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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgtacctcatccttattcatcataatattagagaagaaactcagagctcctcttatgcttccacttgccatttgtctaaaatttggctttctcgttcctggacatttcgctttggcagGATAAGCACAATTCTTGCCCAATCTGTCGGCATGAACTGCTCACTGATGATCGTGCCTATGAGAGCTGGAAGCAGAGGGAGAAGGAGGCGGAAGAAGAGA

Basic information

species Vitis vinifera
transcript Vv04s0008g02290.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0008g02290.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA14G12380.2 (Glycine max), 3'ss of exon 4
gtaatgtacctcatcctt---attcatcataatattagagaagaaactcagagctcctctt-atgc-ttccact---tgccatttgtctaaaatttggctttctcgttcctggacat-ttcgcttt------------ggcagGATAAGCACAATTCTTGCCCAATCTGTCGGCATGAACTGCTCACTGATGATCGTGCCTATGAGAGCTGGAAGCAGAGGGAGAAGGAGGCGGAAGAAGAGA
||| ||| ||| |  |     ||  ||   ||  ||   |       |  ||  ||  ||| |||| ||  | |   ||  |||  |  | || |    |   | | |    ||  | |||  |||            |||||||| ||||||||||||| || |||||||||||||| ||||  |||||||||| ||||||||||||||||||| || | || ||||| || ||||||||||
gtattgtccctaactccacagatctattggaaattttatgttcttcttttgaaatcaacttcatgcattttattctatggaattcttgaagaaatgacatgattagatataagatgtgttcagttttatcctttatgtggcagGATGAGCACAATTCTTGTCCCATCTGTCGGCATGAGCTGCAAACTGATGATCATGCCTATGAGAGCTGGAAGGAGCGTGAAAAGGAAGCTGAAGAAGAGA

upper sequence: Vv04s0008g02290.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA17G33630.1 (Glycine max), 3'ss of exon 4
gtaatgtacctcatcctt---attcatcataatattagagaagaaactcagagctcctctt-atgc-ttccact---tgccatttgtctaaaatttggctttctc-----------gttcctggacatttcgctt---tggcagGATAAGCACAATTCTTGCCCAATCTGTCGGCATGAACTGCTCACTGATGATCGTGCCTATGAGAGCTGGAAGCAGAGGGAGAAGGAGGCGGAAGAAGAGA
||| ||| ||| |  |     ||  ||   ||  ||   |       |  ||  ||  ||| |||| ||  | |   ||  |||  | ||| |  || | |  |            ||         | ||  ||   ||||||||| ||||||||||||| || |||||||||||||| ||||  |||||||||| ||||||||||||||||||| || | || ||||| || ||||||||||
gtattgtccctaactccacagatctattggaaattttatgttcttcttttgatatcaacttcatgcattttattctatggaattcttttaagaaatgacatgattagatataaggtgtgttcaattttatcctttatgtggcagGATGAGCACAATTCTTGTCCCATCTGTCGGCATGAGCTGCAAACTGATGATCATGCCTATGAGAGCTGGAAGGAGCGTGAAAAGGAAGCTGAAGAAGAGA

upper sequence: Vv04s0008g02290.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA14G12380.1 (Glycine max), 3'ss of exon 4
gtaatgtacctcatcct---tattcatcataatattagagaagaaactcagagctcctctt-atgc-ttccact---tgccatttgtctaaaatttggctttctcgttcctggacat-ttcgcttt------------ggcagGATAAGCACAATTCTTGCCCAATCTGTCGGCATGAACTGCTCACTGATGATCGTGCCTATGAGAGCTGGAAGCAGAGGGAGAAGGAGGCGGAAGAAGAGA
||| ||| ||| |  |     ||  ||   ||  ||   |       |  ||  ||  ||| |||| ||  | |   ||  |||  |  | || |    |   | | |    ||  | |||  |||            |||||||| ||||||||||||| || |||||||||||||| ||||  |||||||||| ||||||||||||||||||| || | ||                    
gtattgtccctaactccacagatctattggaaattttatgttcttcttttgaaatcaacttcatgcattttattctatggaattcttgaagaaatgacatgattagatataagatgtgttcagTTTTATCCTTTATGTGGCAGGATGAGCACAATTCTTGTCCCATCTGTCGGCATGAGCTGCAAACTGATGATCATGCCTATGAGAGCTGGAAGGAGCGTGA--------------------

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|110387031|gb|EC951670.1|EC951670
EST:     AGTTGCCCTGCAAGCACACATTTCACCCTCCCTGTTTAAAGCCGTGGCTG                         GATAAGCACAATTCTTGCCCAATCTGTCGGCATGAACTGCTCACTGATGAT
genomic: AGTTGCCCTGCAAGCACACATTTCACCCTCCCTGTTTAAAGCCGTGGCTGgtaatgtacc ... gctttggcagGATAAGCACAATTCTTGCCCAATCTGTCGGCATGAACTGCTCACTGATGAT
EST: gi|22009632|gb|BQ794666.1|BQ794666
EST:     AGTTGCCCTGCAAGCACACATTTCACCCTCCCTGTTTAAAGCCGTGGCTG                         GATAAGCACAATTCTTGCCCAATCTGTCGGCATGAACTGCTCACTGATGAT
genomic: AGTTGCCCTGCAAGCACACATTTCACCCTCCCTGTTTAAAGCCGTGGCTGgtaatgtacc ... gctttggcagGATAAGCACAATTCTTGCCCAATCTGTCGGCATGAACTGCTCACTGATGAT
EST: gi|110359196|gb|EC920296.1|EC920296
EST:     AGTTGCCCTGCAAGCACACATTTCACCCTCCCTGTTTAAAGCCGTGGCTG                         GATAAGCACAATTCTTGCCCAATCTGTCGGCATGAACTGCTCACTGATGAT
genomic: AGTTGCCCTGCAAGCACACATTTCACCCTCCCTGTTTAAAGCCGTGGCTGgtaatgtacc ... gctttggcagGATAAGCACAATTCTTGCCCAATCTGTCGGCATGAACTGCTCACTGATGAT
EST: gi|351027748|gb|FQ446915.1|FQ446915
EST:     AGTTGCCCTGCAAGCACACATTTCACCCTCCCTGTTTAAAGCCGTGGCTG                         GATAAGCACAATTCTTGCCCAATCTGTCGGCATGAACTGCTCACTGATGAT
genomic: AGTTGCCCTGCAAGCACACATTTCACCCTCCCTGTTTAAAGCCGTGGCTGgtaatgtacc ... gctttggcagGATAAGCACAATTCTTGCCCAATCTGTCGGCATGAACTGCTCACTGATGAT
EST: gi|22009633|gb|BQ794667.1|BQ794667
EST:     AGTTGCCCTGCAAGCACACATTTCACCCTCCCTGTTTAAAGCCGTGGCTG                         GATAAGCACAATTCTTGCCCAATCTGTCGGCATGAACTGCTCACTGATGAT
genomic: AGTTGCCCTGCAAGCACACATTTCACCCTCCCTGTTTAAAGCCGTGGCTGgtaatgtacc ... gctttggcagGATAAGCACAATTCTTGCCCAATCTGTCGGCATGAACTGCTCACTGATGAT
EST: gi|33402318|gb|CF207945.1|CF207945
EST:     AGTTGCCCTGCAAGCACACATTTCACCCTCCCTGTTTAAAGCCGTGGCTG                         GATAAGCACAATTCTTGCCCAATCTGTCGGCATGAACTGCTCACTGATGAT
genomic: AGTTGCCCTGCAAGCACACATTTCACCCTCCCTGTTTAAAGCCGTGGCTGgtaatgtacc ... gctttggcagGATAAGCACAATTCTTGCCCAATCTGTCGGCATGAACTGCTCACTGATGAT
EST: gi|349830496|gb|FQ416794.1|FQ416794
EST:     AGTTGCCCTGCAAGCACACATTTCACCCTCCCTGTTTAAAGCCGTGGCTG                         GGATA-GCACCATTCTT
genomic: AGTTGCCCTGCAAGCACACATTTCACCCTCCCTGTTTAAAGCCGTGGCTGgtaatgtacc ... gctttggcagG-ATAAGCACAATTCTT
EST: gi|110409640|gb|EC975307.1|EC975307
EST:     AGTTGCCCTGCAAGCACACATTTCACCCTCCCTGTTTAAAGCCGTGGCTG                         GATAAGCACAATTCTTGCCCAATCTGTCGGCATGAACTGCTCACTGATGAT
genomic: AGTTGCCCTGCAAGCACACATTTCACCCTCCCTGTTTAAAGCCGTGGCTGgtaatgtacc ... gctttggcagGATAAGCACAATTCTTGCCCAATCTGTCGGCATGAACTGCTCACTGATGAT
EST: gi|22008390|gb|BQ793424.1|BQ793424
EST:     AGTTGCCCTGCAAGCACACATTTCACCCTCCCTGTTTAAAGCCGTGGCTG                         GATAAGCACAATTCTTGCCCAATCTGTCGGCATGAACTGCTCACTGATGAT
genomic: AGTTGCCCTGCAAGCACACATTTCACCCTCCCTGTTTAAAGCCGTGGCTGgtaatgtacc ... gctttggcagGATAAGCACAATTCTTGCCCAATCTGTCGGCATGAACTGCTCACTGATGAT
EST: gi|110375238|gb|EC940205.1|EC940205
EST:     AGTTGCCCTGCAAGCACACATTTCACCCTCCCTGTTTAAAGCCGTGGCTG                         GATAAGCACAATTCTTGCCCCATCTGTCGGCATGAACTGCTCACTGATG
genomic: AGTTGCCCTGCAAGCACACATTTCACCCTCCCTGTTTAAAGCCGTGGCTGgtaatgtacc ... gctttggcagGATAAGCACAATTCTTGCCCAATCTGTCGGCATGAACTGCTCACTGATG
EST: gi|22008718|gb|BQ793752.1|BQ793752
EST:     AGTTGCCCTGCAAGCACACATTTCACCCTCCCTGTTTAAAGCCGTGGCTG                         GATAAGCACAATTCTTGCCCAATCTGTCGGCATGAACTGCTCACTGATGAT
genomic: AGTTGCCCTGCAAGCACACATTTCACCCTCCCTGTTTAAAGCCGTGGCTGgtaatgtacc ... gctttggcagGATAAGCACAATTCTTGCCCAATCTGTCGGCATGAACTGCTCACTGATGAT
EST: gi|349825321|gb|FQ418053.1|FQ418053
EST:     AGTTGCCCTGCAAGCACACATTTCACCCTCCCTGTTTAAGGCCGTGGCTG                         GATAAGCACAATTCTTGCCCAATCTGTCGGCATGAACTGCTCACTGA
genomic: AGTTGCCCTGCAAGCACACATTTCACCCTCCCTGTTTAAAGCCGTGGCTGgtaatgtacc ... gctttggcagGATAAGCACAATTCTTGCCCAATCTGTCGGCATGAACTGCTCACTGA
EST: gi|22009328|gb|BQ794362.1|BQ794362
EST:     AGTTGCCCTGCAAGCACACATTTCACCCTCCCTGTTTAAAGCCGTGGCTG                         GATAAGCACAATTCTTGCCCAATCTGTCGGCATGAACTGCTCACTGATGAT
genomic: AGTTGCCCTGCAAGCACACATTTCACCCTCCCTGTTTAAAGCCGTGGCTGgtaatgtacc ... gctttggcagGATAAGCACAATTCTTGCCCAATCTGTCGGCATGAACTGCTCACTGATGAT
EST: gi|22009660|gb|BQ794694.1|BQ794694
