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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgagttttctatgtcattctctctctctctcacacacacgcgcgcacatggctcttttgttaaaatgatgcattattgctagagcttttgtagatcactgactttcgtcgttgtctttgcctttgtctgcttttctaagGTTGTCCATAAGCTTTTGGGGAGGGAACTGGAGCCATGGGAAACAATTGCAGTCGGGGCTTTATCTGGTGGTCTGGCAGCTGTTGTCACAACACCTTTTG

Basic information

species Vitis vinifera
transcript Vv13s0019g03870.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0019g03870.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA20G31800.1 (Glycine max), 3'ss of exon 7
gtacgagttttctatgtcattctctctctctctcacacacacgcgcgcacatggctcttttgttaaaatgatgcattattgctagagcttttgtagatcactgactttcgtcgttgtctttgcctttgtctgcttttctaagGTTGTCCATAAGCTTTTGGGGAGGGAACTGGAGCCATGGGAAACAATTGCAGTCGGGGCTTTATCTGGTGGTCTGGCAGCTGTTGTCACAACACCTTTTG
                                |   |   || |     ||| |    |||| |    |     |  | ||      ||||  |    ||||||  |   |  ||||| | || ||||  |       | |||||| | |    ||  | | | ||||||| |  || | |||||||||||| || || ||||||||||||||  |||| |||||||| ||||| || || |
------------------------------aattgtatgtacaccttggcatagtatgtttgcttggct-----accagtgagtctcctttaatgccacactgaaatggttaattgtcatggcatttgatt-------ttagGTTGCCGAACGACTACTAGAGCGGGAACTCGGTCCCTTGGAAACAATTGCTGTTGGAGCTTTATCTGGTGGCTTGGCGGCTGTTGTTACAACGCCGTTCG

upper sequence: Vv13s0019g03870.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA10G35730.1 (Glycine max), 3'ss of exon 7
gtacgagttttctatgtcattctctctctctctcacacacacgcgcgcacatggctcttttgttaaaatgatgcattattgctagagcttttgtagatcactgactttcgtcgttgtctttgcctttgtctgcttttctaagGTTGTCCATAAGCTTTTGGGGAGGGAACTGGAGCCATGGGAAACAATTGCAGTCGGGGCTTTATCTGGTGGTCTGGCAGCTGTTGTCACAACACCTTTTG
                                             |        ||| |||  |   |   |  |       |  |    ||     |||  ||   |    |    |  |||  ||| |   |  | | ||||||   |    ||  | | | ||||||| |  || | |||||||||||| || || ||||||||||||||  |||| |||||||| ||||| || ||||
------------------------------------------ctaccagtgaatctcctttaatgccacactaaagccacattgaaatggttaattgtcatggatggtaactgagtgcaatgctattggcatttgattttagGTTGCAGAACGACTACTAGAGCGGGAACTCGGTCCCTTGGAAACAATTGCTGTTGGAGCTTTATCTGGTGGCTTGGCGGCTGTTGTTACAACGCCGTTTG
















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|30328516|gb|CD011778.1|CD011778
EST:     AGGTTCCATTCTATGTTGCGGGCATGGGGCTCTATGCCGAGTCCAAAAAG                         GTTGTCCATAAGCTTTTGGGGAGGGAACTGGAGCCATGGGAAACAATTGCA
genomic: AGGTTCCATTCTATGTTGCGGGCATGGGGCTCTATGCCGAGTCCAAAAAGgtacgagttt ... cttttctaagGTTGTCCATAAGCTTTTGGGGAGGGAACTGGAGCCATGGGAAACAATTGCA
EST: gi|30135404|gb|CB920742.1|CB920742
EST:     AGGTTCCATTCTATGTTGCGGGCATGGGGCTCTATGCCGAGTCCAAAAAG                         GTTGTCCATAAGCTTTTGGGGAGGGAACTGGAGCCATGGGAAACAATTGCA
genomic: AGGTTCCATTCTATGTTGCGGGCATGGGGCTCTATGCCGAGTCCAAAAAGgtacgagttt ... cttttctaagGTTGTCCATAAGCTTTTGGGGAGGGAACTGGAGCCATGGGAAACAATTGCA
EST: gi|30134663|gb|CB920001.1|CB920001
EST:     AGGTTCCATTCTATGTTGCGGGCATGGGGCTCTATGCCGAGTCCAAAAAG                         GTTGTCCATAAGCTTTTGGGGAGGGAACTGGAGCCATGGGAAACAATTGCA
genomic: AGGTTCCATTCTATGTTGCGGGCATGGGGCTCTATGCCGAGTCCAAAAAGgtacgagttt ... cttttctaagGTTGTCCATAAGCTTTTGGGGAGGGAACTGGAGCCATGGGAAACAATTGCA
EST: gi|161712726|gb|FC062298.1|FC062298
EST:     AGGTTCCATTCTATGTTGCGGGCATGGGGCTCTATGCCGAGTCCAAAAAG                         GTTGTCCATAAGCTTTTGGGGAGGGAACTGGAGCCATGGGAAACAATTGCA
genomic: AGGTTCCATTCTATGTTGCGGGCATGGGGCTCTATGCCGAGTCCAAAAAGgtacgagttt ... cttttctaagGTTGTCCATAAGCTTTTGGGGAGGGAACTGGAGCCATGGGAAACAATTGCA
EST: gi|110375503|gb|EC940493.1|EC940493
EST:     AGGTTCCATTCTATGTTGCGGGCATGGGGCTCTATGCCGAGTCCAAAAAG                         GTTGTCCATAAGCTTTTGGGGAGGGAACTGGAGCCATGGGAAACAATTGCA
genomic: AGGTTCCATTCTATGTTGCGGGCATGGGGCTCTATGCCGAGTCCAAAAAGgtacgagttt ... cttttctaagGTTGTCCATAAGCTTTTGGGGAGGGAACTGGAGCCATGGGAAACAATTGCA
EST: gi|30328837|gb|CD012099.1|CD012099
EST:     AGGTTCCATTCTATGTTGCGGGCATGGGGCTCTATGCCGAGTCCAAAAAG                         GTTGTCCATAAGCTTTTGGGGAGGGAACTGGAGCCATGGGAAACAATTGCA
genomic: AGGTTCCATTCTATGTTGCGGGCATGGGGCTCTATGCCGAGTCCAAAAAGgtacgagttt ... cttttctaagGTTGTCCATAAGCTTTTGGGGAGGGAACTGGAGCCATGGGAAACAATTGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttttgtagatcactgactttcgtcgttgtctttgcctttgtctgcttttctaagGTTGTCCATAAGCTTTTGGGGAGGGAACTGGAGCCATGGGAAACAATTGCAGTCGGGGCTTTATCTGGTGGTCTGGCAGCTGTTGTCACAACACCTTTTG
           cactgac  putative branch site (score: 2)
                             tctttgcctttgtctg  putative PPT
                                              ttttctaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgagttttctatgtcattctctctctctctcacacacacgcgcgcacatggctcttttgttaaaatgatgcattattgctagagcttttgtagatcactgactttcgtcgttgtctttgcctttgtctgcttttctaagGTTGTCCATAAGCTTTTGGGGAGGGAACTGGAGCCATGGGAAACAATTGCAGTCGGGGCTTTATCTGGTGGTCTGGCAGCTGTTGTCACAACACCTTTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT