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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATTTTCAGAAAGATATTGTTAGAGCAGGGGAAGCATTCACAGCCATAGGATATAAACAAATCGAAACAGgtgaaaaagtaattcatactttctccaaatatgtatttcatggcaacatacttctcataatttggaggactgtgcaattagctcttaaaaatctgttccaaataaatgatctagtttacaatagtaacttaccatttgcgtttattctttacaatctgtatggttatcag

Basic information

species Vitis vinifera
transcript Vv10s0003g02590.t01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv10s0003g02590.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA05G29700.2 (Glycine max), 5'ss of exon 3
GATTTTCAGAAAGATATTGTTAGAGCAGGGGAAGCATTCACAGCCATAGGATATAAACAAATCGAAACAGgtgaaaaagtaattcatactttctccaaatatgtatttcatggcaacatacttctcataatttggaggactgtgcaattagctcttaaaaatctgttccaaataaatgatctagtttacaatagtaacttaccatttgcgtttattctt---tacaatctgtatggttatcag
|| || |||||||| ||||||| |||||  ||| |||| ||||| ||||| ||||| || || ||||||||||||||  ||  |  |  ||  |           |||| ||  ||   | ||  | |   |   | | ||    |    |     |  |||  |    ||  |  ||  | |||||    || | |||||  |||||  |  || ||     |||||    |||||   |||
GACTTCCAGAAAGAAATTGTTAAAGCAGCAGAAACATTTACAGCTATAGGTTATAAGCATATTGAAACAGgtgaaaat-tagcttttgtttcttt----------tttcctgcaaattcagtttacct---tgacaagtcttgatagcatgtgtccaggaatgag----aagcacctg--caagttttgtttattgacttatgatttgattaaatcctcataaacaatacccatggtagacag
















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|77579639|gb|DV218672.1|DV218672
EST:     TAGAGCAGGGGAAGCATTCACAGCCATAGGATATAAACAAATCGAAACAG                         GAACAAAGTTGTCTGAGGATTGCTGCAGATATGGTGCTGAAAACATCAATG
genomic: TAGAGCAGGGGAAGCATTCACAGCCATAGGATATAAACAAATCGAAACAGgtgaaaaagt ... tggttatcagGAACAAAGTTGTCTGAGGATTGCTGCAGATATGGTGCTGAAAACATCAATG
EST: gi|161714829|gb|FC063277.1|FC063277
EST:     TAGAGCAGGGGAAGCATTCACAGCCATAGGATATAAACAAATCGAAACAG                         GAACAAAGTTGTCTGAGGATTGCTGCAGATATGGTGCTGAAAACATCAATG
genomic: TAGAGCAGGGGAAGCATTCACAGCCATAGGATATAAACAAATCGAAACAGgtgaaaaagt ... tggttatcagGAACAAAGTTGTCTGAGGATTGCTGCAGATATGGTGCTGAAAACATCAATG
EST: gi|351045795|gb|FQ440980.1|FQ440980
EST:     CAAATCGAAACAG                         GAACAAAGTTGTCTGAGGATTGCTGCAGATATGGTGCTGAAAACATCAATG
genomic: CAAATCGAAACAGgtgaaaaagt ... tggttatcagGAACAAAGTTGTCTGAGGATTGCTGCAGATATGGTGCTGAAAACATCAATG
EST: gi|110384739|gb|EC949198.1|EC949198
EST:     TAGAGCAGGGGAAGCATTCACAGCCATAGGATATAAACAAATCGAAACAG                         GAACAAAGTTGTCTGAGGATTGCTGCAGATATGGTGCTGAAAACATCAATG
genomic: TAGAGCAGGGGAAGCATTCACAGCCATAGGATATAAACAAATCGAAACAGgtgaaaaagt ... tggttatcagGAACAAAGTTGTCTGAGGATTGCTGCAGATATGGTGCTGAAAACATCAATG
EST: gi|349832459|gb|FQ421020.1|FQ421020
EST:     CAAATCGAAACAG                         GAACAAAGTTGTCTGAGGATTGCTGCAGATATGGTGCTGAAAACATCAATG
genomic: CAAATCGAAACAGgtgaaaaagt ... tggttatcagGAACAAAGTTGTCTGAGGATTGCTGCAGATATGGTGCTGAAAACATCAATG
EST: gi|110693825|gb|EE070405.1|EE070405
EST:     TAGAGCAGGGGAAGCATTCACAGCCATAGGATATAAACAAATCGAAACAG                         GAACAAAGTTGTCTGAGGATTGCTGCAGATATGGTGCTGAAAACATCAATG
genomic: TAGAGCAGGGGAAGCATTCACAGCCATAGGATATAAACAAATCGAAACAGgtgaaaaagt ... tggttatcagGAACAAAGTTGTCTGAGGATTGCTGCAGATATGGTGCTGAAAACATCAATG
EST: gi|349808085|gb|FQ402476.1|FQ402476
EST:     CAAATCGAAACAG                         GAACAAAGTTGTCTGAGGATTGCTGCAGATATGGTGCTGAAAACATCAATG
genomic: CAAATCGAAACAGgtgaaaaagt ... tggttatcagGAACAAAGTTGTCTGAGGATTGCTGCAGATATGGTGCTGAAAACATCAATG
EST: gi|110391854|gb|EC956857.1|EC956857
EST:     TAGAGCAGGGGAAGCATTCACAGCCATAGGATATAAACAAATCGAAACAG                         GAACAAAGTTGTCTGAGGATTGCTGCAGATATGGTGCTGAAAACATCAATG
genomic: TAGAGCAGGGGAAGCATTCACAGCCATAGGATATAAACAAATCGAAACAGgtgaaaaagt ... tggttatcagGAACAAAGTTGTCTGAGGATTGCTGCAGATATGGTGCTGAAAACATCAATG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATTTTCAGAAAGATATTGTTAGAGCAGGGGAAGCATTCACAGCCATAGGATATAAACAAATCGAAACAGgtgaaaaagtaattcatactttctccaaatatgtatttcatggcaacatacttctcataatttggaggactgtgcaattagctcttaaaaatctgttccaaataaatgatctagtttacaatagtaacttaccatttgcgtttattctttacaatctgtatggttatcag

- - - - - - - - - -  AGAGCA
- - - - - - - - - - - GAGCAG