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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggcttctgaacaagagtattatccataaaaatatatttagcctgcaaactgcccctcaatttgaatttttgtctattgactcagGTTTACTTAAACGCAAGAAACCATCGAACCTTGAGCATGCTGTCAAAGCTGCACGCACCAAAGCAGCTAAACCACA

Basic information

species Vitis vinifera
transcript Vv04s0044g01840.t01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0044g01840.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA16G21840.1 (Glycine max), 3'ss of exon 9
gtatggcttctgaacaagagtattatccataaaaatatatttagcctgcaaactgcccctcaatttgaatttttgtctattgactcagGTTTACTTAAACGCAAGAAACCATCGAACCTTGAGCATGCTGTCAAAGCTGCACGCACCAAAGCAGCTAAACCACA------------
||||||    | | |   | |  ||||  |   ||    ||||   |||    ||   || ||  |   |       ||||| ||||| ||||||||||||||||||| ||||| ||   |   ||| ||||||||  |||| ||   || || ||| ||||||            
gtatggtccttcatctt-actgctatcatttttaac---tttaaagtgctgcatgattctaaagattc-tccccccttattggctcagATTTACTTAAACGCAAGAAATCATCGGACACCGTTAATGTTGTCAAAGTGGCACACAGTCAACCATCTAGACCACAGTTAAGACACAT

upper sequence: Vv04s0044g01840.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA16G21840.2 (Glycine max), 3'ss of exon 9
gtatggcttctgaacaagagtattatccataaaaatatatttagcctgcaaactgcccctcaatttgaatttttgtctattgactcagGTTTACTTAAACGCAAGAAACCATCGAACCTTGAGCATGCTGTCAAAGCTGCACGCACCAAAGCAGCTAAACCACA
||||||    | | |   | |  ||||  |   ||    ||||   |||    ||   || ||  |   |       ||||| ||||| ||||||||||||||||||| ||||| ||   |   ||| ||||||||  |||| ||   || || ||| ||||||
gtatggtccttcatctt-actgctatcatttttaac---tttaaagtgctgcatgattctaaagattc-tccccccttattggctcagATTTACTTAAACGCAAGAAATCATCGGACACCGTTAATGTTGTCAAAGTGGCACACAGTCAACCATCTAGACCACA
















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|110703600|gb|EE080590.1|EE080590
EST:     TAAGAGCTCCATTTCTTTGCAAAAGCGGGAAAAACAGCTCAAAAACATTG                         GTTTACTTAAACGCAAGAAACCATCGAACCTTGAGCATGCTGTCAAAGCTG
genomic: TAAGAGCTCCATTTCTTTGCAAAAGCGGGAAAAACAGCTCAAAAACATTGgtatggcttc ... attgactcagGTTTACTTAAACGCAAGAAACCATCGAACCTTGAGCATGCTGTCAAAGCTG
EST: gi|351041413|gb|FQ447540.1|FQ447540
EST:     TAAGAGCTCCATTTCTTTGCAAAAGCGGGAAAAACAGCTCAAAAACATTG                         GTTTACTTAAACGCAAGAAACCATCGAACCTTGAGCATGCTGTCAAAGCTG
genomic: TAAGAGCTCCATTTCTTTGCAAAAGCGGGAAAAACAGCTCAAAAACATTGgtatggcttc ... attgactcagGTTTACTTAAACGCAAGAAACCATCGAACCTTGAGCATGCTGTCAAAGCTG
EST: gi|352794399|gb|FQ481630.1|FQ481630
EST:     TAAGAGCCCCATTTCTTTGCAAAAGCGGGAAAAACAGCTCAAAAACATTG                         GTTTACTTAAACGCAAGAAACCATCGAACCTTGAGCATGCTGTCAAAGCTG
genomic: TAAGAGCTCCATTTCTTTGCAAAAGCGGGAAAAACAGCTCAAAAACATTGgtatggcttc ... attgactcagGTTTACTTAAACGCAAGAAACCATCGAACCTTGAGCATGCTGTCAAAGCTG
EST: gi|30302776|gb|CB979570.1|CB979570
EST:     TAAGAGCTCCATTTCTTTGCAAAAGCGGGAAAAACAGCTCAAAAACATTG                         GTTTACTTAAACGCAAGAAACCATCGAACCTTGAGCATGCTGTCAAAGCTG
genomic: TAAGAGCTCCATTTCTTTGCAAAAGCGGGAAAAACAGCTCAAAAACATTGgtatggcttc ... attgactcagGTTTACTTAAACGCAAGAAACCATCGAACCTTGAGCATGCTGTCAAAGCTG
EST: gi|110688872|gb|EE067920.1|EE067920
EST:     TAAGAGCTCCATTTCTTTGCAAAAGCGGGAAAAACAGCTCAAAAACATTG                         GTTTACTTAAACGCAAGAAACCATCGAACCTTGAGCATGCTGTCAAAGCTG
genomic: TAAGAGCTCCATTTCTTTGCAAAAGCGGGAAAAACAGCTCAAAAACATTGgtatggcttc ... attgactcagGTTTACTTAAACGCAAGAAACCATCGAACCTTGAGCATGCTGTCAAAGCTG
EST: gi|71880737|gb|DT029792.1|DT029792
EST:     TAAGAGCTCCATTTCTTTGCAAAAGCGGGAAAAACAGCTCAAAAACATTG                         GTTTACTTAAACGCAAGAAACCATCGAACCTTGAGCATGCTGTCAAAGCTG
genomic: TAAGAGCTCCATTTCTTTGCAAAAGCGGGAAAAACAGCTCAAAAACATTGgtatggcttc ... attgactcagGTTTACTTAAACGCAAGAAACCATCGAACCTTGAGCATGCTGTCAAAGCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatatatttagcctgcaaactgcccctcaatttgaatttttgtctattgactcagGTTTACTTAAACGCAAGAAACCATCGAACCTTGAGCATGCTGTCAAAGCTGCACGCACCAAAGCAGCTAAACCACA
                                            tattgac  putative branch site (score: 2)
                          tcaatttgaattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatggcttctgaacaagagtattatccataaaaatatatttagcctgcaaactgcccctcaatttgaatttttgtctattgactcagGTTTACTTAAACGCAAGAAACCATCGAACCTTGAGCATGCTGTCAAAGCTGCACGCACCAAAGCAGCTAAACCACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT