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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctttttgaatctttctagctcttaggcttgtgaaaatgataaacattttctattgttatatagtttttgagcttataattatatgtttgttgcatttagTGCAAAAGAGAAGGCTTTGTCCAAAAGGTTAAAGAGGAAGAAGGTGAAGGATGCAATGTCTATGGCTTTTTAGAAGTTAATAAAGTTGCAGGAAACTTTC

Basic information

species Vitis vinifera
transcript Vv12s0178g00020.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv12s0178g00020.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT1G22200.1 (Arabidopsis thaliana), 3'ss of exon 6
-----------------------------------------------------------------------tctttttgaatctttctagctcttaggcttgtgaaaatgataaacattttctattgttatatagtt-tttgagcttataattatatgtt------------tgttgcattt-agTGCAAAAGAGAAGGCTTTGTCCAAAAGGTTAAAGAGGAAGAAGGTGAAGGATGCAATGTCTATGGCTTTTTAGAAGTTAATAAAGTTGCAGGAAACTTTC
                                                                        | || |    |  |  |     ||    |    |||  ||    || |  | ||    |  || | |     | | || || |||| |              || ||||| |||| ||||||||||||||||| |||||||| ||||| |||||||||||||| || |||||  | || || || |||||||| |||||||| || |||||||
gtatactgacgttccttcactaacaacaaaattgggttgatcttggtacttagtttgaaacaaatagtgacaccttgtttggcactaaaatggatatatctaaagaaaccatgggtatctggtctttcgtttcagctatccccacatctagttgtatgatattcttactcatcatttcatttcagTGTAAAAGAGAAGGCTTTGTGCAAAAGGTAAAAGATGAAGAAGGTGAAGGTTGTAATGTTCACGGTTTCTTGGAAGTTAACAAAGTTGCTGGGAACTTTC
















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|349830254|gb|FQ420514.1|FQ420514
EST:     CATATAGAAAGAAAGGTTGGGGGATGACAAATCCAGATTTGATTGATCAG                         TGCAAAAGAGAAGGCTTTGTCCAAAAGGTTAAAGAGGAAGAAGGTGAAGGA
genomic: CATATAGAAAGAAAGGTTGGGGGATGACAAATCCAGATTTGATTGATCAGgttggttatc ... ttgcatttagTGCAAAAGAGAAGGCTTTGTCCAAAAGGTTAAAGAGGAAGAAGGTGAAGGA
EST: gi|351017588|gb|FQ435941.1|FQ435941
EST:     CATATAGAAAGAAAGGTTGGGGGATGACAAATCCAGATTTGATTGATCAG                         TGCAAAAGAGAAGGCTTTGTCCAAAAGGTTAAAGAGGAAGAAGGTGAAGGA
genomic: CATATAGAAAGAAAGGTTGGGGGATGACAAATCCAGATTTGATTGATCAGgttggttatc ... ttgcatttagTGCAAAAGAGAAGGCTTTGTCCAAAAGGTTAAAGAGGAAGAAGGTGAAGGA
EST: gi|351032592|gb|FQ458957.1|FQ458957
EST:     CATATAGAAAGAAAGGTTGGGGGATGACAAATCCAGATTTGATTGATCAG                         TGCAAAAGAGAAGGCTTTGTCCAAAAGGTTAAAGAGGAAGAAGGTGAAGGA
genomic: CATATAGAAAGAAAGGTTGGGGGATGACAAATCCAGATTTGATTGATCAGgttggttatc ... ttgcatttagTGCAAAAGAGAAGGCTTTGTCCAAAAGGTTAAAGAGGAAGAAGGTGAAGGA
EST: gi|351046419|gb|FQ453035.1|FQ453035
EST:     CATATAGAAAGAAAGGTTGGGGGATGACAAATCCAGATTTGATTGATCAG                         TGCATAAGAGAAAGCTTTGTCCAAAAGGTTAAAGAGGAAGAAGGTGAAGGA
genomic: CATATAGAAAGAAAGGTTGGGGGATGACAAATCCAGATTTGATTGATCAGgttggttatc ... ttgcatttagTGCAAAAGAGAAGGCTTTGTCCAAAAGGTTAAAGAGGAAGAAGGTGAAGGA
EST: gi|351032954|gb|FQ461843.1|FQ461843
EST:     CATATAGAAAGAAAGGTTGGGGGATGACAAATCCAGATTTGATTGATCAG                         TGCAAAAGAGAAGGCTTTGTCCAAAAGGTTAAAGAGGAAGAAGGTGAAGGA
genomic: CATATAGAAAGAAAGGTTGGGGGATGACAAATCCAGATTTGATTGATCAGgttggttatc ... ttgcatttagTGCAAAAGAGAAGGCTTTGTCCAAAAGGTTAAAGAGGAAGAAGGTGAAGGA
EST: gi|110712317|gb|EE089798.1|EE089798
EST:     CATATAGAAAGAAAGGTTGGGGGATGACAAATCCAGATTTGATTGATCAG                         TGCAAAAGAGAAAGCTTTGTCCAAAAGGTTAAAGAAGAAGAAGGTGAANGG
genomic: CATATAGAAAGAAAGGTTGGGGGATGACAAATCCAGATTTGATTGATCAGgttggttatc ... ttgcatttagTGCAAAAGAGAAGGCTTTGTCCAAAAGGTTAAAGAGGAAGAAGGTGAA-GG
EST: gi|352791378|gb|FQ480957.1|FQ480957
EST:     CATATAGAAAGAAAGGTTGGGGGATGACAAATCCAGATTTGATTGATCAG                         TGCAAAAGAGAAGGCTTTGTCCAAAAGGTTAAAGAGGAAGAAGGTGAAGGA
genomic: CATATAGAAAGAAAGGTTGGGGGATGACAAATCCAGATTTGATTGATCAGgttggttatc ... ttgcatttagTGCAAAAGAGAAGGCTTTGTCCAAAAGGTTAAAGAGGAAGAAGGTGAAGGA
EST: gi|351037083|gb|FQ465075.1|FQ465075
EST:     CATATAGAAAGAAAGGTTGGGGGATGACAAATCCAGATTTGATTGATCAG                         TGCAAAAGAGAAGGCTTTGTCCAAAAGGTTAAAGAGGAAGAAGGTGAAGGA
genomic: CATATAGAAAGAAAGGTTGGGGGATGACAAATCCAGATTTGATTGATCAGgttggttatc ... ttgcatttagTGCAAAAGAGAAGGCTTTGTCCAAAAGGTTAAAGAGGAAGAAGGTGAAGGA
EST: gi|161708936|gb|FC060479.1|FC060479
EST:     CATATAGAAAGAAAGGTTGGGGGATGACAAATCCAGATTTGATTGATCAG                         TGCAAAAGAGAAGGCTTTGTCCAAAAGGTTAAAGAGGAAGAAGGTGAAGGA
genomic: CATATAGAAAGAAAGGTTGGGGGATGACAAATCCAGATTTGATTGATCAGgttggttatc ... ttgcatttagTGCAAAAGAGAAGGCTTTGTCCAAAAGGTTAAAGAGGAAGAAGGTGAAGGA
EST: gi|351051772|gb|FQ455186.1|FQ455186
EST:     CATATAGAAAGAAAGGTTGGGGGATGACAAATCCAGATTTGATTGATCAG                         TGCAAAAGAGAAGGCTTTGTCCAAAAGGTTAAAGAGGAAGAAGGTGAAGGA
genomic: CATATAGAAAGAAAGGTTGGGGGATGACAAATCCAGATTTGATTGATCAGgttggttatc ... ttgcatttagTGCAAAAGAGAAGGCTTTGTCCAAAAGGTTAAAGAGGAAGAAGGTGAAGGA
EST: gi|351038305|gb|FQ460997.1|FQ460997
EST:     CATATAGAAAGAAAGGTTGGGGGATGACAAATCCAGATTTGATTGATCAG                         TGCAAAAGAGAAGGCTTTGTCCAAAAGGTTAAAGAGGAAGAAGGTGAAGGA
genomic: CATATAGAAAGAAAGGTTGGGGGATGACAAATCCAGATTTGATTGATCAGgttggttatc ... ttgcatttagTGCAAAAGAGAAGGCTTTGTCCAAAAGGTTAAAGAGGAAGAAGGTGAAGGA
EST: gi|351036806|gb|FQ457519.1|FQ457519
EST:     CATATAGAAAGAAAGGTTGGGGGATGACAAATCCAGATTTGATTGATCAG                         TGCAAAAGAGAAGGCTTTGTCCAAAAGGTTAAAGAGGAAGAAGGTGAAGGA
genomic: CATATAGAAAGAAAGGTTGGGGGATGACAAATCCAGATTTGATTGATCAGgttggttatc ... ttgcatttagTGCAAAAGAGAAGGCTTTGTCCAAAAGGTTAAAGAGGAAGAAGGTGAAGGA
EST: gi|351044765|gb|FQ449019.1|FQ449019
EST:     CATATAGAAAGAAAGGTTGGGGGATGACAAATCCAGATTTGATTGATCAG                         TGCAAAAGAGAAGGCTTTGTCCAAAAGGTTAAAGAGGAAGAAGGTGAAGGA
genomic: CATATAGAAAGAAAGGTTGGGGGATGACAAATCCAGATTTGATTGATCAGgttggttatc ... ttgcatttagTGCAAAAGAGAAGGCTTTGTCCAAAAGGTTAAAGAGGAAGAAGGTGAAGGA
EST: gi|351025136|gb|FQ433553.1|FQ433553
EST:     CATATAGAAAGAAAGGTTGGGGGATGACAAATCCAGATTTGATTGATCAG                         TGCAAAAGAGAAGGCTTTGTCCAAAAGGTTAAAGAGGAAGAAGGTGAAGGA
genomic: CATATAGAAAGAAAGGTTGGGGGATGACAAATCCAGATTTGATTGATCAGgttggttatc ... ttgcatttagTGCAAAAGAGAAGGCTTTGTCCAAAAGGTTAAAGAGGAAGAAGGTGAAGGA
EST: gi|351031032|gb|FQ444859.1|FQ444859
EST:     CATATAGAAAGAAAGGTTGGGGGATGACAAATCCAGATTTGATTGATCAG                         TGCAAAAGAGAAGGCTTTGTCCAAAAGGTTAAAGAGGAAGAAGGTGAAGGA
genomic: CATATAGAAAGAAAGGTTGGGGGATGACAAATCCAGATTTGATTGATCAGgttggttatc ... ttgcatttagTGCAAAAGAGAAGGCTTTGTCCAAAAGGTTAAAGAGGAAGAAGGTGAAGGA
EST: gi|110711767|gb|EE088624.1|EE088624
EST:     CATATAGAAAGAAAGGTTGGGGGATGACAAATCCAGATTTGATTGATCAG                         TGCAAAAGAGAAGGCTTTGTCCAAAAGGTTAAAGAGGAAGAAGGTGAAGGA
genomic: CATATAGAAAGAAAGGTTGGGGGATGACAAATCCAGATTTGATTGATCAGgttggttatc ... ttgcatttagTGCAAAAGAGAAGGCTTTGTCCAAAAGGTTAAAGAGGAAGAAGGTGAAGGA
EST: gi|349832977|gb|FQ416355.1|FQ416355
EST:     CATATAGAAAGAAAGGTTGGGGGATGACAAATCCAGATTTGATTGATCAG                         TGCAAAAGAGAAGGCTTTGTCCAAAAGGTTAAAGAGGAAGAAGGTGAAGGA
genomic: CATATAGAAAGAAAGGTTGGGGGATGACAAATCCAGATTTGATTGATCAGgttggttatc ... ttgcatttagTGCAAAAGAGAAGGCTTTGTCCAAAAGGTTAAAGAGGAAGAAGGTGAAGGA
EST: gi|351053700|gb|FQ440210.1|FQ440210
EST:     CATATAGAAAGAAAGGTTGGGGGATGACAAATCCAGATTTGATTGATCAG                         TGCAAAAGAGAAGGCTTTGTCCAAAAGGTTAAAGAGGAAGAAGGTGAAGGA
genomic: CATATAGAAAGAAAGGTTGGGGGATGACAAATCCAGATTTGATTGATCAGgttggttatc ... ttgcatttagTGCAAAAGAGAAGGCTTTGTCCAAAAGGTTAAAGAGGAAGAAGGTGAAGGA
EST: gi|351015973|gb|FQ431928.1|FQ431928
EST:     CATATAGAAAGAAAGGTTGGGGGATGACAAATCCAGATTTGATTGATCAG                         TGCAAAAGAGAAGGCTTTGTCCAAAAGGTTAAAGAGGAAGAAGGTGAAGGA
genomic: CATATAGAAAGAAAGGTTGGGGGATGACAAATCCAGATTTGATTGATCAGgttggttatc ... ttgcatttagTGCAAAAGAGAAGGCTTTGTCCAAAAGGTTAAAGAGGAAGAAGGTGAAGGA
EST: gi|352786840|gb|FQ481215.1|FQ481215
EST:     CATATAGAAAGAAAGGTTGGGGGATGACAAATCCAGATTTGATTGATCAG                         TGCAAAAGAGAAGGCTTTGTCCAAAAGGTTAAAGAGGAAGAAGGTGAAGGA
genomic: CATATAGAAAGAAAGGTTGGGGGATGACAAATCCAGATTTGATTGATCAGgttggttatc ... ttgcatttagTGCAAAAGAGAAGGCTTTGTCCAAAAGGTTAAAGAGGAAGAAGGTGAAGGA
EST: gi|351053378|gb|FQ455714.1|FQ455714
EST:     CATATAGAAAGAAAGGTTGGGGGATGACAAATCCAGATTTGATTGATCAG                         TGCAAAAGAGAAGGCTTTGTCCAAAAGGTTAAAGAGGAAGAAGGTGAAGGA
genomic: CATATAGAAAGAAAGGTTGGGGGATGACAAATCCAGATTTGATTGATCAGgttggttatc ... ttgcatttagTGCAAAAGAGAAGGCTTTGTCCAAAAGGTTAAAGAGGAAGAAGGTGAAGGA
EST: gi|351013633|gb|FQ429774.1|FQ429774
EST:     CATATAGAAAGAAAGGTTGGGGGATGACAAATCCAGATTTGATTGATCAG                         TGCAAAAGAGAAGGCTTTGTCCAAAAGGTTAAAGAGGAAGAAGGTGAAGGA
genomic: CATATAGAAAGAAAGGTTGGGGGATGACAAATCCAGATTTGATTGATCAGgttggttatc ... ttgcatttagTGCAAAAGAGAAGGCTTTGTCCAAAAGGTTAAAGAGGAAGAAGGTGAAGGA
EST: gi|351014796|gb|FQ437996.1|FQ437996
EST:     CATATAGAAAGAAAGGTTGGGGGATGACAAATCCAGATTTGATTGATCAA                         TGCAAAAGAGAAGGCTTTGTCCAAAAGGTTAAAGAGGAAAAAGGTGAATGA
genomic: CATATAGAAAGAAAGGTTGGGGGATGACAAATCCAGATTTGATTGATCAGgttggttatc ... ttgcatttagTGCAAAAGAGAAGGCTTTGTCCAAAAGGTTAAAGAGGAAGAAGGTGAAGGA
EST: gi|351013590|gb|FQ429731.1|FQ429731
EST:     CATATAGAAAGAAAGGTTGGGGGATGACAAATCCAGATTTGATTGATCAG                         TGCAAAAGAGAAGGCTTTGTCCAAAAGGTTAAAGAGGAAGAAGGTGAAGGA
genomic: CATATAGAAAGAAAGGTTGGGGGATGACAAATCCAGATTTGATTGATCAGgttggttatc ... ttgcatttagTGCAAAAGAGAAGGCTTTGTCCAAAAGGTTAAAGAGGAAGAAGGTGAAGGA
EST: gi|161718985|gb|FC068640.1|FC068640
EST:     CATATAGAAAGAAAGGTTGGGGGATGACAAATCCAGATTTGATTGATCAG                         TGCAAAAGAGAAGGCTTTGTCCAAAA
genomic: CATATAGAAAGAAAGGTTGGGGGATGACAAATCCAGATTTGATTGATCAGgttggttatc ... ttgcatttagTGCAAAAGAGAAGGCTTTGTCCAAAA
EST: gi|349825901|gb|FQ423196.1|FQ423196
EST:     CATATAGAAAGAAAGGTTGGGGGATGACAAATCCAGATTTGATTGATCAG                         TGCAAAAGAGAAGGCTTTGTCCAAAAGGTTAAAGAGGAAGAAGGTGAAGGA
genomic: CATATAGAAAGAAAGGTTGGGGGATGACAAATCCAGATTTGATTGATCAGgttggttatc ... ttgcatttagTGCAAAAGAGAAGGCTTTGTCCAAAAGGTTAAAGAGGAAGAAGGTGAAGGA
EST: gi|110689266|gb|EE065350.1|EE065350
EST:     CATATAGAAAGAAAGGTTGGGGGATGACAAATCCAGATTTGATTGATCAG                         TGCAAAAGAGAAGGCTTTGTCCAAAAGGTTAAAGAGGAAGAAGGTGAAGGA
genomic: CATATAGAAAGAAAGGTTGGGGGATGACAAATCCAGATTTGATTGATCAGgttggttatc ... ttgcatttagTGCAAAAGAGAAGGCTTTGTCCAAAAGGTTAAAGAGGAAGAAGGTGAAGGA
EST: gi|351034302|gb|FQ448099.1|FQ448099
EST:     CATATAGAAAGAAAGGTTGGGGGATGACAAATCCAGATTTGATTGATCAG                         TGCAAAAGAGAAGGCTTTGTCCAAAAGGTTAAAGAGGAAGAAGGTGAAGGA
genomic: CATATAGAAAGAAAGGTTGGGGGATGACAAATCCAGATTTGATTGATCAGgttggttatc ... ttgcatttagTGCAAAAGAGAAGGCTTTGTCCAAAAGGTTAAAGAGGAAGAAGGTGAAGGA
EST: gi|351016879|gb|FQ424306.1|FQ424306
EST:     CATATAGAAAGAAAGGTTGGGGGATGACAAATCCAGATTTGATTGATCAG                         TGCAAAAGAGAAGGCTTTGTCCAAAAGGTTAAAGAGGAAGAAGGTGAAGGA
genomic: CATATAGAAAGAAAGGTTGGGGGATGACAAATCCAGATTTGATTGATCAGgttggttatc ... ttgcatttagTGCAAAAGAGAAGGCTTTGTCCAAAAGGTTAAAGAGGAAGAAGGTGAAGGA
EST: gi|352789786|gb|FQ478601.1|FQ478601
EST:     CATATAGAAAGAAAGGTTGGGGGATGACAAATCCAGATTTGATTGATCAG                         TGCAAAAGAGAAGGCTTTGTCCAAAAGGTTAAAGAGGAAGAAGGTGAAGGA
genomic: CATATAGAAAGAAAGGTTGGGGGATGACAAATCCAGATTTGATTGATCAGgttggttatc ... ttgcatttagTGCAAAAGAGAAGGCTTTGTCCAAAAGGTTAAAGAGGAAGAAGGTGAAGGA
EST: gi|110359140|gb|EC920148.1|EC920148
EST:     CATATAGAAAGAAAGGTTGGGGGATGACAAATCCAGATTTGATTGATCAG                         TGCAAAAGAGAAGGCTTTGTCCAAAAGGTTAAAGAGGAAGAAGGTGAAGGA
genomic: CATATAGAAAGAAAGGTTGGGGGATGACAAATCCAGATTTGATTGATCAGgttggttatc ... ttgcatttagTGCAAAAGAGAAGGCTTTGTCCAAAAGGTTAAAGAGGAAGAAGGTGAAGGA
EST: gi|351029738|gb|FQ427578.1|FQ427578
EST:     CATATAGAAAGAAAGGTTGGGGGATGACAAATCCAGATTTGATTGATCAG                         TGCAAAAGAGAAGGCTTTGTCCAAAAGGTTAAAGAGGAAGAAGGTGAAGGA
genomic: CATATAGAAAGAAAGGTTGGGGGATGACAAATCCAGATTTGATTGATCAGgttggttatc ... ttgcatttagTGCAAAAGAGAAGGCTTTGTCCAAAAGGTTAAAGAGGAAGAAGGTGAAGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attttctattgttatatagtttttgagcttataattatatgtttgttgcatttagTGCAAAAGAGAAGGCTTTGTCCAAAAGGTTAAAGAGGAAGAAGGTGAAGGATGCAATGTCTATGGCTTTTTAGAAGTTAATAAAGTTGCAGGAAACTTTC
      tattgttatatagttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctttttgaatctttctagctcttaggcttgtgaaaatgataaacattttctattgttatatagtttttgagcttataattatatgtttgttgcatttagTGCAAAAGAGAAGGCTTTGTCCAAAAGGTTAAAGAGGAAGAAGGTGAAGGATGCAATGTCTATGGCTTTTTAGAAGTTAATAAAGTTGCAGGAAACTTTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - - - - - - - - - - - - gcttgtg
- - - - - - - - - - - - - - - - - - - gataaac