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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattgatatttcatagcattttcgcttatactgatacattaacatgttgcatagagtaatccagtcctggtaccaacttttgagtgcccaaacagGTCCTTGCTATTTCACGTGTCATGGTGGCATGGCAACCGATTGGTATATCAATGGGGGTGTTTGATGTCTGCCATCG

Basic information

species Oryza sativa
transcript LOC_Os01g06600.2
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g06600.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM5G862219_T03 (Zea mays), 3'ss of exon 9
gtattgatatttcatagcattttcgcttatactgatacattaacatgttgcatag--agtaatccagtcctggt-accaacttttga-gtgcccaaacagGTCCTTGCTATTTCACGTGTCATGGTGGCATGGCAACCGATTGGTATATCAATGGGGGTGTTTGATGTCTGCCATCG-----------------------
|||  |      ||   |  || || || | ||  | |  |  ||   |  |      || ||  |   ||| |  || | | |    |||  ||| ||||| || || ||||||||  | |||||||||||||||||| |||| |||||||||||||| || ||  | ||||| ||                       
gtaccggc----caacactcttccgattctgcttctgccgtgccaaactataagctcggtgatgtaaatctgcttgcctattctcactgtgtgcaagcagGTGCTCGCCATTTCACGCATTATGGTGGCATGGCAACCGGTTGGCATATCAATGGGGGTCTTCGACATGTGCCACCGGTACGTGGCGCCATACGTTCTGA

upper sequence: LOC_Os01g06600.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM5G862219_T02 (Zea mays), 3'ss of exon 9
gtattgatatttcatagcattttcgcttatactgatacattaacatgttgcatag--agtaatccagtcctggt-accaacttttga-gtgcccaaacagGTCCTTGCTATTTCACGTGTCATGGTGGCATGGCAACCGATTGGTATATCAATGGGGGTGTTTGATGTCTGCCATCG
|||  |      ||   |  || || || | ||  | |  |  ||   |  |      || ||  |   ||| |  || | | |    |||  ||| ||||| || || ||||||||  | |||||||||||||||||| |||| |||||||||||||| || ||  | ||||| ||
gtaccggc----caacactcttccgattctgcttctgccgtgccaaactataagctcggtgatgtaaatctgcttgcctattctcactgtgtgcaagcagGTGCTCGCCATTTCACGCATTATGGTGGCATGGCAACCGGTTGGCATATCAATGGGGGTCTTCGACATGTGCCACCG

upper sequence: LOC_Os01g06600.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA03G07540.1 (Glycine max), 3'ss of exon 9
--gtattgatatttcatagcattttcgcttatactgatacattaacatgttgcatagagtaatccagtcctggtaccaactt-ttgagtgccc---aaacagGTCCTTGCTATTTCACGTGTCATGGTGGCATGGCAACCGATTGGTATATCAATGGGGGTGTTTGATGTCTGCCATCG
  | ||   |   |  |   || |  | || |  |    |||  ||||||  | |    ||   || | |   | |  | || || |   | |   |||||||| |||||| ||||||| || ||||| || |||||||| ||||||||||| |||||  | |  ||| | || ||  |
ttgcatcagttaattttttaatatgtgtttgtcatctgtcatgcacatgt--cttgatttacatcattaccattgcttatttgtttaacactcttaaaacagGTACTTGCTGTTTCACGCGTAATGGTTGCTTGGCAACCCATTGGTATATCGATGGGCATCTACGATATGTGTCACAG

upper sequence: LOC_Os01g06600.1 (Oryza sativa), 3'ss of exon 9
lower sequence: Vv08s0105g00460.t01 (Vitis vinifera), 3'ss of exon 9
------gtattgatatttcatagcattttcgcttatactgatacattaacatgttgcatagagtaatccagtcctggtaccaacttttgagtgcccaaacagGTCCTTGCTATTTCACGTGTCATGGTGGCATGGCAACCGATTGGTATATCAATGGGGGTGTTTGATGTCTGCCATCG
        ||   ||| || |  |||| |   || | ||  ||     |  |||||| ||   |   ||| |  |  | | || |           |||||||| |||||| |||||||||||||||| || |||||||| || || || |||||||| |  | |||| | || ||  |
tgcctctgatgcttatctcctctcattgt-attttttcttgtatccatatctgttgcttaatttttcccattgtttat-ctaaataccaccattggaaacagGTGCTTGCTGTTTCACGTGTCATGGTTGCCTGGCAACCTATAGGCATTTCAATGGGAGCCTATGATATGTGTCACAG

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|29666427|gb|CB662702.1|CB662702
EST:     CTGAGGGAGATCGACTGCCAGGTGTCAATTCATTTCAGGATATAAGCAAG                         GGTCCTTGCTATTTC
genomic: CTGAGGAAGATCGACTGCCAGGTGTCAATTCATTTCAGGATATAAGCAAGgtattgatat ... gcccaaacagG-TCCTTGCTATTTC
EST: gi|29666426|gb|CB662701.1|CB662701
EST:     CTGAGGAAGATCGACTGCCAGGTGTCAATTCATTTCAGGATATAAGCAAG                         GTCCTTGCTATTTCACGTGTCATGGTGGCATGGCAACCGATTGGTATATCA
genomic: CTGAGGAAGATCGACTGCCAGGTGTCAATTCATTTCAGGATATAAGCAAGgtattgatat ... gcccaaacagGTCCTTGCTATTTCACGTGTCATGGTGGCATGGCAACCGATTGGTATATCA
EST: gi|14713699|gb|AU197670.1|AU197670
EST:     CTGAGGAAGATCGACTGCCAGGTGTCAATTCATTTCAGGATATAAGCAAG                         GTCCTTGCTATTTCACGTGTCATGGTGGCATGGCAACCGATTGGTATATCA
genomic: CTGAGGAAGATCGACTGCCAGGTGTCAATTCATTTCAGGATATAAGCAAGgtattgatat ... gcccaaacagGTCCTTGCTATTTCACGTGTCATGGTGGCATGGCAACCGATTGGTATATCA
EST: gi|33683998|gb|CF312237.1|CF312237
EST:     CTGAGGAAGATCGACTGCCAGGTGTCAATTCATTTCAGGATATAAGCAAG                         GTCCTTGCTATTTCACGTGTCATGGTGGCATGGCAACCGATTG
genomic: CTGAGGAAGATCGACTGCCAGGTGTCAATTCATTTCAGGATATAAGCAAGgtattgatat ... gcccaaacagGTCCTTGCTATTTCACGTGTCATGGTGGCATGGCAACCGATTG
EST: gi|88344179|gb|CI654609.1|CI654609
EST:     CTGAGGAAGATCGACTGCCAGGTGTCAATTCATTTCAGGATATAAGCAAG                         GTCCTTGCTATTTCACGTGCCATGGTGGCATGGCAACCGATTGGTATATCA
genomic: CTGAGGAAGATCGACTGCCAGGTGTCAATTCATTTCAGGATATAAGCAAGgtattgatat ... gcccaaacagGTCCTTGCTATTTCACGTGTCATGGTGGCATGGCAACCGATTGGTATATCA
EST: gi|13165132|gb|AU173929.1|AU173929
EST:     CTGAGGAAGATCGACTGCCAGGTGTCAATTCATTTCAGGATATAAGCAAG                         GTCCTTGCTATTTCACGTGTCATGGTGGCATGGCAACCGATTGGTATATCA
genomic: CTGAGGAAGATCGACTGCCAGGTGTCAATTCATTTCAGGATATAAGCAAGgtattgatat ... gcccaaacagGTCCTTGCTATTTCACGTGTCATGGTGGCATGGCAACCGATTGGTATATCA
EST: gi|56157778|gb|C26441.2|C26441
EST:     CTGAGGAAGATCGACTGCCAGGTGTCAATTCATTTCAGGATATAAGCAAG                         GTCCTTGCTATTTCACGTGTCATGGTGGCATGGCAACCGATTGGTATATCA
genomic: CTGAGGAAGATCGACTGCCAGGTGTCAATTCATTTCAGGATATAAGCAAGgtattgatat ... gcccaaacagGTCCTTGCTATTTCACGTGTCATGGTGGCATGGCAACCGATTGGTATATCA
EST: gi|29660291|gb|CB656566.1|CB656566
EST:     AGGTGTCAATTCATTTCAGGATATAAGCAAG                         GTCCTTGCTATTTCACGTGTCATGGTGGCATGGCAACCGATTGGTATATCA
genomic: AGGTGTCAATTCATTTCAGGATATAAGCAAGgtattgatat ... gcccaaacagGTCCTTGCTATTTCACGTGTCATGGTGGCATGGCAACCGATTGGTATATCA
EST: gi|29678764|gb|CB675039.1|CB675039
EST:     CTGAGGAAGATCGACTGCCAGGTGTCAATTCATTTCAGGATATAAGCAAG                         GTCCTTGCTATTTCACGTGTCATGGTGGCATGGCAACCGATTGGTATATCA
genomic: CTGAGGAAGATCGACTGCCAGGTGTCAATTCATTTCAGGATATAAGCAAGgtattgatat ... gcccaaacagGTCCTTGCTATTTCACGTGTCATGGTGGCATGGCAACCGATTGGTATATCA

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: 74 (upstream exon), 73 (downstream exon)
Score: 35

TCTCAGAATGGTTCAGAACGGTGATATAGTTTTTAATAAAGTATTTGTCCCTGAGGAAGATCGACTGCCAGGTGTCAATTCATTTCAGGATATAAGCAAGgtattgatat ... gcccaaacagGTCCTTGCTATTTCACGTGTCATGGTGGCATGGCAACCGATTGGTATATCAATGGGGGTGTTTGATGTCTGCCATCG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aacatgttgcatagagtaatccagtcctggtaccaacttttgagtgcccaaacagGTCCTTGCTATTTCACGTGTCATGGTGGCATGGCAACCGATTGGTATATCAATGGGGGTGTTTGATGTCTGCCATCG
 cattaac  putative branch site (score: 35)
                                  aactttt  TA-rich tract