagAGTAAAGCAGATGCCTTTGAATATGCTGACCAAGTTTTGGAGAGGTGGTAT
EST: gi|351040265|gb|FQ425351.1|FQ425351
EST:     AGTCCAGGAAGAACTTGCGCATCAATTTCATCACTGTTCGGAAGCTCACT                         AGTAAAGCAGATGCCTTTGAATATGCTGACCAAGTTTTGGAGAGGTGGTAT
genomic: AGTCCAGGAAGAACTTGCGCATCAATTTCATCACTGTTCGGAAGCTCACTgtaagtttag ... tggtttgcagAGTAAAGCAGATGCCTTTGAATATGCTGACCAAGTTTTGGAGAGGTGGTAT
EST: gi|110422621|gb|EC988948.1|EC988948
EST:     AGTCCAGGAAGAACTTGCGCATCAATTTCATCACTGTTCGGAAGCTCACT                         AGTAAAGCAGATGCCTTTGAATATGCTGACCAAGTTTTGGAGAGGTGGTAT
genomic: AGTCCAGGAAGAACTTGCGCATCAATTTCATCACTGTTCGGAAGCTCACTgtaagtttag ... tggtttgcagAGTAAAGCAGATGCCTTTGAATATGCTGACCAAGTTTTGGAGAGGTGGTAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtgtaagggtttggattttaggtatgaaaattgtgatttgaattggtttgcagAGTAAAGCAGATGCCTTTGAATATGCTGACCAAGTTTTGGAGAGGTGGTATCCCACAATTGAAGAAGGCAGCAATAAGGGTATTGTTGTGCTTGTCACCA
                        tatgaaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcttggcatatgtgaatagaaaaatatgaaatttaagattgcaattgtgtaagggtttggattttaggtatgaaaattgtgatttgaattggtttgcagAGTAAAGCAGATGCCTTTGAATATGCTGACCAAGTTTTGGAGAGGTGGTATCCCACAATTGAAGAAGGCAGCAATAAGGGTATTGTTGTGCTTGTCACCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - gcatatg
- - - - - - - - - - aaaaata
- - - - - - - - - - - - - - - - - - - - - - - - - - -gggtttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - atgaaaa