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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatgcctattagaaccttatattgtttcaaattccagtagtattatctaaggaatttagatttttgtaactcagaatgttcctgtttaaacaatctgcagGAAGATTTGTTCCTGGATGTTACACCCTTGCTGTTTCAGAGGCACTTCCAGAGGACTTGCAG

Basic information

species Vitis vinifera
transcript Vv10s0071g01040.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv10s0071g01040.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT5G08565.1 (Arabidopsis thaliana), 3'ss of exon 3
--tatgcctattagaaccttatattgt---ttcaaattccagtagtattatctaaggaatttagatttttgtaactcagaatgttcctgtttaaacaatctgcagGAAGATTTGTTCCTGGATGTTACACCCTTGCTGTTTCAGAGGCACTTCCAGAGGACTTGCAG
  |||| || | |  |||| || ||||     | |||      ||  || | | ||  |   |||    |  ||   |  |  || |  | |      | | |||| |  |||| |||||| || ||||| |||||||| ||||||||||| ||||||||  |||||
tttatggct-tgatgacctgatgttgtattccctaatattgccagctttgtttcagacaga-agagaaata-aatctaacacattgcaatatc--ttgtttccagGGAAGTTTGCTCCTGGTTGCTACACTCTTGCTGTCTCAGAGGCACTCCCAGAGGAAATGCAG
















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|110408198|gb|EC973824.1|EC973824
EST:     TTCGATGATGGATCCAAGTAGAAGTTGGGCTGCTCGGTGGCTTCGAATCG                         GAAGATTTGTTCCTGGATGTTACACCCTTGCTGTTTCAGAGGCACTTCCAG
genomic: TTCGATGATGGATCCAAGTAGAAGTTGGGCTGCTCGGTGGCTTCGAATCGgtatgtcgaa ... caatctgcagGAAGATTTGTTCCTGGATGTTACACCCTTGCTGTTTCAGAGGCACTTCCAG
EST: gi|110384025|gb|EC948438.1|EC948438
EST:     TTCGATGATGGATCCAAGTAGAAGTTGGGCTGCTCGGTGGCTTCGAATCG                         GAAGATTTGTTCCTGGATGTTACACCCTTGCTGTTTCAGAGGCACTTCCAG
genomic: TTCGATGATGGATCCAAGTAGAAGTTGGGCTGCTCGGTGGCTTCGAATCGgtatgtcgaa ... caatctgcagGAAGATTTGTTCCTGGATGTTACACCCTTGCTGTTTCAGAGGCACTTCCAG
EST: gi|33408217|gb|CF213844.1|CF213844
EST:     TTCGATGATGGATCCAAGTAGAAGTTGGGCTGCTCGGTGGCTTCGAATCG                         GAAGATTTGTTCCTGGATGTTACACCCTTGCTGTTTCAGAGGCACTTCCAG
genomic: TTCGATGATGGATCCAAGTAGAAGTTGGGCTGCTCGGTGGCTTCGAATCGgtatgtcgaa ... caatctgcagGAAGATTTGTTCCTGGATGTTACACCCTTGCTGTTTCAGAGGCACTTCCAG
EST: gi|352795434|gb|FQ476549.1|FQ476549
EST:     TTCGATGATGGATCCCAGTAGAAGTTGGGCTGCTCGGTGGCTTCGAATCG                         GAAGATTTGTTCCTGGATGTTACACCCTTGCTGTTTCAGAGGCACTTCCAG
genomic: TTCGATGATGGATCCAAGTAGAAGTTGGGCTGCTCGGTGGCTTCGAATCGgtatgtcgaa ... caatctgcagGAAGATTTGTTCCTGGATGTTACACCCTTGCTGTTTCAGAGGCACTTCCAG
EST: gi|110688876|gb|EE067932.1|EE067932
EST:     TTCGATGATGGATCCAAGTAGAAGTTGGGCTGCTCGGTGGCTTCGAATCG                         GAAGATTTGTTCCTGGATGTTACACCCTTGCTGTTTCAGAGGCACTTCCAG
genomic: TTCGATGATGGATCCAAGTAGAAGTTGGGCTGCTCGGTGGCTTCGAATCGgtatgtcgaa ... caatctgcagGAAGATTTGTTCCTGGATGTTACACCCTTGCTGTTTCAGAGGCACTTCCAG
EST: gi|110426189|gb|EC992587.1|EC992587
EST:     AGAAGTTGGGCTGCTCGGTGGCTTCGAATCG                         GAAGATTTGTTCCTGGATGTTACACCCTTGCTGTTTCAGAGGCACTTCCAG
genomic: AGAAGTTGGGCTGCTCGGTGGCTTCGAATCGgtatgtcgaa ... caatctgcagGAAGATTTGTTCCTGGATGTTACACCCTTGCTGTTTCAGAGGCACTTCCAG
EST: gi|30296227|gb|CB973021.1|CB973021
EST:     TTCGATGATGGATCCAAGTAGAAGTTGGGCTGCTCGGTGGCTTCGAATCG                         GAAGATTTGTTCCTGGATGTTACACCCTTGCTGTTTCAGAGGCACTTCCAG
genomic: TTCGATGATGGATCCAAGTAGAAGTTGGGCTGCTCGGTGGCTTCGAATCGgtatgtcgaa ... caatctgcagGAAGATTTGTTCCTGGATGTTACACCCTTGCTGTTTCAGAGGCACTTCCAG
EST: gi|33408305|gb|CF213932.1|CF213932
EST:     TTCGATGATGGATCCAAGTAGAAGTTGGGCTGCTCGGTGGCTTCGAATCG                         GAAGATTTGTTCCTGGATGTTACACCCTTGCTGTTTCAGAGGCACTTCCAG
genomic: TTCGATGATGGATCCAAGTAGAAGTTGGGCTGCTCGGTGGCTTCGAATCGgtatgtcgaa ... caatctgcagGAAGATTTGTTCCTGGATGTTACACCCTTGCTGTTTCAGAGGCACTTCCAG
EST: gi|110407013|gb|EC972604.1|EC972604
EST:     TTCGATGATGGATCCAAGTAGAAGTTGGGCTGCTCGGTGGCTTCGAATCG                         GAAGATTTGTTCCTGGATGTTACACCCTTGCTGTTTCAGAGGCACTTCCAG
genomic: TTCGATGATGGATCCAAGTAGAAGTTGGGCTGCTCGGTGGCTTCGAATCGgtatgtcgaa ... caatctgcagGAAGATTTGTTCCTGGATGTTACACCCTTGCTGTTTCAGAGGCACTTCCAG
EST: gi|351049428|gb|FQ450029.1|FQ450029
EST:     TTCGATGATGGATCCAACTAGAAGTTGGGCTGCTCGGTGGCTTCGAATCG                         GAAGATTTGTTCCTGGATGTTACACCCTTGCTGTTTCAGAGGCAATTCCAG
genomic: TTCGATGATGGATCCAAGTAGAAGTTGGGCTGCTCGGTGGCTTCGAATCGgtatgtcgaa ... caatctgcagGAAGATTTGTTCCTGGATGTTACACCCTTGCTGTTTCAGAGGCACTTCCAG
EST: gi|110412486|gb|EC978236.1|EC978236
EST:     TTCGATGATGGATCCAAGTAGAAGTTGGGCTGCTCGGTGGCTTCGAATCG                         GAAGATTTGTTCCTGGATGTTACACCCTTGCTGTTTCAGAGGCACTTCCAG
genomic: TTCGATGATGGATCCAAGTAGAAGTTGGGCTGCTCGGTGGCTTCGAATCGgtatgtcgaa ... caatctgcagGAAGATTTGTTCCTGGATGTTACACCCTTGCTGTTTCAGAGGCACTTCCAG
EST: gi|294964123|gb|GW837926.1|GW837926
EST:     TTCGATGATGGATCCAAGTAGAAGTTGGGCTGCTCGGTGGCTGCGAATCA                         GAAGATTTGTTCCTGGATGTTACACCCTTGCTGTTTCAGAGGCACTTCCAG
genomic: TTCGATGATGGATCCAAGTAGAAGTTGGGCTGCTCGGTGGCTTCGAATCGgtatgtcgaa ... caatctgcagGAAGATTTGTTCCTGGATGTTACACCCTTGCTGTTTCAGAGGCACTTCCAG
EST: gi|30296163|gb|CB972957.1|CB972957
EST:     TTCGATGATGGATCCAAGTAGAAGTTGGGCTGCTCGGTGGCTTCGAATCG                         GAAGATTTGTTCCTGGATGTTACACCCTTGCTGTTTCAGAGGCACTTCCAG
genomic: TTCGATGATGGATCCAAGTAGAAGTTGGGCTGCTCGGTGGCTTCGAATCGgtatgtcgaa ... caatctgcagGAAGATTTGTTCCTGGATGTTACACCCTTGCTGTTTCAGAGGCACTTCCAG
EST: gi|30296421|gb|CB973215.1|CB973215
EST:     TTCGATGATGGATCCAAGTAGAAGTTGGGCTGCTCGGTGGCTTCGAATCG                         GAAGATTTGTTCCTGGATGTTACACCCTTGCTGTTTCAGAGGCACTTCCAG
genomic: TTCGATGATGGATCCAAGTAGAAGTTGGGCTGCTCGGTGGCTTCGAATCGgtatgtcgaa ... caatctgcagGAAGATTTGTTCCTGGATGTTACACCCTTGCTGTTTCAGAGGCACTTCCAG
EST: gi|26258793|gb|CA809856.1|CA809856
EST:     TTCGATGATGGATCCAAGTAGAAGTTGGGCTGCTCGGTGGCTTCGAATCG                         GAAGATTTGTTCCTGGATGTTACACCCTTGCTGTTTCAGAGGCACTTCCAG
genomic: TTCGATGATGGATCCAAGTAGAAGTTGGGCTGCTCGGTGGCTTCGAATCGgtatgtcgaa ... caatctgcagGAAGATTTGTTCCTGGATGTTACACCCTTGCTGTTTCAGAGGCACTTCCAG
EST: gi|26264415|gb|CA815478.1|CA815478
EST:     TTCGATGATGGATCCAAGTAGAAGTTGGGCTGCTCGGTGGCTTCGAATCG                         GAAGATTTGTCCCTGGATGTTACACCCTTGCTGTTTCAGAGGCACTTCCAG
genomic: TTCGATGATGGATCCAAGTAGAAGTTGGGCTGCTCGGTGGCTTCGAATCGgtatgtcgaa ... caatctgcagGAAGATTTGTTCCTGGATGTTACACCCTTGCTGTTTCAGAGGCACTTCCAG
EST: gi|77585520|gb|DV221849.1|DV221849
EST:     TTCGATGATGGATCCAAGTAGAAGTTGGGCTGCTCGGTGGCTTCGAATCG                         GAAGATTTGTTCCTGGATGTTACACCCTTGCTGTTTCAGAGGCACTTCCAG
genomic: TTCGATGATGGATCCAAGTAGAAGTTGGGCTGCTCGGTGGCTTCGAATCGgtatgtcgaa ... caatctgcagGAAGATTTGTTCCTGGATGTTACACCCTTGCTGTTTCAGAGGCACTTCCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctaaggaatttagatttttgtaactcagaatgttcctgtttaaacaatctgcagGAAGATTTGTTCCTGGATGTTACACCCTTGCTGTTTCAGAGGCACTTCCAGAGGACTTGCAG
                  ttgtaac  putative branch site (score: 2)
       aatttagatttttgta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatgcctattagaaccttatattgtttcaaattccagtagtattatctaaggaatttagatttttgtaactcagaatgttcctgtttaaacaatctgcagGAAGATTTGTTCCTGGATGTTACACCCTTGCTGTTTCAGAGGCACTTCCAGAGGACTTGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
tatgcct
- - - - - - - - - - - - - - - - - - - - - - - -taaggaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cagaatg