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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agatatgttcaatatttgaaataaaagtttgaagatttgaaatatgtaaaccctgacagcattaaattgactgtgatggcttgtgcaaccaaacttgcagGCCCCATTATAATTTGAATTTGCAGAGCATCTCTGTCAATGGGAAATCGTTAGCCATTGACCCAGAGGTGTTTGCAACATCAACCAACCGAGGAACCATT

Basic information

species Vitis vinifera
transcript Vv06s0061g01030.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0061g01030.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA12G08870.1 (Glycine max), 3'ss of exon 4
agatatgttcaatatttgaaataaaagt-ttgaa--gatttgaaatatgtaaaccctgacagcattaaattgactgtgatggcttgtgcaaccaaacttgcagGCCCCATTATAATTTGAATTTGCAGAGCATCTCTGTCAATGGGAAATCGTTAGCCATTGACCCAGAGGTGTTTGCAACATCAACCAACCGAGGAACCATT
    |  |  | || |  || ||   || |||||  |  ||  ||    ||  |  ||  | || |   | ||||   || ||||      | ||  || |||||| ||||| ||||| ||| |||||||||||||||| |||||  ||    |  | |||| ||| |  || ||||| ||||||| |||| |||| ||||||
-tccaaatatattactaaaattatttgtattgaaatggctttgaaagaatattctttgtgaacaatggttagacta--attgcttccttggcaaatatttcagGCCACATTACAATTTAAATCTGCAGAGCATCTCTGTTAATGGCCAAATTGTGCCAATTGCCCCTGCAGTTTTTGCTACATCAAACAACAGAGGTACCATT

upper sequence: Vv06s0061g01030.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA11G19640.2 (Glycine max), 3'ss of exon 4
agatatgttcaatatttgaaataaaagtttgaagatttgaaatatgtaaaccctgacagcattaaattgactg--tgatggcttgtgcaaccaaacttgcagGCCCCATTATAATTTGAATTTGCAGAGCATCTCTGTCAATGGGAAATCGTTAGCCATTGACCCAGAGGTGTTTGCAACATCAACCAACCGAGGAACCATT
    |  |  | || |  | |||   || |   || | |   |     ||   |    |    ||||||   |  | || ||||        ||  || |||||| ||||| ||||| ||| |||||||||||||||| |||||  ||    |    |||| |||    || ||||| ||||||| |||| |||| ||||||
--ccaaatatattactaaacatatttgtattgggaatggctttggaagaatattctttgtgaaaaattgttagactaattgcttccttgggaaatatttcagGCCTCATTACAATTTAAATCTGCAGAGCATCTCTGTTAATGGCCAAATTGTGCGGATTGCCCCTTCAGTTTTTGCTACATCAAACAACAGAGGTACCATT
















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|352791504|gb|FQ481083.1|FQ481083
EST:     GGCGAGATTGTGGAGGAAGATATAGTTTATAGTCCACTTGTGCCTTCACA                         GCCCCATTATAATTTGAATTTGCAGAGCATCTCTGTCAATGGGAAATCGTT
genomic: GGCGAGATTGTGGAGGAAGATATAGTTTATAGTCCACTTGTGCCTTCACAgtaagttttt ... aaacttgcagGCCCCATTATAATTTGAATTTGCAGAGCATCTCTGTCAATGGGAAATCGTT
EST: gi|351043367|gb|FQ451419.1|FQ451419
EST:     GGCGAGATTGTGGAGGAAGATATAGTTTATAGTCCACTTGTGCCTTCACA                         GCCCCATTATAATTTGAATTTGCAGAGCATCTCTGTCAATGGGAAATCGTT
genomic: GGCGAGATTGTGGAGGAAGATATAGTTTATAGTCCACTTGTGCCTTCACAgtaagttttt ... aaacttgcagGCCCCATTATAATTTGAATTTGCAGAGCATCTCTGTCAATGGGAAATCGTT
EST: gi|352789949|gb|FQ479559.1|FQ479559
EST:     GGCGAGATTGTGGAGGAAGATATAGTTTATAGTCCACTTGTGCCTTCACA                         GCCCCATTATAATTTGAATTTGCAGAGCATCTCTGTCAATGGGAAATCGTT
genomic: GGCGAGATTGTGGAGGAAGATATAGTTTATAGTCCACTTGTGCCTTCACAgtaagttttt ... aaacttgcagGCCCCATTATAATTTGAATTTGCAGAGCATCTCTGTCAATGGGAAATCGTT
EST: gi|349811312|gb|FQ407538.1|FQ407538
EST:     GGCGAGATTGTGGAGGAAGATATAGTTTATAGTCCACTTGTGCCTTCCCA                         GCCCCATTATAATTTGAATTTGCAGAGCATCTCTGTCAATGGGAAATCGTT
genomic: GGCGAGATTGTGGAGGAAGATATAGTTTATAGTCCACTTGTGCCTTCACAgtaagttttt ... aaacttgcagGCCCCATTATAATTTGAATTTGCAGAGCATCTCTGTCAATGGGAAATCGTT
EST: gi|351057266|gb|FQ450973.1|FQ450973
EST:     GGCGAGATTGTGGAGGAAGATATAGTTTATAGTCCACTTGTGCCTTCACA                         GCCCCATTATAATTTGAATTTGCAGAGCATCTCTGTCAATGGGAAATCGTT
genomic: GGCGAGATTGTGGAGGAAGATATAGTTTATAGTCCACTTGTGCCTTCACAgtaagttttt ... aaacttgcagGCCCCATTATAATTTGAATTTGCAGAGCATCTCTGTCAATGGGAAATCGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaaaccctgacagcattaaattgactgtgatggcttgtgcaaccaaacttgcagGCCCCATTATAATTTGAATTTGCAGAGCATCTCTGTCAATGGGAAATCGTTAGCCATTGACCCAGAGGTGTTTGCAACATCAACCAACCGAGGAACCATT
                   aattgac  putative branch site (score: 3)
               attaaattga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agatatgttcaatatttgaaataaaagtttgaagatttgaaatatgtaaaccctgacagcattaaattgactgtgatggcttgtgcaaccaaacttgcagGCCCCATTATAATTTGAATTTGCAGAGCATCTCTGTCAATGGGAAATCGTTAGCCATTGACCCAGAGGTGTTTGCAACATCAACCAACCGAGGAACCATT

- - - - - - - - tgaaata
- - - - - - - - - aaataaa
- - - - - - - - - - - - - - - - - - - - - - - - - ccctgac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaattga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtgatgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cttgtgc