EST:     AGTTGCCCTGCAAGCACACATTTCACCCTCCCTGTTTAAAGCCGTGGCTG                         GATAAGCACAATTCTTGCCCAATCTGTCGGCATGAACTGCTCACTGATGAT
genomic: AGTTGCCCTGCAAGCACACATTTCACCCTCCCTGTTTAAAGCCGTGGCTGgtaatgtacc ... gctttggcagGATAAGCACAATTCTTGCCCAATCTGTCGGCATGAACTGCTCACTGATGAT
EST: gi|349823912|gb|FQ415323.1|FQ415323
EST:     AGTTGCCCTGCAAGCACACATTTCACCCTCCCTGTTTAAAGCCGTGGCTG                         GATAANCACAATTCTTGCCCAATCTG
genomic: AGTTGCCCTGCAAGCACACATTTCACCCTCCCTGTTTAAAGCCGTGGCTGgtaatgtacc ... gctttggcagGATAAGCACAATTCTTGCCCAATCTG
EST: gi|110398241|gb|EC964460.1|EC964460
EST:     AGTTGCCCTGCAAGCACACATTTCACCCTCCCTGTTTAAAGCCGTGGCTG                         GATAAGCACAATTCTTGCCCAATCTGTCGGCATGAACTGCTCACTGATGAT
genomic: AGTTGCCCTGCAAGCACACATTTCACCCTCCCTGTTTAAAGCCGTGGCTGgtaatgtacc ... gctttggcagGATAAGCACAATTCTTGCCCAATCTGTCGGCATGAACTGCTCACTGATGAT
EST: gi|352763367|gb|FQ471679.1|FQ471679
EST:     AGTTGCCCTGCAAGCACACATTTCACCCTCCCTGTTTAAAGCCGTGGCTG                         GATAAGCACAATTCTTGCCCAATCTGTCGGCA
genomic: AGTTGCCCTGCAAGCACACATTTCACCCTCCCTGTTTAAAGCCGTGGCTGgtaatgtacc ... gctttggcagGATAAGCACAATTCTTGCCCAATCTGTCGGCA
EST: gi|110428728|gb|EC995207.1|EC995207
EST:     AAGCACACATTTCACCCTCCCTGTTTAAAGCCGTGGCTG                         GATAAGCACAATTCTTGCCCAATCTGTCGGCATGAACTGCTCACTGATGAT
genomic: AAGCACACATTTCACCCTCCCTGTTTAAAGCCGTGGCTGgtaatgtacc ... gctttggcagGATAAGCACAATTCTTGCCCAATCTGTCGGCATGAACTGCTCACTGATGAT
EST: gi|110429507|gb|EC996001.1|EC996001
EST:     AGTTGCCCTGCAAGCACACATTTCACCCTCCCTGTTTAAAGCCGTGGCTG                         GATAAGCACAATTCTTGCCCAATCTGTCGGCATGAACTGCTCACTGATGAT
genomic: AGTTGCCCTGCAAGCACACATTTCACCCTCCCTGTTTAAAGCCGTGGCTGgtaatgtacc ... gctttggcagGATAAGCACAATTCTTGCCCAATCTGTCGGCATGAACTGCTCACTGATGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttgccatttgtctaaaatttggctttctcgttcctggacatttcgctttggcagGATAAGCACAATTCTTGCCCAATCTGTCGGCATGAACTGCTCACTGATGATCGTGCCTATGAGAGCTGGAAGCAGAGGGAGAAGGAGGCGGAAGAAGAGA
          gtctaaa  putative branch site (score: 3)
                                         tttcgcttt  putative PPT
      atttgtctaaaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatgtacctcatccttattcatcataatattagagaagaaactcagagctcctcttatgcttccacttgccatttgtctaaaatttggctttctcgttcctggacatttcgctttggcagGATAAGCACAATTCTTGCCCAATCTGTCGGCATGAACTGCTCACTGATGATCGTGCCTATGAGAGCTGGAAGCAGAGGGAGAAGGAGGCGGAAGAAGAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA