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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCGTATCTTCAACCAGACAAGGAATCCGATTTCGATGCAGAGCTTAATTTGCCAGCTGCACCTACCGCTCCTGCAGCAGTCCCAGTAAGCAGGCAGCAGgttagtttatattattgttatttttattcagatgcttgctttgtcatgatgattcgagaactatctagtcccatgtatgtactagaggaatgaatgatga...

Basic information

species Oryza sativa
transcript LOC_Os01g01350.1
intron # 6
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|117215705|gb|CT861534.1|CT861534
EST:     TGCCAGCTGCACCTACCGCTCCTGCAGCAGTCCCAGTAAGCAGGCAGCAG                         GTGGATGAGCTAGGATTGCCAGCAGTCCCTCGAGCATCAATCCGCAGTTAG
genomic: TGCCAGCTGCACCTACCGCTCCTGCAGCAGTCCCAGTAAGCAGGCAGCAGgttagtttat ... tctggtgcagGTGGATGAGCTAGGATTGCCAGCAGTCCCTCGAGCATCAATCCGCAGTTAG
EST: gi|88532305|gb|CI461783.1|CI461783
EST:     TACCGCTCCTGCACCAGTCCCATTAAGCAGGCAGCAG                         GTGGATGAGCTAGGATTGCCAGCAGTCCCTCGAGCATCAATCCGCAGTTAG
genomic: TACCGCTCCTGCAGCAGTCCCAGTAAGCAGGCAGCAGgttagtttat ... tctggtgcagGTGGATGAGCTAGGATTGCCAGCAGTCCCTCGAGCATCAATCCGCAGTTAG
EST: gi|33803103|gb|CF327422.1|CF327422
EST:     TGCCAGCTGCACCTACCGCTCCTGCAGCAGTCCCAGTAAGCAGGCAGCAG                         GTGGATGAGCTAGGATTGCCAGCAGTCCCTCGAGCATCAATCCGCAGTTAG
genomic: TGCCAGCTGCACCTACCGCTCCTGCAGCAGTCCCAGTAAGCAGGCAGCAGgttagtttat ... tctggtgcagGTGGATGAGCTAGGATTGCCAGCAGTCCCTCGAGCATCAATCCGCAGTTAG
EST: gi|88532022|gb|CI461477.1|CI461477
EST:     TGCCAGCTGCACCTACCGCTCCTNCAGCAGTCCCAGTAAGCAGGCAGCAG                         GTGGATGAGGTAGGATTGCCAGCAGTCCCTCGAGCATCAATCCGCAGTTAG
genomic: TGCCAGCTGCACCTACCGCTCCTGCAGCAGTCCCAGTAAGCAGGCAGCAGgttagtttat ... tctggtgcagGTGGATGAGCTAGGATTGCCAGCAGTCCCTCGAGCATCAATCCGCAGTTAG
EST: gi|88532113|gb|CI461575.1|CI461575
EST:     CCTGCACCAGTCCCANTAAGCAGGCAGCAG                         GTGGATGAGCTAGGATTGCCAGCAGTCCCTCGAGCATCAATCCGCAGTTAG
genomic: CCTGCAGCAGTCCCAGTAAGCAGGCAGCAGgttagtttat ... tctggtgcagGTGGATGAGCTAGGATTGCCAGCAGTCCCTCGAGCATCAATCCGCAGTTAG
EST: gi|88557001|gb|CI487372.1|CI487372
EST:     CAGTCCCAGTAAGCAGGCAGCAG                         GTGGATGAGCTAGGATTGCCAGCAGTCCCTCGAGCATCAATCCGCAGTTAG
genomic: CAGTCCCAGTAAGCAGGCAGCAGgttagtttat ... tctggtgcagGTGGATGAGCTAGGATTGCCAGCAGTCCCTCGAGCATCAATCCGCAGTTAG
EST: gi|88218574|gb|CI218423.1|CI218423
EST:     TGCCAGCTGCACCTACCGCTCCTGCAGCAGTCCCAGTAAGCAGGCAGCAG                         GTGGATGAGCTAGGATTGCCAGCAGTCCCTCGAGCATCAATCCGCAGTTAG
genomic: TGCCAGCTGCACCTACCGCTCCTGCAGCAGTCCCAGTAAGCAGGCAGCAGgttagtttat ... tctggtgcagGTGGATGAGCTAGGATTGCCAGCAGTCCCTCGAGCATCAATCCGCAGTTAG
EST: gi|88551594|gb|CI481665.1|CI481665
EST:     CAGTCCCAGTAAGCAGGCAGCAG                         GTGGATGAGCTAGGATTGCCAGCAGTCCCTCGAGCATCAATCCGCAGTTAG
genomic: CAGTCCCAGTAAGCAGGCAGCAGgttagtttat ... tctggtgcagGTGGATGAGCTAGGATTGCCAGCAGTCCCTCGAGCATCAATCCGCAGTTAG
EST: gi|88534217|gb|CI462923.1|CI462923
EST:     GCACCTACCGCTCCTGCAGCAGTCCCAGTAAGCAGGCAGCAG                         GTGGATGAGCTAGGATTGCCAGCAGTCCCTCGAGCATCAATCCGCAGTTAG
genomic: GCACCTACCGCTCCTGCAGCAGTCCCAGTAAGCAGGCAGCAGgttagtttat ... tctggtgcagGTGGATGAGCTAGGATTGCCAGCAGTCCCTCGAGCATCAATCCGCAGTTAG
EST: gi|88528837|gb|CI457106.1|CI457106
EST:     GCTCCTGCAGCAGTCCCAGTAAGCAGGCAGCAG                         GTGGATGAGCTAGGATTGCCAGCAGTCCCTCGAGCATCAATCCGCAGTTAG
genomic: GCTCCTGCAGCAGTCCCAGTAAGCAGGCAGCAGgttagtttat ... tctggtgcagGTGGATGAGCTAGGATTGCCAGCAGTCCCTCGAGCATCAATCCGCAGTTAG
EST: gi|86511478|gb|CI154111.1|CI154111
EST:     TGCCAGCTGCACCTACCGCTCCTGCAGCAGTCCCAGTAAGCAGGCAGCAG                         GTGGATGAGCTAGGATTGCCAGCAGTCCCTCGAGCATCAATCCGCAGTTAG
genomic: TGCCAGCTGCACCTACCGCTCCTGCAGCAGTCCCAGTAAGCAGGCAGCAGgttagtttat ... tctggtgcagGTGGATGAGCTAGGATTGCCAGCAGTCCCTCGAGCATCAATCCGCAGTTAG

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: 65 (upstream exon), 18 (downstream exon)
Score: 2

ATCGTATCTTCAACCAGACAAGGAATCCGATTTCGATGCAGAGCTTAATTTGCCAGCTGCACCTACCGCTCCTGCAGCAGTCCCAGTAAGCAGGCAGCAGgttagtttat ... tctggtgcagGTGGATGAGCTAGGATTGCCAGCAGTCCCTCGAGCATCAATCCGCAGTTAGAACAGTAATTCATGTACCTTTGCTTGTGATTGGCATTGACGTGAGAACC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATCGTATCTTCAACCAGACAAGGAATCCGATTTCGATGCAGAGCTTAATTTGCCAGCTGCACCTACCGCTCCTGCAGCAGTCCCAGTAAGCAGGCAGCAGgttagtttatattattgttatttttattcagatgcttgctttgtcatgatgattcgagaactatctagtcccatgtatgtactagaggaatgaatgatga

- - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG