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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtgtgtgtgtgtgtgtgtgtgtattgtgcataattttcaattctcattgtagactgaagataaaattcattagtaaccgataatggtgtttctttatcagAATGGCCCCACTGTGTATCGTAGCAGAACTGTATTTGAGGATGCAACTCCCGAGGTGGTTAGAGATTTCTTCTGGGATGATGAGTTTAGACCTAAATGGG

Basic information

species Vitis vinifera
transcript Vv05s0020g04870.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0020g04870.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os07g08760.2 (Oryza sativa), 3'ss of exon 1
gtgtgtgtgtgtgtgtgtgtgtattgtgcataattttcaattctcattgtagactgaagataaaattcatt--agtaaccgataa--tggtgtttctttatc---agAATGGCCCCACTGTGTATCGTAGCAGAACTGTATTTGAGGATGCAACTCCCGAGGTGGTTAGAGATTTCTTCTGGGATGATGAGTTTAGACCTAAATGGG
         |   ||| | |  | ||    ||  ||| |  |  |    |  |  | | |||   |  | |  |  | |  ||    || | || ||||      ||   || || |   ||||  ||||  | ||| | ||||||||||| ||||| ||| | |||||||||||||||||||||||||| ||| | |  || ||||
-------atttcctgtcttttcaatgaatctacgtttgatgtgaccaaatcaatagcatataggttatagtgcaacatctaatggactgatcttcctttgcttgtagGTGGGACCTATCATGTACTGTAGTCGCACTATTTTTGAGGATGCTACTCCTGAGCTTGTTAGAGATTTCTTCTGGGATGATGAATTTCGTCTGAAGTGGG

upper sequence: Vv05s0020g04870.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G121223_T02 (Zea mays), 3'ss of exon 3
-------gtgtgtgtgtgtgtgtgtgtgtattgtgcataattttcaattctcattgtagactgaagataaaattcattagtaaccgataatggtgtttctttatcagAATGGCCCCACTGTGTATCGTAGCAGAACTGTATTTGAGGATGCAACTCCCGAGGTGGTTAGAGATTTCTTCTGGGATGATGAGTTTAGACCTAAATGGG
           |  ||        | ||| |  ||  ||| | |   ||  |||  || | |    ||| |  || | |||      |||     |   ||||| || | || || |   ||||  | ||| | ||| | ||||||||||| ||||| ||  |||||||||||||||||||||||| ||| ||| | |  || ||||
aacagttagaagattgcagtaaaatctgtgtcatgactaaatgtt--ttaccataatatatttgt-atacatatcctgagtttattttaa----atacatttattagGAGGGACCTATAATGTACTGCAGCCGCACTATTTTTGAGGATGCTACTCCTGAACTGGTTAGAGATTTCTTCTGGGATGGTGATTTTCGTCTAAAGTGGG

upper sequence: Vv05s0020g04870.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G124965_T02 (Zea mays), 3'ss of exon 2
---gtgtgtgtgtgtgtgtgtgtgtattgtgcataattttcaattctc-attgtagactgaagataaaattcattagtaaccgataatggtgtttctttatcagAATGGCCCCACTGTGTATCGTAGCAGAACTGTATTTGAGGATGCAACTCCCGAGGTGGTTAGAGATTTCTTCTGGGATGATGAGTTTAGACCTAAATGGG
   |    |    ||   | |||||| ||   | |||  | ||| ||  |   ||   |     || |  |||   | |     |     |||   ||||   | | || || |   ||||  | ||| | ||| | ||||||||||| || || ||  |||||||||||||||||||||||| ||| ||| | |  || ||||
tcagaagattgcagttaatctgtgtaatgacta-aatggtaaatgctttaccataatttcttcgtatacatcaactgaatttattttaaatgtaatttta---gGAGGGACCTATAATGTACTGCAGCCGCACTATTTTTGAGGATGCTACACCTGAACTGGTTAGAGATTTCTTCTGGGATGGTGATTTTCGTCTAAAGTGGG

upper sequence: Vv05s0020g04870.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA11G01030.1 (Glycine max), 3'ss of exon 2
-gtgtgtgtgtgtgtgtgtgtgtattgtgcataattttcaattctcattgtagactgaagataaaattcattagtaaccgataatggtgtttct-ttatcagAATGGCCCCACTGTGTATCGTAGCAGAACTGTATTTGAGGATGCAACTCCCGAGGTGGTTAGAGATTTCTTCTGGGATGATGAGTTTAGACCTAAATGGG
    | | |||   ||  | | |  | |   |  ||||  |||  ||   |||| |  | ||| |  |||  |      | |     ||  ||| ||| ||||  || || || || || ||||| |||||||| ||||| ||||||||||| ||| |||| || |||||||||||||||||||| ||| | ||||||||||
accatctatgttgatgattatttgatttatttctttttgtatttccaccttagattagaaatata--tcaccatctgatgttggacatggatctgttaacagACAGGTCCTACAGTTTACCGTAGTAGAACTGTCTTTGATGATGCAACTCCAGAGTTGGTGAGGGATTTCTTCTGGGATGATGACTTTCGTCCTAAATGGG

upper sequence: Vv05s0020g04870.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA01G44500.1 (Glycine max), 3'ss of exon 2
-gtgtgtgtgtgtgtgtgtgtgtattgtgcataattttcaattctcattgtagactgaagataaaat-tcattagtaaccgataatggtgtttctttatcagAATGGCCCCACTGTGTATCGTAGCAGAACTGTATTTGAGGATGCAACTCCCGAGGTGGTTAGAGATTTCTTCTGGGATGATGAGTTTAGACCTAAATGGG
    | | ||    ||  | | |  | |   |  ||||  |||  ||   |||| |  | ||| |   ||||  |     |    |||   ||  ||| ||||  || || ||||| ||  |||| |||||||| || || ||||||||||| ||| |||| || |||||||||||||||||||| ||| | ||||||||||
accatctatgctgttgattatttgatttatttctttttgtatttccaccttagattagaaatataccatcatctgatgttggacctgga--tttgttaacagACAGGTCCTACTGTTTACTGTAGTAGAACTGTCTTCGATGATGCAACTCCAGAGTTGGTGAGGGATTTCTTCTGGGATGATGACTTTCGTCCTAAATGGG

upper sequence: Vv05s0020g04870.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT4G14500.1 (Arabidopsis thaliana), 3'ss of exon 2
gtgtgtgtgtgtgtgtgtgtgtattgtgcataattttcaattct---cattgtagactgaagataaaatt-cattagtaaccgataatggtgt-ttctttatcagAATGGCCCCACTGTGTATCGTAGCAGAACTGTATTTGAGGATGCAACTCCCGAGGTGGTTAGAGATTTCTTCTGGGATGATGAGTTTAGACCTAAATGGG
    ||||   ||      || | || | | | | || ||| ||      |  | ||    ||| |||||   || ||| ||    | |  || || |||||||||  || ||   | | ||||| ||| | ||||| ||||||||||||||||| ||  | ||||| |||||||||||||||||||||||| ||||||||||||
----gtgttcttgctataatgaaatgggga-attcttaaatactagatgatagaaacatttgatcaaattgtgtttgtagcctgataggtcgtattgtttatcagACAGGTCCTGTTATTTATCGCAGCCGGACTGTGTTTGAGGATGCAACTCCAGATATTGTTAGGGATTTCTTCTGGGATGATGAGTTTCGACCTAAATGGG

upper sequence: Vv05s0020g04870.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT3G23080.2 (Arabidopsis thaliana), 3'ss of exon 3
gtgtgtgtgtgtgtgtgtgtgtattgtgcataattttcaattctcattgt--agactgaagataaaattcattagtaaccgataatggtgtttctttatcagAATGGCCCCACTGTGTATCGTAGCAGAACTGTATTTGAGGATGCAACTCCCGAGGTGGTTAGAGATTTCTTCTGGGATGATGAGTTTAGACCTAAATGGG
                              ||| | | | || | |        |||  | || |  ||  ||  | |  | |  |  ||||  ||  |||||  || ||   ||| ||||||||  ||||||| |||||||||| ||| || ||  | ||||| |||||||||||||| ||||||||| ||||||||||||
-----------------------------gtaaatctaagttttaaagactctaactttatatgac-ttagttcctgaaaggtggttatgttggtt-gtcagATAGGTCCTGTTGTTTATCGTAGTCGAACTGTTTTTGAGGATGTAACACCAGACATTGTTAGGGATTTCTTCTGGGACGATGAGTTTCGACCTAAATGGG

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|161709868|gb|FC058054.1|FC058054
EST:     AACGGTCAACCCCAAATATGTCATACCAAGCTTGGCGCCATGAGCCCGAG                         AATGGCCCCACTGTGTATCGTAGCAGAACTGTATTTGAGGATGCAACTCCC
genomic: AACGGTCAACCCCAAATATGTCATACCAAGCTTGGCGCCATGAGCCCGAGgtaggttctt ... tctttatcagAATGGCCCCACTGTGTATCGTAGCAGAACTGTATTTGAGGATGCAACTCCC
EST: gi|30252882|gb|CB970433.1|CB970433
EST:     AACGGTCAACCCCAAATATGTCATACCAAGCTTGGCGCCATGAGCCCGAG                         AATGGCCCCACTGTGTATCGTAGCAGAACTGTATTTGAGGATGCAACTCCC
genomic: AACGGTCAACCCCAAATATGTCATACCAAGCTTGGCGCCATGAGCCCGAGgtaggttctt ... tctttatcagAATGGCCCCACTGTGTATCGTAGCAGAACTGTATTTGAGGATGCAACTCCC
EST: gi|110389589|gb|EC954442.1|EC954442
EST:     AACGGTCAACCCCAAATATGTCATACCAAGCTTGGCGCCATGAGCCCGAG                         AATGGCCCCACTGTGTATCGTAGCAGAACTGTATTTGAGGATGCAACTCCC
genomic: AACGGTCAACCCCAAATATGTCATACCAAGCTTGGCGCCATGAGCCCGAGgtaggttctt ... tctttatcagAATGGCCCCACTGTGTATCGTAGCAGAACTGTATTTGAGGATGCAACTCCC
EST: gi|161718153|gb|FC065659.1|FC065659
EST:     AACGGTCAACCCCAAATATGTCATACCAAGCTTGGCGCCATGAGCCCGAG                         AATGGCCCCACTGTGTATCGTAGCAGAACTGTATTTGAGGATGCAACTCCC
genomic: AACGGTCAACCCCAAATATGTCATACCAAGCTTGGCGCCATGAGCCCGAGgtaggttctt ... tctttatcagAATGGCCCCACTGTGTATCGTAGCAGAACTGTATTTGAGGATGCAACTCCC
EST: gi|161719072|gb|FC065699.1|FC065699
EST:     AACGGTCAACCCCAAATATGTCATACCAAGCTTGGCGCCATGAGCCCGAG                         AATGGCCCCACTGTGTATCGTAGCAGAACTGTATTTGAGGATGCAACTCCC
genomic: AACGGTCAACCCCAAATATGTCATACCAAGCTTGGCGCCATGAGCCCGAGgtaggttctt ... tctttatcagAATGGCCCCACTGTGTATCGTAGCAGAACTGTATTTGAGGATGCAACTCCC
EST: gi|37185234|gb|CF604587.1|CF604587
EST:     AACGGTCAACCCCAAATATGTCATACCAAGCTTGGCGCCATGACCCCGAG                         AATGGCCCCACTGTGTATCGTAGCAGAACTGTATTTGAGGATGCAACTCCC
genomic: AACGGTCAACCCCAAATATGTCATACCAAGCTTGGCGCCATGAGCCCGAGgtaggttctt ... tctttatcagAATGGCCCCACTGTGTATCGTAGCAGAACTGTATTTGAGGATGCAACTCCC
EST: gi|110688125|gb|EE066317.1|EE066317
EST:     AACGGTCAACCCCAAATATGTCATACCAAGCTTGGCGCCATGAGCCCGAG                         AATGGCCCCACTGTGTATCGTAGCAGAACTGTATTTGANGATGCAACTCCC
genomic: AACGGTCAACCCCAAATATGTCATACCAAGCTTGGCGCCATGAGCCCGAGgtaggttctt ... tctttatcagAATGGCCCCACTGTGTATCGTAGCAGAACTGTATTTGAGGATGCAACTCCC
EST: gi|33409206|gb|CF214833.1|CF214833
EST:     AACGGTCAACCCCAAATATGTCATACCAAGCTTGGCGCCATGAGCCCGAG                         AATGGCCCCACTGTGTATCGTAGCAGAACTGTATTTGAGGATGCAACTCCC
genomic: AACGGTCAACCCCAAATATGTCATACCAAGCTTGGCGCCATGAGCCCGAGgtaggttctt ... tctttatcagAATGGCCCCACTGTGTATCGTAGCAGAACTGTATTTGAGGATGCAACTCCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attgtagactgaagataaaattcattagtaaccgataatggtgtttctttatcagAATGGCCCCACTGTGTATCGTAGCAGAACTGTATTTGAGGATGCAACTCCCGAGGTGGTTAGAGATTTCTTCTGGGATGATGAGTTTAGACCTAAATGGG
                         tagtaac  putative branch site (score: 1)
                                           tttctttatc  putative PPT
              ataaaattcattagta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtgtgtgtgtgtgtgtgtgtattgtgcataattttcaattctcattgtagactgaagataaaattcattagtaaccgataatggtgtttctttatcagAATGGCCCCACTGTGTATCGTAGCAGAACTGTATTTGAGGATGCAACTCCCGAGGTGGTTAGAGATTTCTTCTGGGATGATGAGTTTAGACCTAAATGGG

gtgtgtg
- - - - - - - - - - - - -gtgcata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - gataaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tggtgtt