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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagccaatcaaattattgagtatcttctttgtatttctcttgtgttatttatgtatcatctttgttttcatacatacctgtcttagtgtgagcaaatttttgtggcatattctataaggagtaggcatcttttgaggttcgaatatcttagctgttggtttctgtgtgcagATATGGAAGATCTAAAAGCCTTTGCTAAAGAGTCTGCTTCTCCAGAAGCCAATGACCTGGCTCACTGGGACCTAAGCTTCTGGAGTGAACGACTCCGGGA

Basic information

species Oryza sativa
transcript LOC_Os02g58340.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g58340.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G133919_T01 (Zea mays), 3'ss of exon 7
gtagccaatcaaattattgagtatcttctttgtatttctcttgtgttatttatgtatcatctttgttttcatacatacctgtcttagtgtgagcaaatttttgtggcatattctataaggagtaggcatcttttgaggttcgaatatcttagctgttggtttctgtgtgcagATATGGAAGATCTAAAAGCCTTTGCTAAAGAGTCTGCTTCTCCAGAAGCCAATGACCTGGCTCACTGGGACCTAAGCTTCTGGAGTGAACGACTCCGGGA
                                                          || ||| ||||||   ||   |||||   |   ||  ||  |  |  | |  |  |           || | | |  |    |  ||||  || | | || ||| ||| | |||||||||||||||| |||| |||||| ||||| |||| |||||| ||||| |||||  || ||||||||||||| | ||||||||||||||||||  | ||
---------------------------------------------------------aatatttcttttcagcaatcattgtctcttttgtagggaaagtaggctgaacttctt-----------gcttttctcca----cacatataataacagctgatttgtgtattcagATATGGAAGATCTGAAAGTCTTTGCGAAAGATTCTGGTTCTCCTGAAGCTAATGATTTGACTCACTGGGACCTTACCTTCTGGAGTGAACGACTGAGAGA
















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|33677982|gb|CF306221.1|CF306221
EST:     AGAGCTTCTTGAGAAACTCCGTGCTGCCTCCTGGGATCATGCTGTTAAAG                         ATATGGAAGATCTAAAAGCCTTTGCTAAAGAGTCTGCTTCTCCAGAAGCCA
genomic: AGAGCTTCTTGAGAAACTCCGTGCTGCCTCCTGGGATCATGCTGTTAAAGgtagccaatc ... ctgtgtgcagATATGGAAGATCTAAAAGCCTTTGCTAAAGAGTCTGCTTCTCCAGAAGCCA
EST: gi|88375308|gb|CI681071.1|CI681071
EST:     GTGCTGCCTCCTGGGATCATGCTGTTAAAG                         ATATGGAAGATCTAAAAGCCTTTGCTAAAGAGTCTGCTTCTCCAGAAGCCA
genomic: GTGCTGCCTCCTGGGATCATGCTGTTAAAGgtagccaatc ... ctgtgtgcagATATGGAAGATCTAAAAGCCTTTGCTAAAGAGTCTGCTTCTCCAGAAGCCA

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), 55 (downstream exon)
Score: 55

GTAAGCATGGCTCAGAAAATGGCAACTGTTGACCGTGTAGAAGAGCTTCTTGAGAAACTCCGTGCTGCCTCCTGGGATCATGCTGTTAAAGgtagccaatc ... ctgtgtgcagATATGGAAGATCTAAAAGCCTTTGCTAAAGAGTCTGCTTCTCCAGAAGCCAATGACCTGGCTCACTGGGACCTAAGCTTCTGGAGTGAACGACTCCGGGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aggagtaggcatcttttgaggttcgaatatcttagctgttggtttctgtgtgcagATATGGAAGATCTAAAAGCCTTTGCTAAAGAGTCTGCTTCTCCAGAAGCCAATGACCTGGCTCACTGGGACCTAAGCTTCTGGAGTGAACGACTCCGGGA
                                          tttctgt  CT-rich tract
                         aatatctta  TA-rich tract