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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggccacctggaatggaattatctcaatatcttatttcctgaggcgtctaatctagaagctagatcttgtcgtgttttatttatttgttttttctttccagAAATAACATGGGGGGAGGTGCTGAATGGGACAATCGAATGATGGATAACCTGAAAAATTTTGATCTCAGCAGTCCCGAGGTCAAGCAGCAATTTG

Basic information

species Vitis vinifera
transcript Vv18s0041g01360.t01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0041g01360.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA11G31810.1 (Glycine max), 3'ss of exon 10
-ggccacctggaatggaattatctcaatatcttatttcctgaggcgtctaa-----tctagaagctagatcttgtcgtgttttatttatttgttttttctttccagAAATAACATGGGGGGAGGTGCTGAATGGGACAATCGAATGATGGATAACCTGAAAAATTTTGATCTCAGCAGTCCCGAGGTCAAGCAGCAATTTG
     |  || |      || |    ||||   || | ||  || || |||       || | |||  ||| | || | |||| |  |  |||||  | |   |||||| |||||||| ||| |  ||||||||||||||||||||||||||| | |||| |||||||| || |  ||||| || || |||||||||||||
taaatatatgcat--attttgttaagatataaaatcttctctggtgtgtaaagattcatatatgctgaatcct-tcctcttttttcaacatgtttgattt---cagAAACAACATGGGTGGAAGCACTGAATGGGACAATCGAATGATGGATACCTTGAAGAATTTTGACCTTAATAGTCCTGAAGTGAAGCAGCAATTTG
















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|30133605|gb|CB918944.1|CB918944
EST:     GGATGCTACAAAATCCACAATATCGTCAACAGCTGCAGGACATGCT                         AAATAACATGGGGGGAGGTGCTGAATGGGACAATCGAATGATGGATAACCT
genomic: GGATGCTACAAAATCCACAATATCGTCAACAGCTGCAGGACATGCTgtaagtttct ... ttctttccagAAATAACATGGGGGGAGGTGCTGAATGGGACAATCGAATGATGGATAACCT
EST: gi|30137643|gb|CB922981.1|CB922981
EST:     GGATGCTACAAAATCCACAATATCGTCAACAGCTGCAGGACATGCT                         AAATAACATGGGGGGAGGTGCTGAATGGGACAATCGAA
genomic: GGATGCTACAAAATCCACAATATCGTCAACAGCTGCAGGACATGCTgtaagtttct ... ttctttccagAAATAACATGGGGGGAGGTGCTGAATGGGACAATCGAA
EST: gi|110369051|gb|EC933194.1|EC933194
EST:     GGATGCTACAAAATCCACAATATCGTCAACAGCTGCAGGACATGCT                         AAATAACATGGGGGGAGGTGCTGAATGGGACAATCGAATGATGGATAACCT
genomic: GGATGCTACAAAATCCACAATATCGTCAACAGCTGCAGGACATGCTgtaagtttct ... ttctttccagAAATAACATGGGGGGAGGTGCTGAATGGGACAATCGAATGATGGATAACCT
EST: gi|37183876|gb|CF603230.1|CF603230
EST:     GGATGCTACAAAATCCACAATATCGTCAACAGCTGCAGGACATGCT                         AAATAACATGGGGGGAGGTGCTGAATGGGACAATCGAATGATGGATAACCT
genomic: GGATGCTACAAAATCCACAATATCGTCAACAGCTGCAGGACATGCTgtaagtttct ... ttctttccagAAATAACATGGGGGGAGGTGCTGAATGGGACAATCGAATGATGGATAACCT
EST: gi|30136598|gb|CB921936.1|CB921936
EST:     GGATGCTACAAAATCCACAATATCGTCAACAGCTGCAGGACATGCT                         AAATAACATGGGGGGAGGTGCTGAATGGGACAATCGAATGATGGATAACCT
genomic: GGATGCTACAAAATCCACAATATCGTCAACAGCTGCAGGACATGCTgtaagtttct ... ttctttccagAAATAACATGGGGGGAGGTGCTGAATGGGACAATCGAATGATGGATAACCT
EST: gi|32268986|gb|CD718145.1|CD718145
EST:     GGATGCTACAAAATCCACAATATCGTCAACAGCTGCAGGACATGCT                         AAATAACATGGGGGGAGGTGCTGAATGGGACAATCGAATGATGGATAACCT
genomic: GGATGCTACAAAATCCACAATATCGTCAACAGCTGCAGGACATGCTgtaagtttct ... ttctttccagAAATAACATGGGGGGAGGTGCTGAATGGGACAATCGAATGATGGATAACCT
EST: gi|30136267|gb|CB921605.1|CB921605
EST:     GGATGCTACAAAATCCACAATATCGTCAACAGCTGCAGGACATGCT                         AAATAACATGGGGG
genomic: GGATGCTACAAAATCCACAATATCGTCAACAGCTGCAGGACATGCTgtaagtttct ... ttctttccagAAATAACATGGGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctaatctagaagctagatcttgtcgtgttttatttatttgttttttctttccagAAATAACATGGGGGGAGGTGCTGAATGGGACAATCGAATGATGGATAACCTGAAAAATTTTGATCTCAGCAGTCCCGAGGTCAAGCAGCAATTTG
 gtctaat  putative branch site (score: 3)
                          tgttttatttatttgt  putative PPT
                          tgttttatttatttgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggccacctggaatggaattatctcaatatcttatttcctgaggcgtctaatctagaagctagatcttgtcgtgttttatttatttgttttttctttccagAAATAACATGGGGGGAGGTGCTGAATGGGACAATCGAATGATGGATAACCTGAAAAATTTTGATCTCAGCAGTCCCGAGGTCAAGCAGCAATTTG

-gccacct
- - - - - aatggaa
- - - - - - - - - - - - - - - - - ttcctga