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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacatacactatccggtcaccttctttacttgtctctttccgcttcccttcgatgaatctaactttctaagctttggtataaaaaatagGTGATCACAAATGGCAAATACAAGAGTGTGCTGCACAGGGTCGTAGCCCAAACAGACGGCAACAGGATGTCAATAGCTTCATTCTACAACCCTGGAAACG

Basic information

species Vitis vinifera
transcript Vv12s0059g01380.t01
intron # 3
splice site 3'
intron type U2

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|351026123|gb|FQ428135.1|FQ428135
EST:     TTCCTCCAATGCGCCACTCCATTGTGGTCAACCTCGGTGACCAACTTGAG                         GTGATCACAAATGGCAAATACAAGAGTGTGCTGCACAGGGTCGTAGCCCAA
genomic: TTCCTCCAATGCGCCACTCCATTGTGGTCAACCTCGGTGACCAACTTGAGgtacatacac ... taaaaaatagGTGATCACAAATGGCAAATACAAGAGTGTGCTGCACAGGGTCGTAGCCCAA
EST: gi|30252772|gb|CB970323.1|CB970323
EST:     TCCTCCAATGCGCCACTCCATTGTGGTCAACCTCGG-GANCCAACTTGAG                         GTGATCACAAATGGCAAATA
genomic: TCCTCCAATGCGCCACTCCATTGTGGTCAACCTCGGTGA-CCAACTTGAGgtacatacac ... taaaaaatagGTGATCACAAATGGCAAATA
EST: gi|32268302|gb|CD717461.1|CD717461
EST:     TTCCTCCAATGCGCCACTCCATTGTGGTCAACCTCGGTGACCAACTTGAG                         GTGATCACAAATGGCAAATACNAGAGTGTGCTGCACAGGGTCGTAGCCCAA
genomic: TTCCTCCAATGCGCCACTCCATTGTGGTCAACCTCGGTGACCAACTTGAGgtacatacac ... taaaaaatagGTGATCACAAATGGCAAATACAAGAGTGTGCTGCACAGGGTCGTAGCCCAA
EST: gi|110727761|gb|EE104888.1|EE104888
EST:     TTCCTCCAATGCGCCACTCCATTGTGGTCAACCTCGGTGACCAACTTGAG                         GTGATCACAAATGGCAAATACAAGAGTGTGCTGCACAGGGTCGTAACCCAA
genomic: TTCCTCCAATGCGCCACTCCATTGTGGTCAACCTCGGTGACCAACTTGAGgtacatacac ... taaaaaatagGTGATCACAAATGGCAAATACAAGAGTGTGCTGCACAGGGTCGTAGCCCAA
EST: gi|351054949|gb|FQ440288.1|FQ440288
EST:     TTCCTCCAATGCGCCACTCCATTGTGGTCAACCTCGGTGACCAACTTGAG                         GTGATCACAAATGGCAAATACAAGAGTGTGCCGCACAGGGTCGTAGCCCAA
genomic: TTCCTCCAATGCGCCACTCCATTGTGGTCAACCTCGGTGACCAACTTGAGgtacatacac ... taaaaaatagGTGATCACAAATGGCAAATACAAGAGTGTGCTGCACAGGGTCGTAGCCCAA
EST: gi|77583863|gb|DV220968.1|DV220968
EST:     TTCCTCCAATGCGCCACTCCATTGTGGTCAACCTCGGTGACCAACTTGAG                         GTGATCACAAATGGCAAATACAAGAGTGTGCTGCACAGGGTCGT
genomic: TTCCTCCAATGCGCCACTCCATTGTGGTCAACCTCGGTGACCAACTTGAGgtacatacac ... taaaaaatagGTGATCACAAATGGCAAATACAAGAGTGTGCTGCACAGGGTCGT
EST: gi|30252855|gb|CB970406.1|CB970406
EST:     TTCCTCCAATGCGCCACTCCATTGTGGTCAACCTCGGTGACCAACTTGAG                         GTGATCACAAATGGCAAATACAAGAGTGTGCTGCACAGGGTCGTAGCCCAA
genomic: TTCCTCCAATGCGCCACTCCATTGTGGTCAACCTCGGTGACCAACTTGAGgtacatacac ... taaaaaatagGTGATCACAAATGGCAAATACAAGAGTGTGCTGCACAGGGTCGTAGCCCAA
EST: gi|32270249|gb|CD719408.1|CD719408
EST:     TTCCTCCAATGCGCCACTCCATTGTGGTCAACCTCGGTGACCAACTTGAG                         GTGATCACAAATGGCAAATACAAGAGTGTGCTGCACAGGGTCGTAGCCCAA
genomic: TTCCTCCAATGCGCCACTCCATTGTGGTCAACCTCGGTGACCAACTTGAGgtacatacac ... taaaaaatagGTGATCACAAATGGCAAATACAAGAGTGTGCTGCACAGGGTCGTAGCCCAA
EST: gi|45770833|gb|CN006685.1|CN006685
EST:     TGACCAACTTGA-                         GTGATCACAAATGGCAAATACAAGAGTGTGCTGCACAGGGTCGTAGCCCAA
genomic: TGACCAACTTGAGgtacatacac ... taaaaaatagGTGATCACAAATGGCAAATACAAGAGTGTGCTGCACAGGGTCGTAGCCCAA
EST: gi|351022691|gb|FQ428600.1|FQ428600
EST:     TTCCTCCAATGCGCCACTCCATTGTGGTCAACCTCGGTGACCAACTTGAG                         GTGATCACAAATGGCAAATACAAGAGTGTGCTGCACAGGGTCGTAGCCCAA
genomic: TTCCTCCAATGCGCCACTCCATTGTGGTCAACCTCGGTGACCAACTTGAGgtacatacac ... taaaaaatagGTGATCACAAATGGCAAATACAAGAGTGTGCTGCACAGGGTCGTAGCCCAA
EST: gi|161710362|gb|FC058993.1|FC058993
EST:     CAACCCCGGTGACCAACTTGAG                         GTGATC-CAAATGGCAAATACAAGAGTGTGCTGCACAGGGTCGTAGCCCAA
genomic: CAACCTCGGTGACCAACTTGAGgtacatacac ... taaaaaatagGTGATCACAAATGGCAAATACAAGAGTGTGCTGCACAGGGTCGTAGCCCAA
EST: gi|161710557|gb|FC059368.1|FC059368
EST:     TTCCTCCAATGCGCCACTCCATTGTGGTCAACCTCGGTGACCAACTTGAG                         GTGATCACAAATGGCAAATACAAGAGTGTGCTGCACAGGGTCGTTGCCCAA
genomic: TTCCTCCAATGCGCCACTCCATTGTGGTCAACCTCGGTGACCAACTTGAGgtacatacac ... taaaaaatagGTGATCACAAATGGCAAATACAAGAGTGTGCTGCACAGGGTCGTAGCCCAA
EST: gi|349832706|gb|FQ422064.1|FQ422064
EST:     TTCCTCCAATGCGCCACTCCATTGTGGTCAACCTCGGTGACCAACTTGAG                         GTGATCACAAATGGCAAATACAAGAGTGTGCTGCACAGGGTCGTAGCCCAA
genomic: TTCCTCCAATGCGCCACTCCATTGTGGTCAACCTCGGTGACCAACTTGAGgtacatacac ... taaaaaatagGTGATCACAAATGGCAAATACAAGAGTGTGCTGCACAGGGTCGTAGCCCAA
EST: gi|32268560|gb|CD717719.1|CD717719
EST:     TTCCTCCAATGCGCCACTCCATTGTGGTCAACCTCGGTGACCAACTTGAG                         GTGATCACAAATGGCAAATACAAGAGTGTGCTGCACAGGGTCGTAGCCCAA
genomic: TTCCTCCAATGCGCCACTCCATTGTGGTCAACCTCGGTGACCAACTTGAGgtacatacac ... taaaaaatagGTGATCACAAATGGCAAATACAAGAGTGTGCTGCACAGGGTCGTAGCCCAA
EST: gi|161718648|gb|FC068224.1|FC068224
EST:     TTCCTCCA-TGCGCCACTCCAT-GTGGTCACCCTCG-TGACCA-CTTGAG                         GTGATC-CAA-TGGCAA
genomic: TTCCTCCAATGCGCCACTCCATTGTGGTCAACCTCGGTGACCAACTTGAGgtacatacac ... taaaaaatagGTGATCACAAATGGCAA
EST: gi|30256251|gb|CB972094.1|CB972094
EST:     TTCCTCCAATGCGCCACTCCATTGTGGTCAACCTCGGTGACCAACTTGAG                         GTGATCACAAATGGCAAATACAAGAGTGTGCTGCACAGGNTCGTAGCCGAT
genomic: TTCCTCCAATGCGCCACTCCATTGTGGTCAACCTCGGTGACCAACTTGAGgtacatacac ... taaaaaatagGTGATCACAAATGGCAAATACAAGAGTGTGCTGCACAGGGTCGTAGCCCAA
EST: gi|110700838|gb|EE077845.1|EE077845
EST:     TTCCTCCAATGCGCCACTCCATTGTGGTCAACCTCGGTGACCAACTTGAG                         GTGATCACAA-TGGCAAATACAAGAGTGTGCTGCACATGTTCGTATCCCAA
genomic: TTCCTCCAATGCGCCACTCCATTGTGGTCAACCTCGGTGACCAACTTGAGgtacatacac ... taaaaaatagGTGATCACAAATGGCAAATACAAGAGTGTGCTGCACAGGGTCGTAGCCCAA
EST: gi|110688626|gb|EE067394.1|EE067394
EST:     TTCCTCCAATGCGCCACTCCATTGTGGTCAACCTCGGTGAACAACTTGAG                         GTGATCACAAATGGCAAATACNAGAGTGTGCTGCACAGGGT
genomic: TTCCTCCAATGCGCCACTCCATTGTGGTCAACCTCGGTGACCAACTTGAGgtacatacac ... taaaaaatagGTGATCACAAATGGCAAATACAAGAGTGTGCTGCACAGGGT
EST: gi|351055645|gb|FQ452110.1|FQ452110
EST:     TTCCTCCAATGCGCCACTCCATTGTGGTCAACCTCGGTGACCAACTTGAG                         GTGGATCACAAATGGCAA-TACAAGAGTGTGCTGCACAGGGTCGTAGCCCA
genomic: TTCCTCCAATGCGCCACTCCATTGTGGTCAACCTCGGTGACCAACTTGAGgtacatacac ... taaaaaatagGTG-ATCACAAATGGCAAATACAAGAGTGTGCTGCACAGGGTCGTAGCCCA
EST: gi|83275704|gb|DV939712.1|DV939712
EST:     TTCCTCCAATGCGCCACTCCATTGTGGTCAACCTCGGTGACCAACTTGAG                         GTGATCACAAATGGCAAATACAAGAGTGTGCTGCACAGGGTCGTTGCCCAA
genomic: TTCCTCCAATGCGCCACTCCATTGTGGTCAACCTCGGTGACCAACTTGAGgtacatacac ... taaaaaatagGTGATCACAAATGGCAAATACAAGAGTGTGCTGCACAGGGTCGTAGCCCAA
EST: gi|30256316|gb|CB972159.1|CB972159
EST:     TTCCTCCAATGCGCCACTCCATTGTGGTCAACCTCGGTGACCAACTTGAG                         GTGATCACAAATGGCAAATACAAGAGTGTGCTGCACAGGGTCGTAGCCCAA
genomic: TTCCTCCAATGCGCCACTCCATTGTGGTCAACCTCGGTGACCAACTTGAGgtacatacac ... taaaaaatagGTGATCACAAATGGCAAATACAAGAGTGTGCTGCACAGGGTCGTAGCCCAA
EST: gi|110409687|gb|EC975356.1|EC975356
EST:     TTCCTCCAATGCGCCACTCCATTGTGGTCAACCTCGGTGACCAACTTGAG                         GTGATCACAAATGGCAAATACAAGAGTGTGCTGCACAGGGTCGTAGCCCAA
genomic: TTCCTCCAATGCGCCACTCCATTGTGGTCAACCTCGGTGACCAACTTGAGgtacatacac ... taaaaaatagGTGATCACAAATGGCAAATACAAGAGTGTGCTGCACAGGGTCGTAGCCCAA
EST: gi|110361236|gb|EC924694.1|EC924694
EST:     TTCCTCCAATGCGCCACTCCATTGTGGTCAACCTCGGTGACCAACTTGAG                         GTGATCACAAATGGCAAATACAAGAGTGTGCTGCACAGGGTCGTTGCCCAA
genomic: TTCCTCCAATGCGCCACTCCATTGTGGTCAACCTCGGTGACCAACTTGAGgtacatacac ... taaaaaatagGTGATCACAAATGGCAAATACAAGAGTGTGCTGCACAGGGTCGTAGCCCAA
EST: gi|161719282|gb|FC064822.1|FC064822
EST:     TTCCTCCAATGCGCCACTCCATTGTGGTCAACCTCGGTGACCAACTTGAG                         GTGATCACAAATGGCAAATACAAGAGTGTGCTGCACAGGGTCGTAGCCCAA
genomic: TTCCTCCAATGCGCCACTCCATTGTGGTCAACCTCGGTGACCAACTTGAGgtacatacac ... taaaaaatagGTGATCACAAATGGCAAATACAAGAGTGTGCTGCACAGGGTCGTAGCCCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctttccgcttcccttcgatgaatctaactttctaagctttggtataaaaaatagGTGATCACAAATGGCAAATACAAGAGTGTGCTGCACAGGGTCGTAGCCCAAACAGACGGCAACAGGATGTCAATAGCTTCATTCTACAACCCTGGAAACG
                      atctaac  putative branch site (score: 2)
                                      tttggtataaaaaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacatacactatccggtcaccttctttacttgtctctttccgcttcccttcgatgaatctaactttctaagctttggtataaaaaatagGTGATCACAAATGGCAAATACAAGAGTGTGCTGCACAGGGTCGTAGCCCAAACAGACGGCAACAGGATGTCAATAGCTTCATTCTACAACCCTGGAAACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG