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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttgaaacctgtccctatttgtttattcaagcttatatgttaacataatgagtaatgccattcttttcacttgtgaacagGAATCATACATGAATTTGTCTGATGCAACCTTCAAG

Basic information

species Oryza sativa
transcript LOC_Os07g23200.1
intron # 8
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|58685723|gb|CK074410.1|CK074410
EST:     AACTAACATCATTCGGCATCATGAGTCAGAATAATTTGTCATCACTTGAG                         GAATCATACATGAATTTGTCTGATGCAACCTTCAAG
genomic: AACTAACATCATTCGGCATCATGAGTCAGAATA-TTTGTCATCACTTGAGgttgaaacct ... ttgtgaacagGAATCATACATGAATTTGTCTGATGCAACCTTCAAG
EST: gi|86528479|gb|CI168685.1|CI168685
EST:     TAACTAACATCATTCGGCATCATGAGTCAGAATATTTGTCATCACTTGAG                         GAATCATACATGAATTTGTCTGATGCAACCTTCAAG
genomic: TAACTAACATCATTCGGCATCATGAGTCAGAATATTTGTCATCACTTGAGgttgaaacct ... ttgtgaacagGAATCATACATGAATTTGTCTGATGCAACCTTCAAG
EST: gi|86494262|gb|CI136895.1|CI136895
EST:     TAACTAACATCATTCGGCATCATGAGTCAGAATATTTGTCATCACTTGAG                         GAATCATACATGAATTTGTCTGATGCAACCTTCAAG
genomic: TAACTAACATCATTCGGCATCATGAGTCAGAATATTTGTCATCACTTGAGgttgaaacct ... ttgtgaacagGAATCATACATGAATTTGTCTGATGCAACCTTCAAG
EST: gi|27547453|gb|CA765564.2|CA765564
EST:     TAACTAACATCATTCGGCATCATGAGTCAGAATATTTGTCATCACTTGAG                         GAATCATACATGAATTTGTCTGATGCAACCTTCAAG
genomic: TAACTAACATCATTCGGCATCATGAGTCAGAATATTTGTCATCACTTGAGgttgaaacct ... ttgtgaacagGAATCATACATGAATTTGTCTGATGCAACCTTCAAG

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: 64 (upstream exon), 12 (downstream exon)
Score: 1

TCTCCTGAGGAATGTGCAGTATCAATAACTAACATCATTCGGCATCATGAGTCAGAATATTTGTCATCACTTGAGgttgaaacct ... ttgtgaacagGAATCATACATGAATTTGTCTGATGCAACCTTCAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcaagcttatatgttaacataatgagtaatgccattcttttcacttgtgaacagGAATCATACATGAATTTGTCTGATGCAACCTTCAAG
            tgttaac  putative branch site (score: 1)
                                ccattcttttcactt  putative PPT
       ttatatgttaacataa  TA-rich tract