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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCTCTACTACAGGGATGACCATTACTCTTGTTGTTGTTTCTGTGTCATTTTTTGTGAAGgtattgtcattttgccacttaaaaaatttatttggtactatatttaatgttttgtatttcgctgcttgtctagtttcgttcaattaaatcttgattgtgttacctgatattatattccctttgtaacatattttactatcgatcatgaaacag

Basic information

species Oryza sativa
transcript LOC_Os05g50280.1
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g50280.1 (Oryza sativa), 5'ss of exon 13
lower sequence: GRMZM2G097768_T01 (Zea mays), 5'ss of exon 14
ATCTCTACTACAGGGATGACCATTACTCTTGTTGTTGTTTCTGTGTCATTTTTTGTGAAGgtattgtcattttgccacttaaaaaatttatttggtactatatttaatgttttgtatttcgctgcttgtctagtttcgttcaattaaatcttgattgtgttacctgatattatattccctttgtaacatattttactatcgatcatgaaacag
|| || || ||||| |||  ||||||||||||| ||||||||||||||||||||||||||||| ||||| ||         |||| |||| |  |||  ||  |  ||  |||| |   | || ||  |  | |       ||| | ||     | | ||     || ||| |  | ||||| | | ||| | |    ||  |  || | |||
ATTTCCACCACAGGAATGGTCATTACTCTTGTTATTGTTTCTGTGTCATTTTTTGTGAAGgtaatgtcactt---------aaaagtttaat-agtagcatgct--attgtttgcagcacactcctattgaaat-------aatcatattgct-tagagtctatcgacattgtcattcctttctgaaatactcttgcttcacttctggagcag
















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|87008327|gb|CI301085.1|CI301085
EST:     CAGGGATGACCATTACTCTTGTTGTTGTTTCTGTGTCATTTTTTGTGAAG                         GACAACATAACTAATGGTTCTCATTTATACTCTGTAATGAGTATGCTTTCG
genomic: CAGGGATGACCATTACTCTTGTTGTTGTTTCTGTGTCATTTTTTGTGAAGgtattgtcat ... catgaaacagGACAACATAACTAATGGTTCTCATTTATACTCTGTAATGAGTATGCTTTCG
EST: gi|29678789|gb|CB675064.1|CB675064
EST:     CAGGGATGACCATTACTCTTGTTGTTGTTTCTGTGTCATTTTTTGTGAAG                         GACAACATAACTAATGGTTCTCATTTATACTCTGTAATGAGTATGCTTTCG
genomic: CAGGGATGACCATTACTCTTGTTGTTGTTTCTGTGTCATTTTTTGTGAAGgtattgtcat ... catgaaacagGACAACATAACTAATGGTTCTCATTTATACTCTGTAATGAGTATGCTTTCG
EST: gi|29678790|gb|CB675065.1|CB675065
EST:     CAGGGATGACCATTACTCTTGTTGTTGTTTCTGTGTCATTTTTTGTGAAG                         GACAACATAACTAATGGTTCTCATTTATACTCTGTAATGAGTATGCTTTCG
genomic: CAGGGATGACCATTACTCTTGTTGTTGTTTCTGTGTCATTTTTTGTGAAGgtattgtcat ... catgaaacagGACAACATAACTAATGGTTCTCATTTATACTCTGTAATGAGTATGCTTTCG
EST: gi|7274036|gb|AU083580.1|AU083580
EST:     CATTACTCTTGTTGTTGTTTCTGTGTCATTTTTTGTGAAG                         GACAACATAACTAATGGTTCTCATTTATACTCTGTAATGAGTATGCTTTCG
genomic: CATTACTCTTGTTGTTGTTTCTGTGTCATTTTTTGTGAAGgtattgtcat ... catgaaacagGACAACATAACTAATGGTTCTCATTTATACTCTGTAATGAGTATGCTTTCG
EST: gi|29674764|gb|CB671039.1|CB671039
EST:     CAGGGATGACCATTACTCTTGTTGTTGTTTCTGTGTCATTTTTTGTGAAG                         GACAACATAACTAATGGTTCTCATTTATACTCTGTAATGAGTATGCTTTCG
genomic: CAGGGATGACCATTACTCTTGTTGTTGTTTCTGTGTCATTTTTTGTGAAGgtattgtcat ... catgaaacagGACAACATAACTAATGGTTCTCATTTATACTCTGTAATGAGTATGCTTTCG
EST: gi|701858|gb|D48149.1|D48149
EST:     CAGGGATGACCATTACTCTTGTTGTTGTTTCTGTGTCATTTTTTGTGAAG                         GACAACATAACTAATGGTTCTCATTTATACTCTGTAATGAGTATGCTTTCG
genomic: CAGGGATGACCATTACTCTTGTTGTTGTTTCTGTGTCATTTTTTGTGAAGgtattgtcat ... catgaaacagGACAACATAACTAATGGTTCTCATTTATACTCTGTAATGAGTATGCTTTCG
EST: gi|58679421|gb|CK068108.1|CK068108
EST:     CA-GGATGACCATTACTC-TGTTG-TGTTTCTGTGTCATTTTTTGTGAAG                         GACAACATAACTAATGGTTCTCATTTATACTCTGTAATGAGTATGCTTTCG
genomic: CAGGGATGACCATTACTCTTGTTGTTGTTTCTGTGTCATTTTTTGTGAAGgtattgtcat ... catgaaacagGACAACATAACTAATGGTTCTCATTTATACTCTGTAATGAGTATGCTTTCG

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: 57 (upstream exon), 66 (downstream exon)
Score: 21

ATCTCTACTACAGGGATGACCATTACTCTTGTTGTTGTTTCTGTGTCATTTTTTGTGAAGgtattgtcat ... catgaaacagGACAACATAACTAATGGTTCTCATTTATACTCTGTAATGAGTATGCTTTCGCTGGTCGGGCTTGTG




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