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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagagtacagttaatgggtagttgtcatacatcccatatgttaacaagcaagacttcttatttggataccattttcttgatgcagGTTAAAAGCAAGCTTAAAGGCCACTCTAAGAGAATAACTGGCCTTGCCTTCTCTCATGTTCTTAATGTGCTAGTTTCGTCTGGAGCAGATGCTCAG

Basic information

species Vitis vinifera
transcript Vv09s0002g08370.t01
intron # 21
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0002g08370.t01 (Vitis vinifera), 3'ss of exon 21
lower sequence: GLYMA15G00880.1 (Glycine max), 3'ss of exon 21
gtag-agtacagttaatgggtagttgtcatacatcccatatgttaacaagcaagacttcttatttggataccattttcttgatgcagGTTAAAAGCAAGCTTAAAGGCCACTCTAAGAGAATAACTGGCCTTGCCTTCTCTCATGTTCTTAATGTGCTAGTTTCGTCTGGAGCAGATGCTCAG
|||  | | |     ||    | ||       |     ||| | |  ||  | |      | |||    |    ||| |   ||||||| ||||| || |||||||||||  |||| ||||||||||| ||||| || ||||||||  | |||||||||||||| ||||| ||||||||||||
gtatcattgcttcccataaacatttcctgctgagtttttatttgagtaataagg------tgtttatgcatttatttttctttgcagGTAAAAAGTAAACTTAAAGGCCATACTAAAAGAATAACTGGTCTTGCTTTTTCTCATGTGTTAAATGTGCTAGTTTCATCTGGGGCAGATGCTCAG

upper sequence: Vv09s0002g08370.t01 (Vitis vinifera), 3'ss of exon 21
lower sequence: GLYMA13G44420.1 (Glycine max), 3'ss of exon 22
gtag-agtacagttaatgggtagttgtcatacatcccatatgttaacaagcaagacttcttatttggataccattttcttgatgcagGTTAAAAGCAAGCTTAAAGGCCACTCTAAGAGAATAACTGGCCTTGCCTTCTCTCATGTTCTTAATGTGCTAGTTTCGTCTGGAGCAGATGCTCAG
|||  | | | |   ||    | ||      ||     ||| | |  ||  | |  ||    | || ||    |||  |   ||||||||||||| || || ||||||||  |||| ||||||||||| ||||| || ||||||||  | |||||||||||||| ||||| || |||||||||
gtatcattgctgcccataaacatttcctgctcagtttttatttgagtaataaggtgtt----tatgcattttttttcttctttgcagGTTAAAAGTAAACTCAAAGGCCATACTAAAAGAATAACTGGTCTTGCTTTTTCTCATGTGTTGAATGTGCTAGTTTCATCTGGGGCTGATGCTCAG

upper sequence: Vv09s0002g08370.t01 (Vitis vinifera), 3'ss of exon 21
lower sequence: GLYMA07G03180.1 (Glycine max), 3'ss of exon 20
gtagagtacagttaatgggtagttgtcatacatcccatatgttaacaagcaagacttctt-atttggataccattttcttgatgcagGTTAAAAGCAAGCTTAAAGGCCACTCTAAGAGAATAACTGGCCTTGCCTTCTCTCATGTTCTTAATGTGCTAGTTTCGTCTGGAGCAGATGCTCAG
     |||       ||  |   ||| | |||     ||  |||  |    ||| || || || |  || | |  |||||  ||||||||||||| || || ||||||||   ||| ||||| ||||| ||||| |||||||||||  | |||||  ||||||| ||||||||||||||||||
-----gtaacagagctgtctgcctgtaa-acagtttgtac-ttatgatttgagattttttgatgttaatgcaaagttcttt-tgcagGTTAAAAGTAAACTCAAAGGCCATAATAAAAGAATTACTGGTCTTGCTTTCTCTCATGTATTGAATGTATTAGTTTCATCTGGAGCAGATGCTCAG

upper sequence: Vv09s0002g08370.t01 (Vitis vinifera), 3'ss of exon 21
lower sequence: GLYMA08G22910.1 (Glycine max), 3'ss of exon 21
gtagagtacagttaatgggtagttgtcatacatcccatatgttaacaagcaagacttcttatttggataccattttcttgatgcagGTTAAAAGCAAGCTTAAAGGCCACTCTAAGAGAATAACTGGCCTTGCCTTCTCTCATGTTCTTAATGTGCTAGTTTCGTCTGGAGCAGATGCTCAG
         |     ||  |   ||| |  ||     ||  |||  |    ||| || |||| |  || | |  ||| |  ||||||||||||| || || ||||| ||  |||| ||||| ||||| ||||| |||||||||||  | |||||  ||||||| |||||||| |||||||||
-------gtaacagctgtctgcctgtaac-cagtttgtac-ttatgatttgagattttttatgttaatgcaaagttcctt-tgcagGTTAAAAGTAAACTCAAAGGGCATACTAAAAGAATTACTGGTCTTGCTTTCTCTCATGTATTGAATGTATTAGTTTCATCTGGAGCTGATGCTCAG

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|349822443|gb|FQ412707.1|FQ412707
EST:     CCAGATATATAACGTCCGCGTAGATGAG                         GTTAAAAGCAAGCTTAAAGGCCACTCTAAGAGAACAACTGGCCTTGCCTTC
genomic: CCAGATATATAACGTCCGCGTAGATGAGgtagagtaca ... cttgatgcagGTTAAAAGCAAGCTTAAAGGCCACTCTAAGAGAATAACTGGCCTTGCCTTC
EST: gi|351031457|gb|FQ446660.1|FQ446660
EST:     CCAGATATATAACGTCCGCGTAGATGAG                         GTTAAAAGCAAGCTTAAAGGCCACTCTAAGAGAATAACTGGCCTTGCCTTC
genomic: CCAGATATATAACGTCCGCGTAGATGAGgtagagtaca ... cttgatgcagGTTAAAAGCAAGCTTAAAGGCCACTCTAAGAGAATAACTGGCCTTGCCTTC
EST: gi|161717398|gb|FC068869.1|FC068869
EST:     TCGGGATGGATGATTCTACAATCCAGATATATAACGTCCGCGTAGATGAT                         GTTAAAAGCAAGCTTAAAGGCCACTCTAAGAGAATAACTGGCCTTGCCTTC
genomic: TCGGGATGGATGATTCTACAATCCAGATATATAACGTCCGCGTAGATGAGgtagagtaca ... cttgatgcagGTTAAAAGCAAGCTTAAAGGCCACTCTAAGAGAATAACTGGCCTTGCCTTC
EST: gi|349813140|gb|FQ411380.1|FQ411380
EST:     CCAGATATATAACGTCCGCGTAGATGAG                         GTTAAAAGCAAGCTTAAAGGCCACTCTAAGAGAACAACTGGCCTTGCCTTC
genomic: CCAGATATATAACGTCCGCGTAGATGAGgtagagtaca ... cttgatgcagGTTAAAAGCAAGCTTAAAGGCCACTCTAAGAGAATAACTGGCCTTGCCTTC
EST: gi|349829095|gb|FQ419627.1|FQ419627
EST:     CCAGATATATAACGTCCGCGTAGATGAG                         GTTAAAAGCAAGCTTAAAGGCCACTCTAAGAGAATAACTGGCCTTGCCTTC
genomic: CCAGATATATAACGTCCGCGTAGATGAGgtagagtaca ... cttgatgcagGTTAAAAGCAAGCTTAAAGGCCACTCTAAGAGAATAACTGGCCTTGCCTTC
EST: gi|349826376|gb|FQ417873.1|FQ417873
EST:     CCAGATATATAACGTCCGCGTAGATGAG                         GTTAAAAGCAAGCTTAAAGGCCACTCTAAGAGAATAACTGGCCTTGCCTTC
genomic: CCAGATATATAACGTCCGCGTAGATGAGgtagagtaca ... cttgatgcagGTTAAAAGCAAGCTTAAAGGCCACTCTAAGAGAATAACTGGCCTTGCCTTC
EST: gi|71861049|gb|DT010104.1|DT010104
EST:     TCGGGATGGATGATTCTACAATCCAGATATATAACGTCCGCGTAGATGAG                         GTTAAAAGCAAGCTTAAAGGCCACTCTAAGAGAATAACTGGCCTTGCCTTC
genomic: TCGGGATGGATGATTCTACAATCCAGATATATAACGTCCGCGTAGATGAGgtagagtaca ... cttgatgcagGTTAAAAGCAAGCTTAAAGGCCACTCTAAGAGAATAACTGGCCTTGCCTTC
EST: gi|71860540|gb|DT009595.1|DT009595
EST:     TCGGGATGGATGATTCTACAATCCAGATATATAACGTCCGCGTAGATGAG                         GTTAAAAGCAAGCTTAAAGGCCACTCTAAGAGAATAACTGGCCTTGCCTTC
genomic: TCGGGATGGATGATTCTACAATCCAGATATATAACGTCCGCGTAGATGAGgtagagtaca ... cttgatgcagGTTAAAAGCAAGCTTAAAGGCCACTCTAAGAGAATAACTGGCCTTGCCTTC
EST: gi|351048584|gb|FQ448858.1|FQ448858
EST:     CCAGATATATAACGTCCGCGTAGATGAG                         GTTAAAAGCAAGCTTAAAGGCCACTCTAAGAGAATAACTGGCCTTGCCTCC
genomic: CCAGATATATAACGTCCGCGTAGATGAGgtagagtaca ... cttgatgcagGTTAAAAGCAAGCTTAAAGGCCACTCTAAGAGAATAACTGGCCTTGCCTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcccatatgttaacaagcaagacttcttatttggataccattttcttgatgcagGTTAAAAGCAAGCTTAAAGGCCACTCTAAGAGAATAACTGGCCTTGCCTTCTCTCATGTTCTTAATGTGCTAGTTTCGTCTGGAGCAGATGCTCAG
                                      ccattttctt  CT-rich tract
     atatgttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagagtacagttaatgggtagttgtcatacatcccatatgttaacaagcaagacttcttatttggataccattttcttgatgcagGTTAAAAGCAAGCTTAAAGGCCACTCTAAGAGAATAACTGGCCTTGCCTTCTCTCATGTTCTTAATGTGCTAGTTTCGTCTGGAGCAGATGCTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG