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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagcttccatatttctgtggaatgtgacaatatgttagtgaacatttttttttccatttcaagttggttggaagcaagagaatcatcatgtgtttgaattttgtcattttggtgcagGTTCCTTGCTATTTCCATTCAAAGTACAAGTCAAGCCAATCAAGTACCTACAGGAAGAATG

Basic information

species Vitis vinifera
transcript Vv10s0116g01210.t01
intron # 2
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|110723374|gb|EE100612.1|EE100612
EST:     ACACTGGTAGCTCAAACCTGTGGGTTCCATCATCCAAGTGCTATTTCTCG                         GTTCCTTGCTATTTCCATTCAAAGTACAAGTCAAGCCAATCAAGTACCTAC
genomic: ACACTGGTAGCTCAAACCTGTGGGTTCCATCATCCAAGTGCTATTTCTCGgtgagcttcc ... tttggtgcagGTTCCTTGCTATTTCCATTCAAAGTACAAGTCAAGCCAATCAAGTACCTAC
EST: gi|110703507|gb|EE080413.1|EE080413
EST:     ACACTGGTAGCTCAAACCTGTGGGTTCCATCATCCAAGTGCTATTTCTCG                         GTTCCTTGCTATTTCCATTCAAAGTACAAGTCAAGCCAATCAAGTACCTAC
genomic: ACACTGGTAGCTCAAACCTGTGGGTTCCATCATCCAAGTGCTATTTCTCGgtgagcttcc ... tttggtgcagGTTCCTTGCTATTTCCATTCAAAGTACAAGTCAAGCCAATCAAGTACCTAC
EST: gi|71862953|gb|DT012008.1|DT012008
EST:     ACACTGGTAGCTCAAACCTGTGGGTTCCATCATCCAAGTGCTATTTCTCG                         GTTCCTTGCTATTTCCATTCAAAGTACAAGTCAAGCCAATCAAGTACCTAC
genomic: ACACTGGTAGCTCAAACCTGTGGGTTCCATCATCCAAGTGCTATTTCTCGgtgagcttcc ... tttggtgcagGTTCCTTGCTATTTCCATTCAAAGTACAAGTCAAGCCAATCAAGTACCTAC
EST: gi|110726583|gb|EE102492.1|EE102492
EST:     ACACTGGTAGCTCAAACCTGTGGGTTCCATCATCCAAGTGCTATTTCTCG                         GTTCCTTGCTATTTCCATTCAAAGTACAAGTCAAGCCAATCAAGTACCTAC
genomic: ACACTGGTAGCTCAAACCTGTGGGTTCCATCATCCAAGTGCTATTTCTCGgtgagcttcc ... tttggtgcagGTTCCTTGCTATTTCCATTCAAAGTACAAGTCAAGCCAATCAAGTACCTAC
EST: gi|71863294|gb|DT012349.1|DT012349
EST:     ACACTGGTAGCTCAAACCTGTGGGTTCCATCATCCAAGTGCTATTTCTCG                         GTTCCTTGCTATTTCCATTCAAAGTACAAGTCAAGCCAATCAAGTACCTAC
genomic: ACACTGGTAGCTCAAACCTGTGGGTTCCATCATCCAAGTGCTATTTCTCGgtgagcttcc ... tttggtgcagGTTCCTTGCTATTTCCATTCAAAGTACAAGTCAAGCCAATCAAGTACCTAC
EST: gi|110723213|gb|EE100267.1|EE100267
EST:     ACACTGGTAGCTCAAACCTGTGGGTTCCATCATCCAAGTGCTATTTCTCG                         GTTCCTTGCTATTTCCATTCAAAGTACAAGTCAAGCCAATCAAGTACCTAC
genomic: ACACTGGTAGCTCAAACCTGTGGGTTCCATCATCCAAGTGCTATTTCTCGgtgagcttcc ... tttggtgcagGTTCCTTGCTATTTCCATTCAAAGTACAAGTCAAGCCAATCAAGTACCTAC
EST: gi|110724471|gb|EE100330.1|EE100330
EST:     ACACTGGTAGCTCAAACCTGTGGGTTCCATCATCCAAGTGCTATTTCTCG                         GTTCCTTGCTATTTCCATTCAAAGTACAAGTCAAGCCAATCAAGTACCTAC
genomic: ACACTGGTAGCTCAAACCTGTGGGTTCCATCATCCAAGTGCTATTTCTCGgtgagcttcc ... tttggtgcagGTTCCTTGCTATTTCCATTCAAAGTACAAGTCAAGCCAATCAAGTACCTAC
EST: gi|110709179|gb|EE084415.1|EE084415
EST:     ACACTGGTAGCTCAAACCTGTGGGTTCCATCATCCAAGTGCTATTTCTCG                         GTTCCTTGCTATTTCCATTCAAAGTACAAGTCAAGCCAATCAAGTACCTAC
genomic: ACACTGGTAGCTCAAACCTGTGGGTTCCATCATCCAAGTGCTATTTCTCGgtgagcttcc ... tttggtgcagGTTCCTTGCTATTTCCATTCAAAGTACAAGTCAAGCCAATCAAGTACCTAC
EST: gi|110710072|gb|EE086085.1|EE086085
EST:     ACACTGGTAGCTCAAACCTGTGGGTTCCATCATCCAAGTGCTATTTCTCG                         GTTCCTTGCTATTTCCATTCAAAGTACAAGTCAAGCCAATCAAGTACCTAC
genomic: ACACTGGTAGCTCAAACCTGTGGGTTCCATCATCCAAGTGCTATTTCTCGgtgagcttcc ... tttggtgcagGTTCCTTGCTATTTCCATTCAAAGTACAAGTCAAGCCAATCAAGTACCTAC
EST: gi|110708151|gb|EE085368.1|EE085368
EST:     ACACTGGTAGCTCAAACCTGTGGGTTCCATCATCCAAGTGCTATTTCTCG                         GTTCCTTGCTATTTCCATTCAAAGTACAAGTCAAGCCAATCAAGTACCTAC
genomic: ACACTGGTAGCTCAAACCTGTGGGTTCCATCATCCAAGTGCTATTTCTCGgtgagcttcc ... tttggtgcagGTTCCTTGCTATTTCCATTCAAAGTACAAGTCAAGCCAATCAAGTACCTAC
EST: gi|110709842|gb|EE085666.1|EE085666
EST:     ACACTGGTAGCTCAAACCTGTGGGTTCCATCATCCAAGTGCTATTTCTCG                         GTTCCTTGCTATTTCCATTCAAAGTACAAGTCAAGCCAATCAAGTACCTAC
genomic: ACACTGGTAGCTCAAACCTGTGGGTTCCATCATCCAAGTGCTATTTCTCGgtgagcttcc ... tttggtgcagGTTCCTTGCTATTTCCATTCAAAGTACAAGTCAAGCCAATCAAGTACCTAC
EST: gi|71862967|gb|DT012022.1|DT012022
EST:     ACACTGGTAGCTCAAACCTGTGGGTTCCATCATCCAAGTGCTATTTCTCG                         GTTCCTTGCTATTTCCATTCAAAGTACAAGTCAAGCCAATCAAGTACCTAC
genomic: ACACTGGTAGCTCAAACCTGTGGGTTCCATCATCCAAGTGCTATTTCTCGgtgagcttcc ... tttggtgcagGTTCCTTGCTATTTCCATTCAAAGTACAAGTCAAGCCAATCAAGTACCTAC
EST: gi|110697801|gb|EE075199.1|EE075199
EST:     ACACTGGTAGCTCAAACCTGTGGGTTCCATCATCCAAGTGCTATTTCTCG                         GTTCCTTGCTATTTCCATTCAAAGTACAAGTCAAGCCAATCAAGTACCTAC
genomic: ACACTGGTAGCTCAAACCTGTGGGTTCCATCATCCAAGTGCTATTTCTCGgtgagcttcc ... tttggtgcagGTTCCTTGCTATTTCCATTCAAAGTACAAGTCAAGCCAATCAAGTACCTAC
EST: gi|110723493|gb|EE100867.1|EE100867
EST:     ACACTGGTAGCTCAAACCTGTGGGTTCCATCATCCAAGTGCTATTTCTCG                         GTTCCTTGCTATTTCCATTCAAAGTACAAGTCAAGCCAATCAAGTACCTAC
genomic: ACACTGGTAGCTCAAACCTGTGGGTTCCATCATCCAAGTGCTATTTCTCGgtgagcttcc ... tttggtgcagGTTCCTTGCTATTTCCATTCAAAGTACAAGTCAAGCCAATCAAGTACCTAC
EST: gi|30299773|gb|CB976567.1|CB976567
EST:     ACACTGGTAGCTCAAACCTGTAGGTTCCATCATCCAAGTGCTATTTCTCG                         GTTCCTTGCTATTTCCATTCAAAGTACAAGTCAAGCCAATCAAGTACCTAC
genomic: ACACTGGTAGCTCAAACCTGTGGGTTCCATCATCCAAGTGCTATTTCTCGgtgagcttcc ... tttggtgcagGTTCCTTGCTATTTCCATTCAAAGTACAAGTCAAGCCAATCAAGTACCTAC
EST: gi|110724042|gb|EE099523.1|EE099523
EST:     ACACTGGTAGCTCAAACCTGTGGGTTCCATCATCCAAGTGCTATTTCTCG                         GTTCCTTGCTATTTCCATTCAAAGTACAAGTCAAGCCAATCAAGTACCTAC
genomic: ACACTGGTAGCTCAAACCTGTGGGTTCCATCATCCAAGTGCTATTTCTCGgtgagcttcc ... tttggtgcagGTTCCTTGCTATTTCCATTCAAAGTACAAGTCAAGCCAATCAAGTACCTAC
EST: gi|352789600|gb|FQ476198.1|FQ476198
EST:     ACACTGGTAGCTCAAACCTGTGGGTTCCATCATCCAAGTGCTATTTCTCG                         GTTCCTTGCTATTTCCATTCAAAGTACAAGTCAAGCCAATCAAGTACCTAC
genomic: ACACTGGTAGCTCAAACCTGTGGGTTCCATCATCCAAGTGCTATTTCTCGgtgagcttcc ... tttggtgcagGTTCCTTGCTATTTCCATTCAAAGTACAAGTCAAGCCAATCAAGTACCTAC
EST: gi|110684973|gb|EE062864.1|EE062864
EST:     CCAAGTGCT-TTCTCTCG                         GTTCCTTGCTATTTCCATTCAAAGTACAAGTCAAGCCAATCAAGTACCTA
genomic: CCAAGTGCTATT-TCTCGgtgagcttcc ... tttggtgcagGTTCCTTGCTATTTCCATTCAAAGTACAAGTCAAGCCAATCAAGTACCTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttggttggaagcaagagaatcatcatgtgtttgaattttgtcattttggtgcagGTTCCTTGCTATTTCCATTCAAAGTACAAGTCAAGCCAATCAAGTACCTACAGGAAGAATG
                                         tcatttt  CT-rich tract
                                  aattttgtcatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagcttccatatttctgtggaatgtgacaatatgttagtgaacatttttttttccatttcaagttggttggaagcaagagaatcatcatgtgtttgaattttgtcattttggtgcagGTTCCTTGCTATTTCCATTCAAAGTACAAGTCAAGCCAATCAAGTACCTACAGGAAGAATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA