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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtgttttacttcgctcagctttgccatgatattcttctataattcagtatcgggatttgatgaagagattatgaatgggaagtgaacgtggtttgtttgtaaagGTGGAAATGAACCCACTTTGGCAGCAGAAGAAGCTCAGGGAGTTCTGTGCGGAAAAAGGTATCCATATCACGGCATACTCCCCCTTGGGTGCCAAAGGAA

Basic information

species Vitis vinifera
transcript Vv01s0011g06470.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|28965842|gb|CB344875.1|CB344875
EST:     AGCTGGAGGAGTTGCTCCAGACAGCTAGCATCCTTCCGGCAGTCAATCAA                         GTGGAAATGAACCCACTTTGGCAGCAGAAGAAGCTCAGGGAGTTCTGTGCG
genomic: AGCTGGAGGAGTTGCTCCAGACAGCTAGCATCCTTCCGGCAGTCAATCAAgtgagtgttt ... gtttgtaaagGTGGAAATGAACCCACTTTGGCAGCAGAAGAAGCTCAGGGAGTTCTGTGCG
EST: gi|349813733|gb|FQ413967.1|FQ413967
EST:     AGCTGGAGGAGTTGCTCCAGACAGCTAGCATCCTTCCGGCAGTCAATCAA                         GTGGAAATGAACCCACTTTGGCAGCAGAAGAAGCTCAGGGAGTTCTGTGCG
genomic: AGCTGGAGGAGTTGCTCCAGACAGCTAGCATCCTTCCGGCAGTCAATCAAgtgagtgttt ... gtttgtaaagGTGGAAATGAACCCACTTTGGCAGCAGAAGAAGCTCAGGGAGTTCTGTGCG
EST: gi|351035169|gb|FQ458526.1|FQ458526
EST:     AGCTGGAGGAGTTGCTCCAGACAGCTAGCATCCTTCCGGCAGTCAATCAA                         GTGGAAATGAACCCACTTTGGCAGCAGAAGAAGCTCAGGGAGTTCTGTGCG
genomic: AGCTGGAGGAGTTGCTCCAGACAGCTAGCATCCTTCCGGCAGTCAATCAAgtgagtgttt ... gtttgtaaagGTGGAAATGAACCCACTTTGGCAGCAGAAGAAGCTCAGGGAGTTCTGTGCG
EST: gi|351048963|gb|FQ449806.1|FQ449806
EST:     AGCTGGAGGAGTTGCTCCAGACAGCTAGCATCCTTCCGGCAGTCAATCAA                         GTGGAAATGAACCCACTTTGGCAGCAGAAGAAGCTCAGGGAGTTCTGTGCG
genomic: AGCTGGAGGAGTTGCTCCAGACAGCTAGCATCCTTCCGGCAGTCAATCAAgtgagtgttt ... gtttgtaaagGTGGAAATGAACCCACTTTGGCAGCAGAAGAAGCTCAGGGAGTTCTGTGCG
EST: gi|351053660|gb|FQ440169.1|FQ440169
EST:     AGCTGGAGGAGTTGCTCCAGACAGCTAGCATCCTTCCGGCAGTCAATCAA                         GTGGAAATGAACCCACTTTGGCAGCAGAAGAAGCTCAGGGAGTTCTGTGCG
genomic: AGCTGGAGGAGTTGCTCCAGACAGCTAGCATCCTTCCGGCAGTCAATCAAgtgagtgttt ... gtttgtaaagGTGGAAATGAACCCACTTTGGCAGCAGAAGAAGCTCAGGGAGTTCTGTGCG
EST: gi|111125105|gb|EE253723.1|EE253723
EST:     AGCTGGAGGAGTTGCTCCAGACAGCTAGCATCCTTCCGGCAGTCAATCAA                         GTGGAAATGAACCCACTTTGGCAGCAGAAGAAGCTCANGGAGTTCTGTGCG
genomic: AGCTGGAGGAGTTGCTCCAGACAGCTAGCATCCTTCCGGCAGTCAATCAAgtgagtgttt ... gtttgtaaagGTGGAAATGAACCCACTTTGGCAGCAGAAGAAGCTCAGGGAGTTCTGTGCG
EST: gi|351047337|gb|FQ451849.1|FQ451849
EST:     AGCTGGAGGAGTTGCTCCAGACAGCTAGCATCCTTCCGGCAGTCAATCAA                         GTGGAAATGAACCCACTTTGGCAGCAGAAGAAGCTCAGGGAGTTCTGTGCG
genomic: AGCTGGAGGAGTTGCTCCAGACAGCTAGCATCCTTCCGGCAGTCAATCAAgtgagtgttt ... gtttgtaaagGTGGAAATGAACCCACTTTGGCAGCAGAAGAAGCTCAGGGAGTTCTGTGCG
EST: gi|351053726|gb|FQ441492.1|FQ441492
EST:     AGCTGGAGGAGTTGCTCCAGACAGCTAGCATCCTTCCGGCAGTCAATCAA                         GTGGAAATGAACCCACTTTGGCAGCAGAAGAAGCTCAGGGAGTTCTGTACG
genomic: AGCTGGAGGAGTTGCTCCAGACAGCTAGCATCCTTCCGGCAGTCAATCAAgtgagtgttt ... gtttgtaaagGTGGAAATGAACCCACTTTGGCAGCAGAAGAAGCTCAGGGAGTTCTGTGCG
EST: gi|349817504|gb|FQ407294.1|FQ407294
EST:     AGCTGGAGGAGTTGCTCCAGACAGCTAGCATCCTTCCGGCAGTCAATCAA                         GTGGAAATGAACCCACTTTGGCAGCAGAAGAAGCTCAGGGAGTTCTGTGCG
genomic: AGCTGGAGGAGTTGCTCCAGACAGCTAGCATCCTTCCGGCAGTCAATCAAgtgagtgttt ... gtttgtaaagGTGGAAATGAACCCACTTTGGCAGCAGAAGAAGCTCAGGGAGTTCTGTGCG
EST: gi|351032689|gb|FQ462403.1|FQ462403
EST:     AGCTGGAGGAGTTGCTCCAGACAGCTAGCATCCTTCCGGCAGTCAATCAA                         GTGGAAATGAACCCACTTTGGCAGCAGAAGAAGCTCAGGGAGTTCTGTGCG
genomic: AGCTGGAGGAGTTGCTCCAGACAGCTAGCATCCTTCCGGCAGTCAATCAAgtgagtgttt ... gtttgtaaagGTGGAAATGAACCCACTTTGGCAGCAGAAGAAGCTCAGGGAGTTCTGTGCG
EST: gi|349822747|gb|FQ398134.1|FQ398134
EST:     AGCTGGAGGAGTTGCTCCAGACAGCTAGCATCCTTCCGGCAGTCAATCAA                         GTGGAAATGAACCCACTTTGGCAGCAGAAGAAGCTCAGGGAGTTCTGTGCG
genomic: AGCTGGAGGAGTTGCTCCAGACAGCTAGCATCCTTCCGGCAGTCAATCAAgtgagtgttt ... gtttgtaaagGTGGAAATGAACCCACTTTGGCAGCAGAAGAAGCTCAGGGAGTTCTGTGCG
EST: gi|110384776|gb|EC949237.1|EC949237
EST:     AGCTGGAGGAGTTGCTCCAGACAGCTAGCATCCTTCCGGCAGTCAATCAA                         GTGGAAATGAACCCACTTTGGCAGCAGAAGAAGCTCAGGGAGTTCTGTGCG
genomic: AGCTGGAGGAGTTGCTCCAGACAGCTAGCATCCTTCCGGCAGTCAATCAAgtgagtgttt ... gtttgtaaagGTGGAAATGAACCCACTTTGGCAGCAGAAGAAGCTCAGGGAGTTCTGTGCG
EST: gi|351013364|gb|FQ425069.1|FQ425069
EST:     AGCTGGAGGAGTTGCTCCAGACAGCTAGCATCCTTCCGGCAGTCAATCAA                         GTGGAAATGAACCCACTTTGGCAGCAGAAGAAGCTCAGGGAGTTCTGTGCG
genomic: AGCTGGAGGAGTTGCTCCAGACAGCTAGCATCCTTCCGGCAGTCAATCAAgtgagtgttt ... gtttgtaaagGTGGAAATGAACCCACTTTGGCAGCAGAAGAAGCTCAGGGAGTTCTGTGCG
EST: gi|351035143|gb|FQ458500.1|FQ458500
EST:     AGCTGGAGGAGTTGCTCCAGACAGCTAGCATCCTTCCGGCAGTCAATCAA                         GTGGAAATGAACCCACTTTGGCAGCAGAAGAAGCTCAGGGAGTTCTGTGCG
genomic: AGCTGGAGGAGTTGCTCCAGACAGCTAGCATCCTTCCGGCAGTCAATCAAgtgagtgttt ... gtttgtaaagGTGGAAATGAACCCACTTTGGCAGCAGAAGAAGCTCAGGGAGTTCTGTGCG
EST: gi|352794471|gb|FQ481704.1|FQ481704
EST:     AGCTGGAGGAGTTGCTCCAGACAGCTAGCATCCTTCCGGCAGTCAATCAA                         GTGGAAATGAACCCACTTTGGCAGCAGAAGAAGCTCAGGGAGTTCTGTGCG
genomic: AGCTGGAGGAGTTGCTCCAGACAGCTAGCATCCTTCCGGCAGTCAATCAAgtgagtgttt ... gtttgtaaagGTGGAAATGAACCCACTTTGGCAGCAGAAGAAGCTCAGGGAGTTCTGTGCG
EST: gi|349818630|gb|FQ403265.1|FQ403265
EST:     AGCTGGAGGAGTTGCTCCAGACAGCTAGCATCCTTCCGGCAGTCAATCAA                         GTGGAAATGAACCCACTTTGGCAGCAGAAGAAGCTCAGGGAGTTCTGTGCG
genomic: AGCTGGAGGAGTTGCTCCAGACAGCTAGCATCCTTCCGGCAGTCAATCAAgtgagtgttt ... gtttgtaaagGTGGAAATGAACCCACTTTGGCAGCAGAAGAAGCTCAGGGAGTTCTGTGCG
EST: gi|351032310|gb|FQ461563.1|FQ461563
EST:     AGCTGGAGGAGTTGCTCCAGACAGCTAGCATCCTTCCGGCAGTCAATCAA                         GTGGAAATGAACCCACTTTGGCAGCAGAAGAAGCTCAGGGAGTTCTGTGCG
genomic: AGCTGGAGGAGTTGCTCCAGACAGCTAGCATCCTTCCGGCAGTCAATCAAgtgagtgttt ... gtttgtaaagGTGGAAATGAACCCACTTTGGCAGCAGAAGAAGCTCAGGGAGTTCTGTGCG
EST: gi|349814452|gb|FQ399092.1|FQ399092
EST:     AGCTGGAGGAGTTGCTCCAGACAGCTAGCATCCTTCCGGCAGTCAATCAA                         GTGGAAATGAACCCACTTTGGCAGCAGAAGAAGCTCAGGGAGTTCTGTGCG
genomic: AGCTGGAGGAGTTGCTCCAGACAGCTAGCATCCTTCCGGCAGTCAATCAAgtgagtgttt ... gtttgtaaagGTGGAAATGAACCCACTTTGGCAGCAGAAGAAGCTCAGGGAGTTCTGTGCG
EST: gi|349814016|gb|FQ414250.1|FQ414250
EST:     AGCTGGAGGAGTTGCTCCAGACAGCTAGCATCCTTCCGGCAGTCAATCAA                         GTGGAAATGAACCCACTTTGGCAGCAGAAGAAGCTCAGGGAGTTCTGTGCG
genomic: AGCTGGAGGAGTTGCTCCAGACAGCTAGCATCCTTCCGGCAGTCAATCAAgtgagtgttt ... gtttgtaaagGTGGAAATGAACCCACTTTGGCAGCAGAAGAAGCTCAGGGAGTTCTGTGCG
EST: gi|349821554|gb|FQ408113.1|FQ408113
EST:     AGCTGGAGGAGTTGCTCCAGACAGCTAGCATCCTTCCGGCAGTCAATCAA                         GTGGAAATGAACCCACTTTGGCAGCAGAAGAAGCTCAGGGAGTTCTGTGCG
genomic: AGCTGGAGGAGTTGCTCCAGACAGCTAGCATCCTTCCGGCAGTCAATCAAgtgagtgttt ... gtttgtaaagGTGGAAATGAACCCACTTTGGCAGCAGAAGAAGCTCAGGGAGTTCTGTGCG
EST: gi|349814748|gb|FQ409971.1|FQ409971
EST:     AGCTGGAGGAGTTGCTCCAGACAGCTAGCATCCTTCCGGCAGTCAATCAA                         GTGGAAATGAACCCACTTTGGCAGCAGAAGAAGCTCAGGGAGTTCTGTGCG
genomic: AGCTGGAGGAGTTGCTCCAGACAGCTAGCATCCTTCCGGCAGTCAATCAAgtgagtgttt ... gtttgtaaagGTGGAAATGAACCCACTTTGGCAGCAGAAGAAGCTCAGGGAGTTCTGTGCG
EST: gi|351031264|gb|FQ445289.1|FQ445289
EST:     AGCTGGAGGAGTTGCTCCAGACAGCTAGCATCCTTCCGGCAGTCAATCAA                         GTGGAAATGAACCCACTTTGGCAGCAGAAGAAGCTCAGGGAGTTCTGTGCG
genomic: AGCTGGAGGAGTTGCTCCAGACAGCTAGCATCCTTCCGGCAGTCAATCAAgtgagtgttt ... gtttgtaaagGTGGAAATGAACCCACTTTGGCAGCAGAAGAAGCTCAGGGAGTTCTGTGCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcgggatttgatgaagagattatgaatgggaagtgaacgtggtttgtttgtaaagGTGGAAATGAACCCACTTTGGCAGCAGAAGAAGCTCAGGGAGTTCTGTGCGGAAAAAGGTATCCATATCACGGCATACTCCCCCTTGGGTGCCAAAGGAA
     atttgat  putative branch site (score: 5)
                                          tttgttt  putative PPT
                  attatgaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtgttttacttcgctcagctttgccatgatattcttctataattcagtatcgggatttgatgaagagattatgaatgggaagtgaacgtggtttgtttgtaaagGTGGAAATGAACCCACTTTGGCAGCAGAAGAAGCTCAGGGAGTTCTGTGCGGAAAAAGGTATCCATATCACGGCATACTCCCCCTTGGGTGCCAAAGGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA