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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttcctgtagacagcttcatgtgcttggtttttgtgatcttattattttttgacataaagacacggcctgaccagagattgcttcatttttgctgtgtagCACACGGGCTTAAGAGGCTCAATTGACCCACTGCTAGAGGAAGCTGATATTGACAAAGATGGGAGGATAAGCTTGGCAGAATTCCGAAGGCTTCTAAGAA

Basic information

species Vitis vinifera
transcript Vv04s0023g03420.t01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0023g03420.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA16G23870.2 (Glycine max), 3'ss of exon 13
tttcctgtagacagcttca--tgtgcttggtttttgtgatcttattattttttgacataaagacacggcctgaccagagattgcttcatttttgctgtgtagCACACGGGCTTAAGAGGCTCAATTGACCCACTGCTAGAGGAAGCTGATATTGACAAAGATGGGAGGATAAGCTTGGCAGAATTCCGAAGGCTTCTAAGAA
     | |    || || |   |||| |   | |    ||   | |      | |  || | |||  |      |||  | |  | | |||| ||| |  |||| ||  |||| ||||||||  |||| ||  ||||||||||||||||||||||||||||||| |  |||||| |  |||| || || || ||||| ||||
--agatctgcttagtttgagccgtgcatatctgtaaaaataaaagttaaaaataatttacatacatagttgctgcagctaatattcctttttggcttttcagCATACATGCTTGAGAGGCTCCGTTGATCCTTTGCTAGAGGAAGCTGATATTGACAAAGATGGAAAAATAAGCCTACCAGAGTTTCGGAGACTTCTTAGAA

upper sequence: Vv04s0023g03420.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA02G05440.1 (Glycine max), 3'ss of exon 11
tttcctgtagacagcttcatgtgcttggtttttgtgatcttattattttt---tgacataaagacacggcctgaccagagattgcttcatttttgctgtgtagCACACGGGCTTAAGAGGCTCAATTGACCCACTGCTAGAGGAAGCTGATATTGACAAAGATGGGAGGATAAGCTTGGCAGAATTCCGAAGGCTTCTAAGAA
  ||   |   ||| || |  || |   | | ||| |   ||  | ||     | |  || | |||  |      |||  | |  | | |||| ||| |  |||| ||  |||| ||||||||  |||| ||  ||||||||||||||||||||||||||||||| |  |||||| |  |||| || || || || |||||||
--tctgcttctcagtttgagctg-tgaatatctgtaaaaataaaagttaaaaataatttacatacatagttgctgcagctaattttcctttttggcttttcagCATACATGCTTGAGAGGCTCCGTTGATCCTTTGCTAGAGGAAGCTGATATTGACAAAGATGGAAAAATAAGCCTACCAGAGTTTCGTAGACTCCTAAGAA
















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|110716188|gb|EE090961.1|EE090961
EST:     GATGGGTTCATAACCCCAGAGGAACTTAAACTG                         CACACGGGCTTAAGAGGCTCAATTGACCCACTGCTAGAGGAAGCTGATATT
genomic: GATGGGTTCATAACCCCAGAGGAACTTAAACTGgtgagtttta ... tgctgtgtagCACACGGGCTTAAGAGGCTCAATTGACCCACTGCTAGAGGAAGCTGATATT
EST: gi|30126914|gb|CB912253.1|CB912253
EST:     CCCAGAGGAACTTAAACTG                         CACACGGGCTTAAGAGGCTCAATTGACCCACTGCTAGAGGAAGCTGATATT
genomic: CCCAGAGGAACTTAAACTGgtgagtttta ... tgctgtgtagCACACGGGCTTAAGAGGCTCAATTGACCCACTGCTAGAGGAAGCTGATATT
EST: gi|30128033|gb|CB913372.1|CB913372
EST:     AATTTGATGTGGATAGGGATGGGTTCATAACCCCAGAGGAACTTAAACTG                         CACACGGGCTTAAGAGGCTCAATTGACCCACTGCTAGAGGAAGCTGATATT
genomic: AATTTGATGTGGATAGGGATGGGTTCATAACCCCAGAGGAACTTAAACTGgtgagtttta ... tgctgtgtagCACACGGGCTTAAGAGGCTCAATTGACCCACTGCTAGAGGAAGCTGATATT
EST: gi|352773310|gb|FQ470897.1|FQ470897
EST:     AATTTGATGTGGATAGGGATGGGTTCATAACCCCAGAGGAACTTAAACTG                         CACACGGGCTTAAGAGGCTCAATTGACCCACTGCTAGAGGAAGCTGATATT
genomic: AATTTGATGTGGATAGGGATGGGTTCATAACCCCAGAGGAACTTAAACTGgtgagtttta ... tgctgtgtagCACACGGGCTTAAGAGGCTCAATTGACCCACTGCTAGAGGAAGCTGATATT
EST: gi|30255795|gb|CB971927.1|CB971927
EST:     AATTTGATGTGGATAGGGATGGGTTCATAACCCCAGAGGAACTTAAACTG                         CACACGGGCTTAAGAGGCTCAATTGACCCACTGCTAGAGGAAGCTGATATT
genomic: AATTTGATGTGGATAGGGATGGGTTCATAACCCCAGAGGAACTTAAACTGgtgagtttta ... tgctgtgtagCACACGGGCTTAAGAGGCTCAATTGACCCACTGCTAGAGGAAGCTGATATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttttgacataaagacacggcctgaccagagattgcttcatttttgctgtgtagCACACGGGCTTAAGAGGCTCAATTGACCCACTGCTAGAGGAAGCTGATATTGACAAAGATGGGAGGATAAGCTTGGCAGAATTCCGAAGGCTTCTAAGAA
                    gcctgac  putative branch site (score: 3)
                                    cttcattttt  putative PPT
                                     ttcattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttcctgtagacagcttcatgtgcttggtttttgtgatcttattattttttgacataaagacacggcctgaccagagattgcttcatttttgctgtgtagCACACGGGCTTAAGAGGCTCAATTGACCCACTGCTAGAGGAAGCTGATATTGACAAAGATGGGAGGATAAGCTTGGCAGAATTCCGAAGGCTTCTAAGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
-ttcctgt
- - - - - - - - -catgtgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - ataaaga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cctgacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcttca