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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cgcttacttcagtagcctagctatattcagtgatgaagcctttactgttccgtttcattctttgacgatatcatgtgagtgattgttcttttgctttcagGCTACGGCATGGAGGTCAGTGGCTTCATGAAAG

Basic information

species Oryza sativa
transcript LOC_Os05g29974.1
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|88342813|gb|CI640146.1|CI640146
EST:     CTGGCTTCCTGCTTCTTCCTCCCCCAAGGCGCTCATCTTCCTTTGCCATG                         GCTACGGCATGGAGGTCAGTGGCTTCATGAAAG
genomic: CTGGCTTCCTGCTTCTTCCTCCCCCAAGGCGCTCATCTTCCTTTGCCATGgtaggtacac ... ttgctttcagGCTACGGCATGGAGGTCAGTGGCTTCATGAAAG
EST: gi|88356078|gb|CI627526.1|CI627526
EST:     CTGGCTTCCTGCTTCTTCCTCCCCCAAGGCGCTCATCTTCCTTTGCCATG                         GCTACGGCATGGAGGTCAGTGGCTTCATGAAAG
genomic: CTGGCTTCCTGCTTCTTCCTCCCCCAAGGCGCTCATCTTCCTTTGCCATGgtaggtacac ... ttgctttcagGCTACGGCATGGAGGTCAGTGGCTTCATGAAAG
EST: gi|88368238|gb|CI575120.1|CI575120
EST:     CTGGCTTCCTGCTTCTTCCTCCCCCAAGGCGCTCATCTTCCTTTGCCATG                         GCTACGGCATGGAGGTCAGTGGCTTCATGAAAG
genomic: CTGGCTTCCTGCTTCTTCCTCCCCCAAGGCGCTCATCTTCCTTTGCCATGgtaggtacac ... ttgctttcagGCTACGGCATGGAGGTCAGTGGCTTCATGAAAG
EST: gi|88760430|gb|CI769986.1|CI769986
EST:     CTGGCTTCCTGCTTCTTCCTCCCCCAAGGCGCTCATCTTCCTTTGCCATG                         GCTACGGCATGGAGGTCAGTGGCTTCATGAAAG
genomic: CTGGCTTCCTGCTTCTTCCTCCCCCAAGGCGCTCATCTTCCTTTGCCATGgtaggtacac ... ttgctttcagGCTACGGCATGGAGGTCAGTGGCTTCATGAAAG
EST: gi|29656345|gb|CB652620.1|CB652620
EST:     CTGGCTTCCTGCTTCTTCCTCCCCCAAGGCGCTCATCTTCCTTTGCCATG                         GCTACGGCATGGAGGTCAGTGGCTTCATGAAAG
genomic: CTGGCTTCCTGCTTCTTCCTCCCCCAAGGCGCTCATCTTCCTTTGCCATGgtaggtacac ... ttgctttcagGCTACGGCATGGAGGTCAGTGGCTTCATGAAAG
EST: gi|88743266|gb|CI766774.1|CI766774
EST:     CTGGCTTCCTGCTTCTTCCTCCCCCAAGGCGCTCATCTTCCTTTGCCATG                         GCTACGGCATGGAGGTCAGTGGCTTCATGAAAG
genomic: CTGGCTTCCTGCTTCTTCCTCCCCCAAGGCGCTCATCTTCCTTTGCCATGgtaggtacac ... ttgctttcagGCTACGGCATGGAGGTCAGTGGCTTCATGAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttccgtttcattctttgacgatatcatgtgagtgattgttcttttgctttcagGCTACGGCATGGAGGTCAGTGGCTTCATGAAAG
              ctttgac  putative branch site (score: 4)
                                     ttgttcttttgctttc  putative PPT
       tttcatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cgcttacttcagtagcctagctatattcagtgatgaagcctttactgttccgtttcattctttgacgatatcatgtgagtgattgttcttttgctttcagGCTACGGCATGGAGGTCAGTGGCTTCATGAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG