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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtgtggcagttccttttttgtgttatcacactgttatttgtactattttcagatggcataccaatctgtaccaaatttcctgcagATGAACATGGTCTTGATTTTGAGCAATATGGCATCCTTATAAAGGTCAAGTTTAG

Basic information

species Oryza sativa
transcript LOC_Os05g51790.1
intron # 23
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g51790.2 (Oryza sativa), 3'ss of exon 23
lower sequence: GRMZM2G440916_T01 (Zea mays), 3'ss of exon 23
gtatgtgtggcagttccttttttgtgttatcacactgttatttgtactattttcagatggcataccaatc--tgtaccaaa--tttcctgcagATGAACATGGTCTTGATTTTGAGCAATATGGCATCCTTATAAAGGTCAAGTTTAG
|||||| ||            || ||||    | |  || |||||  | |||   |||  ||  | |||    ||  ||||  |||| ||||||||| || ||| |||||||||| || ||||| || ||||||||||| || |||||
gtatgtatga-----------ttttgtttcttcgccattgtttgttttgttt---gataacaccctaattgtcgtgtcaaacctttcttgcagATGAGCACGGTATTGATTTTGATCACTATGGTATTCTTATAAAGGTGAAATTTAG
















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|87019115|gb|CI297316.1|CI297316
EST:     GTTTAGTCGTAACTTTCAAGAAATGGCTGTTGCTGGAGAAGTTTCACTTG                         ATGAACATGGTCTTGATTTTGAGCAATATGGCATCCTTATAAAGGTCAAGT
genomic: GTTTAGTCGTAACTTTCAAGAAATGGCTGTTGCTGGAGAAGTTTCACTTGgtatgtgtgg ... tttcctgcagATGAACATGGTCTTGATTTTGAGCAATATGGCATCCTTATAAAGGTCAAGT
EST: gi|66914986|gb|CX101834.1|CX101834
EST:     GTTTAGTCGTAACTTTCAAGAAATGGCTGTTGCTGGAGAAGTTTCACTTG                         ATGAACATGGTCTTGATTTTGAGCAATATGGCATCCTTATAAAGGTCAAGT
genomic: GTTTAGTCGTAACTTTCAAGAAATGGCTGTTGCTGGAGAAGTTTCACTTGgtatgtgtgg ... tttcctgcagATGAACATGGTCTTGATTTTGAGCAATATGGCATCCTTATAAAGGTCAAGT
EST: gi|218486434|gb|FG966621.1|FG966621
EST:     GTTTAGTCGTAACTTTCAAGAAATGGCTGTTGCTGGAGAAGTTTCACTTG                         ATGAACATGGTCTTGATTTTGAGCAATATGGCATCCTTATAAAGGTCAAGT
genomic: GTTTAGTCGTAACTTTCAAGAAATGGCTGTTGCTGGAGAAGTTTCACTTGgtatgtgtgg ... tttcctgcagATGAACATGGTCTTGATTTTGAGCAATATGGCATCCTTATAAAGGTCAAGT
EST: gi|29628420|gb|CB633431.1|CB633431
EST:     GTTTAGTCGTAACTTTCAAGAAATGGCTGTTGCTGGAGAAGTTTCACTTG                         ATGAACATGGTCTTGATTTTGAGCAATATGGCATCCTTATAAAGGTCAAGT
genomic: GTTTAGTCGTAACTTTCAAGAAATGGCTGTTGCTGGAGAAGTTTCACTTGgtatgtgtgg ... tttcctgcagATGAACATGGTCTTGATTTTGAGCAATATGGCATCCTTATAAAGGTCAAGT

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: 70 (upstream exon), 64 (downstream exon)
Score: 18

GGCAAATGGCTTCCAACTCTGCGCACTCTTGTTTCAAAAATAAACAGCACGTTTAGTCGTAACTTTCAAGAAATGGCTGTTGCTGGAGAAGTTTCACTTGgtatgtgtgg ... tttcctgcagATGAACATGGTCTTGATTTTGAGCAATATGGCATCCTTATAAAGGTCAAGTTTAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgttatttgtactattttcagatggcataccaatctgtaccaaatttcctgcagATGAACATGGTCTTGATTTTGAGCAATATGGCATCCTTATAAAGGTCAAGTTTAG
                                             tttcctgc  CT-rich tract
     atttgtactatttt  TA-rich tract