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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agtcaaatcctgggattttgacctgggactgaatcttatagctagaaatggagccttggtattgacattttcatctgttttttttcctgatgaaccgcagCATTTCTTTGCATCAATTGAGAAAGCAAAGAGCGTTCTTGGGTGGAAACCCGAATTCGACCTGGTGGAAGGTCTTGCAGATTCATACAACCTGGATTTTG

Basic information

species Vitis vinifera
transcript Vv14s0060g00820.t01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0060g00820.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA19G41540.2 (Glycine max), 3'ss of exon 9
--agtcaaatcctgggattttgacctggg-actgaatcttatagctagaaatggagccttggt-attgacattttcatctgttttttttcctgatgaaccgcagCATTTCTTTGCATCAATTGAGAAAGCAAAGAGCGTTCTTGGGTGGAAACCCGAATTCGACCTGGTGGAAGGTCTTGCAGATTCATACAACCTGGATTTTG
  | | || |      |     | |||      |  |  | |    |    || |    || | | | | |||   || | | |||||   || ||    |||||||||||||||||||||||||||||||||||| || ||||||||| |||| ||||| |  || || || ||||||||||| || ||||||||||| ||||
taatttaattaacaaaagaaaaaactgaatggcgtgttcttttttcattggtgaaattatgatgaataatattgatattt-tatttttctttgttg---tgcagCATTTCTTTGCATCAATTGAGAAAGCAAAGAGAGTGCTTGGGTGGGAACCTGAATTTGGGCTTGTAGAGGGTCTTGCAGACTCGTACAACCTGGACTTTG

upper sequence: Vv14s0060g00820.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA03G38930.1 (Glycine max), 3'ss of exon 9
------------------------------------------------------------------------------------------agtcaaatcctgggattttga-cctgggactgaatcttatagctagaaatggag---ccttggtattgacattttcatctgttttttttcctgatgaaccgcagCATTTCTTTGCATCAATTGAGAAAGCAAAGAGCGTTCTTGGGTGGAAACCCGAATTCGACCTGGTGGAAGGTCTTGCAGATTCATACAACCTGGATTTTG
                                                                                          | | | || |||  | |   | | |   |   ||  | | | ||       |||     ||   |||| |    | ||    |||  ||     |     ||||||||||||||||||| ||||||||||||||||||| ||||| | | |||| ||||| |  || || || ||||| ||||| || ||||||||||| ||||
gtgataaaaacaaccacacaaatcagatacaatatgaaaagtgtttgtaacttgtatagtttattaaaaattgacataattatatagtctaatgatatactgaaagtagaaacatattaacaaaagtaaaaactgagtggcgagttctttttacattggcgaaataatgatatttaattttcattattgtgcagCATTTCTTTGCATCAGTTGAGAAAGCAAAGAGCGTGCTTGGATTGGAACCTGAATTTGGACTTGTAGAGGGTCTAGCAGACTCGTACAACCTGGACTTTG

upper sequence: Vv14s0060g00820.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: AT1G09340.1 (Arabidopsis thaliana), 3'ss of exon 9
agtcaaatcc-tgggattttgac--ctgggactgaatcttatagctagaaatggagccttggtattgacattttcatctgttttttttcctgatgaaccgcagCATTTCTTTGCATCAATTGAGAAAGCAAAGAGCGTTCTTGGGTGGAAACCCGAATTCGACCTGGTGGAAGGTCTTGCAGATTCATACAACCTGGATTTTG
 || ||| ||      || | |     | | ||| | | |  |      | |  |   | |   |||| ||||| || | | | | |||          ||||||||||||||||||  | ||||||||||||   || || || |||||||| || |||||| | ||||| |||||  | || ||||||||||| ||||| |
-gtaaaaaccacaacgttctaatgatcgaggctgcaacatgaac----gattccaatttagaagttgagattttgatatatgtatattctc------ttgcagCATTTCTTTGCATCGGTGGAGAAAGCAAAGCATGTCCTCGGATGGAAACCGGAGTTCGACTTAGTGGAGGGTCTCACTGACTCATACAACCTTGATTTCG

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|351016728|gb|FQ424155.1|FQ424155
EST:     CCAAGGAGTTCGATTTTGGCAAAAAGAAAGCATTCCCATTCCGTGACCAG                         CATTTCTTTGCATCAATTGAGAAAGCGAAGAGCGTTCTTGGGTGGAAACCC
genomic: CCAAGGAGTTCGATTTTGGCAAAAAGAAAGCATTCCCATTCCGTGACCAGgtaaaaatgg ... tgaaccgcagCATTTCTTTGCATCAATTGAGAAAGCAAAGAGCGTTCTTGGGTGGAAACCC
EST: gi|110377806|gb|EC942895.1|EC942895
EST:     CCAAGGAGTTCGATTTTGGCAAAAAGAAAGCATTCCCATTCCGTGACCAG                         CATTTCTTTGCATCAATTGAGAAAGCGAAGAGCGTTCTTGGGTGGAAACCC
genomic: CCAAGGAGTTCGATTTTGGCAAAAAGAAAGCATTCCCATTCCGTGACCAGgtaaaaatgg ... tgaaccgcagCATTTCTTTGCATCAATTGAGAAAGCAAAGAGCGTTCTTGGGTGGAAACCC
EST: gi|349817662|gb|FQ407651.1|FQ407651
EST:     TCAAGGAGTTCGATTTTGGCAAAAAGAAAGCATTCCCATTCCGTGACCAG                         CATTTCTTTGCATCAATTGAGAAAGCGAAGAGCGTTCTTGGGTGGAAACCC
genomic: CCAAGGAGTTCGATTTTGGCAAAAAGAAAGCATTCCCATTCCGTGACCAGgtaaaaatgg ... tgaaccgcagCATTTCTTTGCATCAATTGAGAAAGCAAAGAGCGTTCTTGGGTGGAAACCC
EST: gi|110382725|gb|EC947045.1|EC947045
EST:     CCAAGGAGTTCGATTTTGGCAAAAAGAAAGCATTCCCATTCCGTGACCAG                         CATTTCTTTGCATCAATTGAGAAAGCAAAGAGCGTTCTTGGGTGGAAACCC
genomic: CCAAGGAGTTCGATTTTGGCAAAAAGAAAGCATTCCCATTCCGTGACCAGgtaaaaatgg ... tgaaccgcagCATTTCTTTGCATCAATTGAGAAAGCAAAGAGCGTTCTTGGGTGGAAACCC
EST: gi|351052362|gb|FQ455534.1|FQ455534
EST:     CCAAGGAGTTCGATTTTGGCAAAAAGAAAGCATTCCCATTCCGTGACCAG                         CATTTCTTTGCATCAATTGAGAAAGCGAAGAGCGTTCTTGGGTGGAAACCC
genomic: CCAAGGAGTTCGATTTTGGCAAAAAGAAAGCATTCCCATTCCGTGACCAGgtaaaaatgg ... tgaaccgcagCATTTCTTTGCATCAATTGAGAAAGCAAAGAGCGTTCTTGGGTGGAAACCC
EST: gi|110417826|gb|EC983913.1|EC983913
EST:     CCAAGGAGTTCGATTTTGGCAAAAAGAAAGCATTCCCATTCCGTGACCAG                         CATTTCTTTGCATCAATTGAGAAAGCGAAGAGCGTTCTTGGGTGGAAACCC
genomic: CCAAGGAGTTCGATTTTGGCAAAAAGAAAGCATTCCCATTCCGTGACCAGgtaaaaatgg ... tgaaccgcagCATTTCTTTGCATCAATTGAGAAAGCAAAGAGCGTTCTTGGGTGGAAACCC
EST: gi|349825173|gb|FQ415720.1|FQ415720
EST:     CCAAGGAGTTCGATTTTGGCAAAAAGAAAGCATTCCCATTCCGTGACCAG                         CATTTCTTTGCATCAATTGAGAAAGCGAAGAGCGTTCTTGGGTGGAAACCC
genomic: CCAAGGAGTTCGATTTTGGCAAAAAGAAAGCATTCCCATTCCGTGACCAGgtaaaaatgg ... tgaaccgcagCATTTCTTTGCATCAATTGAGAAAGCAAAGAGCGTTCTTGGGTGGAAACCC
EST: gi|351052958|gb|FQ453945.1|FQ453945
EST:     TCAAGGAGTTCGATTTTGGCAAAAAGAAAGCATTCCCATTCCGTGACCAG                         CATTTCTTTGCATCAATTGAGAAAGCGAAGAGCGTTCTTGGGTGGAAACCC
genomic: CCAAGGAGTTCGATTTTGGCAAAAAGAAAGCATTCCCATTCCGTGACCAGgtaaaaatgg ... tgaaccgcagCATTTCTTTGCATCAATTGAGAAAGCAAAGAGCGTTCTTGGGTGGAAACCC
EST: gi|110380012|gb|EC945247.1|EC945247
EST:     CCAAGGAGTTCGATTTTGGCAAAAAGAAAGCATTCCCATTCCGTGACCAG                         CATTTCTTTGCATCAATTGAGAAAGCGAAGAGCGTTCTTGGGTGGAAACCC
genomic: CCAAGGAGTTCGATTTTGGCAAAAAGAAAGCATTCCCATTCCGTGACCAGgtaaaaatgg ... tgaaccgcagCATTTCTTTGCATCAATTGAGAAAGCAAAGAGCGTTCTTGGGTGGAAACCC
EST: gi|352773974|gb|FQ473106.1|FQ473106
EST:     CCAAGGAGTTCGATTTTGGCAAAAAGAAAGCATTCCCATTCCGTGACCAG                         CATTTCTTTGCATCAATTGAGAAAGCAAAGAGCGTTCTTGGGTGGAAACCC
genomic: CCAAGGAGTTCGATTTTGGCAAAAAGAAAGCATTCCCATTCCGTGACCAGgtaaaaatgg ... tgaaccgcagCATTTCTTTGCATCAATTGAGAAAGCAAAGAGCGTTCTTGGGTGGAAACCC
EST: gi|110363102|gb|EC926672.1|EC926672
EST:     CCAAGGAGTTCGATTTTGGCAAAAAGAAAGCATTCCCATTCCGTGACCAG                         CATTTCTTTGCATCAATTGAGAAAGCGAAGAGCGTTCTTGGGTGGAAACCC
genomic: CCAAGGAGTTCGATTTTGGCAAAAAGAAAGCATTCCCATTCCGTGACCAGgtaaaaatgg ... tgaaccgcagCATTTCTTTGCATCAATTGAGAAAGCAAAGAGCGTTCTTGGGTGGAAACCC
EST: gi|26259188|gb|CA810251.1|CA810251
EST:     CCAAGGAGTT-GATTTTGGCAAAAAGAAAGCATTCCCATTCCGTGACCAG                         CATTTCTTTGCATCAATTGAGAAAGCAAAGAGCGTTCTTGGGTGGAAACCC
genomic: CCAAGGAGTTCGATTTTGGCAAAAAGAAAGCATTCCCATTCCGTGACCAGgtaaaaatgg ... tgaaccgcagCATTTCTTTGCATCAATTGAGAAAGCAAAGAGCGTTCTTGGGTGGAAACCC
EST: gi|349814545|gb|FQ399185.1|FQ399185
EST:     CCAAGGAGTTCGATTTTGGCAAAAAGAGAGCATTCCCATTCCGTGACCAG                         CATTTCTTTGCATCAGTTGAGAAAGCGAAGAGCGTTCTTGCGTGGAAACCC
genomic: CCAAGGAGTTCGATTTTGGCAAAAAGAAAGCATTCCCATTCCGTGACCAGgtaaaaatgg ... tgaaccgcagCATTTCTTTGCATCAATTGAGAAAGCAAAGAGCGTTCTTGGGTGGAAACCC
EST: gi|351012098|gb|FQ429904.1|FQ429904
EST:     TCAAGGAGTTCGATTTTGGCAAAAAGAAAGCATTCCCATTCCGTGACCAG                         CATTTCTTTGCATCAATTGAGAAAGCGAAGAGCGTTCTTGGGTGGAAACCC
genomic: CCAAGGAGTTCGATTTTGGCAAAAAGAAAGCATTCCCATTCCGTGACCAGgtaaaaatgg ... tgaaccgcagCATTTCTTTGCATCAATTGAGAAAGCAAAGAGCGTTCTTGGGTGGAAACCC
EST: gi|110367551|gb|EC931488.1|EC931488
EST:     CCAAGGAGTTCGATTTTGGCAAAAAGAAAGCATTCCCATTCCGTGACCAG                         CATTTCTTTGCATCAATTGAGAAAGCGAAGAGCGTTCTTGGGTGGAAACCC
genomic: CCAAGGAGTTCGATTTTGGCAAAAAGAAAGCATTCCCATTCCGTGACCAGgtaaaaatgg ... tgaaccgcagCATTTCTTTGCATCAATTGAGAAAGCAAAGAGCGTTCTTGGGTGGAAACCC
EST: gi|110418366|gb|EC984513.1|EC984513
EST:     TCGATTTTGGCAAAAAGAAAGCATTCCCATTCCGTGACCAG                         CATTTCTTTGCATCAATTGAGAAAGCAAAGAGCGTTCTTGGGTGGAAACCC
genomic: TCGATTTTGGCAAAAAGAAAGCATTCCCATTCCGTGACCAGgtaaaaatgg ... tgaaccgcagCATTTCTTTGCATCAATTGAGAAAGCAAAGAGCGTTCTTGGGTGGAAACCC
EST: gi|110378072|gb|EC943185.1|EC943185
EST:     CCAAGGAGTTCGATTTTGGCAAAAAGAAAGCATTCCCATTCCGTGACCAG                         CATTTCTTTGCATCAATTGAGAAAGCAAAGAGCGTTCTTGGGTGGAAACCC
genomic: CCAAGGAGTTCGATTTTGGCAAAAAGAAAGCATTCCCATTCCGTGACCAGgtaaaaatgg ... tgaaccgcagCATTTCTTTGCATCAATTGAGAAAGCAAAGAGCGTTCTTGGGTGGAAACCC
EST: gi|351057074|gb|FQ450781.1|FQ450781
EST:     CCAAGGAGTTCGATTTTGGCAAAAAGAAAGCATTCCCATTCCGTGACCAG                         CATTTCTTTGCATCAATTGAGAAAGCGAAGAGCGTTCTTGGGTGGAAACCC
genomic: CCAAGGAGTTCGATTTTGGCAAAAAGAAAGCATTCCCATTCCGTGACCAGgtaaaaatgg ... tgaaccgcagCATTTCTTTGCATCAATTGAGAAAGCAAAGAGCGTTCTTGGGTGGAAACCC
EST: gi|351016507|gb|FQ423934.1|FQ423934
EST:     CCAAGGAGTTCGATTTTGGCAAAAAGAAAGCATTCCCATTCCGTGACCAG                         CATTTCTTTGCATCAATTGAGAAAGCGAAGAGCGTTCTTGGGTGGAAACCC
genomic: CCAAGGAGTTCGATTTTGGCAAAAAGAAAGCATTCCCATTCCGTGACCAGgtaaaaatgg ... tgaaccgcagCATTTCTTTGCATCAATTGAGAAAGCAAAGAGCGTTCTTGGGTGGAAACCC
EST: gi|352763325|gb|FQ471637.1|FQ471637
EST:     CCAAGGAGTTCGATTTTGGCAAAAAGAAAGCATTCCCATTCCGTGACCAG                         CATTTCTTTGCATCAATTGAGAAAGCAAAGAGCGTTCTTGGGTGGAAACCC
genomic: CCAAGGAGTTCGATTTTGGCAAAAAGAAAGCATTCCCATTCCGTGACCAGgtaaaaatgg ... tgaaccgcagCATTTCTTTGCATCAATTGAGAAAGCAAAGAGCGTTCTTGGGTGGAAACCC
EST: gi|349823731|gb|FQ415142.1|FQ415142
EST:     TCAAGGAGTTCGATTTTGGCAAAAAGAAAGCATTCCCATTCCGTGACCAG                         CATTTCTTTGCATCAATTGAGAAAGCGAAGAGCGTTCTTGGGTGGAAACCC
genomic: CCAAGGAGTTCGATTTTGGCAAAAAGAAAGCATTCCCATTCCGTGACCAGgtaaaaatgg ... tgaaccgcagCATTTCTTTGCATCAATTGAGAAAGCAAAGAGCGTTCTTGGGTGGAAACCC
EST: gi|110721160|gb|EE097838.1|EE097838
EST:     CCAAGGAGTTCGATTTTGGCAAAAAGAAAGCATTCCCATTCCGTGACCAG                         CATTTCTTTGCATCAATTGAGAAAGCGAAGAGCGTTCTTGGGTGGAAACCC
genomic: CCAAGGAGTTCGATTTTGGCAAAAAGAAAGCATTCCCATTCCGTGACCAGgtaaaaatgg ... tgaaccgcagCATTTCTTTGCATCAATTGAGAAAGCAAAGAGCGTTCTTGGGTGGAAACCC
EST: gi|349825174|gb|FQ415721.1|FQ415721
EST:     CCAAGGAGTTCGATTTTGGCAAAAAGAAAGCATTCCCATTCCGTGACCAG                         CATTTCTTTGCATCAATTGAGAAAGCGAAGAGCGTTCTTGGGTGGAAACCC
genomic: CCAAGGAGTTCGATTTTGGCAAAAAGAAAGCATTCCCATTCCGTGACCAGgtaaaaatgg ... tgaaccgcagCATTTCTTTGCATCAATTGAGAAAGCAAAGAGCGTTCTTGGGTGGAAACCC
EST: gi|26259994|gb|CA811057.1|CA811057
EST:     CCAAGGAGTT-GATTTTGGCAAAAAGAAAGCATTCCCATTCCGTGACCAG                         CATTTCTTTGCATCAATTGAGAAAGCAAAGAGCGTTCTTGGGTGGAAACCC
genomic: CCAAGGAGTTCGATTTTGGCAAAAAGAAAGCATTCCCATTCCGTGACCAGgtaaaaatgg ... tgaaccgcagCATTTCTTTGCATCAATTGAGAAAGCAAAGAGCGTTCTTGGGTGGAAACCC
EST: gi|110373613|gb|EC937864.1|EC937864
EST:     CCAAGGAGTTCGATTTTGGCAAAAAGAAAGCATTCCCATTCCGTGACCAG                         CATTTCTTTGCATCAATTGAGAAAGCAAAGAGCGTTCTTGGGTGGAAACCC
genomic: CCAAGGAGTTCGATTTTGGCAAAAAGAAAGCATTCCCATTCCGTGACCAGgtaaaaatgg ... tgaaccgcagCATTTCTTTGCATCAATTGAGAAAGCAAAGAGCGTTCTTGGGTGGAAACCC
EST: gi|349821496|gb|FQ408055.1|FQ408055
EST:     CCAAGGAGTTCGATTTTGGCAAAAAGAAAGCATTCCCATTCCGTGACCAG                         CATTTCTTTGCATCAATTGAGAAAAGCGAAGAGCGTTCTTGGGTGGAAACC
genomic: CCAAGGAGTTCGATTTTGGCAAAAAGAAAGCATTCCCATTCCGTGACCAGgtaaaaatgg ... tgaaccgcagCATTTCTTTGCATCAATTGAGAAA-GCAAAGAGCGTTCTTGGGTGGAAACC
EST: gi|351039971|gb|FQ465009.1|FQ465009
EST:     CCAAGGAGTTCGATTTTGGCAAAAAGAAAGCATTCCCATTCCGTGACCAG                         CATTTCTTTGCATCAATTGAGAAAGCGAAGAGCGTTCTTGGGTGGAAACCC
genomic: CCAAGGAGTTCGATTTTGGCAAAAAGAAAGCATTCCCATTCCGTGACCAGgtaaaaatgg ... tgaaccgcagCATTTCTTTGCATCAATTGAGAAAGCAAAGAGCGTTCTTGGGTGGAAACCC
EST: gi|349807769|gb|FQ402160.1|FQ402160
EST:     TCAAGGAGTTCGATTTTGGCAAAAAGAAAGCATTCCCATTCCGTGACCAG                         CATTTCTTTGCATCAATTGAGAAAGCGAAGAGCGTTCTTGGGTGGAAACCC
genomic: CCAAGGAGTTCGATTTTGGCAAAAAGAAAGCATTCCCATTCCGTGACCAGgtaaaaatgg ... tgaaccgcagCATTTCTTTGCATCAATTGAGAAAGCAAAGAGCGTTCTTGGGTGGAAACCC
EST: gi|351055049|gb|FQ440388.1|FQ440388
EST:     TCAAGGAGTTCGATTTTGGCAAAAAGAAAGCATTCCCATTCCGTGACCAG                         CATTTCTTTGCATCAATTGAGAAAGCGAAGAGCGTTCTTGGGTGGAAACCC
genomic: CCAAGGAGTTCGATTTTGGCAAAAAGAAAGCATTCCCATTCCGTGACCAGgtaaaaatgg ... tgaaccgcagCATTTCTTTGCATCAATTGAGAAAGCAAAGAGCGTTCTTGGGTGGAAACCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaatggagccttggtattgacattttcatctgttttttttcctgatgaaccgcagCATTTCTTTGCATCAATTGAGAAAGCAAAGAGCGTTCTTGGGTGGAAACCCGAATTCGACCTGGTGGAAGGTCTTGCAGATTCATACAACCTGGATTTTG
                                ttttttttcctgat  CT-rich tract
                              tgtttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agtcaaatcctgggattttgacctgggactgaatcttatagctagaaatggagccttggtattgacattttcatctgttttttttcctgatgaaccgcagCATTTCTTTGCATCAATTGAGAAAGCAAAGAGCGTTCTTGGGTGGAAACCCGAATTCGACCTGGTGGAAGGTCTTGCAGATTCATACAACCTGGATTTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- -caaatcc
- - - - - - - - - - - - - - - - - - - - - - -aaatgga