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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactattatttaagaagcattattgtgaataacagaaggcagattaggttttgtttcaggaattaggcatacttctttcattgttctgaatctgatatgttaatcaacagcagTGATGCTGACACTGACACCCAGATCGAAGTGCCGTCGCTGCAGAACGTCTGCTGGTTAGAGATCCATGGGAAGCTTGAACGGTCCTATCTTACACCAGGA

Basic information

species Oryza sativa
transcript LOC_Os01g06500.2
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|86415864|gb|CI029875.1|CI029875
EST:     TGGAGTGAAGACCCCAGATTCTGGACTTGGAAACCTCTGAAAGAAGGAAGCAG                       
genomic: TGGAGTGAAGACCCCAGATTCTGGACTTGGAAACCTCTGAAAGAAGG-A--AGgtactattat ... tcaacagc
EST: gi|117243502|gb|CT843098.1|CT843098
EST:     TGGAGTGAAGACCCCAGATTCTGGACTTGGGAACCTCTGAAAGAAGGAAG                         TGATGCTGACACTGACACCCAGATCGAAGTGCCGTCGCTGCAGAACGTCTG
genomic: TGGAGTGAAGACCCCAGATTCTGGACTTGGAAACCTCTGAAAGAAGGAAGgtactattat ... tcaacagcagTGATGCTGACACTGACACCCAGATCGAAGTGCCGTCGCTGCAGAACGTCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggaattaggcatacttctttcattgttctgaatctgatatgttaatcaacagcagTGATGCTGACACTGACACCCAGATCGAAGTGCCGTCGCTGCAGAACGTCTGCTGGTTAGAGATCCATGGGAAGCTTGAACGGTCCTATCTTACACCAGGA
                                       tgttaat  putative branch site (score: 3)
                                    atatgttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactattatttaagaagcattattgtgaataacagaaggcagattaggttttgtttcaggaattaggcatacttctttcattgttctgaatctgatatgttaatcaacagcagTGATGCTGACACTGACACCCAGATCGAAGTGCCGTCGCTGCAGAACGTCTGCTGGTTAGAGATCCATGGGAAGCTTGAACGGTCCTATCTTACACCAGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC