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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCCGCAATGGGTGAAAATTCTGGATTGCAAGAAAATCATGTAGGATCTGTTATGGATCTGGACAATATGGGGCATGACTTTTCACTAAAGGAATGCAGTgtaagtccatatagaagtttccacttgtcttcagacacttgtcagatgacttgtgtttctcttaattccacaatgtagcatgctatacagtacttgcactattttattcagtcgttatttgaagtccatggcataattggtatgctgttcacattgcag

Basic information

species Oryza sativa
transcript LOC_Os01g67250.1
intron # 10
splice site 5'
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|29625772|gb|CB630783.1|CB630783
EST:     TTATGGATCTGGACAATATGGGGCATGACTTTTCACTAAAGGAATGCAGT                         GATTTTGGCAGTGCGATTCAGGGTGTTGACACAG
genomic: TTATGGATCTGGACAATATGGGGCATGACTTTTCACTAAAGGAATGCAGTgtaagtccat ... cacattgcagGATTTTGGCAGTGCGATTCAGGGTGTTGACACAG
EST: gi|58593960|gb|CF992268.1|CF992268
EST:     TTATGGATCTGGACAATATGGGGCATGACTTTTCACTAAAGGAATGCAGT                         GATTTTGGCAGTGCGATTCAGGGTGTTGACACAG
genomic: TTATGGATCTGGACAATATGGGGCATGACTTTTCACTAAAGGAATGCAGTgtaagtccat ... cacattgcagGATTTTGGCAGTGCGATTCAGGGTGTTGACACAG
EST: gi|29629880|gb|CB634889.1|CB634889
EST:     TTATGGATCTGGACAATATGGGGCATGACTTTTCACTAAAGGAATGCAGT                         GATTTTGGCAGTGCGATTCAGGGTGTTGACACAG
genomic: TTATGGATCTGGACAATATGGGGCATGACTTTTCACTAAAGGAATGCAGTgtaagtccat ... cacattgcagGATTTTGGCAGTGCGATTCAGGGTGTTGACACAG
EST: gi|29678405|gb|CB674680.1|CB674680
EST:     TTATGGATCTGGACAATATGGGGCATGACTTTTCACTAAAGGAATGCAGT                         GATTTTGGCAGTGCGATTCAGGGTGTTGACACAG
genomic: TTATGGATCTGGACAATATGGGGCATGACTTTTCACTAAAGGAATGCAGTgtaagtccat ... cacattgcagGATTTTGGCAGTGCGATTCAGGGTGTTGACACAG
EST: gi|29630218|gb|CB635227.1|CB635227
EST:     TTATGGATCTGGACAATATGGGGCATGACTTTTCACTAAAGGAATGCAGT                         GATTTTGGCAGTGCGATTCAGGGTGTTGACACAG
genomic: TTATGGATCTGGACAATATGGGGCATGACTTTTCACTAAAGGAATGCAGTgtaagtccat ... cacattgcagGATTTTGGCAGTGCGATTCAGGGTGTTGACACAG
EST: gi|218495650|gb|FG950472.1|FG950472
EST:     TCATGGATCTGGACAATATGGGGCATGACTTTTCACTAAAGGAATGCAGT                         GATTTTGGCAGTGCGATTCAGGGTGTTGACACAG
genomic: T-ATGGATCTGGACAATATGGGGCATGACTTTTCACTAAAGGAATGCAGTgtaagtccat ... cacattgcagGATTTTGGCAGTGCGATTCAGGGTGTTGACACAG
EST: gi|29630627|gb|CB635636.1|CB635636
EST:     TTATGGATCTGGACAATATGGGGCATGACTTTTCACTAAAGGAATGCAGT                         GATTTTGGCAGTGCGATTCAGGGTGTTGACACAG
genomic: TTATGGATCTGGACAATATGGGGCATGACTTTTCACTAAAGGAATGCAGTgtaagtccat ... cacattgcagGATTTTGGCAGTGCGATTCAGGGTGTTGACACAG
EST: gi|218479724|gb|FG953391.1|FG953391
EST:     TTATGGATCTGGACAATATGGGGCATGACTTTTCACTAAAGGAATGCAGT                         GATTTTGGCAGTGCGATTCAGGGTGTTGACACAG
genomic: TTATGGATCTGGACAATATGGGGCATGACTTTTCACTAAAGGAATGCAGTgtaagtccat ... cacattgcagGATTTTGGCAGTGCGATTCAGGGTGTTGACACAG
EST: gi|86481978|gb|CI124611.1|CI124611
EST:     TTATGGATCTGGACAATATGGGGCATGACTTTTCACTAAAGGAATGCAGT                         GATTTTGGCAGTGCGATTCAGGGTGTTGACACAG
genomic: TTATGGATCTGGACAATATGGGGCATGACTTTTCACTAAAGGAATGCAGTgtaagtccat ... cacattgcagGATTTTGGCAGTGCGATTCAGGGTGTTGACACAG
EST: gi|58609260|gb|CK037293.1|CK037293
EST:     TTATGGATCTGGACAATATGGGGCATGACTTTTCACTAAAGGAATGCAGT                         GATTTTGGCAGTGCGATTCAGGGTGTTGACACAG
genomic: TTATGGATCTGGACAATATGGGGCATGACTTTTCACTAAAGGAATGCAGTgtaagtccat ... cacattgcagGATTTTGGCAGTGCGATTCAGGGTGTTGACACAG
EST: gi|33796069|gb|CF323901.1|CF323901
EST:     TTATGGATCTGGACAATATGGGGCATGACTTTTCACTAAAGGAATGCAGT                         GATTTTGGCAGTGCGATTCAGGGTGTTGACACAG
genomic: TTATGGATCTGGACAATATGGGGCATGACTTTTCACTAAAGGAATGCAGTgtaagtccat ... cacattgcagGATTTTGGCAGTGCGATTCAGGGTGTTGACACAG
EST: gi|58683098|gb|CK071785.1|CK071785
EST:     TTATGGATCTGGACAATATGGGGCATGACTTTTCACTAAAGGAATGCAGT                         GATTTTGGCAGTGCGATTCAGGGTGTTGACACAG
genomic: TTATGGATCTGGACAATATGGGGCATGACTTTTCACTAAAGGAATGCAGTgtaagtccat ... cacattgcagGATTTTGGCAGTGCGATTCAGGGTGTTGACACAG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 62 (upstream exon), 50 (downstream exon)
Score: 36

GTCCGCAATGGGTGAAAATTCTGGATTGCAAGAAAATCATGTAGGATCTGTTATGGATCTGGACAATATGGGGCATGACTTTTCACTAAAGGAATGCAGTgtaagtccat ... cacattgcagGATTTTGGCAGTGCGATTCAGGGTGTTGACACAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCCGCAATGGGTGAAAATTCTGGATTGCAAGAAAATCATGTAGGATCTGTTATGGATCTGGACAATATGGGGCATGACTTTTCACTAAAGGAATGCAGTgtaagtccatatagaagtttccacttgtcttcagacacttgtcagatgacttgtgtttctcttaattccacaatgtagcatgctatacagtacttgcactattttattcagtcgttatttgaagtccatggcataattggtatgctgttcacattgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA