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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtttgtcttggttgttgattttaggaactcggttgcattttcccttggttttattattccgttaatgatgtgcttgaaaaatttttacagGGGGAGAAGTTAAAGCTTTTCTACAATCCAGTAGCTAGCAAACTTGTTCCAAATGAAGATTTTGGGATTGGTTTTAATG

Basic information

species Vitis vinifera
transcript Vv09s0002g06980.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|110377543|gb|EC942616.1|EC942616
EST:     GGAGGGCTCCTGTCTACTGGAAGACCATGAATGGCCTTCCTCCTAGTTCT                         GGGGAGAAGTTAAAGCTTTTCTACAATCCAGTAGCTAGCAAACTTGTTCCA
genomic: GGAGGGCTCCTGTCTACTGGAAGACCATGAATGGCCTTCCTCCTAGTTCTgtatgtttgt ... atttttacagGGGGAGAAGTTAAAGCTTTTCTACAATCCAGTAGCTAGCAAACTTGTTCCA
EST: gi|26256962|gb|CA808025.1|CA808025
EST:     GGAGGGCTCCTGTCTACTGGAAGACCATGAATGGCCTTCCTCCTAGTTCT                         GGGGAGAAGTTAAAGCTTTTCTACAATCCAGTAGCTAGCAAACTTGTTCCA
genomic: GGAGGGCTCCTGTCTACTGGAAGACCATGAATGGCCTTCCTCCTAGTTCTgtatgtttgt ... atttttacagGGGGAGAAGTTAAAGCTTTTCTACAATCCAGTAGCTAGCAAACTTGTTCCA
EST: gi|32249446|gb|CD715265.1|CD715265
EST:     GGAGGGCTCCTGTCTACTGGAAGACCATGAATGGCCTTCCTCCTAGTTCT                         GGGGAGAAGTTAAAGCTTTTCTACAATCCAGTAGCTAGCAAACTTGTTCCA
genomic: GGAGGGCTCCTGTCTACTGGAAGACCATGAATGGCCTTCCTCCTAGTTCTgtatgtttgt ... atttttacagGGGGAGAAGTTAAAGCTTTTCTACAATCCAGTAGCTAGCAAACTTGTTCCA
EST: gi|32249285|gb|CD715104.1|CD715104
EST:     GGAGGGCTCCTGTCTACTGGAAGACCATGAATGGCCTTCCTCCTAGTTCT                         GGGGAGAAGTTAAAGCTTTTCTACAATCCAGTAGCTAGCAAACTTGTTCCA
genomic: GGAGGGCTCCTGTCTACTGGAAGACCATGAATGGCCTTCCTCCTAGTTCTgtatgtttgt ... atttttacagGGGGAGAAGTTAAAGCTTTTCTACAATCCAGTAGCTAGCAAACTTGTTCCA
EST: gi|110363813|gb|EC927432.1|EC927432
EST:     GGAGGGCTCCTGTTTACTGGAAGACCATGAATGGCCTTCCTCCTAGTTCT                         GGGGAGAAGTTAAAGCTTTTTCTACAATCCAGTAGCTAGCAAACTTGTTCC
genomic: GGAGGGCTCCTGTCTACTGGAAGACCATGAATGGCCTTCCTCCTAGTTCTgtatgtttgt ... atttttacagGGGGAGAAGTTAAAGC-TTTTCTACAATCCAGTAGCTAGCAAACTTGTTCC
EST: gi|28961921|gb|CB340979.1|CB340979
EST:     GGAGGGCTCCTGTCTACTGGAAGACCATGAATGGCCTTCCTCCTAGTTCT                         GGGGAGAAGTTAAAGCTTTTCTACAATCCAGTAGCTAGCAAA--TGTTCCA
genomic: GGAGGGCTCCTGTCTACTGGAAGACCATGAATGGCCTTCCTCCTAGTTCTgtatgtttgt ... atttttacagGGGGAGAAGTTAAAGCTTTTCTACAATCCAGTAGCTAGCAAACTTGTTCCA
EST: gi|110385730|gb|EC950281.1|EC950281
EST:     GGAGGGCTCCTGTCTACTGGAAGACCATGAATGGCCTTCCTCCTAGTTCT                         GGGGAGAAGTTAAAGCTTTTCTACAATCCAGTAGCTAGCAAACTTGTTCCA
genomic: GGAGGGCTCCTGTCTACTGGAAGACCATGAATGGCCTTCCTCCTAGTTCTgtatgtttgt ... atttttacagGGGGAGAAGTTAAAGCTTTTCTACAATCCAGTAGCTAGCAAACTTGTTCCA
EST: gi|32269789|gb|CD718948.1|CD718948
EST:     GGAGGGCTCCTGTCTACTGGAAGACCATGAATGGCCTTCCTCCTAGTTCT                         GGGGAGAAGTTAAAGCTTTTCTACAATCCAGTAGCTAGCAAACTTGTTCCA
genomic: GGAGGGCTCCTGTCTACTGGAAGACCATGAATGGCCTTCCTCCTAGTTCTgtatgtttgt ... atttttacagGGGGAGAAGTTAAAGCTTTTCTACAATCCAGTAGCTAGCAAACTTGTTCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cattttcccttggttttattattccgttaatgatgtgcttgaaaaatttttacagGGGGAGAAGTTAAAGCTTTTCTACAATCCAGTAGCTAGCAAACTTGTTCCAAATGAAGATTTTGGGATTGGTTTTAATG
                        cgttaat  putative branch site (score: 4)
                                              tttttac  putative PPT
                                      ttgaaaaatttttaca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtttgtcttggttgttgattttaggaactcggttgcattttcccttggttttattattccgttaatgatgtgcttgaaaaatttttacagGGGGAGAAGTTAAAGCTTTTCTACAATCCAGTAGCTAGCAAACTTGTTCCAAATGAAGATTTTGGGATTGGTTTTAATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA