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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcgtgatagcgtgtggctctgtttgctaccaaatgcgccgccagtaaagctcaactgattgtttgctgtcgtttctgtggcttcagGAGCCTCTAAAGTTGGATTTTGTCATAAGCTTTCCTGACCATGGGTTCCACCTGCGCTTCGATCCTTGGTCACAG

Basic information

species Oryza sativa
transcript LOC_Os06g49990.3
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g49990.3 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G116434_T01 (Zea mays), 3'ss of exon 2
gttcgtgatagcgtgtggctctgtttgctaccaaatgcgccgccagtaaagctcaactgattgtttgctgtcgtttctgtggcttcagGAGCCTCTAAAGTTGGATTTTGTCATAAGCTTTCCTGACCATGGGTTCCACCTGCGCTTCGATCCTTGGTCACAG
||| |||| |    |||     ||||| |     ||||    | |   |  || | ||||| |   | ||| | |||||||||||||||||||||| ||| |||| |||||||| |||||||| |||||||| || ||||| ||||| ||||||||||| |||
gtttgtgagacgaggtgcacgcgtttgttg---gatgc----caaaatattcttacctgatcggc-gttgttggttctgtggcttcagGAGCCTCTCAAGCTGGACTTTGTCATTAGCTTTCCGGACCATGGATTTCACCTACGCTTTGATCCTTGGTCCCAG

upper sequence: LOC_Os06g49990.3 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA01G37380.1 (Glycine max), 3'ss of exon 2
------------------------------------------------------------------------gttcgtgatagcgtg--tggctctgtttgctaccaaatgcgccgccag----taaagctcaactgattgtttgctgtcg----tttctgtggcttcagGAGCCTCTAAAGTTGGATTTTGTCATAAGCTTTCCTGACCATGGGTTCCACCTGCGCTTCGATCCTTGGTCACAG
                                                                        ||   |||  |  ||  |  | | | || |||| |  || | |         ||    | ||  |||| ||  ||        ||| ||    | ||||| || || ||||||||| |||| || ||||||||||| ||||| ||||| || || |||||||| ||||| |||
gtttgtcacatatgattatcacttaacaccttgtcagttgtgtcgtctatgattttgtgtgaacttgaacgagtaattgactgtctgcttcacgcaggttactactatctgtggctttgcgttttattttttaagagattcttgacttcttctactttatgcacatgcagGAACCCCTGAAGTTGGATATTGTTATTAGCTTTCCTGATCATGGATTCCATCTTCGTTTCGATCCGTGGTCTCAG

upper sequence: LOC_Os06g49990.3 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA11G07910.1 (Glycine max), 3'ss of exon 2
-----------------------------------------------------------------------------------------------gttcgtgatagcgtgtggctctg--tttgcta----ccaaatgcgccgccagt--aaagctcaactgattgtttgctgtcgtttctgtggctt---------cagGAGCCTCTAAAGTTGGATTTTGTCATAAGCTTTCCTGACCATGGGTTCCACCTGCGCTTCGATCCTTGGTCACAG
                                                                                               | |    |     ||| ||| ||  ||||  |    ||   ||         |  |||| |  | |  || ||  ||   |||  | |   |          ||||| || || ||||||||| |||| || ||||||||||| ||||| ||||| || ||||| ||||| ||||| |||
gtttgtcgcatatgatttatggcttaacttactgtcatttatgttttctattattgtttgaacttgcactagcaattgactgtctgcttcgggcaggttactactatctgttgctttgcctttgtgaggctcctgttgttttattttttgaaagatgcatttgtttttatcttgagttcttctacttaatgcacatgcagGAACCCCTGAAGTTGGATGTTGTTATTAGCTTTCCTGATCATGGCTTCCATCTTCGCTTTGATCCGTGGTCTCAG

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|11442702|gb|BF430605.1|BF430605
EST:     AGGGCCAGCCAACACTCTACGACGTTGTCCACGTGAAGTACTTCGATGAG                         GAGCCTCTAAAGTTGGATTTTGTCATAAGCTTTCCTGACCATGGGTTCCAC
genomic: AGGGCCAGCCAACACTCTACGACGTTGTCCACGTGAAGTACTTCGATGAGgttcgtgata ... gtggcttcagGAGCCTCTAAAGTTGGATTTTGTCATAAGCTTTCCTGACCATGGGTTCCAC
EST: gi|33675671|gb|CF303910.1|CF303910
EST:     AGGGCCAGCCAACACTCTACGACGTTGTCCACGTGAAGTACTTCGATGAG                         GAGCCTCTAAAGTTGGATTTTGTCATAAGCTTTCCTGACCATGGGTTCCAC
genomic: AGGGCCAGCCAACACTCTACGACGTTGTCCACGTGAAGTACTTCGATGAGgttcgtgata ... gtggcttcagGAGCCTCTAAAGTTGGATTTTGTCATAAGCTTTCCTGACCATGGGTTCCAC

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: 56 (upstream exon), 31 (downstream exon)
Score: 3

GGATGCCGATTTCCGATGCGTTCGCGCAGATAGAGGGCCAGCCAACACTCTACGACGTTGTCCACGTGAAGTACTTCGATGAGgttcgtgata ... gtggcttcagGAGCCTCTAAAGTTGGATTTTGTCATAAGCTTTCCTGACCATGGGTTCCACCTGCGCTTCGATCCTTGGTCACAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatgcgccgccagtaaagctcaactgattgtttgctgtcgtttctgtggcttcagGAGCCTCTAAAGTTGGATTTTGTCATAAGCTTTCCTGACCATGGGTTCCACCTGCGCTTCGATCCTTGGTCACAG
                     aactgat  putative branch site (score: 3)
                                        tttctgt  putative PPT
                          attgttt  TA-rich tract