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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttatgaattagtaatggatgaaatttcacatttgtgcttgtagatagtgcaattctctctcttataaaatttgaaatatggtgtttgcattttatttcagGGTTTACATTTACGGAAGTCAGCTCCGTTAGAGCGAGTGCAAGTAAAGTTATCTGTTGCCACTTCTCATCAGATGGAAAACTGCTTGCTAGTGGTGGCCA

Basic information

species Vitis vinifera
transcript Vv04s0008g04890.t01
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0008g04890.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GLYMA17G30910.1 (Glycine max), 3'ss of exon 12
ttatgaattagtaatggatgaaatttcacatttgtgcttgtaga-tagtgcaatt--ctctctcttataaaatttgaaatatggtgtttgcattttatttcagGGTTTACATTTACGGAAGTCAGCTCCGTTAGAGCGAGTGCAAGTAAAGTTATCTGTTGCCACTTCTCATCAGATGGAAAACTGCTTGCTAGTGGTGGCCA
 |     ||     | | || | | |  |  ||    || | || | |   || |   | |  ||  |||||||      ||||   ||  ||||  ||||||| || |||||| | ||| | |  || ||  | || ||  | |  ||||||  ||||||||| || ||||| ||||| ||| |||||||||||||||||||
-tgctttttttatgtaggtggattgttgctctttaatttattgacttgcataaatagatattactgctaaaattgaggccatgga--ttcaatttattttcagGTTTCACATTTTCTGAAATAAATTCTGTACGTGCAAGCACTACCAAAGTTGGCTGTTGCCATTTTTCATCTGATGGGAAATTGCTTGCTAGTGGTGGCCA
















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|110711263|gb|EE087569.1|EE087569
EST:     TGATACAGACCCTAGAGATACAGTTGGTCGTTGTATGGATGTCAGTAAAG                         GGTTTACATTTACGGAAGTCAGCTCCGTTAGAGCGAGTGCAAGTAAAGTTA
genomic: TGATACAGACCCTAGAGATACAGTTGGTCGTTGTATGGATGTCAGTAAAGgtgaggtgat ... tttatttcagGGTTTACATTTACGGAAGTCAGCTCCGTTAGAGCGAGTGCAAGTAAAGTTA
EST: gi|56408846|gb|CX017098.1|CX017098
EST:     TGATACAGACCCTAGAGATACAGTTGGTCGTTGTATGGATGTCAGTAAAG                         GGTTTACATTTACGGAAGTCAGCTCCGTTCGAGCGAGTGCAAGTAAAGTTA
genomic: TGATACAGACCCTAGAGATACAGTTGGTCGTTGTATGGATGTCAGTAAAGgtgaggtgat ... tttatttcagGGTTTACATTTACGGAAGTCAGCTCCGTTAGAGCGAGTGCAAGTAAAGTTA
EST: gi|56408912|gb|CX017164.1|CX017164
EST:     TGATACAGACCCTAGAGATACAGTTGGTCGTTGTATGGATGTCAGTAAAG                         GGTTTACATTTACGGAAGTCAGCTCCGTTCGAGCGAGTGCAAGTAAAGTTA
genomic: TGATACAGACCCTAGAGATACAGTTGGTCGTTGTATGGATGTCAGTAAAGgtgaggtgat ... tttatttcagGGTTTACATTTACGGAAGTCAGCTCCGTTAGAGCGAGTGCAAGTAAAGTTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtgcaattctctctcttataaaatttgaaatatggtgtttgcattttatttcagGGTTTACATTTACGGAAGTCAGCTCCGTTAGAGCGAGTGCAAGTAAAGTTATCTGTTGCCACTTCTCATCAGATGGAAAACTGCTTGCTAGTGGTGGCCA
                                            ttttatttc  CT-rich tract
            tctcttataaaatttg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttatgaattagtaatggatgaaatttcacatttgtgcttgtagatagtgcaattctctctcttataaaatttgaaatatggtgtttgcattttatttcagGGTTTACATTTACGGAAGTCAGCTCCGTTAGAGCGAGTGCAAGTAAAGTTATCTGTTGCCACTTCTCATCAGATGGAAAACTGCTTGCTAGTGGTGGCCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - tggatga
- - - - - - - - - - - - - - - - -gtgcttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgaaata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtttgc