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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAATTTACCCACCTTTTCACCCAATGATTGGATTACAGTTCTATACTTGCGGAAAGCTTGAATGgtatggaatacttttccctattcacctacttactgtgttcatatatcgcggagtaacaactttcattgtccagtataagctttggcctttggctatttca...

Basic information

species Oryza sativa
transcript LOC_Os03g49730.2
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g49730.2 (Oryza sativa), 5'ss of exon 13
lower sequence: GRMZM2G457881_T01 (Zea mays), 5'ss of exon 15
GAATTTACCCACCTTTTCACCCAATGATTGGATTACAGTTCTATACTTGCGGAAAGCTTGAATGgtatggaatacttttccctattcacctacttactgtgttcatatatcgcggagtaacaactttcattgtccagtataagctttggcctttggctatttca--
|| |||| ||||||||||| || |||||||||||||| ||||||||||| ||||||||||||||||||||| || |   || ||   |  ||| |         | | |        | |     ||| || ||||||||||   || ||  ||   | | | |  
GAGTTTATCCACCTTTTCATCCGATGATTGGATTACAATTCTATACTTGTGGAAAGCTTGAATGgtatggactattagcccttacctatttacctcacacaaggaca-acaatcatatgagtttattccttatccagtataaatgtttgctgttaa-tgtcttatg
















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|87029842|gb|CI274523.1|CI274523
EST:     TTTCACCCAATGATTGGATTACAGTTCTATACTTGCGGAAAGCTTGAATG                         GTTGCTTGAGTACACAGAGGATGCTCTGATGTCTTTAACCAGGGCAGCAGA
genomic: TTTCACCCAATGATTGGATTACAGTTCTATACTTGCGGAAAGCTTGAATGgtatggaata ... cctgttgcagGTTGCTTGAGTACACAGAGGATGCTCTGATGTCTTTAACCAGGGCAGCAGA
EST: gi|58684796|gb|CK073483.1|CK073483
EST:     TTTCACCCAATGATTGGATTACAGTTCTATACTTGCGGAAAGCTTGAATG                         GTTGCTTGAGTACACAGAGGATGCTCTGATGTCTTTAACCAGGGCAGCAGA
genomic: TTTCACCCAATGATTGGATTACAGTTCTATACTTGCGGAAAGCTTGAATGgtatggaata ... cctgttgcagGTTGCTTGAGTACACAGAGGATGCTCTGATGTCTTTAACCAGGGCAGCAGA
EST: gi|86426152|gb|CI071249.1|CI071249
EST:     TTTCACCCAATGATTGGATTACAGTTCTATACTTGCGGAAAGCTTGAATG                         GTTGCTTGAGTACACAGAGGATGCTCTGATGTCTTTAACCAGGGCAGCAGA
genomic: TTTCACCCAATGATTGGATTACAGTTCTATACTTGCGGAAAGCTTGAATGgtatggaata ... cctgttgcagGTTGCTTGAGTACACAGAGGATGCTCTGATGTCTTTAACCAGGGCAGCAGA
EST: gi|88908158|gb|CI090754.1|CI090754
EST:     TTTCACCCAATGATTGGATTACAGTTCTATACTTGCGGAAAGCTTGAATG                         GTTGCTTGAGTACACAGAGGATGCTCTGATGTCTTTAACCAGGGCAGCAGG
genomic: TTTCACCCAATGATTGGATTACAGTTCTATACTTGCGGAAAGCTTGAATGgtatggaata ... cctgttgcagGTTGCTTGAGTACACAGAGGATGCTCTGATGTCTTTAACCAGGGCAGCAGA
EST: gi|87029746|gb|CI274427.1|CI274427
EST:     TTTCACCCAATGATTGGATTACAGTTCTATACTTGCGGAAAGCTTGAATG                         GTTGCTTGAGTACACAGAGGATGCTCTGATGTCTTTAACCAGGGCAGCAGA
genomic: TTTCACCCAATGATTGGATTACAGTTCTATACTTGCGGAAAGCTTGAATGgtatggaata ... cctgttgcagGTTGCTTGAGTACACAGAGGATGCTCTGATGTCTTTAACCAGGGCAGCAGA
EST: gi|86259978|gb|CI065851.1|CI065851
EST:     TTTCACCCAATGATTGGATTACAGTTCTATACTTGCGGAAAGCTTGAATG                         GTTGCTTGAGTACACAGAGGATGCTCTGATGTCTTTAACCAGGGCAGCAGA
genomic: TTTCACCCAATGATTGGATTACAGTTCTATACTTGCGGAAAGCTTGAATGgtatggaata ... cctgttgcagGTTGCTTGAGTACACAGAGGATGCTCTGATGTCTTTAACCAGGGCAGCAGA
EST: gi|66918158|gb|CX105006.1|CX105006
EST:     TTT-ACCCAATGATTGGATTACAGTTCTATACTTGCGGAAAGCTTGAATG                         GTTGCTTGAGTACACAGAGGATGCTCTGATGTCTTTAACCAGGGCAGCAGA
genomic: TTTCACCCAATGATTGGATTACAGTTCTATACTTGCGGAAAGCTTGAATGgtatggaata ... cctgttgcagGTTGCTTGAGTACACAGAGGATGCTCTGATGTCTTTAACCAGGGCAGCAGA
EST: gi|88255533|gb|CI354357.1|CI354357
EST:     ACAGTTCTATACTTGCGGAAAGCTTGAATG                         GTTGCTTGAGTACACAGAGGATGCTCTGATGTCTTTAACCAGGGCAGCAGA
genomic: ACAGTTCTATACTTGCGGAAAGCTTGAATGgtatggaata ... cctgttgcagGTTGCTTGAGTACACAGAGGATGCTCTGATGTCTTTAACCAGGGCAGCAGA
EST: gi|7332557|gb|AU085903.1|AU085903
EST:     TTTCACCCAATGATTGGATTACAGTTCTATACTTGCGGAAAGCTTGAATG                         GTTGCTTGAGTACACAGAGGATGCTCTGATGTCTTTAACCAGGGCAGCAGA
genomic: TTTCACCCAATGATTGGATTACAGTTCTATACTTGCGGAAAGCTTGAATGgtatggaata ... cctgttgcagGTTGCTTGAGTACACAGAGGATGCTCTGATGTCTTTAACCAGGGCAGCAGA

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: 71 (upstream exon), 22 (downstream exon)
Score: 2

GAATTTACCCACCTTTTCACCCAATGATTGGATTACAGTTCTATACTTGCGGAAAGCTTGAATGgtatggaata ... cctgttgcagGTTGCTTGAGTACACAGAGGATGCTCTGATGTCTTTAACCAGGGCAGCAGATATACTTCGCATAACGCATGGGACTAAATCCGAGTTCATGAAGGAACTT




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