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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTCAGTGGACAGTTCCTGACACTGAGCTGCGAGAGTCTCTGAGGCTTGCAGTTGCTGAAGTGTTGTTACCAGCGTACAGAAATTTCATTAAACGTTTTGGgtttgttttctcataattcacaacctttttatttatttttttattttggaagggatgtgagatttagaatgttttcttttggctctgtagcatttgaaag...

Basic information

species Vitis vinifera
transcript Vv13s0073g00170.t01
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0073g00170.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: GLYMA10G34000.1 (Glycine max), 5'ss of exon 11
CTCAGTGGACAGTTCCTGACACTGAGCTGCGAGAGTCTCTGAGGCTTGCAGTTGCTGAAGTGTTGTTACCAGCGTACAGAAATTTCATTAAACGTTTTGGgtttgttttc-tcataattcacaacctttttatttatttttttattttggaagggatgtgagatttagaatgttttcttttggctctgtagcatttgaaag-
|||| ||||||||||||||||||||| ||||||||||||| |||||||||||||||||||| ||||| || || || |||   ||  | ||||| |||||||||||| || |  |  ||||   ||    |  |||| |  ||  | |  | ||   || | | |  |    |      |  |   | ||  ||   |    
CTCAATGGACAGTTCCTGACACTGAGTTGCGAGAGTCTCTTAGGCTTGCAGTTGCTGAAGTCTTGTTGCCTGCCTATAGATCATTTGTCAAACGATTTGGgtttgttctcattttggttcatttccaacgttattatgtcatttctatcaaggga--gttaaagtatgttcatcaaacatgagtagtttataatgcaagtct

upper sequence: Vv13s0073g00170.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: GLYMA20G33590.1 (Glycine max), 5'ss of exon 11
CTCAGTGGACAGTTCCTGACACTGAGCTGCGAGAGTCTCTGAGGCTTGCAGTTGCTGAAGTGTTGTTACCAGCGTACAGAAATTTCATTAAACGTTTTGGgtttgttttctcataattcacaacctttttatttatttttttattttggaagggatgtgagattta-gaatgttttcttttggctctgtagcatttgaaag-----
| || ||||||||||| ||| | ||| ||||||| ||||| ||||| |||||||||||||| ||||| || || || |||   ||  | ||||| |||||||||||| ||     |||   |  |  || |    || || | |  |  | ||||| |   || || | ||||    |  ||  | |||  | ||||  |      
CGCAATGGACAGTTCCAGACTCCGAGTTGCGAGAATCTCTTAGGCTAGCAGTTGCTGAAGTCTTGTTGCCTGCCTATAGATCGTTTGTCAAACGATTTGGgtttgttctc-----atttttattcacttcaaacgttattatgtcatttaggggat-tattatctatggatgtgaaataatgtgtttgtcccctttgtgacaaaaa

upper sequence: Vv13s0073g00170.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: GLYMA10G23810.1 (Glycine max), 5'ss of exon 11
CTCAGTGGACAGTTCCTGACACTGAGCTGCGAGAGTCTCTGAGGCTTGCAGTTGCTGAAGTGTTGTTACCAGCGTACAGAAATTTCATTAAACGTTTTGGgtttgttttctcataattcacaacctttttatttatttttttattttggaagggatgtgagatttagaatgtttt---cttttggctctgtagcatttgaaag--------
||||||||||||| || ||  | ||| ||||||||||||| |  ||||||||||||||||| ||| |||| || || |||   ||  | |||||||||||||  || ||||| |  |   ||||  ||| | ||||            | | | ||      ||||  |   | |   || || |||       |||||||||        
CTCAGTGGACAGTACCAGATGCAGAGTTGCGAGAGTCTCTTATTCTTGCAGTTGCTGAAGTCTTGCTACCTGCCTATAGATCATTTGTGAAACGTTTTGGgtgcgtattctccttttaaccaactgtttgaattat-----------agcaagtatactctttttaacacactctaaactattagctgaaatttatttgaaagtagaaact

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|352778157|gb|FQ468819.1|FQ468819
EST:     GTTGCTGAAGTGTTGTTACCAGCGTACAGAAATTTCATTAAACGTTTTGG                         GCCACTGGTTGAGAGTGGGAAGAATCCCCAGAAGTACATTCGATTCACAGC
genomic: GTTGCTGAAGTGTTGTTACCAGCGTACAGAAATTTCATTAAACGTTTTGGgtttgttttc ... tcaatggcagGCCACTGGTTGAGAGTGGGAAGAATCCCCAGAAGTACATTCGATTCACAGC
EST: gi|110363112|gb|EC926682.1|EC926682
EST:     GTTGCTGAAGTGTTGTTACCAGCGTACAGAAATTTCATTAAACGTTTTGG                         GCCACTGGTTGAGAGTGGGAAGAATCCCCAGAAGTACATTCGATTCACAGC
genomic: GTTGCTGAAGTGTTGTTACCAGCGTACAGAAATTTCATTAAACGTTTTGGgtttgttttc ... tcaatggcagGCCACTGGTTGAGAGTGGGAAGAATCCCCAGAAGTACATTCGATTCACAGC
EST: gi|352781497|gb|FQ468341.1|FQ468341
EST:     GTTGCTGAAGTGTTGTTACCAGCGTACAGAAATTTCATTAAACGTTTTGG                         GCCACTGGTTGAGAGTGGGAAGAATCCCCAGAAGTACATTCGATTCACAGC
genomic: GTTGCTGAAGTGTTGTTACCAGCGTACAGAAATTTCATTAAACGTTTTGGgtttgttttc ... tcaatggcagGCCACTGGTTGAGAGTGGGAAGAATCCCCAGAAGTACATTCGATTCACAGC
EST: gi|110730993|gb|EE108709.1|EE108709
EST:     GTTGCTGAAGTGTTGTTACCAGCGTACAGAAATTTCATTAAACGTTTTGG                         GCCACTGGTTGAGAGTGGAAAGAATCCCCAGAAGTACATTCGATTCACAGC
genomic: GTTGCTGAAGTGTTGTTACCAGCGTACAGAAATTTCATTAAACGTTTTGGgtttgttttc ... tcaatggcagGCCACTGGTTGAGAGTGGGAAGAATCCCCAGAAGTACATTCGATTCACAGC
EST: gi|110693382|gb|EE069563.1|EE069563
EST:     GTTGCTGAAGTGTTGTTACCAGCATACAGAAATTTCATTAAACGTTTTGG                         GCCACTGGTTGAGAGTGGAAAGAATCCCCAGAAGTACATTCGATTCACTGC
genomic: GTTGCTGAAGTGTTGTTACCAGCGTACAGAAATTTCATTAAACGTTTTGGgtttgttttc ... tcaatggcagGCCACTGGTTGAGAGTGGGAAGAATCCCCAGAAGTACATTCGATTCACAGC
EST: gi|352769772|gb|FQ468700.1|FQ468700
EST:     GTTGCTGAAGTGTTGTTACCAGCGTACAGAAATTTCATTAAACGTTTTGG                         GCCACTGGTTGAGAGTGGGAAGAATCCCCAGAAGTACATTCGATTCACAGC
genomic: GTTGCTGAAGTGTTGTTACCAGCGTACAGAAATTTCATTAAACGTTTTGGgtttgttttc ... tcaatggcagGCCACTGGTTGAGAGTGGGAAGAATCCCCAGAAGTACATTCGATTCACAGC
EST: gi|30134289|gb|CB919627.1|CB919627
EST:     GTTGCTGAAGTGTTGTTACCAGCGTACAGAAATTTCATTAAACGTTTTGG                         GCCACTGGTTGAGAGTGGGAAGAATCCCCAGAAGTACATTCGATTCACAGC
genomic: GTTGCTGAAGTGTTGTTACCAGCGTACAGAAATTTCATTAAACGTTTTGGgtttgttttc ... tcaatggcagGCCACTGGTTGAGAGTGGGAAGAATCCCCAGAAGTACATTCGATTCACAGC
EST: gi|30136995|gb|CB922333.1|CB922333
EST:     GTTGCTGAAGTGTTGTTACCAGCGTACAGAAATTTCATTAAACGTTTTGG                         GCCACTGGTTGAGAGTGGGAAGAATCCCCAGAAGTACATTCGATTCACAGC
genomic: GTTGCTGAAGTGTTGTTACCAGCGTACAGAAATTTCATTAAACGTTTTGGgtttgttttc ... tcaatggcagGCCACTGGTTGAGAGTGGGAAGAATCCCCAGAAGTACATTCGATTCACAGC
EST: gi|352773551|gb|FQ472333.1|FQ472333
EST:     GTTGTTGAAGTGTTGTTACCAGCGTACAGAAATTTCATTAAACGTTTTGG                         GCCACTGGTTGAGAGTGGGAAGAATCCCCAGAAGTACATTCGATTCACAGC
genomic: GTTGCTGAAGTGTTGTTACCAGCGTACAGAAATTTCATTAAACGTTTTGGgtttgttttc ... tcaatggcagGCCACTGGTTGAGAGTGGGAAGAATCCCCAGAAGTACATTCGATTCACAGC
EST: gi|30297777|gb|CB974571.1|CB974571
EST:     GTTGCTGAAGTGTTGTTACCAGCGTACAGAAATTTCATTAAACGTTTTGG                         GCCACTGGTTGAGAGTGGGAAGAATCCCCAGAAGTACATTCGATTCCCAGC
genomic: GTTGCTGAAGTGTTGTTACCAGCGTACAGAAATTTCATTAAACGTTTTGGgtttgttttc ... tcaatggcagGCCACTGGTTGAGAGTGGGAAGAATCCCCAGAAGTACATTCGATTCACAGC
EST: gi|110361233|gb|EC924691.1|EC924691
EST:     GTTGCTGAAGTGTTGTTACCAGCGTACAGAAATTTCATTAAACGTTTTGG                         GCCACTGGTTGAGAGTGGAAAGAATCCCCAGAAGTACATTCGATTCACAGC
genomic: GTTGCTGAAGTGTTGTTACCAGCGTACAGAAATTTCATTAAACGTTTTGGgtttgttttc ... tcaatggcagGCCACTGGTTGAGAGTGGGAAGAATCCCCAGAAGTACATTCGATTCACAGC
EST: gi|352773081|gb|FQ470696.1|FQ470696
EST:     GTTGCTGAAGTGTTGTTACCAGCGTACAGAAATTTCATTAAACGTTTTGG                         GCCACTGGTTGAGAGTGGGAAGAATCCCCAGAAGTACATTCGATTCACAGC
genomic: GTTGCTGAAGTGTTGTTACCAGCGTACAGAAATTTCATTAAACGTTTTGGgtttgttttc ... tcaatggcagGCCACTGGTTGAGAGTGGGAAGAATCCCCAGAAGTACATTCGATTCACAGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTCAGTGGACAGTTCCTGACACTGAGCTGCGAGAGTCTCTGAGGCTTGCAGTTGCTGAAGTGTTGTTACCAGCGTACAGAAATTTCATTAAACGTTTTGGgtttgttttctcataattcacaacctttttatttatttttttattttggaagggatgtgagatttagaatgttttcttttggctctgtagcatttgaaag

- - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaagggat