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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taaattgttattggtgaatatttagctgtttgcttcacataattcaaattatgttatcctttaatttgttactgattgttaaaatgaaaatttgttcaagCTGGTGAGATGCTTCATGTTGCGGAAGCTTTCATAGACAAAAACTTTCACCCTACAGTCATATGTCGAG

Basic information

species Vitis vinifera
transcript Vv17s0000g08170.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv17s0000g08170.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA20G35760.1 (Glycine max), 3'ss of exon 3
--taaattgttattggtgaatatttagctgtttgcttcacataattcaaat-tatgttatcctttaatttgttactgattgttaaaatgaaaatttgttcaagCTGGTGAGATGCTTCATGTTGCGGAAGCTTTCATAGACAAAAACTTTCACCCTACAGTCATATGTCGAG
  |   |  | |||| ||| |  |    | | |  |  || ||||  |     |  |  |  ||| |||| ||   |  | |               ||  |||||||||||||||||||||||| |||||  ||||||| || || | ||| |||||||| || || ||||
catggctcttgattgatga-tgctagattttgttgtgtacttaatggagggacagatctttatttgatttattg--ggctatatgttgtctccccccttgcagCTGGTGAGATGCTTCATGTTGCTGAAGCACTCATAGATAAGAATTATCATCCTACAGTTATTTGCCGAG

upper sequence: Vv17s0000g08170.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA16G33380.1 (Glycine max), 3'ss of exon 6
---------------------------------taaattgttattggtgaatatttagctgtttgcttcacataattcaaattat--gttatcctttaatttgttactgattgttaaaat---gaaaatttgttcaagCTGGTGAGATGCTTCATGTTGCGGAAGCTTTCATAGACAAAAACTTTCACCCTACAGTCATATGTCGAG
                                 | | ||  |  |  |  |||   |   |        |  | | |  | ||||  |  | | | |  | | ||    ||| | || ||   | |  || | |  ||||||||||||||||||||| || || || ||||| |||||||   ||||||||||||| || || ||||
gtatgtttctgcatgatttaatagcaaaattcttgattttgttatattatataccgaatggacgatcagatcttagttgatttattgggcagcatattctctttttacaattttcaatattttgtattttcggtgcagCTGGTGAGATGCTTCATGTCGCCGATGCATTCATTGACAAAA---TTCACCCTACAGTTATTTGCCGAG

upper sequence: Vv17s0000g08170.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA09G28650.1 (Glycine max), 3'ss of exon 6
----------------------------------taaattgttattgg--tgaatatttagctgtttgcttcacataattcaaattat--gttatcctttaatttgttactgattgttaaaat---gaaaatttgttca-agCTGGTGAGATGCTTCATGTTGCGGAAGCTTTCATAGACAAAAACTTTCACCCTACAGTCATATGTCGAG
                                   |  || |||||    |  ||| | |   |        |  | | |  | || |  |  | ||| |  | | ||    ||| | || ||   | |  ||||     ||||||||||||||||||||| || || || ||||| |||||||   ||||||||||||| || || ||||
gtatgtttctgcatgatttaatagcaaaattctagatgtttttattatattatatactgaatggaggatcagatcttagttgatttgttgggcagcctattctctttttacaattttcaatatcttgtatttttgggtgcagCTGGTGAGATGCTTCATGTCGCCGATGCATTCATTGACAAAA---TTCACCCTACAGTTATTTGCCGAG

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|352773628|gb|FQ472410.1|FQ472410
EST:     CACACAAGATGAAGAAGTTGGTGATGGAACTACTTCAGTCATTGTTCTTG                         CTGGTGAGATGCTTCATGTTGCGGAAGCTTTCATAGACAAAAACTTTCACC
genomic: CACACAAGATGAAGAAGTTGGTGATGGAACTACTTCAGTCATTGTTCTTGgtacatctct ... tttgttcaagCTGGTGAGATGCTTCATGTTGCGGAAGCTTTCATAGACAAAAACTTTCACC
EST: gi|352764588|gb|FQ472945.1|FQ472945
EST:     CACACAAGATGAAGAAGTTGGTGATGGAACTACTTCAGTCATTGTTCTTG                         CTGGTGAGATGCTTCATGTTGCGGAAGCTTTCATAGACAAAAACTTTCACC
genomic: CACACAAGATGAAGAAGTTGGTGATGGAACTACTTCAGTCATTGTTCTTGgtacatctct ... tttgttcaagCTGGTGAGATGCTTCATGTTGCGGAAGCTTTCATAGACAAAAACTTTCACC
EST: gi|37189192|gb|CF608541.1|CF608541
EST:     CACACAAGATGAAGAAGTTGGTGATGGAACTACTTCAGTCATTGTTCTTG                         CTGGTGAGATGCTTCATGTCGCGGAAGCTTTCATAGACAAAAACTTTCACC
genomic: CACACAAGATGAAGAAGTTGGTGATGGAACTACTTCAGTCATTGTTCTTGgtacatctct ... tttgttcaagCTGGTGAGATGCTTCATGTTGCGGAAGCTTTCATAGACAAAAACTTTCACC
EST: gi|352769725|gb|FQ468653.1|FQ468653
EST:     CACACAAGATGAAGAAGTTGGTGATGGAACTACTTCAGTCATTGTTCTTG                         CTGGTGAGATGCTTCATGTTGCGGAAGCTTTCATAGACAAAAACTTTCACC
genomic: CACACAAGATGAAGAAGTTGGTGATGGAACTACTTCAGTCATTGTTCTTGgtacatctct ... tttgttcaagCTGGTGAGATGCTTCATGTTGCGGAAGCTTTCATAGACAAAAACTTTCACC
EST: gi|71857425|gb|DT006480.1|DT006480
EST:     CACACAAGATGAAGAAGTTGGTGATGGAACTACTTCAGTCATTGTTCTTG                         CTGGTGAGATGCTTCATGTCGCGGAAGCTTTCATAGACAAAAACTTTCACC
genomic: CACACAAGATGAAGAAGTTGGTGATGGAACTACTTCAGTCATTGTTCTTGgtacatctct ... tttgttcaagCTGGTGAGATGCTTCATGTTGCGGAAGCTTTCATAGACAAAAACTTTCACC
EST: gi|71857213|gb|DT006268.1|DT006268
EST:     CACACAAGATGAAGAAGTTGGTGATGGAACTACTTCAGTCATTGTTCTTG                         CTGGTGAGATGCTTCATGTCGCGGAAGCTTTCATAGACAAAAACTTTCACC
genomic: CACACAAGATGAAGAAGTTGGTGATGGAACTACTTCAGTCATTGTTCTTGgtacatctct ... tttgttcaagCTGGTGAGATGCTTCATGTTGCGGAAGCTTTCATAGACAAAAACTTTCACC
EST: gi|71857633|gb|DT006688.1|DT006688
EST:     CACACAAGATGAAGAAGTTGGTGATGGAACTACTTCAGTCATTGTTCTTG                         CTGGTGAGATGCTTCATGTCGCGGAAGCTTTCATAGACAAAAACTTTCACC
genomic: CACACAAGATGAAGAAGTTGGTGATGGAACTACTTCAGTCATTGTTCTTGgtacatctct ... tttgttcaagCTGGTGAGATGCTTCATGTTGCGGAAGCTTTCATAGACAAAAACTTTCACC
EST: gi|71857432|gb|DT006487.1|DT006487
EST:     CACACAAGATGAAGAAGTTGGTGATGGAACTACTTCAGTCATTGTTCTTG                         CTGGTGAGATGCTTCATGTCGCGGAAGTTTTCATAGACAAAAACTTTCACC
genomic: CACACAAGATGAAGAAGTTGGTGATGGAACTACTTCAGTCATTGTTCTTGgtacatctct ... tttgttcaagCTGGTGAGATGCTTCATGTTGCGGAAGCTTTCATAGACAAAAACTTTCACC
EST: gi|71859366|gb|DT008421.1|DT008421
EST:     CACACAAGATGAAGAAGTTGGTGATGGAACTACTTCAGTCATTGTTCTTG                         CTGGTGAGATGCTTCATGTCGCGGAAGCTTTCATAGACAAAAACTTTCACC
genomic: CACACAAGATGAAGAAGTTGGTGATGGAACTACTTCAGTCATTGTTCTTGgtacatctct ... tttgttcaagCTGGTGAGATGCTTCATGTTGCGGAAGCTTTCATAGACAAAAACTTTCACC
EST: gi|71857184|gb|DT006239.1|DT006239
EST:     CACACAAGATGAAGAAGTTGGTGATGGAACTACTTCAGTCATTGTTCTTG                         CTGGTGAGATGCTTCATGTCGCGGAAGCTTTCATAGACAAAAACTTTCACC
genomic: CACACAAGATGAAGAAGTTGGTGATGGAACTACTTCAGTCATTGTTCTTGgtacatctct ... tttgttcaagCTGGTGAGATGCTTCATGTTGCGGAAGCTTTCATAGACAAAAACTTTCACC
EST: gi|71856945|gb|DT006000.1|DT006000
EST:     CACACAAGATGAAGAAGTTGGTGATGGAACTACTTCAGTCATTGTTCTTG                         CTGGTGAGATGCTTCATGTCGCGGAAGCTTTCATAGACAAAAACTTTCACC
genomic: CACACAAGATGAAGAAGTTGGTGATGGAACTACTTCAGTCATTGTTCTTGgtacatctct ... tttgttcaagCTGGTGAGATGCTTCATGTTGCGGAAGCTTTCATAGACAAAAACTTTCACC
EST: gi|71857006|gb|DT006061.1|DT006061
EST:     CACACAAGATGAAGAAGTTGGTGATGGAACTACTTCAGTCATTGTTCTTG                         CTGGTGAGATGCTTCATGTCGCGGAAGCTTTCATAGACAAAAACTTTCACC
genomic: CACACAAGATGAAGAAGTTGGTGATGGAACTACTTCAGTCATTGTTCTTGgtacatctct ... tttgttcaagCTGGTGAGATGCTTCATGTTGCGGAAGCTTTCATAGACAAAAACTTTCACC
EST: gi|71858194|gb|DT007249.1|DT007249
EST:     CACACAAGATGAAGAAGTTGGTGATGGAACTACTTCAGTCATTGTTCTTG                         CTGGTGAGATGCTTCATGTCGCGGAAGCTTTCATAGACAAAAACTTTCACC
genomic: CACACAAGATGAAGAAGTTGGTGATGGAACTACTTCAGTCATTGTTCTTGgtacatctct ... tttgttcaagCTGGTGAGATGCTTCATGTTGCGGAAGCTTTCATAGACAAAAACTTTCACC
EST: gi|71855063|gb|DT004118.1|DT004118
EST:     CACACAAGATGAAGAAGTTGGTGATGGAACTACTTCAGTCATTGTTCTTG                         CTGGTGAGATGCTTCATGTCGCGGAAGCTTTCAT
genomic: CACACAAGATGAAGAAGTTGGTGATGGAACTACTTCAGTCATTGTTCTTGgtacatctct ... tttgttcaagCTGGTGAGATGCTTCATGTTGCGGAAGCTTTCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaattatgttatcctttaatttgttactgattgttaaaatgaaaatttgttcaagCTGGTGAGATGCTTCATGTTGCGGAAGCTTTCATAGACAAAAACTTTCACCCTACAGTCATATGTCGAG
                        tactgat  putative branch site (score: 2)
                                             tttgttc  putative PPT
              tttaatttgttactga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taaattgttattggtgaatatttagctgtttgcttcacataattcaaattatgttatcctttaatttgttactgattgttaaaatgaaaatttgttcaagCTGGTGAGATGCTTCATGTTGCGGAAGCTTTCATAGACAAAAACTTTCACCCTACAGTCATATGTCGAG

- - - - - - - - - - - - -ctgtttg
- - - - - - - - - - - - - - - - cttcaca
- - - - - - - - - - - - - - - - - - - - - - caaatta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgattg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaatgaa