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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcaatgtgatattttatttttctattgatcaaccttcaagatttatgaggtaataaaaaatcttgaacatgaaactgatattggtaacttgttatctcagGATTAGAGTTGTGCTCCACCACCAAATATCAGGAACTGATGTGCAGTATACATTGTCATGCATTCAG

Basic information

species Vitis vinifera
transcript Vv14s0036g00520.t01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0036g00520.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA10G30880.1 (Glycine max), 3'ss of exon 8
gcaatgtgatattttatt--tttctattgatcaaccttcaagatttatgaggtaataaaaaatcttgaacatgaaactgatattggtaacttgtta-tctcagGATTAGAGTTGTGCTCCACCACCAAATATCAGGAACTGATGTGCAGTATACATTGTCATGCATTCAG---------------------------------
   || ||  | || |||  ||  ||||    |||  |     ||| || |  |||     |  |  | || || ||||||  | ||  ||  ||| |  ||| || |||||||| ||||||||||||||||||| || ||||||||| ||| ||||||| ||| |||||                                 
tatatatgtgaattaattagttcgtattagataactattgcactttgtg-gacaatgtgctaatt--agcaagagactgatgatagtgtctgtttaattccagAATGAGAGTTGTTCTCCACCACCAAATATCAGCAAGTGATGTGCAATATGCATTGTCGTGCTTTCAGGTGATGATGACTACAAATCAACTAAACTCTTTT

upper sequence: Vv14s0036g00520.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA10G30880.3 (Glycine max), 3'ss of exon 8
gcaatgtgatattttatt--tttctattgatcaaccttcaagatttatgaggtaataaaaaatcttgaacatgaaactgatattggtaacttgtta-tctcagGATTAGAGTTGTGCTCCACCACCAAATATCAGGAACTGATGTGCAGTATACATTGTCATGCATTCAG
   || ||  | || |||  ||  ||||    |||  |     ||| || |  |||     |  |  | || || ||||||  | ||  ||  ||| |  ||| || |||||||| ||||||||||||||||||| || ||||||||| ||| ||||||| ||| |||||
tatatatgtgaattaattagttcgtattagataactattgcactttgtg-gacaatgtgctaatt--agcaagagactgatgatagtgtctgtttaattccagAATGAGAGTTGTTCTCCACCACCAAATATCAGCAAGTGATGTGCAATATGCATTGTCGTGCTTTCAG

upper sequence: Vv14s0036g00520.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA20G36590.2 (Glycine max), 3'ss of exon 8
-gcaatgtgatattttattt--ttctattgatcaaccttcaagatttatgaggtaataaaaaatcttgaacatgaaactgatattggtaacttgttatctcagGATTAGAGTTGTGCTCCACCACCAAATATCAGGAACTGATGTGCAGTATACATTGTCATGCATTCAG
  | || ||  | || ||||  |  ||||    |||| |      || || |  |||      |  | | || || ||||||  | ||  ||  | ||  ||| || |||||||| ||||| ||||||||||||| || ||||||||| ||  | ||||||||| |||||
ttctatatgtgaattaatttgttcgtattagataaccattgcacgttgtg-gacaatgtgc--ttataagcaagagactgatgatagtgtctgttaattccagAATGAGAGTTGTTCTCCATCACCAAATATCAGCAAGTGATGTGCAATACGCCTTGTCATGCTTTCAG

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|30300481|gb|CB977275.1|CB977275
EST:     AAGTACTTGCAAGAACATGGCGTGCTTATGATGCCAGAGAGCTCGTCGAG                         GATTAGAGTTGTGCTCCACCACCAAATATCAGGAACTGATGTGCAGTATAC
genomic: AAGTACTTGCAAGAACATGGCGTGCTTATGATGCCAGAGAGCTCGTCGAGgtgtgtctca ... gttatctcagGATTAGAGTTGTGCTCCACCACCAAATATCAGGAACTGATGTGCAGTATAC
EST: gi|110379523|gb|EC944723.1|EC944723
EST:     AAGTACTTGCAAGAACATGGCGTGCTTATGATGCCAGAGAGCTCGTCGAG                         GATTAGAGTTGTGCTCCACCACCAAATATCAGGAACTGATGTGCAGTATAC
genomic: AAGTACTTGCAAGAACATGGCGTGCTTATGATGCCAGAGAGCTCGTCGAGgtgtgtctca ... gttatctcagGATTAGAGTTGTGCTCCACCACCAAATATCAGGAACTGATGTGCAGTATAC
EST: gi|110727225|gb|EE103744.1|EE103744
EST:     AAGTACTTGCAAGAACATGGCGTGCTTATGATGCCAGAGAGCTCGTCGAG                         GATTAGAGTTGTGCTCCACCACCAAATATCAGGAACTGATGTGCAGTATAC
genomic: AAGTACTTGCAAGAACATGGCGTGCTTATGATGCCAGAGAGCTCGTCGAGgtgtgtctca ... gttatctcagGATTAGAGTTGTGCTCCACCACCAAATATCAGGAACTGATGTGCAGTATAC
EST: gi|110362584|gb|EC926127.1|EC926127
EST:     AAGTACTTGCAAGAACATGGCGTGCTTATGATGCCAGAGAGCTCGTCGAG                         GATTAGAGTTGTGCTCCACCACCAAATATCAGGAACTGATGTGCAGTATAC
genomic: AAGTACTTGCAAGAACATGGCGTGCTTATGATGCCAGAGAGCTCGTCGAGgtgtgtctca ... gttatctcagGATTAGAGTTGTGCTCCACCACCAAATATCAGGAACTGATGTGCAGTATAC
EST: gi|30130413|gb|CB915752.1|CB915752
EST:     AAGTACTTGCAAGAACATGGCGTGCTTATGATGCCAGAGAGCTCGTCGAG                         GATTAGAGTTGTGCTCCACCACCAAATATCAGGAACTGATGTGCAGTATAC
genomic: AAGTACTTGCAAGAACATGGCGTGCTTATGATGCCAGAGAGCTCGTCGAGgtgtgtctca ... gttatctcagGATTAGAGTTGTGCTCCACCACCAAATATCAGGAACTGATGTGCAGTATAC
EST: gi|46918393|gb|CN547722.1|CN547722
EST:     AAGTACTTGCAAGAACATGGCGTGCTTATGATGCCAGAGAGCTCGTCGAG                         GATTAGAGTTGTGCTCCACCACCAAATATCAGGAACTGATGTGCAGTATAC
genomic: AAGTACTTGCAAGAACATGGCGTGCTTATGATGCCAGAGAGCTCGTCGAGgtgtgtctca ... gttatctcagGATTAGAGTTGTGCTCCACCACCAAATATCAGGAACTGATGTGCAGTATAC
EST: gi|110422750|gb|EC989080.1|EC989080
EST:     AAGTACTTGCAAGAACATGGCGTGCTTATGATGCCAGAGAGCTCGTCGAG                         GATTAGAGTTGTGCTCCACCACCAAATATCAGGAACTGATGTGCAGTATAC
genomic: AAGTACTTGCAAGAACATGGCGTGCTTATGATGCCAGAGAGCTCGTCGAGgtgtgtctca ... gttatctcagGATTAGAGTTGTGCTCCACCACCAAATATCAGGAACTGATGTGCAGTATAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaggtaataaaaaatcttgaacatgaaactgatattggtaacttgttatctcagGATTAGAGTTGTGCTCCACCACCAAATATCAGGAACTGATGTGCAGTATACATTGTCATGCATTCAG
                                    tggtaac  putative branch site (score: 2)
                                              ttatctc  putative PPT
     taataaaaaatcttga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcaatgtgatattttatttttctattgatcaaccttcaagatttatgaggtaataaaaaatcttgaacatgaaactgatattggtaacttgttatctcagGATTAGAGTTGTGCTCCACCACCAAATATCAGGAACTGATGTGCAGTATACATTGTCATGCATTCAG

-caatgtg
- - - - - - - - - - - - - -atcaacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaacatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaactga