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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gacccatataacaattttaatattaaagtactggtaaaatcatatttttaacatggagattgcctcccatctaactgcctatcatgaacttttcttgcagGGGTTGGTCAGCAGAACCTATCATTTTCAGAGGTCATACAGATGGTGTATCTGGATTTTCTGTATGGGGCCAAGATATAATTTCAATTTCCAAAAACAAG

Basic information

species Vitis vinifera
transcript Vv05s0020g00560.t01
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0020g00560.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: GLYMA20G28920.1 (Glycine max), 3'ss of exon 8
-gacccatataacaattttaatattaaagtactggtaaaatcatatttttaacatggagattgcctcccatctaactgcctatcatgaacttttcttgcagGGGTTGGTCAGCAGAACCTATCATTTTCAGAGGTCATACAGATGGTGTATCTGGATTTTCTGTATGGGGCCAAGATATAATTTCAATTTCCAAAAACAAG
      |||||    |   |  |   || |   ||| | |   | | |||  |||     |        |||     ||| ||| |    | | ||||||||  |  | ||    | || || ||||||||||||||| |||||||  ||||  | || || || |||||||||||| | ||||||||||||   || |  
ttgaagatatattcctaaaagaacctaaatgaaggtgataagctttctttctcatttccgtaaggatatatcctgaagcccatc-tctgttatccttgcagGAATCTGCCATTGCAGCCCATTATTTTCAGAGGTCATTCAGATGGCATATCCAGTTTCTCCGTTTGGGGCCAAGATGTTATTTCAATTTCCCGGAATAGA
















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|26264567|gb|CA815630.1|CA815630
EST:     CTCGTGTCCAGCTCTCTTGATAGGACTTTACGAATTTGGGATCTCAGAAG                         GGGATGGTCAGCAGAACCTATCATTTTCAGAGGTCATACAGATGGTGTATC
genomic: CTCGTGTCCAGCTCTCTTGATAGGACTTTACGAATTTGGGACCTCAGAAGgtaataacaa ... tttcttgcagGGGTTGGTCAGCAGAACCTATCATTTTCAGAGGTCATACAGATGGTGTATC
EST: gi|110372279|gb|EC936432.1|EC936432
EST:     CTCGTGTCCAGCTCTCTTGATAGGACTTTACGAATTTGGGATCTCAGAAG                         GGGTTGGTCAGCAGAACCTATCATTTTCAGAGGTCATACAGATGGTGTATC
genomic: CTCGTGTCCAGCTCTCTTGATAGGACTTTACGAATTTGGGACCTCAGAAGgtaataacaa ... tttcttgcagGGGTTGGTCAGCAGAACCTATCATTTTCAGAGGTCATACAGATGGTGTATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttaacatggagattgcctcccatctaactgcctatcatgaacttttcttgcagGGGTTGGTCAGCAGAACCTATCATTTTCAGAGGTCATACAGATGGTGTATCTGGATTTTCTGTATGGGGCCAAGATATAATTTCAATTTCCAAAAACAAG
                       atctaac  putative branch site (score: 2)
                                           cttttcttgc  putative PPT
                                         aactttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gacccatataacaattttaatattaaagtactggtaaaatcatatttttaacatggagattgcctcccatctaactgcctatcatgaacttttcttgcagGGGTTGGTCAGCAGAACCTATCATTTTCAGAGGTCATACAGATGGTGTATCTGGATTTTCTGTATGGGGCCAAGATATAATTTCAATTTCCAAAAACAAG

-acccata
- - - - -aacaatt
- - - - - - - - - - - - - - - - ggtaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - -catggag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -actgcct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catgaac