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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAACTTGGGGATTCAGTACTTCGGCCATTTCTCCAGgttgatactagactattgttctaaaccactgtgattccctgcaaagtgaaaatctcagcttccgatatttacttgaattgtgtatttgtag

Basic information

species Oryza sativa
transcript LOC_Os08g32630.5
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g32630.5 (Oryza sativa), 5'ss of exon 14
lower sequence: GRMZM5G851815_T02 (Zea mays), 5'ss of exon 15
AAACTTGGGGATTCAGTACTTCGGCCATTTCTCCAGgttgatactagactattgttctaaaccactgtgattccctgcaaagtgaaaatctcagcttccgatatttacttgaattgtgtatttgtag
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AAACTAGGGGATTCGGTACTTCGGCCATTTCTACAGgttgctgcttggacattgt----atgcgttgttatatcc---ataaagaaatacttgtctttc---actta-tgggactgcacatttgtag
















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|29670150|gb|CB666425.1|CB666425
EST:     AAACTTGGGGATTCAGTACTTCGGCCATTTCTCCAG                         GATGTAATACAATTTGGACCTCTGGTTAAAACTCTGGGTCTAGTAATGATC
genomic: AAACTTGGGGATTCAGTACTTCGGCCATTTCTCCAGgttgatacta ... gtatttgtagGATGTAATACAATTTGGACCTCTGGTTAAAACTCTGGGTCTAGTAATGATC
EST: gi|29670151|gb|CB666426.1|CB666426
EST:     AAACTTGGGGATTCAGTACTTCGGCCATTTCTCCAG                         GATGTAATACAATTTGGACCTCTGGTTAAAACTCTGGGTCTAGTAATGATC
genomic: AAACTTGGGGATTCAGTACTTCGGCCATTTCTCCAGgttgatacta ... gtatttgtagGATGTAATACAATTTGGACCTCTGGTTAAAACTCTGGGTCTAGTAATGATC
EST: gi|22305644|gb|BQ906866.1|BQ906866
EST:     GGGATTTCAGTACTTCGCCCATTTCTCCAG                         GATGTAATACCATTTGGACCTCTGGTTAAAACTCTGGGTCTAGTAATGATC
genomic: GGGA-TTCAGTACTTCGGCCATTTCTCCAGgttgatacta ... gtatttgtagGATGTAATACAATTTGGACCTCTGGTTAAAACTCTGGGTCTAGTAATGATC
EST: gi|29677474|gb|CB673749.1|CB673749
EST:     AAACTTGGGGATTCAGTACTTCGGCCATTTCTCCAG                         GATGTAATACAATTTGGACCTCTGGTTAAAACTCTGGGTCTAGTAATGATC
genomic: AAACTTGGGGATTCAGTACTTCGGCCATTTCTCCAGgttgatacta ... gtatttgtagGATGTAATACAATTTGGACCTCTGGTTAAAACTCTGGGTCTAGTAATGATC
EST: gi|88244952|gb|CI244801.1|CI244801
EST:     TTCGGCCATTTCTNCAG                         GATGTAATACAATTTGGACCTCTGGTTAAAACTCTGGGTCTAGTAATGATC
genomic: TTCGGCCATTTCTCCAGgttgatacta ... gtatttgtagGATGTAATACAATTTGGACCTCTGGTTAAAACTCTGGGTCTAGTAATGATC
EST: gi|88847633|gb|CI018324.1|CI018324
EST:     AAACTTGGGGATTCAGTACTTCGGCCATTTCTCCAG                         GATGTAATACAATTTGGACCTCTGGTTAAAACTCTGGGTCTAGTAATGATC
genomic: AAACTTGGGGATTCAGTACTTCGGCCATTTCTCCAGgttgatacta ... gtatttgtagGATGTAATACAATTTGGACCTCTGGTTAAAACTCTGGGTCTAGTAATGATC
EST: gi|88245161|gb|CI245010.1|CI245010
EST:     CCATTTCTCCAG                         GATGTAATACAATTTGGACCTCTGGTTAAAACTCTGGGTCTAGTAATGATC
genomic: CCATTTCTCCAGgttgatacta ... gtatttgtagGATGTAATACAATTTGGACCTCTGGTTAAAACTCTGGGTCTAGTAATGATC
EST: gi|88841109|gb|CI001071.1|CI001071
EST:     AAACTTGGGGATTCAGTACTTCGGCCATTTCTCCAG                         GATGTAATACAATTTGGACCTCTGGTTAAAACTCTGGGTCTAGTAATGATC
genomic: AAACTTGGGGATTCAGTACTTCGGCCATTTCTCCAGgttgatacta ... gtatttgtagGATGTAATACAATTTGGACCTCTGGTTAAAACTCTGGGTCTAGTAATGATC
EST: gi|29679962|gb|CB676237.1|CB676237
EST:     AAACTTGGGGATTCAGTACTTCGGCCATTTCTCCAG                         GATGTAATACAATTTGGACCTCTGGTTAAAACTCTGGGTCTAGTAATGATC
genomic: AAACTTGGGGATTCAGTACTTCGGCCATTTCTCCAGgttgatacta ... gtatttgtagGATGTAATACAATTTGGACCTCTGGTTAAAACTCTGGGTCTAGTAATGATC

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: 36 (upstream exon), 48 (downstream exon)
Score: 11

AAACTTGGGGATTCAGTACTTCGGCCATTTCTCCAGgttgatacta ... gtatttgtagGATGTAATACAATTTGGACCTCTGGTTAAAACTCTGGGTCTAGTAATGATCACTCGACCACAGATTTTGCCTTCCATTTTTAAGCAG




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