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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatctgatgctttttcatgatgcaattagtgttttgtgttgacttaaataaatatcgtcacctgcttattcagtgattactgatcgtaatactacgtggtttgttttctgcagGTCATGGTGGAGCTCGAGCAGCAGAATTCGTCAAGCAGAACCTCTTCACCAATTTAATCAAGCACCCAAAGTTATTCAGTGATACCAAGTCTGCAATTG

Basic information

species Oryza sativa
transcript LOC_Os06g48300.1
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|33680920|gb|CF309159.1|CF309159
EST:     AATTGATGGTGTCGATGGAGAGACCGTTGGACTGTTTGGTGTCTTTGATG                         GTCATGGTGGAGCTCGAGCAGCAGAATTCGTCAAGCAGAACCTCTTCACCA
genomic: AATTGATGGTGTCGATGGAGAGACCGTTGGACTGTTTGGTGTCTTTGATGgtaatctgat ... ttttctgcagGTCATGGTGGAGCTCGAGCAGCAGAATTCGTCAAGCAGAACCTCTTCACCA
EST: gi|88391402|gb|CI598220.1|CI598220
EST:     AATTGATGGTGTCGATGGAGAGACCGTTGGACTGTTTGGTGTCTTTGATG                         GTCATGGTGGAGCTCGAGCAGCAGAATTCGTCAAGCAGAACCTCTTCACCA
genomic: AATTGATGGTGTCGATGGAGAGACCGTTGGACTGTTTGGTGTCTTTGATGgtaatctgat ... ttttctgcagGTCATGGTGGAGCTCGAGCAGCAGAATTCGTCAAGCAGAACCTCTTCACCA
EST: gi|88377052|gb|CI597836.1|CI597836
EST:     AATTGATGGTGTCGATGGAGAGACCGTTGGACTGTTTGGTGTCTTTGATG                         GTCATGGTGGAGCTCGAGCAGCAGAATTCGTCAAGCAGAACCTCTTCACCA
genomic: AATTGATGGTGTCGATGGAGAGACCGTTGGACTGTTTGGTGTCTTTGATGgtaatctgat ... ttttctgcagGTCATGGTGGAGCTCGAGCAGCAGAATTCGTCAAGCAGAACCTCTTCACCA
EST: gi|218481440|gb|FG958928.1|FG958928
EST:     AATTGATGGTGTCGATGGAGAGACCGTTGGACTGTTTGGTGTCTTTGATG                         GTCATGGTGGAGCTCGAGCAGCAGAATTCGTCAAGCAGAACCTCTTCACCA
genomic: AATTGATGGTGTCGATGGAGAGACCGTTGGACTGTTTGGTGTCTTTGATGgtaatctgat ... ttttctgcagGTCATGGTGGAGCTCGAGCAGCAGAATTCGTCAAGCAGAACCTCTTCACCA
EST: gi|66913181|gb|CX100029.1|CX100029
EST:     AATTGATGGTGTCGATGGAGAGACCGTTGGACTGTTTGGTGTCTTTGATG                         GTCATGGTGGAGCTCGAGCAGCAGAATTCGTCAAGCAGAACCTCTTCACCA
genomic: AATTGATGGTGTCGATGGAGAGACCGTTGGACTGTTTGGTGTCTTTGATGgtaatctgat ... ttttctgcagGTCATGGTGGAGCTCGAGCAGCAGAATTCGTCAAGCAGAACCTCTTCACCA
EST: gi|33682770|gb|CF311009.1|CF311009
EST:     AATTGATGGTGTCGATGGAGAGACCGTTGGACTGTTTGGTGTCTTTGATG                         GTCATGGTGGAGCTCGAGCAGCAGAATTCGTCAAGCAGAACCTCTTCACCA
genomic: AATTGATGGTGTCGATGGAGAGACCGTTGGACTGTTTGGTGTCTTTGATGgtaatctgat ... ttttctgcagGTCATGGTGGAGCTCGAGCAGCAGAATTCGTCAAGCAGAACCTCTTCACCA

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: 75 (upstream exon), 75 (downstream exon)
Score: 38

GCGAGCTCTCCTGGAAAAAGATCCTCCATGGAGGACTTCTATGACACCAGAATTGATGGTGTCGATGGAGAGACCGTTGGACTGTTTGGTGTCTTTGATGgtaatctgat ... ttttctgcagGTCATGGTGGAGCTCGAGCAGCAGAATTCGTCAAGCAGAACCTCTTCACCAATTTAATCAAGCACCCAAAGTTATTCAGTGATACCAAGTCTGCAATTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cacctgcttattcagtgattactgatcgtaatactacgtggtttgttttctgcagGTCATGGTGGAGCTCGAGCAGCAGAATTCGTCAAGCAGAACCTCTTCACCAATTTAATCAAGCACCCAAAGTTATTCAGTGATACCAAGTCTGCAATTG
                   tactgat  putative branch site (score: 38)
                                         tttgttttct  putative PPT
                            taatacta  TA-rich tract