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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attccccttgctctcatgaaaacatggtcacacacaaaagcaagaataacaaggaagaataagcgtgtgtttcttctcttagaattttcttctgctgcagGATGGAGCAATACTGGCATGGAAATTTAATGCAGTTTCCAACTGCTTTGAACCAGCTGCCTCACTCAAAGGTCACACTCAATCAGTGATCACGCTAGTTG

Basic information

species Vitis vinifera
transcript Vv16s0100g00320.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv16s0100g00320.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA09G27300.1 (Glycine max), 3'ss of exon 4
----attccccttgctctcatgaaaacatggtcacacacaaaagcaagaataacaaggaagaataagcgtgtgtttct-tctcttagaattttcttctgctgcagGATGGAGCAATACTGGCATGGAAATTTAATGCAGTTTCCAACTGCTTTGAACCAGCTGCCTCACTCAAAGGTCACACTCAATCAGTGATCACGCTAGTTG
    ||  |    |    ||  | || |   || |||  |    ||    |     | || |  |    | | ||| | ||||  |  |  | |||||||||||||| ||| | ||| |||||||||| ||||||| || | ||||||||||||| || ||||| ||||| ||||||||  |||     ||  |  |  ||||||
gaaaatgacaacagaatacactagaaaagattctcacttatctacatattt-----gtaataccatctttatttttttatctcaaatgaaatacttctgctgcagGACGGATCTATATTGGCATGGAAGTTTAATGTAGCTACCAACTGCTTTGAGCCGGCTGCATCACTTAAAGGTCATTCTCGGGGTGTTGTTTCATTAGTTG

upper sequence: Vv16s0100g00320.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA16G32370.1 (Glycine max), 3'ss of exon 4
-attccccttgctctcatgaaaacatggtcacacacaaaagcaagaataacaaggaagaataagcgtgtgtttcttctcttagaattttcttctgctgcagGATGGAGCAATACTGGCATGGAAATTTAATGCAGTTTCCAACTGCTTTGAACCAGCTGCCTCACTCAAAGGTCACACTCAATCAGTGATCACGCTAGTTG
 |||     ||    || ||| |||     | |        |  |  ||   |     ||||    | | |||  ||||  |  |  | ||||| |||||||| ||| | ||| |||||||||| ||||||| || | ||||||||||||| || ||||| ||||| ||||||||  |||     ||  |  |  ||||||
tattgaaaatgaaaaca-gaatacacaagaaaaggttctcacttgtctacatatttgtaatatcatttttttttatctcaaatgaaatacttctcctgcagGACGGATCTATATTGGCATGGAAGTTTAATGTAGCTACCAACTGCTTTGAGCCGGCTGCATCACTTAAAGGTCATTCTCGGGGTGTTGTTTCATTAGTTG
















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|22009453|gb|BQ794487.1|BQ794487
EST:     AAGTTTATGCATTGGTTGTTGGTAATGATCTGCTCTTTGCTGGTGTACAG                         GATGGAGCAATACTGGCATGGAAATTTAATGCAGTTTCCAACTGCTTTGAA
genomic: AAGTTTATGCATTGGTTGTTGGTAATGATCTGCTCTTTGCTGGTGTACAGgtaattcttt ... tctgctgcagGATGGAGCAATACTGGCATGGAAATTTAATGCAGTTTCCAACTGCTTTGAA
EST: gi|351049271|gb|FQ429014.1|FQ429014
EST:     AAGTTTATGCATTGGTTGTTGGTAATGATCTGCTCTTTGCTGGTGTACAG                         GATGGAGCAATACTGGCATGGAAATTTAATGCAGT
genomic: AAGTTTATGCATTGGTTGTTGGTAATGATCTGCTCTTTGCTGGTGTACAGgtaattcttt ... tctgctgcagGATGGAGCAATACTGGCATGGAAATTTAATGCAGT
EST: gi|349829433|gb|FQ419965.1|FQ419965
EST:     AAGTTTATGCATTGGTTGTTGGTAATGATCTGCTCTTTGCTGGTGTACAG                         GATGGAGCAATACTGGCATGGAAATTTAATGCAGTTTCAAACTGCTTTGAA
genomic: AAGTTTATGCATTGGTTGTTGGTAATGATCTGCTCTTTGCTGGTGTACAGgtaattcttt ... tctgctgcagGATGGAGCAATACTGGCATGGAAATTTAATGCAGTTTCCAACTGCTTTGAA
EST: gi|30322438|gb|CD005700.1|CD005700
EST:     TTTGCTGGTGTA-AG                         GATGGAGC-CTACTGGCATGGAAATTTAATGCAGTTTCCAACTGCTTTGAA
genomic: TTTGCTGGTGTACAGgtaattcttt ... tctgctgcagGATGGAGCAATACTGGCATGGAAATTTAATGCAGTTTCCAACTGCTTTGAA
EST: gi|161721021|gb|FC069636.1|FC069636
EST:     AAGTTTATGCATTGGTTGTTGGTAATGATCTGCTCTTTGCTGGTGTACAG                         GATGGAGCAATACTGGCATGGAAATTTAATGCAGTTTCCAACTGCTTTGAA
genomic: AAGTTTATGCATTGGTTGTTGGTAATGATCTGCTCTTTGCTGGTGTACAGgtaattcttt ... tctgctgcagGATGGAGCAATACTGGCATGGAAATTTAATGCAGTTTCCAACTGCTTTGAA
EST: gi|22009470|gb|BQ794504.1|BQ794504
EST:     AAGTTTATGCATTGGTTGTTGGTAATGATCTGCTCTTTGCTGGTGTACAG                         GATGGAGCAATACTGGCATGGAAATTTAATGCAGTTTCCAACTGCTTTGAA
genomic: AAGTTTATGCATTGGTTGTTGGTAATGATCTGCTCTTTGCTGGTGTACAGgtaattcttt ... tctgctgcagGATGGAGCAATACTGGCATGGAAATTTAATGCAGTTTCCAACTGCTTTGAA
EST: gi|22009471|gb|BQ794505.1|BQ794505
EST:     AAGTTTATGCATTGGTTGTTGGTAATGATCTGCTCTTTGCTGGTGTACAG                         GATGGAGCAATACTGGCATGGAAATTTAATGCAGTTTCCAACTGCTTTGAA
genomic: AAGTTTATGCATTGGTTGTTGGTAATGATCTGCTCTTTGCTGGTGTACAGgtaattcttt ... tctgctgcagGATGGAGCAATACTGGCATGGAAATTTAATGCAGTTTCCAACTGCTTTGAA
EST: gi|30305654|gb|CB982448.1|CB982448
EST:     AAGTTTATGCATTGGTTGTTGGTAATGATCTGCTCTTTGCTGGTGTACAG                         GATGGAGCAATACTGGCATGGAAATTTAATGCAGTTTCCAACTGCTTTGAA
genomic: AAGTTTATGCATTGGTTGTTGGTAATGATCTGCTCTTTGCTGGTGTACAGgtaattcttt ... tctgctgcagGATGGAGCAATACTGGCATGGAAATTTAATGCAGTTTCCAACTGCTTTGAA
EST: gi|34545194|gb|CF513426.1|CF513426
EST:     AAGTTTATGCATTGGTTGTTGGTAATGATCTGCCCTTTGCTGGTGTACAG                         GATGGAGCAATACTGGCATGGAAATTTAATGCAGTTTCCAACTGCTTTGAA
genomic: AAGTTTATGCATTGGTTGTTGGTAATGATCTGCTCTTTGCTGGTGTACAGgtaattcttt ... tctgctgcagGATGGAGCAATACTGGCATGGAAATTTAATGCAGTTTCCAACTGCTTTGAA
EST: gi|34546189|gb|CF514421.1|CF514421
EST:     AGTTTATGCATTGGTTGTTGGTAATGATC-GACCCTTTGCGGGTGTACAG                         GATGGAGCAATACTGGCATGGAAATTTAATGCAGTTTCCAACTGCTTTGAA
genomic: AGTTTATGCATTGGTTGTTGGTAATGATCTG-CTCTTTGCTGGTGTACAGgtaattcttt ... tctgctgcagGATGGAGCAATACTGGCATGGAAATTTAATGCAGTTTCCAACTGCTTTGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataacaaggaagaataagcgtgtgtttcttctcttagaattttcttctgctgcagGATGGAGCAATACTGGCATGGAAATTTAATGCAGTTTCCAACTGCTTTGAACCAGCTGCCTCACTCAAAGGTCACACTCAATCAGTGATCACGCTAGTTG
 gaataac  putative branch site (score: 2)
                                       ttttcttctgctgc  putative PPT
                                 ttagaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attccccttgctctcatgaaaacatggtcacacacaaaagcaagaataacaaggaagaataagcgtgtgtttcttctcttagaattttcttctgctgcagGATGGAGCAATACTGGCATGGAAATTTAATGCAGTTTCCAACTGCTTTGAACCAGCTGCCTCACTCAAAGGTCACACTCAATCAGTGATCACGCTAGTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- tcccctt
- - - - - ctctcat
- - - - - - - - -gaaaaca
- - - - - - - - - - - - - -tcacaca
- - - - - - - - - - - - - - - - - - aaagcaa
- - - - - - - - - - - - - - - - - - - - - -gaataac
- - - - - - - - - - - - - - - - - - - - - - - - - - ggaagaa