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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTATGGACCAATGGGGTTTGATATAGGCGCATTTTTAGGAAACTTGATTTTGGCTTACTTTGCACAAGATGGGCATGCTGATCAAGTGAATGATAGAAAAgtatgtctgtgttcttaacttcgtttctatggtttttcccatttccccaaagtttgaaaatatttagctgtccatagtctagtgttaattttcttgtttc...

Basic information

species Vitis vinifera
transcript Vv03s0091g00080.t01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv03s0091g00080.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: LOC_Os04g57410.1 (Oryza sativa), 5'ss of exon 4
TTATGGACCAATGGGGTTTGATATAGGCGCATTTTTAGGAAACTTGATTTTGGCTTACTTTGCACAAGATGGGCATGCTGATCAAGTGAATGATAGAAAAgtatgtctgtgttcttaacttcgtttctatggtt-----tttcccatttccccaaagtt-tgaaaatatttagctgtccatagtctagtgttaattttcttgtttc
 ||||| |||||||| |  ||||| || || ||  | || |||||||||||||| || ||| |||||||||| |||||||||||||  |||||| | || || ||| ||  ||  |    |  |     |   |     |     || |  ||   ||  | ||  | ||| ||  |   ||   || ||  ||     |      
CTATGGCCCAATGGGTTACGATATTGGGGCCTTCCTGGGGAACTTGATTTTGGCATATTTTTCACAAGATGGACATGCTGATCAAGCAAATGATCGTAAGgtgtgtatggatttattggctaataatagtaaatgaaagtgcgtaatcttacctgggtggttaagttgttttgcgtttgctaagataatggcaaccacat------

upper sequence: Vv03s0091g00080.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: LOC_Os04g57400.1 (Oryza sativa), 5'ss of exon 4
TTATGGACCAATGGGGTTTGATATAGGCGCATTTTTAGGAAACTTGATTTTGGCTTACTTTGCACAAGATGGGCATGCTGATCAAGTGAATGATAGAAAAgtatgtctgtgttcttaacttcgtt----tctatggtttttcccatttccccaaagtttgaaaatatttagctgtccatagtctagtgttaattttcttgtttc
 ||||| |||||||| |  || || || || ||  | || |||||||||||||| || ||| |||||||||| || ||||||||||  |||||| | || |||||| ||  ||  |    |  |     |  |||    |    | ||   |   ||    |||| |     | |   |  |   |||  ||     | |||  
CTATGGCCCAATGGGTTACGACATTGGGGCCTTCCTGGGGAACTTGATTTTGGCATATTTTTCACAAGATGGACACGCTGATCAAGCAAATGATCGTAAGgtatgtatggatttattggctaataatagtaaatgaaagtgtgtacttttacctggtccacaaatgtcctctttttttt--ttatgtgacaaaaagatagtt--

upper sequence: Vv03s0091g00080.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GRMZM2G464137_T03 (Zea mays), 5'ss of exon 4
TTATGGACCAATGGGGTTTGATATAGGCGCATTTTTAGGAAACTTGATTTTGGCTTACTTTGCACAAGATGGGCATGCTGATCAAGTGAATGATAGAAAAgtatgtctgtgttcttaacttcgtttctatggtttttcccatttccccaaagtttgaaaatatttagctgtccatagtctagtgtta-attttcttgtttc
 ||||| |||||||| |||||||| || || ||  | |||||| |||||||||| |||| ||||||  |||||||||||||||||| ||||||| | || |||||  ||  |   | |  | |||  | | |        ||    |||| || |  ||   |     | | ||| || || |  || || | ||||  | 
CTATGGGCCAATGGGTTTTGATATTGGAGCCTTCCTTGGAAACCTGATTTTGGCATACTATGCACAGAATGGGCATGCTGATCAAGCGAATGATCGTAAGgtatgcatgaatctgttagcttgttaattttgcaccctttataattccaa-gtctccaatggtagtattatacatggtttactcatacatgtacttggctt

upper sequence: Vv03s0091g00080.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA10G40730.1 (Glycine max), 5'ss of exon 4
TTATGGACCAATGGGGTTTGATATAGGCGCATTTTTAGGAAACTTGATTTTGGCTTACTTTGCACAAGATGGGCATGCTGATCAAGTGAATGATAGAAAAgtatgtctgtgttcttaacttcgtttctatggtttttcccatttccccaaagtttgaaaatatttagctgtccatagtctagt-gttaattttcttgtttc-
||||||||||||||| |||||||| || ||||| || ||||||||||||||||||| |||||| ||||||||||||||||||||||  |||||| |||||||| |||    || |  |  ||  |||| ||||  ||  | | | |      |   | | |  |||  ||  || | | |  | |||| | | | |  |   
TTATGGACCAATGGGTTTTGATATTGGAGCATTCTTGGGAAACTTGATTTTGGCTTTCTTTGCTCAAGATGGGCATGCTGATCAAGCAAATGATCGAAAAgtaggtcccctttttccatgtc--ttctgtggtccttgtcctcttctttgcatactatagttgttatttggtcacatttttcttgttattctccataatcta

upper sequence: Vv03s0091g00080.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA20G26580.1 (Glycine max), 5'ss of exon 4
TTATGGACCAATGGGGTTTGATATAGGCGCATTTTTAGGAAACTTGATTTTGGCTTACTTTGCACAAGATGGGCATGCTGATCAAGTGAATGATAGAAAAgtatgtctgtgttcttaacttcgtttctatggtttttcc----catttccccaaagtttgaaaatatttagctgtccatagtctagtgttaattttcttgtttc
||||||||||||||| |||||||| || ||||| || ||||||||||||||||||| |||||| ||||||||||||||||||||||  |||||| |||||||| |||    || |  |  ||  |||| ||||  || |    | | | |      |   | | |  |||  |   || | | |  ||||| | | | |  |  
TTATGGACCAATGGGTTTTGATATTGGAGCATTCTTGGGAAACTTGATTTTGGCTTTCTTTGCTCAAGATGGGCATGCTGATCAAGCAAATGATCGAAAAgtaggtcccctttttccatgtc--ttctgtggtccttacttgtcctcttctttgcatactatagttgttatttagtcaca-tttcttgttattctccataatc-

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|34362855|gb|CF404440.1|CF404440
EST:     CACAAGATGGGCATGCTGATCAAGTGAATGATAGAAAA                         ACATATAAAGAATGGATTTTGAAGACAATAGAACAGACTTGGAATCTTTTC
genomic: CACAAGATGGGCATGCTGATCAAGTGAATGATAGAAAAgtatgtctgt ... tcttttgcagACATATAAAGAATGGATTTTGAAGGCAATAGAACAGACTTGGAATCTTTTC
EST: gi|110727535|gb|EE104406.1|EE104406
EST:     TGGCTTACTTTGCACAAGATGGGCATGCTGATCAAGTGAATGATAGAAAA                         ACATATAAAGAATGGATTTTGAAGGCAATAGAACAGACTTGGAATCTTTTC
genomic: TGGCTTACTTTGCACAAGATGGGCATGCTGATCAAGTGAATGATAGAAAAgtatgtctgt ... tcttttgcagACATATAAAGAATGGATTTTGAAGGCAATAGAACAGACTTGGAATCTTTTC
EST: gi|33403054|gb|CF208681.1|CF208681
EST:     TGGCTTACTTTGCACAAGATGGGCATGCTGATCAAGTGAATGATAGAAAA                         ACATATAAAGAATGGATTTTGAAGGCAATAGAACAGACTTGGAATCTTTTC
genomic: TGGCTTACTTTGCACAAGATGGGCATGCTGATCAAGTGAATGATAGAAAAgtatgtctgt ... tcttttgcagACATATAAAGAATGGATTTTGAAGGCAATAGAACAGACTTGGAATCTTTTC
EST: gi|32269752|gb|CD718911.1|CD718911
EST:     TGGCTTACTTTGCACAAGATGGGCATGCTGATCAAGTGAATGATAGAAAA                         ACATATAAAGAATGGATTTTGA
genomic: TGGCTTACTTTGCACAAGATGGGCATGCTGATCAAGTGAATGATAGAAAAgtatgtctgt ... tcttttgcagACATATAAAGAATGGATTTTGA
EST: gi|22013296|gb|BQ798330.1|BQ798330
EST:     TGCTGATCAAGTGAATGATAGAAAA                         ACATATAAAGAATGGATTTTGAAGGCAATAGAACAGACTTGGAATCTTTTC
genomic: TGCTGATCAAGTGAATGATAGAAAAgtatgtctgt ... tcttttgcagACATATAAAGAATGGATTTTGAAGGCAATAGAACAGACTTGGAATCTTTTC
EST: gi|33402966|gb|CF208593.1|CF208593
EST:     TGGCTTACTTTGCACAAGATGGGCATGCTGATCAAGTGAATGATAGAAAA                         ACATATAAAGAATGGATTTTGAAGGCAATAGAACAGACTTGGAATCTTTTC
genomic: TGGCTTACTTTGCACAAGATGGGCATGCTGATCAAGTGAATGATAGAAAAgtatgtctgt ... tcttttgcagACATATAAAGAATGGATTTTGAAGGCAATAGAACAGACTTGGAATCTTTTC
EST: gi|22013448|gb|BQ798482.1|BQ798482
EST:     ATGGGCATGCTGATCAAGTGAATGATAGAAAA                         ACATATAAAGAATGGATTTTGAAGGCAATAGAACAGACTTGGAATCTTTTC
genomic: ATGGGCATGCTGATCAAGTGAATGATAGAAAAgtatgtctgt ... tcttttgcagACATATAAAGAATGGATTTTGAAGGCAATAGAACAGACTTGGAATCTTTTC
EST: gi|32247178|gb|CD712997.1|CD712997
EST:     TGGCTTACTTTGCACAAGATGGGCATGCTGATCAAGTGAATGATAGAAAA                         ACATATAAAGAATGGATTTTGAAGGCAATAGAACAGACTTGGAATCTTTTC
genomic: TGGCTTACTTTGCACAAGATGGGCATGCTGATCAAGTGAATGATAGAAAAgtatgtctgt ... tcttttgcagACATATAAAGAATGGATTTTGAAGGCAATAGAACAGACTTGGAATCTTTTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTATGGACCAATGGGGTTTGATATAGGCGCATTTTTAGGAAACTTGATTTTGGCTTACTTTGCACAAGATGGGCATGCTGATCAAGTGAATGATAGAAAAgtatgtctgtgttcttaacttcgtttctatggtttttcccatttccccaaagtttgaaaatatttagctgtccatagtctagtgttaattttcttgtttc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tttcccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaaaata