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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatcctaaacaattttattgttagagtttcatttggactatctattatatatttagcttttgatcacttgagttaagacaactactgacaaaattgtctgagtgaggaagtacactgttaattccttgacttgtatgtccagATATTTTGGAGTTGATATCAATGCCATAATAGAATATGCCAATACATTTGATGACATTCAACACTTGCGAGCTGAAATAAG

Basic information

species Vitis vinifera
transcript Vv00s0250g00020.t01
intron # 6
splice site 3'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv00s0250g00020.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA10G34370.1 (Glycine max), 3'ss of exon 6
gtatcctaaacaattttattgttagagtttcatttggactatctattatatatttagcttttgatcacttgagttaagacaactactgacaaaattgtctgagtgaggaagtacactgtta-attccttgacttgtatgtccagATATTTTGGAGTTGATATCAATGCCATAATAGAATATGCCAATACATTTGATGACATTCAACACTTGCGAGCTGAAATAAG
                          || || |    | | ||| | |||   ||  ||||   | | |||||  || | |   | |  |  |  | | | |   ||  |||  ||  ||   || ||| ||   ||  |  |||||||||||||||||||| |||||||||  |||||||||||| ||||   ||||||||||||||||||| ||||| |||||
--------------------------gtatcctaatcagtttctttaataagattcactttcagt-atttgagacaa-atatgaaatacctca--tatttaatctagctagtgaaccattgtgtttctttacaactactt--agATATTTTGGAGTTGATATTAATGCCATACGAGAATATGCCAAGACATGCAATGACATTCAACACTTGCGTGCTGAGATAAG

upper sequence: Vv00s0250g00020.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA20G33190.1 (Glycine max), 3'ss of exon 6
gtatcctaaacaattttattgttagagtttcatttggactatctattatatatttagcttttgatcacttgagttaagacaactactgacaaaattgtctgagtgaggaagtacactgttaattccttgacttgtatgtccagATATTTTGGAGTTGATATCAATGCCATAATAGAATATGCCAATACATTTGATGACATTCAACACTTGCGAGCTGAAATAAG
                        |  |   | |  |  | | || || | ||| |   ||| |  | ||||   || |  |      ||| | ||     ||  ||  |   || |||   ||| ||        |    |||||||| ||||||||||| |||||||||  |||||||||||| ||||   ||||||||||||||||||| || || |||||
------------------------gtatcctaatcagtttgtttaata-agattca--ctttcagtatttgaacaaatatgaaataccacatatttaatctagcaagtgaac-cattgt-ggttcttta---caactacttagATATTTCGGAGTTGATATTAATGCCATACGAGAATATGCCAAGACATGCAATGACATTCAACACTTGCGTGCGGAGATAAG
















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|37188932|gb|CF608281.1|CF608281
EST:     AGTATTGGGGTGAAAACCATTTTTTGCTTACAACAAGATTCAGATCTTGA                         ATATTTTGGAGTTGATATCAATGCCATAATAGAATATGCCAATACATTTGA
genomic: AGTATTGGGGTGAAAACCATTTTTTGCTTACAACAAGATTCAGATCTTGAgtatcctaaa ... gtatgtccagATATTTTGGAGTTGATATCAATGCCATAATAGAATATGCCAATACATTTGA
EST: gi|71860017|gb|DT009072.1|DT009072
EST:     AGTATTGGGGTGAAAACCATTTTTTGCGTACAACAAGATTCAGATCTTGA                         ATATTTTGGAGTTGATATCAATGCCATAATAGAATATGCCAATACATTTGA
genomic: AGTATTGGGGTGAAAACCATTTTTTGCTTACAACAAGATTCAGATCTTGAgtatcctaaa ... gtatgtccagATATTTTGGAGTTGATATCAATGCCATAATAGAATATGCCAATACATTTGA
EST: gi|110731715|gb|EE106367.1|EE106367
EST:     AGTATTGGGGTGAAAACCATTTTTTGCTTACAACAAGATTCAGATCTTGA                         ATATTTTGGAGTTGATATCAATGCCATAATAGAATATGCCAATACATTTGA
genomic: AGTATTGGGGTGAAAACCATTTTTTGCTTACAACAAGATTCAGATCTTGAgtatcctaaa ... gtatgtccagATATTTTGGAGTTGATATCAATGCCATAATAGAATATGCCAATACATTTGA
EST: gi|110725728|gb|EE102561.1|EE102561
EST:     AGTATTGGGGTGAAAACCATTTTTTGCTTACAACAAGATTCAGATCTTGA                         ATATTTTGGAGTTGATATCAATGCCATAATAGAATATGCCAATACATTTGA
genomic: AGTATTGGGGTGAAAACCATTTTTTGCTTACAACAAGATTCAGATCTTGAgtatcctaaa ... gtatgtccagATATTTTGGAGTTGATATCAATGCCATAATAGAATATGCCAATACATTTGA
EST: gi|110390476|gb|EC955386.1|EC955386
EST:     AGTATTGGGGTGAAAACCATTTTTTGCTTACAACAAGATTCAGATCTTGA                         ATATTTTGGAGTTGATATCAATGCCATAATAGAATATGCCAATACATTTGA
genomic: AGTATTGGGGTGAAAACCATTTTTTGCTTACAACAAGATTCAGATCTTGAgtatcctaaa ... gtatgtccagATATTTTGGAGTTGATATCAATGCCATAATAGAATATGCCAATACATTTGA
EST: gi|27582920|gb|CB005615.1|CB005615
EST:     AGTATTGGGGTGAAAACCATTTTTTGCTTACAACAAGATTCAGATCTTGA                         ATATTTTGGAGTTGATATCAATGCCATAATAGAATATGCCAATACATTTGA
genomic: AGTATTGGGGTGAAAACCATTTTTTGCTTACAACAAGATTCAGATCTTGAgtatcctaaa ... gtatgtccagATATTTTGGAGTTGATATCAATGCCATAATAGAATATGCCAATACATTTGA
EST: gi|110719002|gb|EE096483.1|EE096483
EST:     AGTATTGGGGTGAAAACCATTTTTTGCTTACAACAAGATTCAGATCTTGA                         ATATTTTGGAGTTGATATCAATGCCATAATAGAATATGCCAATACATTTGA
genomic: AGTATTGGGGTGAAAACCATTTTTTGCTTACAACAAGATTCAGATCTTGAgtatcctaaa ... gtatgtccagATATTTTGGAGTTGATATCAATGCCATAATAGAATATGCCAATACATTTGA
EST: gi|71858350|gb|DT007405.1|DT007405
EST:     AGTATTGGGGTGAAAACCATTTTTTGCTTACAACAAGATTCAGATCTTGA                         ATATTTTGGAGTTGATATCAATGCCATAATAGAATATGCCAATACATTTGA
genomic: AGTATTGGGGTGAAAACCATTTTTTGCTTACAACAAGATTCAGATCTTGAgtatcctaaa ... gtatgtccagATATTTTGGAGTTGATATCAATGCCATAATAGAATATGCCAATACATTTGA
EST: gi|110723499|gb|EE100881.1|EE100881
EST:     AGTATTGGGGTGAAAACCATTTTTTGCTTACAACAAGATTCAGATCTTGA                         ATATTTTGGAGTTGATATCAATGCCATAATAGAATATGCCAATACATTTGA
genomic: AGTATTGGGGTGAAAACCATTTTTTGCTTACAACAAGATTCAGATCTTGAgtatcctaaa ... gtatgtccagATATTTTGGAGTTGATATCAATGCCATAATAGAATATGCCAATACATTTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acaaaattgtctgagtgaggaagtacactgttaattccttgacttgtatgtccagATATTTTGGAGTTGATATCAATGCCATAATAGAATATGCCAATACATTTGATGACATTCAACACTTGCGAGCTGAAATAAG
 ttccttgac  putative branch site 
                            tgttaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatcctaaacaattttattgttagagtttcatttggactatctattatatatttagcttttgatcacttgagttaagacaactactgacaaaattgtctgagtgaggaagtacactgttaattccttgacttgtatgtccagATATTTTGGAGTTGATATCAATGCCATAATAGAATATGCCAATACATTTGATGACATTCAACACTTGCGAGCTGAAATAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA