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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...catatgacttggtttttgactcgtatcaattagcatttgaggttagataagatattcttttacataggagattcatcatgaacttattctggtgtaccagGTCTTCCAAAAACGTTTACCTCCAGAAGCTGTGGATTTAGTTTGTAGGTTTTTCCAGTACTCCCCCAATCTGCGATGCACAGCT

Basic information

species Vitis vinifera
transcript Vv12s0035g01060.t01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv12s0035g01060.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA12G28730.1 (Glycine max), 3'ss of exon 10
-catatgacttggtttttgactcgtatcaattagcatttgaggttagataagatattcttttacataggagattcatcatgaacttattctggtgtaccagGTCTTCCAAAAACGTTTACCTCCAGAAGCTGTGGATTTAGTTTGTAGGTTTTTCCAGTACTCCCCCAATCTGCGATGCACAGCT
 |||||   |     ||   |  | ||    || | |      ||  | | |||  |   ||  ||  |||||| |   ||   | || ||  | |   ||||||| || ||||||||||| |||||||| |||||  | || |||||||| || ||||||||||||||| || ||||||| || 
acatattggtaaaacttgtgcgtgaat-gtctaacctacattatttcaaaggattcttggttgaatgtgagatttactgtgttatgatcctaatttgatagGTCTTTCAGAAACGTTTACCCCCAGAAGCAGTGGACCTTGTCTGTAGGTTCTTTCAGTACTCCCCCAATTTGAGATGCACTGCA

upper sequence: Vv12s0035g01060.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA16G00400.2 (Glycine max), 3'ss of exon 9
catatgacttggtttttgactcgtatcaat---tagcatttgaggttagataagatattcttttacataggagattcatcatgaacttattctggtgtaccagGTCTTCCAAAAACGTTTACCTCCAGAAGCTGTGGATTTAGTTTGTAGGTTTTTCCAGTACTCCCCCAATCTGCGATGCACAGCT
              |   ||| |||| |||   || | |      ||  | | |||  |   ||   |  |||||| |   |||  | || ||  | |   |||| || || ||||||||||| |||||||| |||||  | || |||||||| || |||||||| |||||| || ||||||| || 
------------ggtaaaacttgtatgaatgtctaacctacattatttcaaaggattcttggttgactgtgagatttactgtgatatgatcctaatttgataggtttttcagAAACGTTTACCCCCAGAAGCAGTGGACCTTGTCTGTAGGTTCTTTCAGTACTCTCCCAATTTGAGATGCACTGCA

upper sequence: Vv12s0035g01060.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA16G00400.1 (Glycine max), 3'ss of exon 9
catatgacttggtttttgactcgtatcaat---tagcatttgaggttagataagatattcttttacataggagattcatcatgaacttattctggtgtaccagGTCTTCCAAAAACGTTTACCTCCAGAAGCTGTGGATTTAGTTTGTAGGTTTTTCCAGTACTCCCCCAATCTGCGATGCACAGCT
|| |  | | |   |   ||| |||| |||   || | |      ||  | | |||  |   ||   |  |||||| |   |||  | || ||  | |   |||| || || ||||||||||| |||||||| |||||  | || |||||||| || |||||||| |||||| || ||||||| || 
caaagtattgg---taaaacttgtatgaatgtctaacctacattatttcaaaggattcttggttgactgtgagatttactgtgatatgatcctaatttgatagGTTTTTCAGAAACGTTTACCCCCAGAAGCAGTGGACCTTGTCTGTAGGTTCTTTCAGTACTCTCCCAATTTGAGATGCACTGCA

upper sequence: Vv12s0035g01060.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: AT1G09840.2 (Arabidopsis thaliana), 3'ss of exon 11
-catatgacttggttt--ttgactc--gtatcaattagcat-ttgaggttagataagatattcttttacataggagattcatcatgaac-ttattctggtgtaccagGTCTTCCAAAAACGTTTACCTCCAGAAGCTGTGGATTTAGTTTGTAGGTTTTTCCAGTACTCCCCCAATCTGCGATGCACAGCT
   ||  |   |||||  ||||||   ||   ||||| |   ||||| || | |      |   | |  ||      | |  ||||||  || |  |  ||   ||||| |||||||||||||| || |||||||| || ||| |  |||||||||| ||||| || ||||||||| || |||| ||||||
tagtaaaaaaaggtttaattgacttcagtgataattatctccttgagcttcgct------tctctctgaatccttattactgcatgaatattctatttatgc-tcagGTGTTCCAAAAACGTTTGCCACCAGAAGCAGTTGATCTTCTTTGTAGGTTCTTCCAATATTCCCCCAATTTGAGATGTACAGCT

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|30126156|gb|CB911495.1|CB911495
EST:     ACTATACCGAATTTAAATTCCCACAAATAAAGCCTCATCCATGGCACAAG                         GTCTTCCAAAAACGTTTACCTCCAGAAGCTGTGGATTTAGTTTGTAGGTTT
genomic: ACTACACCGAATTTAAATTCCCACAAATAAAGCCTCATCCATGGCACAAGgtatgctctt ... ggtgtaccagGTCTTCCAAAAACGTTTACCTCCAGAAGCTGTGGATTTAGTTTGTAGGTTT
EST: gi|110726124|gb|EE101641.1|EE101641
EST:     ACTACACCGAATTTAAATTCCCACAAATAAAGCCTCATCCATGGCACAAG                         GTCTTCCAAAAACGTTTACCTCCAGAAGCTGTGGATTTAGTTTGTAGGTTT
genomic: ACTACACCGAATTTAAATTCCCACAAATAAAGCCTCATCCATGGCACAAGgtatgctctt ... ggtgtaccagGTCTTCCAAAAACGTTTACCTCCAGAAGCTGTGGATTTAGTTTGTAGGTTT
EST: gi|27580396|gb|CB003091.1|CB003091
EST:     ACTATACCGAATTTAAATTCCCACAAATAAAGCCTCATCCATGGCACAAG                         GTCTTCCAAAAACGTTTACCTCCAGAAGCTGTGGATTTAGTTTGTAGGTTT
genomic: ACTACACCGAATTTAAATTCCCACAAATAAAGCCTCATCCATGGCACAAGgtatgctctt ... ggtgtaccagGTCTTCCAAAAACGTTTACCTCCAGAAGCTGTGGATTTAGTTTGTAGGTTT
EST: gi|161715603|gb|FC067769.1|FC067769
EST:     ACTACACCGAATTTAAATTCCCACAAATAAAGCCTCATCCATGGCACAAG                         GTCTTCCCAAAACGTTTACCTCCAGAAGCTGTGGATTTAGTTTG
genomic: ACTACACCGAATTTAAATTCCCACAAATAAAGCCTCATCCATGGCACAAGgtatgctctt ... ggtgtaccagGTCTTCCAAAAACGTTTACCTCCAGAAGCTGTGGATTTAGTTTG
EST: gi|27579322|gb|CB002017.1|CB002017
EST:     ACTATACCGAATTTAAATTCCCACAAATAAAGCCTCATCCATGGCACAAG                         GTCTTCCAAAAACGTTTACCTCCAGAAGCTGTGGATTTAGTTTGTAGGTTT
genomic: ACTACACCGAATTTAAATTCCCACAAATAAAGCCTCATCCATGGCACAAGgtatgctctt ... ggtgtaccagGTCTTCCAAAAACGTTTACCTCCAGAAGCTGTGGATTTAGTTTGTAGGTTT
EST: gi|156736132|gb|EV240253.1|EV240253
EST:     ACTACACCGAATTTAAATTCCCACAAATAAAGCCTCATCCATGGCACAAG                         GTCTTCCAAAAACGTTTACCTCCAGAAGCTGTGGATTTAGTTTGTAGGTTT
genomic: ACTACACCGAATTTAAATTCCCACAAATAAAGCCTCATCCATGGCACAAGgtatgctctt ... ggtgtaccagGTCTTCCAAAAACGTTTACCTCCAGAAGCTGTGGATTTAGTTTGTAGGTTT
EST: gi|27581595|gb|CB004290.1|CB004290
EST:     ACTATACCGAATTTAAATTCCCACAAATAAAGCCTCATCCATGGCACAAG                         GTCTTCCAAAAACGTTTACCTCCAGAAGCTGTGGATTTAGTTTGTAGGTTT
genomic: ACTACACCGAATTTAAATTCCCACAAATAAAGCCTCATCCATGGCACAAGgtatgctctt ... ggtgtaccagGTCTTCCAAAAACGTTTACCTCCAGAAGCTGTGGATTTAGTTTGTAGGTTT
EST: gi|27581007|gb|CB003702.1|CB003702
EST:     ACTATACCGAATTTAAATTCCCACAAATAAAGCCTCATCCATGGCACAAG                         GTCTTCCAAAAACGTTTACCTCCAGAAGCTGTGGATTTAGTTTGTAGGTTT
genomic: ACTACACCGAATTTAAATTCCCACAAATAAAGCCTCATCCATGGCACAAGgtatgctctt ... ggtgtaccagGTCTTCCAAAAACGTTTACCTCCAGAAGCTGTGGATTTAGTTTGTAGGTTT
EST: gi|30130728|gb|CB916067.1|CB916067
EST:     ACTATACCGAATTTAAATTCCCACAAATAAAGCCTCATCCATGGCACAAG                         GTCTTCCAAAAACGTTTACCTCCAGAAGCTGTGGATTTAGTTTGTAGGTTT
genomic: ACTACACCGAATTTAAATTCCCACAAATAAAGCCTCATCCATGGCACAAGgtatgctctt ... ggtgtaccagGTCTTCCAAAAACGTTTACCTCCAGAAGCTGTGGATTTAGTTTGTAGGTTT
EST: gi|110419339|gb|EC985557.1|EC985557
EST:     ATCCATGGCACAAG                         GTCTTCCAAAAACGTTTACCTCCAGAAGCTGTGGATTTAGTTTGTAGGTTT
genomic: ATCCATGGCACAAGgtatgctctt ... ggtgtaccagGTCTTCCAAAAACGTTTACCTCCAGAAGCTGTGGATTTAGTTTGTAGGTTT
EST: gi|27579129|gb|CB001824.1|CB001824
EST:     ACTATACCGAATTTAAATTCCCACAAATAAAGCCTCATCCATGGCACAAG                         GTCTTCCAAAAACGTTTACCTCCAGAAGCTGTGGATTTAGTTTGTAGGTTT
genomic: ACTACACCGAATTTAAATTCCCACAAATAAAGCCTCATCCATGGCACAAGgtatgctctt ... ggtgtaccagGTCTTCCAAAAACGTTTACCTCCAGAAGCTGTGGATTTAGTTTGTAGGTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gataagatattcttttacataggagattcatcatgaacttattctggtgtaccagGTCTTCCAAAAACGTTTACCTCCAGAAGCTGTGGATTTAGTTTGTAGGTTTTTCCAGTACTCCCCCAATCTGCGATGCACAGCT
      atattcttttacata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
catatgacttggtttttgactcgtatcaattagcatttgaggttagataagatattcttttacataggagattcatcatgaacttattctggtgtaccagGTCTTCCAAAAACGTTTACCTCCAGAAGCTGTGGATTTAGTTTGTAGGTTTTTCCAGTACTCCCCCAATCTGCGATGCACAGCT

- - tgacttg
- - - - - - - - - - - - - - - - gcatttg
- - - - - - - - - - - - - - - - - - - - - - -gataaga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catgaac