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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caatacatagaaaagtgactcaatattccttgtggttagcaatctataacaactgtcattgtcattggtgtagctgactgcactcttgctctttctgcagATATGTTTCTTGCACTCGATAAAGATATGAATGGAACATTGAGCAAGCAAGAGCTTCGAGAATATGCAGATGGAACATTAACTGAAATTTTCATTGAGAG

Basic information

species Vitis vinifera
transcript Vv05s0020g01710.t01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0020g01710.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: LOC_Os05g05710.1 (Oryza sativa), 3'ss of exon 9
---------------------------------------caatacatagaaaagtgactcaat--attccttgtggttagcaatctataacaactgt----cattgtcattggtgtagctgactg-cactcttgctctttctgcagATATGTTTCTTGCACTCGATAAAGATATGAATGGAACATTGAGCAAGCAAGAGCTTCGAGAATATGCAGATGGAACATTAACTGAAATTTTCATTGAGAG
                                          |   ||| |     || ||||   | |  |      ||  | || |  | | | |    || | |  ||| || | ||  ||    | | || ||    ||||||||||||||||||||| || |||||||  ||||||||||||||||| || |||||    |||||||||||||| ||||| ||||| || |||||||| ||
gtatgccagccaccctcatgtctggttttctgatttttcttttgggtagcagtagcacacaatcagtgctctccaaaaagttaccttttgccattctattgcagtatagttgatg-atctacctaatgcgcatggtccca-tgcagATATGTTTCTTGCACTTGACAAAGATACAAATGGAACATTGAGCAAACAGGAGCTCAAGGAATATGCAGATGGCACATTGACTGATATCTTCATTGAAAG

upper sequence: Vv05s0020g01710.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GRMZM2G083459_T02 (Zea mays), 3'ss of exon 10
---------caatacatagaaaagtgactcaatattccttgtgg--ttagcaatctataacaac-tgtcattgt-cattggtgta-gctgactgc---actcttgc----tctttctgcagATATGTTTCTTGCACTCGATAAAGATATGAATGGAACATTGAGCAAGCAAGAGCTTCGAGAATATGCAGATGGAACATTAACTGAAATTTTCATTGAGAG
         |   |  ||        | |   | ||||| ||||  ||   |||    | | ||    |||| | |  ||||||| | | | ||    | | || |    |  || |||||| |||||||||||||| ||||| |||| ||| || ||| ||||||| ||||||||    |||||||||||||| || || ||||| ||||||||||| ||
gtatgccagctggaattattgttaatagttgtttttcctcgtggatttgaaaattatcatctacacaccattctactgtggtgtatggttagtgtttgatttttacctcatgcttgtgcagACATGTTTCTTGCACTAGATAAGGATACGAACGGTACACTGAGCAAACAAGAGCTCAAGGAATATGCAGATGGCACGTTGACTGAGATTTTCATTGAAAG

upper sequence: Vv05s0020g01710.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GRMZM2G050800_T01 (Zea mays), 3'ss of exon 2
------------caatacatagaaaagtgactcaatattccttgtggtta----gcaatctataacaactgtcattgtcattggtgtag-ctgactgcactcttgctctt-----tctgcagATATGTTTCTTGCACTCGATAAAGATATGAATGGAACATTGAGCAAGCAAGAGCTTCGAGAATATGCAGATGGAACATTAACTGAAATTTTCATTGAGAG
             ||| |    |||| ||      |   |||||   ||     |   ||| || | || ||  | ||     || |   |||  |  | | |||  ||      | |||||| |||||||||||||| ||||| ||||  ||  | ||| ||||||| ||||| ||    |||||||||||||| ||||| ||||| ||||||||||| ||
gtatgtcagctgtaattctcgcaaaattgttgttttcccccttggatttgtaatgtgttctctacctaccgttctagtgtgctgtatgctctgtatttaatattgacctcatgcctgtgcagACATGTTTCTTGCACTAGATAAGGATACAAACAGTACACTGAGCAAACAAGAACTCAAGGAATATGCAGATGGCACATTGACTGAGATTTTCATTGAAAG

upper sequence: Vv05s0020g01710.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA07G38000.1 (Glycine max), 3'ss of exon 9
--caatacatagaaaagtgactcaatattccttgtggttagcaatctataacaactgtcattgtcattggtgtagctgactgcactcttgctctttctgcagATATGTTTCTTGCACTCGATAAAGATATGAATGGAACATTGAGCAAGCAAGAGCTTCGAGAATATGCAGATGGAACATTAACTGAAATTTTCATTGAGAG
     || ||   |   ||| |  | |||     |   ||   |    ||| |    |   | ||| |  |||   |   |  | || |  | |||||||||| ||||||||||| || ||||||||||  ||||| ||||| |||||||| ||||| ||||||||||||||||  ||  |  |||| ||||| ||||||||
aggcctaaatttcatgatgaattgaaattatgaata--taattacggttaaaattatttcctatcagttttgtgtttatgtttattcctaatttttctgcagACATGTTTCTTGCTCTTGATAAAGATACAAATGGGACATTAAGCAAGCAGGAGCTGCGAGAATATGCAGATGCGACTCTGGCTGATATTTTTATTGAGAG

upper sequence: Vv05s0020g01710.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA17G02700.1 (Glycine max), 3'ss of exon 8
caatacatagaaaagtgactcaatattccttgtggttagcaat-ctataacaactgtcat-tgtcattggtgtagctgactgcactcttgctctttctgcagATATGTTTCTTGCACTCGATAAAGATATGAATGGAACATTGAGCAAGCAAGAGCTTCGAGAATATGCAGATGGAACATTAACTGAAATTTTCATTGAGAG
  |  | || |    |   | |||     || ||  ||  | | |  | | |||| |    | | | |  | |   |   |  | || || | |||||||||| ||||||||||| || ||||||||||  ||||| ||||| |||||||| ||||| |||||||||||||||| |||  |  |||| ||||| || |||||
--aggcctaaatttcttgatgaattgaaattatgaatataattgccgttaaaactatttcctataagttttatgtttatgtttattcctgatttttctgcagACATGTTTCTTGCTCTTGATAAAGATACAAATGGGACATTAAGCAAGCAGGAGCTGCGAGAATATGCAGATGCAACTCTGGCTGACATTTTTATCGAGAG

upper sequence: Vv05s0020g01710.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: AT5G18580.1 (Arabidopsis thaliana), 3'ss of exon 9
--------------------caatacatagaaaagtgactcaatattccttgtggttagcaatctataacaactgtcattgtcattggtgtagctgactgcactcttgctctttctgcagATATGTTTCTTGCACTCGATAAAGATATGAATGGAACATTGAGCAAGCAAGAGCTTCGAGAATATGCAGATGGAACATTAACTGAAATTTTCATTGAGAG
                     ||||  |  | |    |||  | |   ||   | |  |  || | ||| ||||   || |  |||| | |||          |  |  |  ||||| ||||||||| || ||||| ||||||||||||| |||| |  || |||| ||||| |||  ||||||||| ||||| ||  ||||||| ||||||||||| ||
gtgggtgtgctattttgtcttaatagctgcagaga--actggaaacaactctcgttatgtcatat-taagaactaaaatggagattgatctaga-------gtttctctttcttctgtagATATGTTCCTCGCACTTGATAAAGATATGAGTGGATCGCTGTGCAAACAAGAACTTAAAGAATATGCTGATGGGACCCTAACTGAGATTTTCATTGAAAG

upper sequence: Vv05s0020g01710.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: PP1S180_30V6.1 (Physcomitrella patens), 3'ss of exon 9
-----------------------------------------------------------------------------caatacatagaaaa-gtgactcaatattc---cttgtggttagcaatctataacaactgtcattg------tcattggtgtagctgactgcactcttgct------ctttctgcagATATGTTTCTTGCACTCGATAAAGATATGAATGGAACATTGAGCAAGCAAGAGCTTCGAGAATATGCAGATGGAACATTAACTGAAATTTTCATTGAGAG
                                                                             ||||   |  |  | ||   | ||| |       | |  | |  |   | ||   ||  |   ||      | ||  || || | |  |   || ||  |       ||  ||||||||  ||||| |  || ||||| || |||||||||||||| |||||| |||| |||| || |||||| ||||| || || ||||| || ||||||||| |
gtatatactttataaaccattctcttgcagctgctttgcacctacttgatctgtaataatagttttcgaaaagattgcaatttttgcaggatgtttttgaatgtgtgattctattatcaaaaggatgtagtcacgatttatgcaagacttataagtttaacggtatttcctgtttttgaacgatttgatgcagATACATTTCTGGGGCTGGATAAGGACATGAATGGAACATTAAGCAAGGAAGAACTTCAAGCATATGCTGATGGCACCTTGACTGACATCTTCATTGAGCG

upper sequence: Vv05s0020g01710.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: EFJ29777 (Selaginella moellendorffii), 3'ss of exon 9
caatacatagaaaagtgactcaatattccttgtggttagca-atctataacaactgtcattgtcattggtgtagctga--ctgcactcttgctctttctgcagATATGTTTCTTGCACTCGATAAAGATATGAATGGAACATTGAGCAAGCAAGAGCTTCGAGAATATGCAGATGGAACATTAACTGAAATTTTCATTGAGAG
                                  || ||   |||| ||    || || || | ||| || |        ||  |   |||     | || |||| | ||||| || || || ||||||||||| || |||||||||||||| ||||||| ||| ||||| ||||| ||||  |||  ||| || |||||  |
----------------------------------gtgagtgcatctctact--ctttcttttttatttgtatcaacagtcctttaactttgtaaaatttgtagATGTCTTTCTCGCGCTGGACAAAGATATGAACGGTACATTGAGCAAGCAGGAGCTTCAAGACTATGCCGATGGCACATACACTACAATATTTATTGAACG

upper sequence: Vv05s0020g01710.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: EFJ08923 (Selaginella moellendorffii), 3'ss of exon 9
caatacatagaaaagtgactcaatattccttgtggttagca-atctataacaactgtcattgtcattggtgtagctga--ctgcactcttgctctttctgcagATATGTTTCTTGCACTCGATAAAGATATGAATGGAACATTGAGCAAGCAAGAGCTTCGAGAATATGCAGATGGAACATTAACTGAAATTTTCATTGAGAG
                                  || ||   |||| ||     | |  || | ||| || |        ||  |   |||     | || |||| | ||||| || || || ||||||||||| || |||||||||||||| ||||||| ||| ||||| ||||| ||||  |||   || || |||||  |
----------------------------------gtgagtgcatctctactctttat--tttttatttgtatcaacagtcctttaactttgtaaaatttgtagATGTCTTTCTCGCGCTGGACAAAGATATGAACGGTACATTGAGCAAGCAGGAGCTTCAAGACTATGCCGATGGCACATACACTACCATATTTATTGAACG

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|349825677|gb|FQ421776.1|FQ421776
EST:     CGAGCAAGCTGAAAACTGGTTCTCTTTGACATCTGCCCAACGAATATGTG                         ATATGTTTCTTGCACTCGATAAAGATATGAATGGAACATTGAGCAAGCAAG
genomic: CGAGCAAGCTGAAAACTGGTTCTCTTTGACATCTGCCCAACGAATATGTGgtgggtgctt ... ctttctgcagATATGTTTCTTGCACTCGATAAAGATATGAATGGAACATTGAGCAAGCAAG
EST: gi|351036361|gb|FQ458736.1|FQ458736
EST:     CGAGCAAGCTGAAAACTGGTTCTCTTTGACATCTGCCCAACGAATATGTG                         ATATGTTTCTTGCACTCGATAAAGATATGAATGGAACATTGAGCAAGCAAG
genomic: CGAGCAAGCTGAAAACTGGTTCTCTTTGACATCTGCCCAACGAATATGTGgtgggtgctt ... ctttctgcagATATGTTTCTTGCACTCGATAAAGATATGAATGGAACATTGAGCAAGCAAG
EST: gi|161720737|gb|FC069962.1|FC069962
EST:     CGAGCAAGCTGAAAACTGGTTCTCTTTGACATCTGCCCAACGAATATGTG                         ATATGTTTCTTGCACTCGATAAAGATATGAATGGAACATTGAGCAAGCAAG
genomic: CGAGCAAGCTGAAAACTGGTTCTCTTTGACATCTGCCCAACGAATATGTGgtgggtgctt ... ctttctgcagATATGTTTCTTGCACTCGATAAAGATATGAATGGAACATTGAGCAAGCAAG
EST: gi|349812983|gb|FQ411223.1|FQ411223
EST:     CGAGCAAGCTGAAAACTGGTTCTCTTTGACATCTGCCCAACGAATATGTG                         ATATGTTTCTTGCACTCGATAAAGATATGAATGGAACATTGAGCAAGCAAG
genomic: CGAGCAAGCTGAAAACTGGTTCTCTTTGACATCTGCCCAACGAATATGTGgtgggtgctt ... ctttctgcagATATGTTTCTTGCACTCGATAAAGATATGAATGGAACATTGAGCAAGCAAG
EST: gi|352786873|gb|FQ481248.1|FQ481248
EST:     CGAGCAAGCTGAAAACTGGTTCTCTTTGACATCTGCCCAACGAATATGTG                         ATATGTTTCTTGCACTCGATAAAGATATGAATGGAACATTGAGCAAGCAAG
genomic: CGAGCAAGCTGAAAACTGGTTCTCTTTGACATCTGCCCAACGAATATGTGgtgggtgctt ... ctttctgcagATATGTTTCTTGCACTCGATAAAGATATGAATGGAACATTGAGCAAGCAAG
EST: gi|349830110|gb|FQ420370.1|FQ420370
EST:     GAGCAAGCTGAAAAACTGGTTCTCTTTGACATCTGCCCAACGAATATGTG                         ATATGTTTCTTGCACTCGATAAAGATATGAATGGAACATTGAGCAAGCCAG
genomic: GAGCAAGCTGAAAA-CTGGTTCTCTTTGACATCTGCCCAACGAATATGTGgtgggtgctt ... ctttctgcagATATGTTTCTTGCACTCGATAAAGATATGAATGGAACATTGAGCAAGCAAG
EST: gi|351030803|gb|FQ438641.1|FQ438641
EST:     CGAGCAAGCTGAAAACTGGTTCTCTTTGACATCTGCCCAACGAATATGTG                         ATATGTTTCTTGCACTCGATAAAGATATGAATGGAACATTGAGCAAGCAAG
genomic: CGAGCAAGCTGAAAACTGGTTCTCTTTGACATCTGCCCAACGAATATGTGgtgggtgctt ... ctttctgcagATATGTTTCTTGCACTCGATAAAGATATGAATGGAACATTGAGCAAGCAAG
EST: gi|351056495|gb|FQ455147.1|FQ455147
EST:     CGAGCAAGCTGAAAACTGGTTCTCTTTGACATCTGCCCAACGAATATGTG                         ATATGTTTCTTGCACTCGATAAAGATATGAATGGAACATTGAGCAAGCAAG
genomic: CGAGCAAGCTGAAAACTGGTTCTCTTTGACATCTGCCCAACGAATATGTGgtgggtgctt ... ctttctgcagATATGTTTCTTGCACTCGATAAAGATATGAATGGAACATTGAGCAAGCAAG
EST: gi|110362368|gb|EC925897.1|EC925897
EST:     CGAGCAAGCTGAAAACTGGTTCTCTTTGACATCTGCCCAACGAATATGTG                         ATATGTTTCTTGCACTCGATAAAGATATGAATGGAACATTGAGCAAGCAAG
genomic: CGAGCAAGCTGAAAACTGGTTCTCTTTGACATCTGCCCAACGAATATGTGgtgggtgctt ... ctttctgcagATATGTTTCTTGCACTCGATAAAGATATGAATGGAACATTGAGCAAGCAAG
EST: gi|351051731|gb|FQ449545.1|FQ449545
EST:     CGAGCAAGCTGAAAACTGGTTCTCTTTGACATCTGCCCCACGAATATGTG                         GTATGTTTCTTGCACTCGATAAAGATATGAATGGAACATTGAGCAAGCAAG
genomic: CGAGCAAGCTGAAAACTGGTTCTCTTTGACATCTGCCCAACGAATATGTGgtgggtgctt ... ctttctgcagATATGTTTCTTGCACTCGATAAAGATATGAATGGAACATTGAGCAAGCAAG
EST: gi|110363937|gb|EC927571.1|EC927571
EST:     CGAGCAAGCTGAAAACTGGTTCTCTTTGACATCTGCCCAACGAATATGTG                         ATATGTTTCTTGCACTCGATAAAGATATGAATGGAACATTGAGCAAGCAAG
genomic: CGAGCAAGCTGAAAACTGGTTCTCTTTGACATCTGCCCAACGAATATGTGgtgggtgctt ... ctttctgcagATATGTTTCTTGCACTCGATAAAGATATGAATGGAACATTGAGCAAGCAAG
EST: gi|351042975|gb|FQ434416.1|FQ434416
EST:     CGAGCAAGCTGAAAACTGGTTCTCTTTGACATCTGCCCAACGAATATGTG                         ATATGTTTCTTGCACTCGATAAAGATATGAATGGAACATTGAGCAAGCAAG
genomic: CGAGCAAGCTGAAAACTGGTTCTCTTTGACATCTGCCCAACGAATATGTGgtgggtgctt ... ctttctgcagATATGTTTCTTGCACTCGATAAAGATATGAATGGAACATTGAGCAAGCAAG
EST: gi|110689038|gb|EE064912.1|EE064912
EST:     CGAGCAAGCTGAAAACTGGTTCTCTTTGACATCTGCCCAACGAATATGTG                         ATATGTTTCTTGCACTCGATAAAGATATGAATGGAACATTGAGCAAGCAAG
genomic: CGAGCAAGCTGAAAACTGGTTCTCTTTGACATCTGCCCAACGAATATGTGgtgggtgctt ... ctttctgcagATATGTTTCTTGCACTCGATAAAGATATGAATGGAACATTGAGCAAGCAAG
EST: gi|352798699|gb|FQ480724.1|FQ480724
EST:     CGAGCAAGCTGAAAACTGGTTCTCTTTGACATCTGCCCAACGAATATGTG                         ATATGTTTCTTGCACTCGATAAAGATATGAATGGAACATTGAGCAAGCAAG
genomic: CGAGCAAGCTGAAAACTGGTTCTCTTTGACATCTGCCCAACGAATATGTGgtgggtgctt ... ctttctgcagATATGTTTCTTGCACTCGATAAAGATATGAATGGAACATTGAGCAAGCAAG
EST: gi|352793795|gb|FQ481949.1|FQ481949
EST:     CGAGCAAGCTGAAAACTGGTTCTCTTTGACATCTGCCCAACCAATATGTG                         ATATGTTTCTTGCACTCGATAAAGATATGAATGGAACCTTGAGCAAGCCAG
genomic: CGAGCAAGCTGAAAACTGGTTCTCTTTGACATCTGCCCAACGAATATGTGgtgggtgctt ... ctttctgcagATATGTTTCTTGCACTCGATAAAGATATGAATGGAACATTGAGCAAGCAAG
EST: gi|110423040|gb|EC989375.1|EC989375
EST:     CGAGCAAGCTGAAAACTGGTTCTCTTTGACATCTGCCCAACGAATATGTG                         ATATGTTTCTTGCACTCGATAAAGATATGAATGGAACATTGAGCAAGCAAG
genomic: CGAGCAAGCTGAAAACTGGTTCTCTTTGACATCTGCCCAACGAATATGTGgtgggtgctt ... ctttctgcagATATGTTTCTTGCACTCGATAAAGATATGAATGGAACATTGAGCAAGCAAG
EST: gi|33404780|gb|CF210407.1|CF210407
EST:     CGAGCAAGCTGAAAACTGGTTCTCTTTGACATCTGCCCAACGAATATGTG                         ATATGTTTCTTGCACTCGATAAAGATATGAATGGAACATTGAGCAAGCAAG
genomic: CGAGCAAGCTGAAAACTGGTTCTCTTTGACATCTGCCCAACGAATATGTGgtgggtgctt ... ctttctgcagATATGTTTCTTGCACTCGATAAAGATATGAATGGAACATTGAGCAAGCAAG
EST: gi|351035211|gb|FQ458568.1|FQ458568
EST:     CGAGCAAGCTGAAAACTGGTTCTCTTTGACATCTGCCCAACGAATATGTG                         ATATGTTTCTTGCACTCGATAAAGATATGAATGGAACATTGAGCAAGCAAG
genomic: CGAGCAAGCTGAAAACTGGTTCTCTTTGACATCTGCCCAACGAATATGTGgtgggtgctt ... ctttctgcagATATGTTTCTTGCACTCGATAAAGATATGAATGGAACATTGAGCAAGCAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataacaactgtcattgtcattggtgtagctgactgcactcttgctctttctgcagATATGTTTCTTGCACTCGATAAAGATATGAATGGAACATTGAGCAAGCAAGAGCTTCGAGAATATGCAGATGGAACATTAACTGAAATTTTCATTGAGAG
                          agctgac  putative branch site (score: 3)
                                   cactcttgctctttct  putative PPT
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
caatacatagaaaagtgactcaatattccttgtggttagcaatctataacaactgtcattgtcattggtgtagctgactgcactcttgctctttctgcagATATGTTTCTTGCACTCGATAAAGATATGAATGGAACATTGAGCAAGCAAGAGCTTCGAGAATATGCAGATGGAACATTAACTGAAATTTTCATTGAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
caataca
- - - -tagaaaa
- - - - - - - - - - - - -ttccttg
- - - - - - - - - - - - - - - - tggttag
- - - - - - - - - - - - - - - - - - - - - - -ataacaa
- - - - - - - - - - - - - - - - - - - - - - - - - - ctgtcat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tggtgta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgactgc