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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaacagaattcatgtctactttgacataatgaattgaatttcttataacttgcatctgtttctcctttgttttacacattgctgaccttaacacaagtagGAAATAAAGCAGTTGGTGTCATGAAGGCTGGGCAAACCTTCACAATTGAACCTATGATTAACACAG

Basic information

species Vitis vinifera
transcript Vv15s0048g00490.t01
intron # 13
splice site 3'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv15s0048g00490.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GLYMA01G33520.1 (Glycine max), 3'ss of exon 13
------gaacagaattcatgtctactttgacataatgaattgaatttcttataacttgcatctgtttctcctttgttttacacattgctgaccttaacacaagtagGAAATAAAGCAGTTGGTGTCATGAAGGCTGGGCAAACCTTCACAATTGAACCTATGATTAACACAG
         |  |   | |   | | |    | || |||   |  ||  || ||  |  |       |   |    | || |||       | | | |||  | ||||||||||||||||||||| ||||||||||| || ||||| ||||||||||| ||||| ||  | |
ttttctacccctacccccttgattcgtgttaacaaagaacaaagattgctagaaagtagaaagagaacatgtggaatgtatacac------cttaaccactggcagGAAATAAAGCAGTTGGTGTGATGAAGGCTGGACAGACCTTTACAATTGAACCAATGATCAATGCCG

upper sequence: Vv15s0048g00490.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GLYMA03G03350.1 (Glycine max), 3'ss of exon 11
----gaacagaattcatgtc--tactttgacataatgaattgaatttcttataacttgcatctgtttctcctttgttttacacattgctgaccttaacacaagtagGAAATAAAGCAGTTGGTGTCATGAAGGCTGGGCAAACCTTCACAATTGAACCTATGATTAACACAG
        ||  ||  |  |  |||      | || |||   |  ||  || ||  |  | |     |   |    | || |||       | | | |||    ||||||||||||||||||||| |||||||| || || ||||| ||||||||||||||||| ||  | |
gcacctctagcttttctacccgtaccccctaacaaagaacaaaggttgctagaaagtagaacgagaacatatggaatgtatacac------cttaatcactgtcagGAAATAAAGCAGTTGGTGTGATGAAGGCCGGACAGACCTTTACAATTGAACCTATGATCAATGCCG
















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|32268561|gb|CD717720.1|CD717720
EST:     TGGTATTGGAGAGCTGTTTCATTGTGCACCAAATATTCCCCACTATGCCA                         GAAATAAAGCAGTTGGTGTCATGAAGGCTGGGCAAACCTTCACAATTGAAC
genomic: TGGTATTGGAGAGCTGTTTCATTGTGCACCAAATATTCCCCACTATGCCAgtatcctcaa ... acacaagtagGAAATAAAGCAGTTGGTGTCATGAAGGCTGGGCAAACCTTCACAATTGAAC
EST: gi|32270889|gb|CD720048.1|CD720048
EST:     TGGTATTGGAGAGCTGTTTCATTGTGCACCANATATTCCCCACTATGCCA                         GAAATAAAGCAGTTGGTGTCATGAAGGCTGGGCAAACCTTCACAATTGAAC
genomic: TGGTATTGGAGAGCTGTTTCATTGTGCACCAAATATTCCCCACTATGCCAgtatcctcaa ... acacaagtagGAAATAAAGCAGTTGGTGTCATGAAGGCTGGGCAAACCTTCACAATTGAAC
EST: gi|110689166|gb|EE065152.1|EE065152
EST:     TGGTATTGGAGAGCTGTTTCATTGTGCACCAAATATTCCCCACTATGCCA                         GAAATAAAGCAGTTGGTGTCATGAAGGCTGGGCAAACCTTCACAATTGAAC
genomic: TGGTATTGGAGAGCTGTTTCATTGTGCACCAAATATTCCCCACTATGCCAgtatcctcaa ... acacaagtagGAAATAAAGCAGTTGGTGTCATGAAGGCTGGGCAAACCTTCACAATTGAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taacttgcatctgtttctcctttgttttacacattgctgaccttaacacaagtagGAAATAAAGCAGTTGGTGTCATGAAGGCTGGGCAAACCTTCACAATTGAACCTATGATTAACACAG
                                      gaccttaac  putative branch site 
                    tttgtttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaacagaattcatgtctactttgacataatgaattgaatttcttataacttgcatctgtttctcctttgttttacacattgctgaccttaacacaagtagGAAATAAAGCAGTTGGTGTCATGAAGGCTGGGCAAACCTTCACAATTGAACCTATGATTAACACAG

-aacagaa
- - - - -tcatgtc
- - - - - - - - - - - - - - - -aattgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gctgacc