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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAACTTCTTTCTGAGAGCATGCGCTATGCAGACAAGCAGGATGCTTCAGGAAACAAGCTTCTCCAAGATGTTGGGCTGTGGATATCGCAGAAAATCAGGgtagggattctgaccaaagttgtactatatatataaaatcatctacatttatatgattggtttgttggcgcattacatttatctgtctgcttttgtgcac...

Basic information

species Vitis vinifera
transcript Vv11s0016g02850.t01
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0016g02850.t01 (Vitis vinifera), 5'ss of exon 10
lower sequence: GLYMA08G03570.1 (Glycine max), 5'ss of exon 10
GGAACTTCTTTCTGAGAGCATGCGCTATGCAGACAAGCAGGATGCTTCAGGAAACAAGCTTCTCCAAGATGTTGGGCTGTGGATATCGCAGAAAATCAGGgtagggattctgaccaa----agttgtactatatatataaaatcatctacatttatatgattggtttgttggcgcattacatttatctgtctgcttttgtgcac
||||||| ||||||||||||| |  |      |||||||||||||||| |||||||| ||||| |||||||||||||| |||||||| || || || | |||  ||||| |            |||| ||  |||| | ||||    |   || || | | |   |||    |  |||    |   | |  || ||   | |  
GGAACTTGTTTCTGAGAGCATCCAATCCTTGAACAAGCAGGATGCTTCTGGAAACAAACTTCTTCAAGATGTTGGGCTATGGATATCCCAAAAGATAAAGgtgtggattgttgtttgttccgtttgtgctggatatctcaaatgtgattttttaatcttactttcttgaattcagattgaggtc--cggcttgtttccttcc--

upper sequence: Vv11s0016g02850.t01 (Vitis vinifera), 5'ss of exon 10
lower sequence: GLYMA05G36050.1 (Glycine max), 5'ss of exon 10
GGAACTTCTTTCTGAGAGCATGCGCTATGCAGACAAGCAGGATGCTTCAGGAAACAAGCTTCTCCAAGATGTTGGGCTGTGGATATCGCAGAAAATCAGGgtagggattctgaccaa----agttgtactatatatataaaatcatctacatttatatgattggtttgttggcgcattacatttatctgtctgcttttgtgcac
||||||| ||||||||||||| |  |      |||||||||||||||| |||||||| ||||| |||||||||||||| |||||||| || || || | |||  || ||||            |||| ||  |||| | ||||    || | |  ||  |||  ||| |||     | |      |||| ||  |||  | |  
GGAACTTGTTTCTGAGAGCATCCAATCCTTGCACAAGCAGGATGCTTCTGGAAACAAACTTCTTCAAGATGTTGGGCTATGGATATCCCAAAAGATAAAGgtgtggtttcttgtttgttccgtttgtgctggatatctcaaatgcgttatactctta--attcctttcttgaattctgattgaggtctggcttgtttgcttc--

upper sequence: Vv11s0016g02850.t01 (Vitis vinifera), 5'ss of exon 10
lower sequence: GLYMA01G00870.1 (Glycine max), 5'ss of exon 10
GGAACTTCTTTCTGAGAGCATGCGCTATGCAGACAAGCAGGATGCTTCAGGAAACAAGCTTCTCCAAGATGTTGGGCTGTGGATATCGCAGAAAATCAGGgtagggattctgaccaaagttgtact-atatatataaaatcat-ctacatttatat---gattggtttgttggcgcattacatttatctgtctgcttttgtgcac
||||||| ||||||||||  |||  |       ||| || |||||||| |||||||||||| | ||||||||||| || |||||||| || || || ||||| ||  |  |   ||   || || |   ||   |   ||| | || ||||  | |    |||  |||||||       ||    |  ||| |  ||        
GGAACTTGTTTCTGAGAGTGTGCAGTCCATGAGCAAACAAGATGCTTCTGGAAACAAGCTTTTTCAAGATGTTGGCCTATGGATATCCCAAAAGATTAGGgtcggattgttattcatcattctatttgcattcttttcatctttctgcattagtctcttaatttctttgttgaatttaaactcaaacttgtttatttcct-----

upper sequence: Vv11s0016g02850.t01 (Vitis vinifera), 5'ss of exon 10
lower sequence: GLYMA07G15170.1 (Glycine max), 5'ss of exon 10
GGAACTTCTTTCTGAGAGCATGCGCTATGCAGACAAGCAGGATGCTTCAGGAAACAAGCTTCTCCAAGATGTTGGGCTGTGGATATCGCAGAAAATCAGGgt---agggattctgaccaaagttgtactatatatataaaatcatctacatttatatgattggtttgttggcgcatt---acatttatctgtctgcttttgtgcac
 |||||| ||||||||||| |||  |       ||| ||||||||||| ||||| |||||| | ||||||||||| || |||||||| || || || |||||   | || |  | |    | ||| | | | |  ||        || ||||   ||  |   ||  | |  | |||   ||    |  ||| |  ||        
AGAACTTGTTTCTGAGAGCGTGCAGTCAATGAGCAAACAGGATGCTTCTGGAAATAAGCTTTTTCAAGATGTTGGCCTATGGATATCCCAAAAGATTAGGgttagatggttattcattctatttgcattcttttcatctttgttactgcattatcatcttattttcttcgatgaattcgaactcaaacttgtttatttcc------

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|46918678|gb|CN548007.1|CN548007
EST:     GAAACAAGCTTCTCCAAGATGTTGGGCTGTGGATATCGCAGAAAATCAGG                         GATCATTTCTCAACAAGTAAAAGGATGGGCATAACTCTCAAATATATAG
genomic: GAAACAAGCTTCTCCAAGATGTTGGGCTGTGGATATCGCAGAAAATCAGGgtagggattc ... ttgtttgcagGATCATTTCTCAACAAGTAAAAGGATGGGCATAACTCTCAAATATATAG
EST: gi|161717475|gb|FC066878.1|FC066878
EST:     GAAACAAGCTTCTCCCAGATGTTGGGCTGTGGATATCGCAGAAAATCAGG                         GATCATTTTCTCA-CA-GTAAAAGGATGGGCATAACT
genomic: GAAACAAGCTTCTCCAAGATGTTGGGCTGTGGATATCGCAGAAAATCAGGgtagggattc ... ttgtttgcagGATCATTT-CTCAACAAGTAAAAGGATGGGCATAACT
EST: gi|30329681|gb|CD012943.1|CD012943
EST:     AAGATGTTGGGCTGTGGATATCGCAGAAAATCAGG                         GATCATTTCTCANCAAGTAAAAGGATGGGCATAACTCTCAAATATATAG
genomic: AAGATGTTGGGCTGTGGATATCGCAGAAAATCAGGgtagggattc ... ttgtttgcagGATCATTTCTCAACAAGTAAAAGGATGGGCATAACTCTCAAATATATAG
EST: gi|29784840|gb|CB341314.2|CB341314
EST:     GAAACAAGCTTCTCCAAGATGTTGGGCTGTGGATATCGCAGAAAATCAGG                         GATCATTTCTCAACAAGTAAAAGGATGGGCATAACTCTCAAATATATAG
genomic: GAAACAAGCTTCTCCAAGATGTTGGGCTGTGGATATCGCAGAAAATCAGGgtagggattc ... ttgtttgcagGATCATTTCTCAACAAGTAAAAGGATGGGCATAACTCTCAAATATATAG
EST: gi|33409346|gb|CF214973.1|CF214973
EST:     GAAACAAGCTTCTCCAAGATGTTGGGCTGTGGATATCGCAGAAAATCAGG                         GATCATTTCTCAACAAGTAAAAGGATGGGCATAACTCTCAAATATATAG
genomic: GAAACAAGCTTCTCCAAGATGTTGGGCTGTGGATATCGCAGAAAATCAGGgtagggattc ... ttgtttgcagGATCATTTCTCAACAAGTAAAAGGATGGGCATAACTCTCAAATATATAG
EST: gi|30256405|gb|CB972248.1|CB972248
EST:     GAAACAAGCTTCTCCAAGATGTTGGGCTGTGGATATCGCAGAAAATCAGG                         GATCATTTCTCAACAAGTAAAAGGATGGGCATAACTCTCAAATATATAG
genomic: GAAACAAGCTTCTCCAAGATGTTGGGCTGTGGATATCGCAGAAAATCAGGgtagggattc ... ttgtttgcagGATCATTTCTCAACAAGTAAAAGGATGGGCATAACTCTCAAATATATAG
EST: gi|33409425|gb|CF215052.1|CF215052
EST:     AAGATGTTGGGCTGTGGATATCGCAGAAAATCAGG                         GATCATTTCTCAACAAGTAAAAGGATGGGCATAACTCTCAAATATATAG
genomic: AAGATGTTGGGCTGTGGATATCGCAGAAAATCAGGgtagggattc ... ttgtttgcagGATCATTTCTCAACAAGTAAAAGGATGGGCATAACTCTCAAATATATAG
EST: gi|110363721|gb|EC927331.1|EC927331
EST:     GAAACAAGCTTCTCCAAGATGTTGGGCTGTGGATATCGCAGAAAATCAGG                         GATCATTTCTCAACAAGTAAAAGGATGGGCATAACTCTCAAATATATAG
genomic: GAAACAAGCTTCTCCAAGATGTTGGGCTGTGGATATCGCAGAAAATCAGGgtagggattc ... ttgtttgcagGATCATTTCTCAACAAGTAAAAGGATGGGCATAACTCTCAAATATATAG
EST: gi|71884224|gb|DT033279.1|DT033279
EST:     GAAACAAGCTTCTCCAAGATGTTGGGCTGTGGATATCGCAGAAAATCAGG                         GATCATTTCTCAACAAGTAAAAGGATGGGCATAACTCTCAAATATATAG
genomic: GAAACAAGCTTCTCCAAGATGTTGGGCTGTGGATATCGCAGAAAATCAGGgtagggattc ... ttgtttgcagGATCATTTCTCAACAAGTAAAAGGATGGGCATAACTCTCAAATATATAG
EST: gi|110361259|gb|EC924720.1|EC924720
EST:     GAAACAAGCTTCTCCAAGATGTTGGGCTGTGGATATCGCAGAAAATCAGG                         GATCATTTCTCAACAAGTAAAAGGATGGGCATAACTCTCAAATATATAG
genomic: GAAACAAGCTTCTCCAAGATGTTGGGCTGTGGATATCGCAGAAAATCAGGgtagggattc ... ttgtttgcagGATCATTTCTCAACAAGTAAAAGGATGGGCATAACTCTCAAATATATAG
EST: gi|71882578|gb|DT031633.1|DT031633
EST:     GAAACAAGCTTCTCCAAGATGTTGGGCTGTGGATATCGCAGAAAATCAGG                         GATCATTTCTCAACAAGTAAAAGGATGGGCATAACTCTCAAATATATAG
genomic: GAAACAAGCTTCTCCAAGATGTTGGGCTGTGGATATCGCAGAAAATCAGGgtagggattc ... ttgtttgcagGATCATTTCTCAACAAGTAAAAGGATGGGCATAACTCTCAAATATATAG
EST: gi|30256378|gb|CB972221.1|CB972221
EST:     GAAACAAGCTTCTCCAAGATGTTGGGCTGTGGATATCGCAGAAAATCAGG                         GATCATTTCTCAACAAGTAAAAGGATGGGCATAACTCTCAAATATATAG
genomic: GAAACAAGCTTCTCCAAGATGTTGGGCTGTGGATATCGCAGAAAATCAGGgtagggattc ... ttgtttgcagGATCATTTCTCAACAAGTAAAAGGATGGGCATAACTCTCAAATATATAG
EST: gi|30256486|gb|CB972329.1|CB972329
EST:     GAAACAAGCTTCTCCAAGATGTTGGGCTGTGGATATCGCAGAAAATCAGG                         GATCATTTCTCAACAAGTAAAAGGATGGGCATAACTCTCAAATATATAG
genomic: GAAACAAGCTTCTCCAAGATGTTGGGCTGTGGATATCGCAGAAAATCAGGgtagggattc ... ttgtttgcagGATCATTTCTCAACAAGTAAAAGGATGGGCATAACTCTCAAATATATAG
EST: gi|110361880|gb|EC925383.1|EC925383
EST:     GAAACAAGCTTCTCCAAGATGTTGGGCTGTGGATATCGCAGAAAATCAGG                         GATCATTTCTCAACAAGTAAAAGGATGGGCATAACTCTCAAATATATAG
genomic: GAAACAAGCTTCTCCAAGATGTTGGGCTGTGGATATCGCAGAAAATCAGGgtagggattc ... ttgtttgcagGATCATTTCTCAACAAGTAAAAGGATGGGCATAACTCTCAAATATATAG
EST: gi|110729768|gb|EE106084.1|EE106084
EST:     GAAACAAGCTTCTCCAAGATGTTGGGCTGTGGATATCGCAGAAAATCAGG                         GATCATTTCTCAACAAGTAAAAGGATGGGCATAACTCTCAAATATATAG
genomic: GAAACAAGCTTCTCCAAGATGTTGGGCTGTGGATATCGCAGAAAATCAGGgtagggattc ... ttgtttgcagGATCATTTCTCAACAAGTAAAAGGATGGGCATAACTCTCAAATATATAG
EST: gi|351045413|gb|FQ447678.1|FQ447678
EST:     GAAACAAGCTTCTCCAAGATGTTGGGCTGTGGATATCGCAGAAAATCAGG                         GATCATTTCTCAACAAGTAAAAGGATGGGCATAACTCTCAAATATATAG
genomic: GAAACAAGCTTCTCCAAGATGTTGGGCTGTGGATATCGCAGAAAATCAGGgtagggattc ... ttgtttgcagGATCATTTCTCAACAAGTAAAAGGATGGGCATAACTCTCAAATATATAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGAACTTCTTTCTGAGAGCATGCGCTATGCAGACAAGCAGGATGCTTCAGGAAACAAGCTTCTCCAAGATGTTGGGCTGTGGATATCGCAGAAAATCAGGgtagggattctgaccaaagttgtactatatatataaaatcatctacatttatatgattggtttgttggcgcattacatttatctgtctgcttttgtgcac

- - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tataaaa