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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggaaagcatgggggttttggtgcaactattagatcttttaacgtgtcatagctcttttctgttttgttccgtagattctaaccctctgttctgtgtgcagGAATCTTACGAGAACCAGCAGGATATTCAGCTCATGCGGTTCGCCGACTACTTTGGCAGGTCATTTGCAAGCGTGAGCGCCGCCCAGTTCCCCTGGGCGA

Basic information

species Oryza sativa
transcript LOC_Os01g03760.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g03760.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G121683_T01 (Zea mays), 3'ss of exon 1
-------ggaaagcatgggggttttggtgcaactattagatcttttaacgtgtcatagctcttttctgttttgttccgtagattctaaccctctgttctgtgtgcagGAATCTTACGAGAACCAGCAGGATATTCAGCTCATGCGGTTCGCCGACTACTTTGGCAGGTCATTTGCAAGCGTGAGCGCCGCCCAGTTCCCCTGGGCGA
       ||  ||| |  ||| ||||||   |  |||||  | |  ||   ||     | |||| ||||| |||   ||| ||||| |   | ||||||||  ||||| ||| |||||||| || ||||| |||||||||||| |||| || || ||||||||| || ||||||||   ||||||||  | || || || ||||| |
ggatctcggggagc-tctgggctttggtattaggattag--cctgcaaaaggttggtacacttt-ctgttgtgtat-gtatattctgattatttgttctgt--gcagGCATCGTACGAGAATCAACAGGACATTCAGCTCATGAGGTTTGCTGATTACTTTGGCCGGGCATTTGCAGCTGTGAGCGCATCTCAATTTCCATGGGCAA
















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|29645275|gb|CB650282.1|CB650282
EST:     CCGCTCTGATCGACGCCGAGAACCTCGCGGCGCATCTCGTGCAGATCTCG                         GAATCTTACGAGAACCAGCAGGATATTCAGCTCATGCGGTTCGCCGACTAC
genomic: CCGCTCTGATCGACGCCGAGAACCTCGCGGCGCATCTCGTGCAGATCTCGgtaatacccg ... ctgtgtgcagGAATCTTACGAGAACCAGCAGGATATTCAGCTCATGCGGTTCGCCGACTAC
EST: gi|29657372|gb|CB653647.1|CB653647
EST:     CCGCTCTGATCGACGCCGAGAACCTCGCGGCGCATCTCGTGCAGATCTCG                         GAATCTTACGAGAACCAGCAGGATATTCAGCTCATGCGGTTCGCCGACTAC
genomic: CCGCTCTGATCGACGCCGAGAACCTCGCGGCGCATCTCGTGCAGATCTCGgtaatacccg ... ctgtgtgcagGAATCTTACGAGAACCAGCAGGATATTCAGCTCATGCGGTTCGCCGACTAC
EST: gi|29645235|gb|CB650242.1|CB650242
EST:     CCGCTCTGATCGACGCCGAGAACCTCGCGGCGCATCTCGTGCAGATCTCG                         GAATCTTACGAGAACCAGCAGGATATTCAGCTCATGCGGTTCGCCGACTAC
genomic: CCGCTCTGATCGACGCCGAGAACCTCGCGGCGCATCTCGTGCAGATCTCGgtaatacccg ... ctgtgtgcagGAATCTTACGAGAACCAGCAGGATATTCAGCTCATGCGGTTCGCCGACTAC
EST: gi|9055412|gb|AU097610.1|AU097610
EST:     GCTCTGATCGACGCCGAGAACCTCGCGGCGCATCTCGTGCAGATCTCG                         GAATCTTACGAGAACCANCAGGATATTCAGCTCATGCGGTTCGCCGACTAC
genomic: GCTCTGATCGACGCCGAGAACCTCGCGGCGCATCTCGTGCAGATCTCGgtaatacccg ... ctgtgtgcagGAATCTTACGAGAACCAGCAGGATATTCAGCTCATGCGGTTCGCCGACTAC
EST: gi|58587053|gb|CF985361.1|CF985361
EST:     CCGCTCTGATCGACGCCGAGAACCTCGCGGCGCATCTCGTGCAGATCTCG                         GAATCTTACGAGAACCAGCAGGATATTCAGCTCATGCGGTTCGCCGACTAC
genomic: CCGCTCTGATCGACGCCGAGAACCTCGCGGCGCATCTCGTGCAGATCTCGgtaatacccg ... ctgtgtgcagGAATCTTACGAGAACCAGCAGGATATTCAGCTCATGCGGTTCGCCGACTAC

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: 63 (upstream exon), 74 (downstream exon)
Score: 94

GCCCAAGGTGAAGAAGCCGAAGAAGCCCAAGGTGACGGTCGCCGAGGCGGCCGCTCTGATCGACGCCGAGAACCTCGCGGCGCATCTCGTGCAGATCTCGgtaatacccg ... ctgtgtgcagGAATCTTACGAGAACCAGCAGGATATTCAGCTCATGCGGTTCGCCGACTACTTTGGCAGGTCATTTGCAAGCGTGAGCGCCGCCCAGTTCCCCTGGGCGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcatagctcttttctgttttgttccgtagattctaaccctctgttctgtgtgcagGAATCTTACGAGAACCAGCAGGATATTCAGCTCATGCGGTTCGCCGACTACTTTGGCAGGTCATTTGCAAGCGTGAGCGCCGCCCAGTTCCCCTGGGCGA
                              ttctaac  putative branch site (score: 94)
                                    ccctctgttct  CT-rich tract
                ttttgtt  TA-rich tract