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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attaggggttgactaagtgttatgaacatgtgaatgcttgggttgacgagttcatgaaaatcctaatgcttttctttatcatgttgttttgtctcactagCTGTTGAATGATAACGGCATGAAGAGGAAAGGAGCTTCCGACCAG

Basic information

species Vitis vinifera
transcript Vv11s0016g03560.t01
intron # 7
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|71871899|gb|DT020954.1|DT020954
EST:     GTTCAAGGGGAGAGGAATTGTATATTTCCTGAAGACCCTGGCCAG                         CTGTTGAATGATAACGGCATGAAGAGGAAAGGAGCTTCCGACCAG
genomic: GTTCAAGGGGAGAGGAATTGTATATTTCCTGAAGACCCTGGCCAGgtatgcttta ... gtctcactagCTGTTGAATGATAACGGCATGAAGAGGAAAGGAGCTTCCGACCAG
EST: gi|30329176|gb|CD012438.1|CD012438
EST:     ATTTCCTGAAGTCCCTGGCCAG                         CTGTTGAATGATAACGGCATGAAGAGGAAAGGAGCTTCCGTCCAG
genomic: ATTTCCTGAAGACCCTGGCCAGgtatgcttta ... gtctcactagCTGTTGAATGATAACGGCATGAAGAGGAAAGGAGCTTCCGACCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acgagttcatgaaaatcctaatgcttttctttatcatgttgttttgtctcactagCTGTTGAATGATAACGGCATGAAGAGGAAAGGAGCTTCCGACCAG
               tcctaat  putative branch site (score: 2)
                                         ttttgtctc  putative PPT
                        ttttctttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attaggggttgactaagtgttatgaacatgtgaatgcttgggttgacgagttcatgaaaatcctaatgcttttctttatcatgttgttttgtctcactagCTGTTGAATGATAACGGCATGAAGAGGAAAGGAGCTTCCGACCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - ggggttg
- - -gggttga
- - - - - - - - - - - - - catgtga
- - - - - - - - - - - - - - - - - - - - - - - - - - - -gaaaatc