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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taatggaatttaattgtagtagtaaattgtttgtaattacttcttaatttgccattttcttcttgtcctgacttgaaattaatggtgattaatcggtcagGGTGTGTTTGATGGTCCGTGCGGCACGCGGCTGGATCATGGCGTGACGGCCGTTGGATACGGGACGGCCAGCAAGGGACACGATTACATCATCGTGAAGA

Basic information

species Oryza sativa
transcript LOC_Os01g73980.1
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|88972969|gb|CI019588.1|CI019588
EST:     TCAGCGTCGCCATCGAGGCCTCAGGCAGGAACTTCCAGTTCTACAGCGGG                         GGTGTGTTTGATGGTCCGTGCGGCACGCGGCTGGATCATGGCGTGACGGCC
genomic: TCAGCGTCGCCATCGAGGCCTCAGGCAGGAACTTCCAGTTCTACAGCGGGgtatgaaaca ... aatcggtcagGGTGTGTTTGATGGTCCGTGCGGCACGCGGCTGGATCATGGCGTGACGGCC
EST: gi|86251628|gb|CI016917.1|CI016917
EST:     TCAGCGTCGCCATCGAGGCCTCAGGCAGGAACTTCCAGTTCTACAGCGGG                         GGTGTGTTTGATGGTCCGTGCGGCACGCGGCTGGATCATGGCGTGACGGCC
genomic: TCAGCGTCGCCATCGAGGCCTCAGGCAGGAACTTCCAGTTCTACAGCGGGgtatgaaaca ... aatcggtcagGGTGTGTTTGATGGTCCGTGCGGCACGCGGCTGGATCATGGCGTGACGGCC
EST: gi|38471694|gb|CF955825.1|CF955825
EST:     TCAGCGTCGCCATCGAGGCCTCAGGCAGGAACTTCCAGTTCTACAGCGGG                         GGTGTGTTTGATGGTCCGTGCGGCACGCGGCTGGATCATGGCGTGACGGCC
genomic: TCAGCGTCGCCATCGAGGCCTCAGGCAGGAACTTCCAGTTCTACAGCGGGgtatgaaaca ... aatcggtcagGGTGTGTTTGATGGTCCGTGCGGCACGCGGCTGGATCATGGCGTGACGGCC
EST: gi|89172697|gb|CI022576.1|CI022576
EST:     TCAGCGTCGCCATCGAGGCCTCAGGCAGGAACTTCCAGTTCTACAGCGGG                         GGTGTGTTTGATGGTCCGTGCGGCACGCGGCTGGATCATGGCGTGACGGCC
genomic: TCAGCGTCGCCATCGAGGCCTCAGGCAGGAACTTCCAGTTCTACAGCGGGgtatgaaaca ... aatcggtcagGGTGTGTTTGATGGTCCGTGCGGCACGCGGCTGGATCATGGCGTGACGGCC
EST: gi|89168933|gb|CI020473.1|CI020473
EST:     TCAGCGTCGCCATCGAGGCCTCAGGCAGGAACTTCCAGTTCTACAGCGGG                         GGTGTGTTTGATGGTCCGTGCGGCACGCGGCTGGATCATGGCGTGACGGCC
genomic: TCAGCGTCGCCATCGAGGCCTCAGGCAGGAACTTCCAGTTCTACAGCGGGgtatgaaaca ... aatcggtcagGGTGTGTTTGATGGTCCGTGCGGCACGCGGCTGGATCATGGCGTGACGGCC
EST: gi|86261298|gb|CI014365.1|CI014365
EST:     TCAGCGTCGCCATCGAGGCCTCAGGCAGGAACTTCCAGTTCTACAGCGGG                         GGTGTGTTTGATGGTCCGTGCGGCACGCGGCTGGATCATGGCGTGACGGCC
genomic: TCAGCGTCGCCATCGAGGCCTCAGGCAGGAACTTCCAGTTCTACAGCGGGgtatgaaaca ... aatcggtcagGGTGTGTTTGATGGTCCGTGCGGCACGCGGCTGGATCATGGCGTGACGGCC
EST: gi|86261270|gb|CI014337.1|CI014337
EST:     TCAGCGTCGCCATCGAGGCCTCAGGCAGGAACTTCCAGTTCTACAGCGGG                         GGTGTGTTTGATGGTCCGTGCGGCACGCGGCTGGATCATGGCGTGACGGCC
genomic: TCAGCGTCGCCATCGAGGCCTCAGGCAGGAACTTCCAGTTCTACAGCGGGgtatgaaaca ... aatcggtcagGGTGTGTTTGATGGTCCGTGCGGCACGCGGCTGGATCATGGCGTGACGGCC
EST: gi|86486660|gb|CI129293.1|CI129293
EST:     TCAGCGTCGCCATCGAGGCCTCAGGCAGGAACTTCCAGTTCTACAGCGGG                         GGTGTGTTTGATGGTCCGTGCGGCACGCGGCTGGATCATGGCGTGACGGCC
genomic: TCAGCGTCGCCATCGAGGCCTCAGGCAGGAACTTCCAGTTCTACAGCGGGgtatgaaaca ... aatcggtcagGGTGTGTTTGATGGTCCGTGCGGCACGCGGCTGGATCATGGCGTGACGGCC
EST: gi|86251766|gb|CI018958.1|CI018958
EST:     TCAGCGTCGCCATCGAGGCCTCAGGCAGGAACTTCCAGTTCTACAGCGGG                         GGTGTGTTTGATGGTCCGTGCGGCACGCGGCTGGATCATGGCGTGACGGCC
genomic: TCAGCGTCGCCATCGAGGCCTCAGGCAGGAACTTCCAGTTCTACAGCGGGgtatgaaaca ... aatcggtcagGGTGTGTTTGATGGTCCGTGCGGCACGCGGCTGGATCATGGCGTGACGGCC
EST: gi|88225222|gb|CI225138.1|CI225138
EST:     CAGGAACTTCCAGTTTTACAGCGGG                         GGTGTGTTTGATGGTCCGTGCGGCACACGGCTGGATCATGGCGTGACGGCC
genomic: CAGGAACTTCCAGTTCTACAGCGGGgtatgaaaca ... aatcggtcagGGTGTGTTTGATGGTCCGTGCGGCACGCGGCTGGATCATGGCGTGACGGCC
EST: gi|88965159|gb|CI009195.1|CI009195
EST:     CATCGAGGCCTCAGGCAGGAACTTCCAGTTCTACAGCGGG                         GGTGTGTTTGATGGTCCGTGCGGCACGCGGCTGGATCATGGCGTGACGGCC
genomic: CATCGAGGCCTCAGGCAGGAACTTCCAGTTCTACAGCGGGgtatgaaaca ... aatcggtcagGGTGTGTTTGATGGTCCGTGCGGCACGCGGCTGGATCATGGCGTGACGGCC
EST: gi|29626397|gb|CB631408.1|CB631408
EST:     TCAGCGTCGCCATCGAGGCCTCAGGCAGGAACTTCCAGTTCTACAGCGGG                         GGTGTGTTTGATGGTCCGTGCGGCACGCGGCTGGATCATGGCGTGACGGCC
genomic: TCAGCGTCGCCATCGAGGCCTCAGGCAGGAACTTCCAGTTCTACAGCGGGgtatgaaaca ... aatcggtcagGGTGTGTTTGATGGTCCGTGCGGCACGCGGCTGGATCATGGCGTGACGGCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatttgccattttcttcttgtcctgacttgaaattaatggtgattaatcggtcagGGTGTGTTTGATGGTCCGTGCGGCACGCGGCTGGATCATGGCGTGACGGCCGTTGGATACGGGACGGCCAGCAAGGGACACGATTACATCATCGTGAAGA
                           ttgaaattaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taatggaatttaattgtagtagtaaattgtttgtaattacttcttaatttgccattttcttcttgtcctgacttgaaattaatggtgattaatcggtcagGGTGTGTTTGATGGTCCGTGCGGCACGCGGCTGGATCATGGCGTGACGGCCGTTGGATACGGGACGGCCAGCAAGGGACACGATTACATCATCGTGAAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA