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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATTGGCACAAGAGGGTTTGCCTTCAAATGTGGTTGCATCGGCGCAGTGCCTTGCGAATGTGGCAAATTTGTTGAATACAAGAGATACTGAATTGAGTAGgtcggttgggtttgtgttaatattccattaccgatgttccttttttttttttcccctgcttttaggattttgagttttatataaagggagatgtggatttag

Basic information

species Vitis vinifera
transcript Vv05s0049g01470.t01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0049g01470.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA07G09310.1 (Glycine max), 5'ss of exon 2
GATTGGCACAAGAGGGTTTGCCTTCAAATGTGGTTGCATCGGCGCAGTGCCTTGCGAATGTGGCAAATTTGTTGAATACAAGAGATACTGAATTGAGTAGgtcggttgggtttgtgttaatattccattaccgatgttccttttttttttttcccctgcttttaggattttgagttttatataaagggagatgtggatttag
|||||||||| ||| | |||||||| ||||||||| |||| || ||    |||||||||||||| || |||||||||| ||||||||||||| |||||||||  |||  ||||   || |    |||||   | | ||  ||| |   |       ||   || | || ||||  |           |  || ||  |||||
GATTGGCACAGGAGAGCTTGCCTTCTAATGTGGTTACATCCGCACAAGTTCTTGCGAATGTGGCCAACTTGTTGAATATAAGAGATACTGAAATGAGTAGgtgtgttttgtttactttca----ccattgttgttttttgtttctgcatcaatatttgaagtttgaatattgaactcacccct----ggaatctgtgtttag

upper sequence: Vv05s0049g01470.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA09G32470.2 (Glycine max), 5'ss of exon 3
GATTGGCACAAGAGGGTTTGCCTTCAAATGTGGTTGCATCGGCGCAGTGCCTTGCGAATGTGGCAAATTTGTTGAATACAAGAGATACTGAATTGAGTAGgtcggttgggtttgtgttaatattccattaccgatgttccttttttttttttcccctgcttttaggattttgagttttatataaag--ggagatgtggatttag
||||||| || ||| | ||||| || ||||||||| ||||||| ||    ||||||||||| || || |||||||||| ||||||||||||| |||||||||  |||  |||||        || ||  |    ||||    |||  ||| | |     | || | | ||||| | ||  |   |    |  || ||  |||||
GATTGGCGCAGGAGAGCTTGCCCTCCAATGTGGTTACATCGGCACAAGTTCTTGCGAATGTCGCCAACTTGTTGAATATAAGAGATACTGAAATGAGTAGgtgtgttttgtttgc-------tttcaccattcttgttttgctttggtttctgcatcaatatttgaagtttgaatattgaactcaccctggaatctgtgtttag
















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|294964637|gb|GW838440.1|GW838440
EST:     CTTGCGAATGTGGCAAATTTGTTGAATACAAGAGATGCTGAATTGAGTAG                         TTT-CTTGTAACCATGGGG-ACATGTCTT
genomic: CTTGCGAATGTGGCAAATTTGTTGAATACAAGAGATACTGAATTGAGTAGgtcggttggg ... gtggatttagTTTTCTTGTAGCAATGGGGGACATGTCTT
EST: gi|349812735|gb|FQ409894.1|FQ409894
EST:     CTTGCGAATGTGGCAAATTTGTTGAATACAAGAGATACTGAATTGAGTAG                         TTTTCTTGTAGCAATGGGGGACATGTCTTTGAGGAAGACTGGAGTGGAGGA
genomic: CTTGCGAATGTGGCAAATTTGTTGAATACAAGAGATACTGAATTGAGTAGgtcggttggg ... gtggatttagTTTTCTTGTAGCAATGGGGGACATGTCTTTGAGGAAGACTGGAGTGGAGGA
EST: gi|349815651|gb|FQ400807.1|FQ400807
EST:     CTTGCGAATGTGGCAAATTTGTTGAATACAAGAGATACTGAATTGAGTAG                         TTTTCTTGTAGCAATGGGGGACATGTCTTTGAGGAAGACTGGAGTGGAGGA
genomic: CTTGCGAATGTGGCAAATTTGTTGAATACAAGAGATACTGAATTGAGTAGgtcggttggg ... gtggatttagTTTTCTTGTAGCAATGGGGGACATGTCTTTGAGGAAGACTGGAGTGGAGGA
EST: gi|351044677|gb|FQ443208.1|FQ443208
EST:     CTTGCGAATGTGGCAAATTTGTTGAATACAAGAGATACTGAATTGAGTAG                         TTTTCTTGTAGCAATGGGGGACATGTCTTTGAGGAAGACTGGAGTGGAGGA
genomic: CTTGCGAATGTGGCAAATTTGTTGAATACAAGAGATACTGAATTGAGTAGgtcggttggg ... gtggatttagTTTTCTTGTAGCAATGGGGGACATGTCTTTGAGGAAGACTGGAGTGGAGGA
EST: gi|349812781|gb|FQ410423.1|FQ410423
EST:     CTTGCGAATGTGGCAAATTTGTTGAATACAAGAGATACTGAATTGAGTAG                         TTTTCTTGTAGCAATGGGGGACATGTCTTTGAGGAAGACTGGAGTGGAGGA
genomic: CTTGCGAATGTGGCAAATTTGTTGAATACAAGAGATACTGAATTGAGTAGgtcggttggg ... gtggatttagTTTTCTTGTAGCAATGGGGGACATGTCTTTGAGGAAGACTGGAGTGGAGGA
EST: gi|110718784|gb|EE096009.1|EE096009
EST:     CTTGCGAATGTGGCAAATTTGTTGAATACAAGAGATACTGAATTGAGTAG                         TTTTCTTGTAGCAATGGGGGACATGTCTTTGAAGAAGACTGGAGTGGAGGA
genomic: CTTGCGAATGTGGCAAATTTGTTGAATACAAGAGATACTGAATTGAGTAGgtcggttggg ... gtggatttagTTTTCTTGTAGCAATGGGGGACATGTCTTTGAGGAAGACTGGAGTGGAGGA
EST: gi|161713410|gb|FC063390.1|FC063390
EST:     CTTGCGAATGTGGCAAATTTGTTGAATACAAGAGATACTGAATTGAGTAG                         TTTTCTTGTAGCAATGGGGGACATGTCTTTGAGGAAGACTGGAGTGGAGGA
genomic: CTTGCGAATGTGGCAAATTTGTTGAATACAAGAGATACTGAATTGAGTAGgtcggttggg ... gtggatttagTTTTCTTGTAGCAATGGGGGACATGTCTTTGAGGAAGACTGGAGTGGAGGA
EST: gi|110730524|gb|EE107704.1|EE107704
EST:     CTTGCGAATGTGGCAAATTTGTTGAATACAAGAGATACTGAATTGAGTAG                         TTTTCTTGTAGCAATGGGGGACATGTCTTTGAAGAAGACTGGAGTGGANGA
genomic: CTTGCGAATGTGGCAAATTTGTTGAATACAAGAGATACTGAATTGAGTAGgtcggttggg ... gtggatttagTTTTCTTGTAGCAATGGGGGACATGTCTTTGAGGAAGACTGGAGTGGAGGA
EST: gi|351044047|gb|FQ452720.1|FQ452720
EST:     CTTGCGAATGTGGCAAATTTGTTGAATACAAGAGATACTGAATTGAGTAG                         TTTTCTTGTAGCAATGGGGGACATGTCTTTGAGGAAGACTGGAGTGGAGGA
genomic: CTTGCGAATGTGGCAAATTTGTTGAATACAAGAGATACTGAATTGAGTAGgtcggttggg ... gtggatttagTTTTCTTGTAGCAATGGGGGACATGTCTTTGAGGAAGACTGGAGTGGAGGA
EST: gi|110687005|gb|EE064039.1|EE064039
EST:     CTTGCGAATGTGGCAAATTTGTTGAATACAAGAGATACTGAATTGAGTAG                         TTTTCTTGTAGCAATGGGGGACATGTCTTTGAGGAAGACTGGAGTGGAGGA
genomic: CTTGCGAATGTGGCAAATTTGTTGAATACAAGAGATACTGAATTGAGTAGgtcggttggg ... gtggatttagTTTTCTTGTAGCAATGGGGGACATGTCTTTGAGGAAGACTGGAGTGGAGGA
EST: gi|351032507|gb|FQ458872.1|FQ458872
EST:     CTTGCGAATGTGGCAAATTTGTTGAATACAAGAGATACTGAATTGAGTAG                         TTTTCTTGTAGCAATGGGGGACATGTCTTTGAGGAAGACTGGAGTGGAGGA
genomic: CTTGCGAATGTGGCAAATTTGTTGAATACAAGAGATACTGAATTGAGTAGgtcggttggg ... gtggatttagTTTTCTTGTAGCAATGGGGGACATGTCTTTGAGGAAGACTGGAGTGGAGGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATTGGCACAAGAGGGTTTGCCTTCAAATGTGGTTGCATCGGCGCAGTGCCTTGCGAATGTGGCAAATTTGTTGAATACAAGAGATACTGAATTGAGTAGgtcggttgggtttgtgttaatattccattaccgatgttccttttttttttttcccctgcttttaggattttgagttttatataaagggagatgtggatttag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA