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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtactggatttgactagtacttcttgattgaggataccccttctcatcagaagggatagctgtaatcgtttttggaagtcactctttatgtttgtccatgctttgcagGTTGAGGCAGCACTGATGGGAAGTAACTATGTGGATAATATAATGGTATACGCAGATCCCTTGCACAATTATTGTGTAGCTCTGGTGGTCCCTTCACATC

Basic information

species Vitis vinifera
transcript Vv12s0057g01270.t01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv12s0057g01270.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA13G11700.1 (Glycine max), 3'ss of exon 10
gtttgtactggatttgactagtacttcttgattgaggataccccttctcatcagaagggatagctgtaatcgtttttggaagtcactctttatgtttgtccatgctt---tgcagGTTGAGGCAGCACTGATGGGAAGTAACTATGTGGATAATATAATGGTATACGCAGATCCCTTGCACAATTATTGTGTAGCTCTGGTGGTCCCTTCACATC
    |||  | | |    |  |  |||| || |  ||||      |     || |||   | || ||||   ||| | |   | ||    | | ||  |     |||   ||||| |||||||||||||        || |  ||||||||||||||||||| || ||||| ||||| |||||||| ||||| ||||| || ||  |||| ||||
----gtaaagcaataccttgttcattctggaatctggatgaag--tgctgacacaagatct-gcagtaacattttctagggcttacatcatgttttcattatgacttgcttgcagATTGAGGCAGCACTATCATCGTGTGATCATGTGGATAATATAATGGTTTATGCAGACCCCTTTCACAATTACTGTGTGGCTCTAGTTGTTGCTTCGCATC

upper sequence: Vv12s0057g01270.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA20G07280.1 (Glycine max), 3'ss of exon 9
---gtttgtactggatttgactagtacttcttgattgaggataccccttctcatcagaagggatagctgtaatcgtttttggaagtcactctttatgtttgtccatgct---ttgcagGTTGAGGCAGCACTGATGGGAAGTAACTATGTGGATAATATAATGGTATACGCAGATCCCTTGCACAATTATTGTGTAGCTCTGGTGGTCCCTTCACATC
     |   ||   |  |   | ||  ||   |  ||   | |   |||  || ||||        | ||||   ||| |||   | ||    | | ||  |     ||   ||||||||||||||||||||      | || | |||||||| ||||||||||| || ||||| ||||| |||||||| ||||| ||||| || ||  ||||||| |
gtaactcaaaccataccttgttcgt-tttggagtctggataaagtactta-caccagat----ccacagtaactttttctgggccttacgtagtgttttaattatgacttacttgcagGTTGAGGCAGCACTATCATCATGTGATTATGTGGACAATATAATGGTTTATGCAGACCCCTTTCACAATTACTGTGTGGCTCTAGTTGTTGCTTCACAAC

upper sequence: Vv12s0057g01270.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA20G07060.1 (Glycine max), 3'ss of exon 9
---gtttgtactggatttgac-tagtacttcttgattgaggataccccttctcatcagaagggatagctgtaatcgtttttggaagtcactctttatgtttgtccatgctttgcagGTTGAGGCAGCACTGATGGGAAGTAACTATGTGGATAATATAATGGTATACGCAGATCCCTTGCACAATTATTGTGTAGCTCTGGTGGTCCCTTCACATC
     |   |      ||| | |  ||     ||| |||  ||||  |  |   |    || ||    |  |||  |  |    ||| | |   | | |||   | |  || ||||||||||||||||||      | || |||||||||||||||||||||| || ||||| |||||  || |||| ||||| ||||| || ||   |||| |||
gttactcaaatataccttgtcattttagaatctgaatgaa-atactgccacaagtttctagtgaatttttcaat--tcctacatagtgatttcattttttttctcttaatt-gcagGTTGAGGCAGCACTATCATCATGTGACTATGTGGATAATATAATGGTTTATGCAGACCCCTTTTACGATTACTGTGTGGCTCTAGTTGTTGTTTCATATC

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|110688644|gb|EE067428.1|EE067428
EST:     GAAAGATATTGTTAAACTACAGCATGGAGAATATATCTCCCTTGGGGAAG                         -TTGAGGCAGCACTGATGGGGAGTAACTATGTGGATAATATAATG
genomic: GAAGGATATTGTTAAACTACAGCATGGAGAATATATCTCCCTTGGG-AAGgtttgtactg ... tgctttgcagGTTGAGGCAGCACTGATGGGAAGTAACTATGTGGATAATATAATG
EST: gi|110696839|gb|EE073301.1|EE073301
EST:     AGAAGGATATTGTTAAACTACAGCATGGAGAATATATCTCCCTTGGGAAG                         GTTGAGGCAGCACTGATGGGAAGTAACTATGTGGATAATATAATGGTATAC
genomic: AGAAGGATATTGTTAAACTACAGCATGGAGAATATATCTCCCTTGGGAAGgtttgtactg ... tgctttgcagGTTGAGGCAGCACTGATGGGAAGTAACTATGTGGATAATATAATGGTATAC
EST: gi|352786143|gb|FQ478754.1|FQ478754
EST:     AGAAGGATATTGTTAAACTACAGCATGGAGAATATATCTCCCTTGGGAGG                         GTTGAGGTAGCACTGATGGGAAGTAACTATGTGGATAATATATTGGTATAC
genomic: AGAAGGATATTGTTAAACTACAGCATGGAGAATATATCTCCCTTGGGAAGgtttgtactg ... tgctttgcagGTTGAGGCAGCACTGATGGGAAGTAACTATGTGGATAATATAATGGTATAC
EST: gi|351023858|gb|FQ423281.1|FQ423281
EST:     AGAAGGATATTGTTAAACTACAGCATGGAGAATATATCTCCCTTGGGAAG                         GTTGAGGTAGCACTGATGGGAAGTAACTATGTGGATAATATAATGGTATAC
genomic: AGAAGGATATTGTTAAACTACAGCATGGAGAATATATCTCCCTTGGGAAGgtttgtactg ... tgctttgcagGTTGAGGCAGCACTGATGGGAAGTAACTATGTGGATAATATAATGGTATAC
EST: gi|110403223|gb|EC964583.1|EC964583
EST:     AGAAGGATATTGTTAAACTACAGCATGGAGAATATATCTCCCTTGGGAAG                         GTTGAGGCAGCACTGATGGGAAGTAACTATGTGGATAATATAATGGTATAC
genomic: AGAAGGATATTGTTAAACTACAGCATGGAGAATATATCTCCCTTGGGAAGgtttgtactg ... tgctttgcagGTTGAGGCAGCACTGATGGGAAGTAACTATGTGGATAATATAATGGTATAC
EST: gi|351031287|gb|FQ445312.1|FQ445312
EST:     AGAAGGATATTGTTAAACTACAGCATGGAGAATATATCTCCCTTGGGAAG                         GTTGAGGTAGCACTGATGGGAAGTAACTATGTGGATAATATAATGGTATAC
genomic: AGAAGGATATTGTTAAACTACAGCATGGAGAATATATCTCCCTTGGGAAGgtttgtactg ... tgctttgcagGTTGAGGCAGCACTGATGGGAAGTAACTATGTGGATAATATAATGGTATAC
EST: gi|349830561|gb|FQ416859.1|FQ416859
EST:     AGAAGGATATTGTTAAACTACAGCATGGAGAATATATCTCCCTTGGGAAG                         GTTGAGGTAGCACTGATGGGAAGTAACTATGTGGATAATATAATGGTATAC
genomic: AGAAGGATATTGTTAAACTACAGCATGGAGAATATATCTCCCTTGGGAAGgtttgtactg ... tgctttgcagGTTGAGGCAGCACTGATGGGAAGTAACTATGTGGATAATATAATGGTATAC
EST: gi|351023101|gb|FQ430976.1|FQ430976
EST:     AGAAGGATATTGTTAAACTACAGCATGGAGAATATATCTCCCTTGGGAAG                         GTTGAGGTAGCACTGATGGGAAGTAACTATGTGGATAATATAATGGTATAC
genomic: AGAAGGATATTGTTAAACTACAGCATGGAGAATATATCTCCCTTGGGAAGgtttgtactg ... tgctttgcagGTTGAGGCAGCACTGATGGGAAGTAACTATGTGGATAATATAATGGTATAC
EST: gi|351040054|gb|FQ425140.1|FQ425140
EST:     AGAAGGATATTGTTAAACTACAGCATGGAGAATATATCTCCCTTGGGAAG                         GTTGAGGTAGCACTGATGGGAAGTAACTATGTGGATAATATAATGGTATAC
genomic: AGAAGGATATTGTTAAACTACAGCATGGAGAATATATCTCCCTTGGGAAGgtttgtactg ... tgctttgcagGTTGAGGCAGCACTGATGGGAAGTAACTATGTGGATAATATAATGGTATAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggatagctgtaatcgtttttggaagtcactctttatgtttgtccatgctttgcagGTTGAGGCAGCACTGATGGGAAGTAACTATGTGGATAATATAATGGTATACGCAGATCCCTTGCACAATTATTGTGTAGCTCTGGTGGTCCCTTCACATC
                               tttatgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgtactggatttgactagtacttcttgattgaggataccccttctcatcagaagggatagctgtaatcgtttttggaagtcactctttatgtttgtccatgctttgcagGTTGAGGCAGCACTGATGGGAAGTAACTATGTGGATAATATAATGGTATACGCAGATCCCTTGCACAATTATTGTGTAGCTCTGGTGGTCCCTTCACATC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG