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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggcttatgtatattcttctagccacatttgagggcttatttagtaaaataaaccatcagaaagatctaaagaatggcttgctgatgagcatctatttcagGGGTTACTTTATATGGTGGACCAAGGGCAAGTGCCTTGCTGAATCTTCCAGAGGCTCACTCTTTTCATCATGAGTATAATTCAATGGCTTGCACTGTTGA

Basic information

species Vitis vinifera
transcript Vv13s0019g02360.t01
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0019g02360.t01 (Vitis vinifera), 3'ss of exon 15
lower sequence: LOC_Os05g38150.1 (Oryza sativa), 3'ss of exon 14
-ggcttatgta-tattcttctagccacatttgagggcttatttagta-aaataaaccatcagaaagatctaaagaatggcttgctgatgagcatctatttcagGGGTTACTTTATATGGTGGACCAAGGGCAAGTGCCTTGCTGAATCTTCCAGAGGCTCACTCTTTTCATCATGAGTATAATTCAATGGCTTGCACTGTTGA
   |  ||||| |||  |||| |  | | | ||  | || ||   |  | ||| |    ||  |   |||      |   | | | |||    | ||||||||| |||| | | ||||||||||| |  ||          |||    ||||| | |||   || |||||||||||||||| ||| ||||| |||||||||||
tcacagatgtagtatgtttctgg--atactggattgttttttacttgtatatacagggccatgattttctccctgcttcttagataatgc-tgtatatttcagGAGTTAATATTTATGGTGGACCTATTGCGCACAAAGCTCTGGGATTTCCAAAAGCTGTTTCATTTCATCATGAGTATAGTTCTATGGCCTGCACTGTTGA

upper sequence: Vv13s0019g02360.t01 (Vitis vinifera), 3'ss of exon 15
lower sequence: GLYMA14G07120.1 (Glycine max), 3'ss of exon 12
---ggcttatgtatattcttctagccacatttgagggcttatttagtaaaataaaccatcagaaa-gatctaaagaatggcttgctgatgagcatctatttcagGGGTTACTTTATATGGTGGACCAAGGGCAAGTGCCTTGCTGAATCTTCCAGAGGCTCACTCTTTTCATCATGAGTATAATTCAATGGCTTGCACTGTTGA
     ||||||||         || |  ||  |    | ||   | |  ||   |   ||    | | | |   |||||  |   | |||   || |||  |||| ||||  |||||||| ||||||||||||||| |  || | ||| ||||| | || || || |||||||||||||| | |||  ||||||||||||||||
aaaaacttatgtaa---tggggagtcgaatgaggcaccataccaattttaaagcattttcttttatggtttttggaatgattaaattatgtaaatttatg-cagGTGTTAAATTATATGGAGGACCAAGGGCAAGTTCTCTGTTAAATATTCCACAAGCACATTCATTTCATCATGAGTACAGTTCGCTGGCTTGCACTGTTGA
















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|110364352|gb|EC923948.1|EC923948
EST:     AGTGCAGACTGGTGGCCTCAATCAGCTTATCGTAGAGCTCCGCAATGAAG                         GGGTTACTTTATATGGTGGACCAAGGGCAAGTGCCTTGCTGAATCTTCCAG
genomic: AGTGCAGACTGGTGGCCTCAATCAGCTTATCGTAGAGCTCCGCAATGAAGgtggggcatt ... tctatttcagGGGTTACTTTATATGGTGGACCAAGGGCAAGTGCCTTGCTGAATCTTCCAG
EST: gi|29783366|gb|CB349487.2|CB349487
EST:     AGTGCAGACTGGTGGCCTCAATCAGCTTATCGTAGAGCTCCGCAATGAAG                         GGGTTACTTTATATGGTGGACCAAGGGCAAGTGCCTTGCTGAATCTTCCAG
genomic: AGTGCAGACTGGTGGCCTCAATCAGCTTATCGTAGAGCTCCGCAATGAAGgtggggcatt ... tctatttcagGGGTTACTTTATATGGTGGACCAAGGGCAAGTGCCTTGCTGAATCTTCCAG
EST: gi|30297817|gb|CB974611.1|CB974611
EST:     AGTGCAGACTGGTGGCCTCAATCAGCTTATCGTAGAGCTCCGCAATGAAG                         GGGTTACTTTATATGGTGGACCAAGGGCAAGTGCCTTGCTGAATCTTCCAG
genomic: AGTGCAGACTGGTGGCCTCAATCAGCTTATCGTAGAGCTCCGCAATGAAGgtggggcatt ... tctatttcagGGGTTACTTTATATGGTGGACCAAGGGCAAGTGCCTTGCTGAATCTTCCAG
EST: gi|110427351|gb|EC993787.1|EC993787
EST:     AATCAGCTTATCGTAGAGCTCCGCAATGAAG                         GGGTTACTTTATATGGTGGACCAAGGGCAAGTGCCTTGCTGAATCTTCCAG
genomic: AATCAGCTTATCGTAGAGCTCCGCAATGAAGgtggggcatt ... tctatttcagGGGTTACTTTATATGGTGGACCAAGGGCAAGTGCCTTGCTGAATCTTCCAG
EST: gi|33402185|gb|CF207812.1|CF207812
EST:     AGTGCAGACTGGTGGCCTCAATCAGCTTATCGTAGAGCTCCGCAATGAAG                         GGGTTACTTTATATGGTGGACCAAGGGCAAGTGCCTTGCTGAATCTTCCAG
genomic: AGTGCAGACTGGTGGCCTCAATCAGCTTATCGTAGAGCTCCGCAATGAAGgtggggcatt ... tctatttcagGGGTTACTTTATATGGTGGACCAAGGGCAAGTGCCTTGCTGAATCTTCCAG
EST: gi|33402196|gb|CF207823.1|CF207823
EST:     AGTGCAGACTGGTGGCCTCAATCAGCTTATCGTAGAGCTCCGCAATGAAG                         GGGTTACTTTATATGGTGGACCAAGGGCAAGTGCCTTGCTGAATCTTCCAG
genomic: AGTGCAGACTGGTGGCCTCAATCAGCTTATCGTAGAGCTCCGCAATGAAGgtggggcatt ... tctatttcagGGGTTACTTTATATGGTGGACCAAGGGCAAGTGCCTTGCTGAATCTTCCAG
EST: gi|110377214|gb|EC942273.1|EC942273
EST:     AGTGCAGACTGGTGGCCTCAATCAGCTTATCGTAGAGCTCCGCAATGAAG                         GGGTTACTTTATATGGTGGACCAAGGGCAAGTGCCTTGCTGAATCTTCCAG
genomic: AGTGCAGACTGGTGGCCTCAATCAGCTTATCGTAGAGCTCCGCAATGAAGgtggggcatt ... tctatttcagGGGTTACTTTATATGGTGGACCAAGGGCAAGTGCCTTGCTGAATCTTCCAG
EST: gi|110365796|gb|EC929255.1|EC929255
EST:     AGTGCAGACTGGTGGCCTCAATCAGCTTATCGTAGAGCTCCGCAATGAAG                         GGGTTACTTTATATGGTGGACCAAGGGCAAGTGCCTTGCTGAATCTTCCAG
genomic: AGTGCAGACTGGTGGCCTCAATCAGCTTATCGTAGAGCTCCGCAATGAAGgtggggcatt ... tctatttcagGGGTTACTTTATATGGTGGACCAAGGGCAAGTGCCTTGCTGAATCTTCCAG
EST: gi|33402539|gb|CF208166.1|CF208166
EST:     AGTGCAGACTGGTGGCCTCAATCAGCTTATCGTAGAGCTCCGCAATGAAG                         GGGTTACTTTATATGGTGGACCAAGGGCAAGTGCCTTGCTGAATCTTCCAG
genomic: AGTGCAGACTGGTGGCCTCAATCAGCTTATCGTAGAGCTCCGCAATGAAGgtggggcatt ... tctatttcagGGGTTACTTTATATGGTGGACCAAGGGCAAGTGCCTTGCTGAATCTTCCAG
EST: gi|110362804|gb|EC926359.1|EC926359
EST:     AGTGCAGACTGGTGGCCTCAATCAGCTTATCGTAGAGCTCCGCAATGAAG                         GGGTTACTTTATATGGTGGACCAAGGGCAAGTGCCTTGCTGAATCTTCCAG
genomic: AGTGCAGACTGGTGGCCTCAATCAGCTTATCGTAGAGCTCCGCAATGAAGgtggggcatt ... tctatttcagGGGTTACTTTATATGGTGGACCAAGGGCAAGTGCCTTGCTGAATCTTCCAG
