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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attgatccaatctactttatggcacttcattattatttgttttgggcaacttggaaaaacctcctatcacaatcagcttttttaaacaaaatacttgcagGCAAGAGGTACTATTTCTGGGAAATGAAATTGCATTCAATGAGGCCATAATTGAGGAGAGAGAACAGGGAATTAAGGAGATACAAGATCAAATTGGACAG

Basic information

species Vitis vinifera
transcript Vv14s0068g00800.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0068g00800.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA16G05040.1 (Glycine max), 3'ss of exon 4
------------------------------------------------------------------------------attgatccaatctactttatggcacttcattattatttgttttgggc------aact-----tggaaaaacctcctatcacaatcagcttttttaaac------aaaatacttgcagGCAAGAGGTACTATTTCTGGGAAATGAAATTGCATTCAATGAGGCCATAATTGAGGAGAGAGAACAGGGAATTAAGGAGATACAAGATCAAATTGGACAG
                                                                              |   ||  |  |   |||     |  |   |||  |||||||| |||      ||||     | |||  |     | ||    || | |||  |  |       || | |  | |||||||||| ||||  |  |||  ||||||||  | |||||||||||||| ||||| || ||||||||||||||||  ||| || |||| ||||||||||| 
gtaagtctgcaacatttcagctatttaacgggaccaattgacttctgtttaatctttatcttatcattgtaatatataaacaatatatgcgtttttgaaagatatatgtatagtttgtttttggcttattcaactcttgattgaagtataatttttcgaggtctggtttccttgatcgctgaaataaaaatccagGCAAGAGATACTTCTGTTGGACAATGAAATATCCTTCAATGAGGCCATGATTGAAGAAAGAGAACAGGGAATTAGAGAGGTAGAAGAGCAAATTGGACAA
















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|71860322|gb|DT009377.1|DT009377
EST:     GCACTTAATATGGATCAGGAGAACCAGCCTTTTCTAGTAGGACAGAAGAG                         GCAAGAGGTACTATTTCT
genomic: GCACTTAATATGGATCAGGAGAACCAGCCTTTTCTAGTAGGACAGAAGAGgcaagtattt ... atacttgcagGCAAGAGGTACTATTTCT
EST: gi|351039919|gb|FQ464957.1|FQ464957
EST:     GCACTTAATATGGATCAGGAGAACCAGCCTTTTCTAGTAGGACAGAAGAG                         GCAAGAGGTACTATTTCTGGGAAATGAAATTGCATTCAATGAGGCC
genomic: GCACTTAATATGGATCAGGAGAACCAGCCTTTTCTAGTAGGACAGAAGAGgcaagtattt ... atacttgcagGCAAGAGGTACTATTTCTGGGAAATGAAATTGCATTCAATGAGGCC
EST: gi|351032434|gb|FQ458799.1|FQ458799
EST:     GCACTTAATATGGATCAGGAGAACCAGCCTTTTCTAGTAGGACAGAAGAG                         GCAAGAGGTACTATTTCTGGGAAATGAAATTGCATTCAATGAGGCCATAAT
genomic: GCACTTAATATGGATCAGGAGAACCAGCCTTTTCTAGTAGGACAGAAGAGgcaagtattt ... atacttgcagGCAAGAGGTACTATTTCTGGGAAATGAAATTGCATTCAATGAGGCCATAAT
EST: gi|110713687|gb|EE089836.1|EE089836
EST:     GCACTTAATATGGATCAGGAGAACCAGCCTTTTCTAGTAGGACAGAAGAG                         GCAAGAGGTACTATTTCTGGGAAATGAAATTGCATTCAATGAGGCCATAAT
genomic: GCACTTAATATGGATCAGGAGAACCAGCCTTTTCTAGTAGGACAGAAGAGgcaagtattt ... atacttgcagGCAAGAGGTACTATTTCTGGGAAATGAAATTGCATTCAATGAGGCCATAAT
EST: gi|351054689|gb|FQ462719.1|FQ462719
EST:     GCACTTAATATGGATCAGGAGAACCAGCCTTTTCTAGTAGGACAGAAGAG                         GCAAGAGGTACTATTTCTGGGAAATGAAATTGCATTCAATGAGGCCATAAT
genomic: GCACTTAATATGGATCAGGAGAACCAGCCTTTTCTAGTAGGACAGAAGAGgcaagtattt ... atacttgcagGCAAGAGGTACTATTTCTGGGAAATGAAATTGCATTCAATGAGGCCATAAT
EST: gi|110371177|gb|EC934993.1|EC934993
EST:     GCACTTAATATGGATCAGGAGAACCAGCCTTTTCTAGTAGGACAGAAGAG                         GCAAGAGGTACTATTTCTGGGAAATGAAATTGCATTCAATGAGGCCATAAT
genomic: GCACTTAATATGGATCAGGAGAACCAGCCTTTTCTAGTAGGACAGAAGAGgcaagtattt ... atacttgcagGCAAGAGGTACTATTTCTGGGAAATGAAATTGCATTCAATGAGGCCATAAT
EST: gi|351016153|gb|FQ435473.1|FQ435473
EST:     GCACTTAATATGGATCAGGAGAACCAGCCTTTTCTAGTAGGACAGAAGAG                         GCAAGAGGTACTATTTCCGGGAAATGAAATTGCATTCAATGAGGCCATAAT
genomic: GCACTTAATATGGATCAGGAGAACCAGCCTTTTCTAGTAGGACAGAAGAGgcaagtattt ... atacttgcagGCAAGAGGTACTATTTCTGGGAAATGAAATTGCATTCAATGAGGCCATAAT
EST: gi|110718584|gb|EE095585.1|EE095585
EST:     GCACTTAATATGGATCAGGAGAACCAGCCTTTTCTAGTAGGACAGAAGAA                         GCAAGAGGTACTATTTCTGGGAAATGAAATTGCATTCAATGAGGCCATAAT
genomic: GCACTTAATATGGATCAGGAGAACCAGCCTTTTCTAGTAGGACAGAAGAGgcaagtattt ... atacttgcagGCAAGAGGTACTATTTCTGGGAAATGAAATTGCATTCAATGAGGCCATAAT
EST: gi|30252786|gb|CB970337.1|CB970337
EST:     GCACTTAATATGGATCAGGAGAACCAGCCTTTTCTAGTAGGACAGAAGAG                         GCAAGAGGTACTATTTCTGGGAAATGAAATTGCATTCAATGAGGCCATAAT
genomic: GCACTTAATATGGATCAGGAGAACCAGCCTTTTCTAGTAGGACAGAAGAGgcaagtattt ... atacttgcagGCAAGAGGTACTATTTCTGGGAAATGAAATTGCATTCAATGAGGCCATAAT
EST: gi|110405448|gb|EC970989.1|EC970989
EST:     GCACTTAATATGGATCAGGAGAACCAGCCTTTTCTAGTAGGACAGAAGAG                         GCAAGAGGTACTATTTCTGGGAAATGAAATTGCATTCAATGAGGCCATAAT
genomic: GCACTTAATATGGATCAGGAGAACCAGCCTTTTCTAGTAGGACAGAAGAGgcaagtattt ... atacttgcagGCAAGAGGTACTATTTCTGGGAAATGAAATTGCATTCAATGAGGCCATAAT
EST: gi|110406346|gb|EC971916.1|EC971916
EST:     GCACTTAATATGGATCAGGAGAACCAGCCTTTTCTAGTAGGACAGAAGAG                         GCAAGAGGTACTATTTCTGGGAAATGAAATTGCATTCAATGAGGCCATAAT
genomic: GCACTTAATATGGATCAGGAGAACCAGCCTTTTCTAGTAGGACAGAAGAGgcaagtattt ... atacttgcagGCAAGAGGTACTATTTCTGGGAAATGAAATTGCATTCAATGAGGCCATAAT
EST: gi|34415325|gb|CF414079.1|CF414079
EST:     GCACTTAATATGGATCAGGAGAACCAGCCTTTTCTAGTAGGACAGAAGAG                         GCAAGAGGTACTATTTCTGGGAAATGAAATTGCATTCAATGAGGCCATAAT
genomic: GCACTTAATATGGATCAGGAGAACCAGCCTTTTCTAGTAGGACAGAAGAGgcaagtattt ... atacttgcagGCAAGAGGTACTATTTCTGGGAAATGAAATTGCATTCAATGAGGCCATAAT
EST: gi|110403781|gb|EC969537.1|EC969537
EST:     GCACTTAATATGGATCAGGAGAACCAGCCTTTTCTAGTAGGACAGAAGAG                         GCAAGAGGTACTATTTCTGGGAAATGAAATTGCATTCAATGAGGCCATAAT
genomic: GCACTTAATATGGATCAGGAGAACCAGCCTTTTCTAGTAGGACAGAAGAGgcaagtattt ... atacttgcagGCAAGAGGTACTATTTCTGGGAAATGAAATTGCATTCAATGAGGCCATAAT
EST: gi|351034888|gb|FQ458245.1|FQ458245
EST:     GCACTTAATATGGATCAGGAGAACCAGCCTTTTCTAGTAGGACAGAAGAG                         GCAAGAGGTACTATTTCTGGGAAATGAAATTGCATTCAATGAGGCCATAAT
genomic: GCACTTAATATGGATCAGGAGAACCAGCCTTTTCTAGTAGGACAGAAGAGgcaagtattt ... atacttgcagGCAAGAGGTACTATTTCTGGGAAATGAAATTGCATTCAATGAGGCCATAAT
EST: gi|30126331|gb|CB911670.1|CB911670
EST:     GCACTTAATATGGATCAGGAGAACCAGCCTTTTCTAGTAGGACAGAAGAG                         GCAAGAGGTACTATTTCTGGGAAATGAAATTGCATTCAATGAGGCCATAAT
genomic: GCACTTAATATGGATCAGGAGAACCAGCCTTTTCTAGTAGGACAGAAGAGgcaagtattt ... atacttgcagGCAAGAGGTACTATTTCTGGGAAATGAAATTGCATTCAATGAGGCCATAAT
EST: gi|30131604|gb|CB916943.1|CB916943
EST:     GCACTTAATATGGATCAGGAGAACCAGCCTTTTCTAGTAGGACAGAAGAG                         GCAAGAGGTACTATTTCTGGGAAATGAAATTGCATTCAATGAGGCCATAAT
genomic: GCACTTAATATGGATCAGGAGAACCAGCCTTTTCTAGTAGGACAGAAGAGgcaagtattt ... atacttgcagGCAAGAGGTACTATTTCTGGGAAATGAAATTGCATTCAATGAGGCCATAAT
EST: gi|110713854|gb|EE090137.1|EE090137
EST:     GCACTTAATATGGATCAAGAGAACCAGCCTTTTCTAGTANGACAGAAGAG                         GCAAGAAGTACTATTTCTGGGAAATGAAATTGCATTNCA-TGANGCCATAA
genomic: GCACTTAATATGGATCAGGAGAACCAGCCTTTTCTAGTAGGACAGAAGAGgcaagtattt ... atacttgcagGCAAGAGGTACTATTTCTGGGAAATGAAATTGCATT-CAATGAGGCCATAA
EST: gi|34542538|gb|CF510770.1|CF510770
EST:     GCACTTAATATGGATCAGGAGAACCAGCCTTTTCTAGTAGGACAGAAGAG                         GCAAGAGGTACTATTTCTGGGAAATGAAATTGCATTCAATGAGGCCATAAT
genomic: GCACTTAATATGGATCAGGAGAACCAGCCTTTTCTAGTAGGACAGAAGAGgcaagtattt ... atacttgcagGCAAGAGGTACTATTTCTGGGAAATGAAATTGCATTCAATGAGGCCATAAT
EST: gi|110700860|gb|EE077882.1|EE077882
EST:     GCACTTAATATGGATCAGGAGAACCAGCCTTTTCTAGTAGGACAGAAGAG                         GCAAGAGGTACTATTTCTGGGAAATGAAATTGCATTCAATGAGGCCATAAT
genomic: GCACTTAATATGGATCAGGAGAACCAGCCTTTTCTAGTAGGACAGAAGAGgcaagtattt ... atacttgcagGCAAGAGGTACTATTTCTGGGAAATGAAATTGCATTCAATGAGGCCATAAT
EST: gi|110423298|gb|EC989640.1|EC989640
EST:     GCACTTAATATGGATCAGGAGAACCAGCCTTTTCTAGTAGGACAGAAGAG                         GCAAGAGGTACTATTTCTGGGAAATGAAATTGCATTCAATGAGGCCATAAT
genomic: GCACTTAATATGGATCAGGAGAACCAGCCTTTTCTAGTAGGACAGAAGAGgcaagtattt ... atacttgcagGCAAGAGGTACTATTTCTGGGAAATGAAATTGCATTCAATGAGGCCATAAT
EST: gi|351031591|gb|FQ459848.1|FQ459848
EST:     GCACTTAATATGGATCAGGAGAACCAGCCTTTTCTAGTAGGACAGAAGAG                         GCAAGAGGTACTATTTCTGGGAAATGAAATTGCATTCAATGAGGCCATAAT
genomic: GCACTTAATATGGATCAGGAGAACCAGCCTTTTCTAGTAGGACAGAAGAGgcaagtattt ... atacttgcagGCAAGAGGTACTATTTCTGGGAAATGAAATTGCATTCAATGAGGCCATAAT
EST: gi|349824290|gb|FQ417701.1|FQ417701
EST:     GCACTTAATATGGATCAGGAGAACCAGCCTTTTCTAGTAGGACAGAAGAG                         GCAAGAGGTACTATTTCTGG-AAATGAAATTGCATTCAATGAGGCCATAAT
genomic: GCACTTAATATGGATCAGGAGAACCAGCCTTTTCTAGTAGGACAGAAGAGgcaagtattt ... atacttgcagGCAAGAGGTACTATTTCTGGGAAATGAAATTGCATTCAATGAGGCCATAAT
EST: gi|351027941|gb|FQ425842.1|FQ425842
EST:     GCACTTAATATGGATCAGGAGAACCAGCCTTTTCTAGTAGGACAGAAGAG                         GCAAGAGGTACTATTTCTGG-AAATGAAATTGCATTCAATGAGGCCATAAT
genomic: GCACTTAATATGGATCAGGAGAACCAGCCTTTTCTAGTAGGACAGAAGAGgcaagtattt ... atacttgcagGCAAGAGGTACTATTTCTGGGAAATGAAATTGCATTCAATGAGGCCATAAT
EST: gi|34542448|gb|CF510680.1|CF510680
EST:     GCACTTAATATGGATCAGGAGAACCAGCCTTTTCTAGTAGGACAGAAGAG                         GCAAGAGGTACTATTTCTGGGAAATGAAATTGCATTCAATGAGGCCATAAT
genomic: GCACTTAATATGGATCAGGAGAACCAGCCTTTTCTAGTAGGACAGAAGAGgcaagtattt ... atacttgcagGCAAGAGGTACTATTTCTGGGAAATGAAATTGCATTCAATGAGGCCATAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcaacttggaaaaacctcctatcacaatcagcttttttaaacaaaatacttgcagGCAAGAGGTACTATTTCTGGGAAATGAAATTGCATTCAATGAGGCCATAATTGAGGAGAGAGAACAGGGAATTAAGGAGATACAAGATCAAATTGGACAG
                                ttttttaaacaaaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attgatccaatctactttatggcacttcattattatttgttttgggcaacttggaaaaacctcctatcacaatcagcttttttaaacaaaatacttgcagGCAAGAGGTACTATTTCTGGGAAATGAAATTGCATTCAATGAGGCCATAATTGAGGAGAGAGAACAGGGAATTAAGGAGATACAAGATCAAATTGGACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - ccaatct
- - - - - - - - -tatggca
- - - - - - - - - - - - - - - - - - - -ttttggg
- - - - - - - - - - - - - - - - - - - - - - - - - - ggaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acaatca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaacaaa