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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtagaatttcccgtcaagagaatgcattttgctctgttttggctgtatggtttagtttcagtatgttttaattccatttttgtttgatgtttttcttagGACTAAGTTAAGGAGATGGCTAGTGGTGAGGGAAAAAAGTCTGGTGAGGGAAAAAAGGCTAATGCCAATGCAAAGGGTG

Basic information

species Vitis vinifera
transcript Vv07s0005g02620.t01
intron # 1
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|352787275|gb|FQ477895.1|FQ477895
EST:     TTTTCCCTCCCCTGTCTCTGCCTCCGCCGCCAG                         GACTAAGTTAAGGAGATGGCTAGTGGTGAAGGG-AAAAAGTCTGGTGAGGG
genomic: TTTTCCCTCCCCTGTCTCTGCCTCCGCCGCCAGgtatgcacag ... tttttcttagGACTAAGTTAAGGAGATGGCTAGTGGTG-AGGGAAAAAAGTCTGGTGAGGG
EST: gi|161715595|gb|FC068351.1|FC068351
EST:     AAACGAGTTCCTCAGTGTTTTCCCTCCCCTGTCTCTGCCTCCGCCGCCAG                         GACTAAGTTAAGGAGATGGCTAGTGGTGAGGGAAAAAAGTCTGGTGAGGGA
genomic: AAACGAGTTCCTCAGTGTTTTCCCTCCCCTGTCTCTGCCTCCGCCGCCAGgtatgcacag ... tttttcttagGACTAAGTTAAGGAGATGGCTAGTGGTGAGGGAAAAAAGTCTGGTGAGGGA
EST: gi|110712760|gb|EE088090.1|EE088090
EST:     AAACGAGTTCCTCAGCGTTTTTCCT-CCC-GTCTCTGCCTCCGCCGCCAG                         GACTAAGTTAAGGAGATGGCTAGTGGTGAGGGAAAAAAGTCTGGTGAGGGA
genomic: AAACGAGTTCCTCAGTGTTTTCCCTCCCCTGTCTCTGCCTCCGCCGCCAGgtatgcacag ... tttttcttagGACTAAGTTAAGGAGATGGCTAGTGGTGAGGGAAAAAAGTCTGGTGAGGGA
EST: gi|29784140|gb|CB344515.2|CB344515
EST:     AAACGAGTTCCTCAGTGTTTTCCCTCCCCTGTCTCTGCCTCCGCCGCCAG                         GACTAAGTTAAGGAGATGGCTAGTGGTGAGGGAAAAAAGTCTGGTGAGGGA
genomic: AAACGAGTTCCTCAGTGTTTTCCCTCCCCTGTCTCTGCCTCCGCCGCCAGgtatgcacag ... tttttcttagGACTAAGTTAAGGAGATGGCTAGTGGTGAGGGAAAAAAGTCTGGTGAGGGA
EST: gi|110712013|gb|EE089150.1|EE089150
EST:     AAACGAGTTCCTCAGCGTTTTTCCT-CCC-GTCTCTGCCTCCGCCGCCAG                         GACTAAGTTAAGGAGATGGCTAGTGGTGAGGGAAAAAAGTCTGGTGAGGGA
genomic: AAACGAGTTCCTCAGTGTTTTCCCTCCCCTGTCTCTGCCTCCGCCGCCAGgtatgcacag ... tttttcttagGACTAAGTTAAGGAGATGGCTAGTGGTGAGGGAAAAAAGTCTGGTGAGGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtatggtttagtttcagtatgttttaattccatttttgtttgatgtttttcttagGACTAAGTTAAGGAGATGGCTAGTGGTGAGGGAAAAAAGTCTGGTGAGGGAAAAAAGGCTAATGCCAATGCAAAGGGTG
                                           tgtttttctt  CT-rich tract
                     ttttaattccattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtagaatttcccgtcaagagaatgcattttgctctgttttggctgtatggtttagtttcagtatgttttaattccatttttgtttgatgtttttcttagGACTAAGTTAAGGAGATGGCTAGTGGTGAGGGAAAAAAGTCTGGTGAGGGAAAAAAGGCTAATGCCAATGCAAAGGGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - cccgtca
- - - - - - - - - - gaatgca
- - - - - - - - - - - - - - - - - - - - - - tgtatgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cagtatg