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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttggattttttgtattaaagtttaactttattgtcttgtctttatactatatttccactccacttgttgctcatgaagttatccctttcaaatgcttagGAAGAAGAAATTGATGGTGTAGATTTTATAATTATTGCAAGTGATGGACTTTGGAATGTCTTATCAAATAAG

Basic information

species Vitis vinifera
transcript Vv18s0001g15050.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g15050.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA20G38500.1 (Glycine max), 3'ss of exon 7
tttggattttttgtattaaagtttaactttattgtcttgtctttata-ctatatttccactccacttgttgctcatgaagttatccctttcaaat---------gcttagGAAGAAGAAATTGATGGTGTAGATTTTATAATTATTGCAAGTGATGGACTTTGGAATGTCTTATCAAATAAG
          |||  | ||   | | ||| | |  |   ||  |||| || | |    |     ||| |  ||  |||| |  || ||||    |         |||||||| ||||||||||| || || |||||||| || ||||| |||| ||| |||||||||||| ||| ||| |||
---------gttgcctaaatcataagcttcaatacccactcggtatatctgtgtcattatatttcttatgccttctgaattgctcgctttttggtactgttatggcttagGAGGAAGAAATTGACGGAGTCGATTTTATTATAATTGCTAGTGGTGGCCTTTGGAATGTCATATTAAACAAG
















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|110712077|gb|EE089286.1|EE089286
EST:     TTGGGGATAA-CATCTTAAGGCATATGTTGTTGCTGATCCA-AAATTCCG                         GAAGAAAAAAT-GATGGTG
genomic: TTGGGGATAAACTTCTTAAGGCATATGTTGTTGCTGATCCAGAAATTCAGgtaatcttat ... aaatgcttagGAAGAAGAAATTGATGGTG
EST: gi|351030454|gb|FQ432392.1|FQ432392
EST:     TTGGGGATAAACTTCTTAAGGCATATGTTGTTGCTGATCCAGAAATTCAG                         GAAGAAGAAATTGATGGTGTAGATTTTATAATTATTGCAAGTGATGGACTT
genomic: TTGGGGATAAACTTCTTAAGGCATATGTTGTTGCTGATCCAGAAATTCAGgtaatcttat ... aaatgcttagGAAGAAGAAATTGATGGTGTAGATTTTATAATTATTGCAAGTGATGGACTT
EST: gi|45368324|gb|CK906683.1|CK906683
EST:     TTGGGGATAAACTTCTTAAGGCATATGTTGTTGCTGATCCAGAAATTCAG                         GAAGAAGAAATTGATGGTGTAGATTTTATAATTATTGCAAGTGATGGACTT
genomic: TTGGGGATAAACTTCTTAAGGCATATGTTGTTGCTGATCCAGAAATTCAGgtaatcttat ... aaatgcttagGAAGAAGAAATTGATGGTGTAGATTTTATAATTATTGCAAGTGATGGACTT
EST: gi|349815543|gb|FQ400699.1|FQ400699
EST:     TTGGGGATAAACTTCTTAAGGCATATGTTGTTGCTGATCCAGAAATTCAG                         GAAGAAGAAATTGATGGTGTAGATTTTATAATTATTGCAAGTGATGGACTT
genomic: TTGGGGATAAACTTCTTAAGGCATATGTTGTTGCTGATCCAGAAATTCAGgtaatcttat ... aaatgcttagGAAGAAGAAATTGATGGTGTAGATTTTATAATTATTGCAAGTGATGGACTT
EST: gi|32245933|gb|CD711752.1|CD711752
EST:     TTGGGGATAAACTTCTTAAGGCATATGTTGTTGCTGATCCAGAAATTCAG                         GAAGAAGAAATTGATGGTGTAGATTTTATAATTATTGCAAGTGATGGACTT
genomic: TTGGGGATAAACTTCTTAAGGCATATGTTGTTGCTGATCCAGAAATTCAGgtaatcttat ... aaatgcttagGAAGAAGAAATTGATGGTGTAGATTTTATAATTATTGCAAGTGATGGACTT
EST: gi|83274595|gb|DV938692.1|DV938692
EST:     TTGGGGATAAACTTCTTAAGGCATATGTTGTTGCTGATCCAGAAATTCAG                         GAAGAAGAAATTGATGGTGTAGATTTTATAATTATTGCAAGTGATGGACTT
genomic: TTGGGGATAAACTTCTTAAGGCATATGTTGTTGCTGATCCAGAAATTCAGgtaatcttat ... aaatgcttagGAAGAAGAAATTGATGGTGTAGATTTTATAATTATTGCAAGTGATGGACTT
EST: gi|351023467|gb|FQ432850.1|FQ432850
EST:     TTGGGGATAAACTTCTTAAGGCATATGTTGTTGCTGATCCAGAAATTCAG                         GAAGAAGAAATTGATGGTGTAGATTTTATAATTATTGCAAGTGATGGACTT
genomic: TTGGGGATAAACTTCTTAAGGCATATGTTGTTGCTGATCCAGAAATTCAGgtaatcttat ... aaatgcttagGAAGAAGAAATTGATGGTGTAGATTTTATAATTATTGCAAGTGATGGACTT
EST: gi|351029448|gb|FQ436842.1|FQ436842
EST:     TTGGGGATAAACTTCTTAAGGCATATGTTGTTGCTGATCCAGAAATTCAG                         GAAGAAGAAATTGATGGTGTAGATTTTATAATTATTGCAAGTGATGGACTT
genomic: TTGGGGATAAACTTCTTAAGGCATATGTTGTTGCTGATCCAGAAATTCAGgtaatcttat ... aaatgcttagGAAGAAGAAATTGATGGTGTAGATTTTATAATTATTGCAAGTGATGGACTT
EST: gi|349817905|gb|FQ407894.1|FQ407894
EST:     TTGGGGATAAACTTCTTAAGGCATATGTTGTTGCTGATCCAGAAATTCAG                         GAAGAAGAAATTGATGGTGTAGATTTTATAATTATTGCAAGTGATGGACTT
genomic: TTGGGGATAAACTTCTTAAGGCATATGTTGTTGCTGATCCAGAAATTCAGgtaatcttat ... aaatgcttagGAAGAAGAAATTGATGGTGTAGATTTTATAATTATTGCAAGTGATGGACTT
EST: gi|351044250|gb|FQ447604.1|FQ447604
EST:     TTGGGGATAAACTTCTTAAGGCATATGTTGTTGCTGATCCAGAAATTCAG                         GAAGAAGAAATTGATGGTGTAGATTTTATAATTATTGCAAGTGATGGACTT
genomic: TTGGGGATAAACTTCTTAAGGCATATGTTGTTGCTGATCCAGAAATTCAGgtaatcttat ... aaatgcttagGAAGAAGAAATTGATGGTGTAGATTTTATAATTATTGCAAGTGATGGACTT
EST: gi|110371845|gb|EC935970.1|EC935970
EST:     TTGGGGATAAACTTCTTAAGGCATATGTTGTTGCTGATCCAGAAATTCAG                         GAAGAAGAAATTGATGGTGTAGATTTTATAATTATTGCAAGTGATGGACTT
genomic: TTGGGGATAAACTTCTTAAGGCATATGTTGTTGCTGATCCAGAAATTCAGgtaatcttat ... aaatgcttagGAAGAAGAAATTGATGGTGTAGATTTTATAATTATTGCAAGTGATGGACTT
EST: gi|349832452|gb|FQ421013.1|FQ421013
EST:     TTGGGGATAAACTTCTTAAGGCATATGTTGTTGCTGATCCAGAAATTCAG                         GAAGAAGAAATTGATGGTGTAGATTTTATAATTATTGCAAGTGATGGACTT
genomic: TTGGGGATAAACTTCTTAAGGCATATGTTGTTGCTGATCCAGAAATTCAGgtaatcttat ... aaatgcttagGAAGAAGAAATTGATGGTGTAGATTTTATAATTATTGCAAGTGATGGACTT
EST: gi|349815027|gb|FQ410250.1|FQ410250
EST:     TTGGGGATAAACTTCTTAAGGCATATGTTGTTGCTGATCCAGAAATTCAG                         GAAGAAGAAATTGATGGTGTAGATTTTATAATTATTGCAAGTGATGGACTT
genomic: TTGGGGATAAACTTCTTAAGGCATATGTTGTTGCTGATCCAGAAATTCAGgtaatcttat ... aaatgcttagGAAGAAGAAATTGATGGTGTAGATTTTATAATTATTGCAAGTGATGGACTT
EST: gi|351025872|gb|FQ427884.1|FQ427884
EST:     TTGGGGATAAACTTCTTAAGGCATATGTTGTTGCTGATCCAGAAATTCAG                         GAAGAAGAAATTGATGGTGTAGATTTTATAATTATTGCAAGTGATGGACTT
genomic: TTGGGGATAAACTTCTTAAGGCATATGTTGTTGCTGATCCAGAAATTCAGgtaatcttat ... aaatgcttagGAAGAAGAAATTGATGGTGTAGATTTTATAATTATTGCAAGTGATGGACTT
EST: gi|351025088|gb|FQ433505.1|FQ433505
EST:     TTGGGGATAAACTTCTTAAGGCATATGTTGTTGCTGATCCAGAAATTCAG                         GAAGAAGAAATTGATGGTGTAGATTTTATAATTATTGCAAGTGATGGACTT
genomic: TTGGGGATAAACTTCTTAAGGCATATGTTGTTGCTGATCCAGAAATTCAGgtaatcttat ... aaatgcttagGAAGAAGAAATTGATGGTGTAGATTTTATAATTATTGCAAGTGATGGACTT
EST: gi|32245467|gb|CD711286.1|CD711286
EST:     TTGGGGATAAACTTCTTAAGGCATATGTTGTTGCTGATCCAGAAATTCAG                         GAAGAAGAAATTGATGGTGTAGATTTTATAATTATTGCAAGTGATGGACTT
genomic: TTGGGGATAAACTTCTTAAGGCATATGTTGTTGCTGATCCAGAAATTCAGgtaatcttat ... aaatgcttagGAAGAAGAAATTGATGGTGTAGATTTTATAATTATTGCAAGTGATGGACTT
EST: gi|351012826|gb|FQ430389.1|FQ430389
EST:     TTGGGGATAAACTTCTTAAGGCATATGTTGTTGCTGATCCAGAAATTCAG                         GAAGAAGAAATTGATGGTGTAGATTTTATAATTATTGCAAGTGATGGACTT
genomic: TTGGGGATAAACTTCTTAAGGCATATGTTGTTGCTGATCCAGAAATTCAGgtaatcttat ... aaatgcttagGAAGAAGAAATTGATGGTGTAGATTTTATAATTATTGCAAGTGATGGACTT
EST: gi|351030991|gb|FQ439027.1|FQ439027
EST:     TTGGGGATAAACTTCTTAAGGCATATGTTGTTGCTGATCCAGAAATTCAG                         GAAGAAGAAATTGATGGTGTAGATTTTATAATTATTGCAAGTGATGGACTT
genomic: TTGGGGATAAACTTCTTAAGGCATATGTTGTTGCTGATCCAGAAATTCAGgtaatcttat ... aaatgcttagGAAGAAGAAATTGATGGTGTAGATTTTATAATTATTGCAAGTGATGGACTT
EST: gi|349830246|gb|FQ420506.1|FQ420506
EST:     TTGGGGATAAACTTCTTAAGGCATATGTTGTTGCTGATCCAGAAATTCAG                         GAAGAAGAAATTGATGGTGTAGATTTTATAATTATTGCAAGTGATGGACTT
genomic: TTGGGGATAAACTTCTTAAGGCATATGTTGTTGCTGATCCAGAAATTCAGgtaatcttat ... aaatgcttagGAAGAAGAAATTGATGGTGTAGATTTTATAATTATTGCAAGTGATGGACTT
EST: gi|351033310|gb|FQ446542.1|FQ446542
EST:     TTGGGGATAAACTTCTTAAGGCATATGTTGTTGCTGATCCAGAAATTCAG                         GAAGAAGAAATTGATGGTGTAGATTTTATAATTATTGCAAG
genomic: TTGGGGATAAACTTCTTAAGGCATATGTTGTTGCTGATCCAGAAATTCAGgtaatcttat ... aaatgcttagGAAGAAGAAATTGATGGTGTAGATTTTATAATTATTGCAAG
EST: gi|110377520|gb|EC942589.1|EC942589
EST:     TTGGGGATAAACTTCTTAAGGCATATGTTGTTGCTGATCCAGAAATTCAG                         GAAGAAGAAATTGATGGTGTAGATTTTATAATTATTGCAAGTGATGGACTT
genomic: TTGGGGATAAACTTCTTAAGGCATATGTTGTTGCTGATCCAGAAATTCAGgtaatcttat ... aaatgcttagGAAGAAGAAATTGATGGTGTAGATTTTATAATTATTGCAAGTGATGGACTT
EST: gi|351021784|gb|FQ437169.1|FQ437169
EST:     TGGGGATAAACTTCTTAAAGGCATATGTTGTTGCTGATCCAGAAATTCAC                         GAAGAACAAATTGATGGTGTAGATTTTATAATTATTTGTAAGTGATGGACT
genomic: TGGGGATAAACTTCTTAA-GGCATATGTTGTTGCTGATCCAGAAATTCAGgtaatcttat ... aaatgcttagGAAGAAGAAATTGATGGTGTAGATTTTATAATTATT-GCAAGTGATGGACT
EST: gi|351046056|gb|FQ441439.1|FQ441439
EST:     TTGGGGATAAACTTCTTAAGGCATATGTTGTTGCTGATCCAGAAATTCAG                         GAAGAAGAAATTGATGGTGTAGATTTTATAATTATTGCAAGTGATGGACTT
genomic: TTGGGGATAAACTTCTTAAGGCATATGTTGTTGCTGATCCAGAAATTCAGgtaatcttat ... aaatgcttagGAAGAAGAAATTGATGGTGTAGATTTTATAATTATTGCAAGTGATGGACTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tactatatttccactccacttgttgctcatgaagttatccctttcaaatgcttagGAAGAAGAAATTGATGGTGTAGATTTTATAATTATTGCAAGTGATGGACTTTGGAATGTCTTATCAAATAAG
                                     tccctttca  CT-rich tract
                                         tttcaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttggattttttgtattaaagtttaactttattgtcttgtctttatactatatttccactccacttgttgctcatgaagttatccctttcaaatgcttagGAAGAAGAAATTGATGGTGTAGATTTTATAATTATTGCAAGTGATGGACTTTGGAATGTCTTATCAAATAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - tgtcttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctcatga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccctttc