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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttctgcataatctaagagtgaattctgtggatttgttaatgtttactgcttctgttttttattctttctaaagtaaagtatttgtgtttatgggtttagGTTGAAACCCAAAAAGAAGAACCAAAAGAGGCAGAGAGAGCCGAGATTTGCGTTCATCACCAAGAGCGAAGTTGATCATCTTGACGATGGATACAGATGG

Basic information

species Vitis vinifera
transcript Vv05s0077g00730.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0077g00730.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA07G36640.1 (Glycine max), 3'ss of exon 1
tttctgcataatctaagagtgaattctgtggatttgttaatgtttactgcttctgttttttattctttctaaagtaaagtatttgtgtttatgggtttagGTTGAAACCCAAAAAGAAGAACCAAAAGAGGCAGAGAGAGCCGAGATTTGCGTTCATCACCAAGAGCGAAGTTGATCATCTTGACGATGGATACAGATGG
||  |    | |      ||   || |    | || |||   |  |   |  |       | ||  |  | |       |   |    ||    | ||||| | || || ||||||||||||||||||| ||| |||||||| |||||||||||||| || ||||| ||||| ||||| || |||||||| |||||||||
ttaattttgatttcttatgtttgttgttataacttattataatgaaacccaacaaaaacatgttaataattattggtttttgctaaaattccatgcttagGCTCAAGCCAAAAAAGAAGAACCAAAAGAAGCAAAGAGAGCCAAGATTTGCGTTCATGACAAAGAGTGAAGTGGATCACCTCGACGATGGCTACAGATGG

upper sequence: Vv05s0077g00730.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA17G03950.2 (Glycine max), 3'ss of exon 1
---------tttctgcataatctaagagtgaattctgtggatttgttaatgtttactgcttctgttttttattctttctaaagtaaagtatttgtgtttatgggtttagGTTGAAACCCAAAAAGAAGAACCAAAAGAGGCAGAGAGAGCCGAGATTTGCGTTCATCACCAAGAGCGAAGTTGATCATCTTGACGATGGATACAGATGG
         | | ||       ||  |   ||  |     |      ||     |    | |   |  |||||  || |    | || |       |  |||   ||||| | || || ||||||||||||||||| | ||| ||||||||||||||||||||||| || ||||| ||||| ||||| || |||||||| || ||||||
gatttcttatgtttgttgttattataatgaaacccaacaaaaacaaaaacaaaaaaacatgccaataattattggttttttgctcaaat-------tccatg--cttagGCTCAAGCCAAAAAAGAAGAACCAAAAAAAGCAAAGAGAGCCGAGATTTGCGTTCATGACAAAGAGTGAAGTGGATCACCTCGACGATGGCTATAGATGG
















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|156737123|gb|EV241244.1|EV241244
EST:     CTAAAGC-GCGGGAGGAGGAAGAGCAAGATCAGGAGAAGAATAAGCAACA                         GTTGAAACCCAAAAAGAAGAACCAAAAGAGGCAGAGAGAGCCGAGATTTGC
genomic: CTAAAGCGGC-GGAGGAGGAAGAGCAAGATCAGGAGAAGAATAAGCAACAgtgagttccc ... atgggtttagGTTGAAACCCAAAAAGAAGAACCAAAAGAGGCAGAGAGAGCCGAGATTTGC
EST: gi|110719220|gb|EE096949.1|EE096949
EST:     ACTAAAGCGGCGGAGGAGGAAGAGCAAGATCAGGAGAAGAATAAGCAACA                         GTTGAAACCCAAAAAGAAGAACCAAAAGAGGCAGAGAGAGCCGAGATTTGC
genomic: ACTAAAGCGGCGGAGGAGGAAGAGCAAGATCAGGAGAAGAATAAGCAACAgtgagttccc ... atgggtttagGTTGAAACCCAAAAAGAAGAACCAAAAGAGGCAGAGAGAGCCGAGATTTGC
EST: gi|22014586|gb|BQ799620.1|BQ799620
EST:     ACTAAAGCGGC-GAGGAGGAAGAGCAAGATCAGGAGAAGAATAAGCAACA                         GTTGAAACCCAAAAAGAAG-ACCAAAAGAGGCAGAGAGAGCCGAGATTTGC
genomic: ACTAAAGCGGCGGAGGAGGAAGAGCAAGATCAGGAGAAGAATAAGCAACAgtgagttccc ... atgggtttagGTTGAAACCCAAAAAGAAGAACCAAAAGAGGCAGAGAGAGCCGAGATTTGC
EST: gi|71858820|gb|DT007875.1|DT007875
EST:     ACTAAAGCGGCGGAGGAGGAAGAGCAAGATCAGGAGAAGAATAAGCAACA                         GTTGAAACCCAAAAAGAAGAACCAAAAGAGGCAGAGAGAGCCGAGATTTGC
genomic: ACTAAAGCGGCGGAGGAGGAAGAGCAAGATCAGGAGAAGAATAAGCAACAgtgagttccc ... atgggtttagGTTGAAACCCAAAAAGAAGAACCAAAAGAGGCAGAGAGAGCCGAGATTTGC
EST: gi|22014202|gb|BQ799236.1|BQ799236
EST:     ACTAAAGCGGCGGAGGAGGAAGAGCAAGATCAGGAGAAGAATAAGCACCA                         GTTGAACCCCAAAAAGAAGACCCAAAAGAGGCAGAGAGAGCCGAGATTTGC
genomic: ACTAAAGCGGCGGAGGAGGAAGAGCAAGATCAGGAGAAGAATAAGCAACAgtgagttccc ... atgggtttagGTTGAAACCCAAAAAGAAGAACCAAAAGAGGCAGAGAGAGCCGAGATTTGC
EST: gi|110712223|gb|EE089600.1|EE089600
EST:     ACTAAAGCGGCGGAGGAGGAAGAGCAAGATCAGGAGAAGAATAAGCAACA                         GTTGAAACCCAAAAAGAAGAACCAAAAGAGGCAGAGAGAGCCGAGATTTGC
genomic: ACTAAAGCGGCGGAGGAGGAAGAGCAAGATCAGGAGAAGAATAAGCAACAgtgagttccc ... atgggtttagGTTGAAACCCAAAAAGAAGAACCAAAAGAGGCAGAGAGAGCCGAGATTTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actgcttctgttttttattctttctaaagtaaagtatttgtgtttatgggtttagGTTGAAACCCAAAAAGAAGAACCAAAAGAGGCAGAGAGAGCCGAGATTTGCGTTCATCACCAAGAGCGAAGTTGATCATCTTGACGATGGATACAGATGG
                     ttctaaa  putative branch site (score: 2)
          ttttttattctttcta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttctgcataatctaagagtgaattctgtggatttgttaatgtttactgcttctgttttttattctttctaaagtaaagtatttgtgtttatgggtttagGTTGAAACCCAAAAAGAAGAACCAAAAGAGGCAGAGAGAGCCGAGATTTGCGTTCATCACCAAGAGCGAAGTTGATCATCTTGACGATGGATACAGATGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- -ctgcata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aagtaaa