EST: gi|110382148|gb|EC938618.1|EC938618
EST:     AGTGCAGACTGGTGGCCTCAATCAGCTTATCGTAGAGCTCCGCAATGAAG                         GGGTTACTTTATATGGTGGACCAAGGGCAAGTGCCTTGCTGAATCTTCCAG
genomic: AGTGCAGACTGGTGGCCTCAATCAGCTTATCGTAGAGCTCCGCAATGAAGgtggggcatt ... tctatttcagGGGTTACTTTATATGGTGGACCAAGGGCAAGTGCCTTGCTGAATCTTCCAG
EST: gi|110375487|gb|EC940476.1|EC940476
EST:     AGTGCAGACTGGTGGCCTCAATCAGCTTATCGTAGAGCTCCGCAATGAAG                         GGGTTACTTTATATGGTGGACCAAGGGCAAGTGCCTTGCTGAATCTTCCAG
genomic: AGTGCAGACTGGTGGCCTCAATCAGCTTATCGTAGAGCTCCGCAATGAAGgtggggcatt ... tctatttcagGGGTTACTTTATATGGTGGACCAAGGGCAAGTGCCTTGCTGAATCTTCCAG
EST: gi|110388887|gb|EC953685.1|EC953685
EST:     AGTGCAGACTGGTGGCCTCAATCAGCTTATCGTAGAGCTCCGCAATGAAG                         GGGTTACTTTATATGGTGGACCAAGGGCAAGTGCCTTGCTGAATCTTCCAG
genomic: AGTGCAGACTGGTGGCCTCAATCAGCTTATCGTAGAGCTCCGCAATGAAGgtggggcatt ... tctatttcagGGGTTACTTTATATGGTGGACCAAGGGCAAGTGCCTTGCTGAATCTTCCAG
EST: gi|33402105|gb|CF207732.1|CF207732
EST:     AGTGCAGACTGGTGGCCTCAATCAGCTTATCGTAGAGCTCCGCAATGAAG                         GGGTTACTTTATATGGTGGACCAAGGGCAAGTGCCTTGCTGAATCTTCCAG
genomic: AGTGCAGACTGGTGGCCTCAATCAGCTTATCGTAGAGCTCCGCAATGAAGgtggggcatt ... tctatttcagGGGTTACTTTATATGGTGGACCAAGGGCAAGTGCCTTGCTGAATCTTCCAG
EST: gi|29783302|gb|CB349405.2|CB349405
EST:     AGTGCAGACTGGTGGCCTCAATCAGCTTATCGTAGAGCTCCGCAATGAAG                         GGGTTACTTTATATGGTGGACCAAGGGCAAGTGCCTTGCTGAATCTTCCAG
genomic: AGTGCAGACTGGTGGCCTCAATCAGCTTATCGTAGAGCTCCGCAATGAAGgtggggcatt ... tctatttcagGGGTTACTTTATATGGTGGACCAAGGGCAAGTGCCTTGCTGAATCTTCCAG
EST: gi|110414936|gb|EC980800.1|EC980800
EST:     AGTGCAGACTGGTGGCCTCAATCAGCTTATCGTAGAGCTCCGCAATGAAG                         GGGTTACTTTATATGGTGGACCAAGGGCAAGTGCCTTGCTGAATCTTCCAG
genomic: AGTGCAGACTGGTGGCCTCAATCAGCTTATCGTAGAGCTCCGCAATGAAGgtggggcatt ... tctatttcagGGGTTACTTTATATGGTGGACCAAGGGCAAGTGCCTTGCTGAATCTTCCAG
EST: gi|110421820|gb|EC988122.1|EC988122
EST:     AGTGCAGACTGGTGGCCTCAATCAGCTTATCGTAGAGCTCCGCAATGAAG                         GGGTTACTTTATATGGTGGACCAAGGGCAAGTGCCTTGCTGAATCTTCCAG
genomic: AGTGCAGACTGGTGGCCTCAATCAGCTTATCGTAGAGCTCCGCAATGAAGgtggggcatt ... tctatttcagGGGTTACTTTATATGGTGGACCAAGGGCAAGTGCCTTGCTGAATCTTCCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaataaaccatcagaaagatctaaagaatggcttgctgatgagcatctatttcagGGGTTACTTTATATGGTGGACCAAGGGCAAGTGCCTTGCTGAATCTTCCAGAGGCTCACTCTTTTCATCATGAGTATAATTCAATGGCTTGCACTGTTGA
                                 tgctgat  putative branch site (score: 3)
                                             tctatttc  putative PPT
                     taaagaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggcttatgtatattcttctagccacatttgagggcttatttagtaaaataaaccatcagaaagatctaaagaatggcttgctgatgagcatctatttcagGGGTTACTTTATATGGTGGACCAAGGGCAAGTGCCTTGCTGAATCTTCCAGAGGCTCACTCTTTTCATCATGAGTATAATTCAATGGCTTGCACTGTTGA

-gcttatg
- - - - - - - - - - gccacat
- - - - - - - - - - - - - - - - - - - - - - aaaataa
- - - - - - - - - - - - - - - - - - - - - - - - - - ccatcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - taaagaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcttgct