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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtgtttagaaacaaacctattttatgttgcatcaataaagtactctcttccaactatcaattgtgttgctagatccgagctaatatttggtttttaaacctcagGGATCCAAATTTGCGGCCCTCGTTTGCACAGTTAACCAGTGCTTTGAAGACTGTCCAAAGGCTAGTAACCCCTTCTCACCAGGAGTCCCAGAGCCCTCCT

Basic information

species Oryza sativa
transcript LOC_Os03g06410.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g06410.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G038982_T01 (Zea mays), 3'ss of exon 8
gtgagtgtttagaaacaaacctattttatgttgcatcaataaagtactctcttccaactatcaattgtgttgctagatccgagctaatatttggtttttaaacc-tcagGGATCCAAATTTGCGGCCCTCGTTTGCACAGTTAACCAGTGCTTTGAAGACTGTCCAAAGGCTAGTAACCCCTTCTCACCAGGAGTCCCAGAGCCCTCCT
||||||  | ||||  |||||| || | || |        |||||   || |  |    ||     |   |  || ||  | ||||| || || | | | || |  |||||| |||||| |||| || || |||||||||||||| |||||  | |||||||| ||||| ||||| |||||||||||||||||| |||||||||| | |
gtgagttataagaactaaacctgttgtctgat-------caaagtctcctgtctcggtcat----ggcact-ttaaatttgtgctaacatgtgctctgtcaatcgccagGGACCCAAATCTGCGCCCTTCATTTGCACAGTTAACAAGTGCCCTAAAGACTGTTCAAAGACTAGTGACCCCTTCTCACCAGGAGACCCAGAGCCCCCAT

upper sequence: LOC_Os03g06410.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GLYMA10G30070.1 (Glycine max), 3'ss of exon 13
--------------gtgagtgtttagaaacaaacctattttatgttgcat-caataaagtactctcttccaactat-caattgtgttgctagatccgagctaatatttggtttttaaacc-----------tcagGGATCCAAATTTGCGGCCCTCGTTTGCACAGTTAACCAGTGCTTTGAAGACTGTCCAAAGGCTAGTAACCCCTTCTCACCAGGAGTCCCAGAGCCCTCCT
               | |  |||| |    |  ||| |||| |    ||| | || || |  | ||  | || | | ||| |    |   || | | || | ||      ||| |   ||           ||||||||||||||||||||||||||||||| ||  | ||    ||| | ||| || | ||  | || || | ||| ||| | || ||          || |||
gtaagcatgctcaacttaaagttt-gttttattcctttttttttacacataccattaaatgatttcagcaaattttgcaactacact-tcagtttccagtttatgacatttttctggcccccctccccgtttcagGGATCCAAATTTGCGGCCCTCGTTTGCGCAACTCACAGTGGCTCTAAAGCCTCTACAGCGTCTGGTTATCCCATCTTATCAAGATCAGTTAGCTCCACCT

upper sequence: LOC_Os03g06410.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GLYMA20G37330.1 (Glycine max), 3'ss of exon 13
-------------gtgagtgtttagaaacaaacctattttatgttgcat-caataaagtactctcttccaactat-caattgtgttgctagatccgagctaatatttggtt---------tttaaacctcagGGATCCAAATTTGCGGCCCTCGTTTGCACAGTTAACCAGTGCTTTGAAGACTGTCCAAAGGCTAGTAACCCCTTCTCACCAGGAGTCCCAGAGCCCTCCT
              | |  ||||           | |||| |    ||| | || || |  | ||    || | | ||| |    | |    |||    | | ||||   |         |       ||||||||||||||||||||||||||||||||||  | ||    ||| | ||| || | ||  | || || | ||| ||||| || ||          || |||
gtaagcatgctcaattaaagtttgttttattcatttttttcttccacataccattaaatgatttcaggaaattttacaactacacttcattctccagtttgacatttttctgcccccccgtccccgtttcagGGATCCAAATTTGCGGCCCTCGTTTGCACAACTCACAGTGGCTCTAAAGCCTCTGCAGCGTCTGGTTATCCCATCTCATCATGACCAGGTAGCTCCACCT

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|88466419|gb|CI529828.1|CI529828
EST:     AAGGAAATTGATCCTCTAGTTGCAAGGATCATATGGGAATGCTGGCAGAA                         GGATCCAAATTTGCGGCCCTCGTTTGCACAGTTAACCAGTGCTTTGAAGAC
genomic: AAGGAAATTGATCCTCTAGTTGCAAGGATCATATGGGAATGCTGGCAGAAgtgagtgttt ... taaacctcagGGATCCAAATTTGCGGCCCTCGTTTGCACAGTTAACCAGTGCTTTGAAGAC
EST: gi|88472352|gb|CI409623.1|CI409623
EST:     AAGGAAATTGATCCTCTAGTTGCAAGGATCATATGGGGATGCTGGCAGAA                         GGATCCAAATTTGCGGCCCTCGTTTGCACAGTTAACCAGTGCTTTGAAGAC
genomic: AAGGAAATTGATCCTCTAGTTGCAAGGATCATATGGGAATGCTGGCAGAAgtgagtgttt ... taaacctcagGGATCCAAATTTGCGGCCCTCGTTTGCACAGTTAACCAGTGCTTTGAAGAC
EST: gi|2317490|gb|C22544.1|C22544
EST:     AAGGAAATTGATCCTCTAGTTGCAAGGATCATATGGGAATGCTGGCAGAA                         GGATCCAAATTTGCGGCCCTCGTTTGCACAGTTAACCATTGCTTTGAAGAC
genomic: AAGGAAATTGATCCTCTAGTTGCAAGGATCATATGGGAATGCTGGCAGAAgtgagtgttt ... taaacctcagGGATCCAAATTTGCGGCCCTCGTTTGCACAGTTAACCAGTGCTTTGAAGAC
EST: gi|88470256|gb|CI407527.1|CI407527
EST:     AAGGAAATTGATCCTCTAGTTGCAAGGATCATATGGGAATGCTGGCAGAA                         GGATCCAAATTTGCGGCCCTCGTTTGCACAGTTAACCAGTGCTTTGAAGAC
genomic: AAGGAAATTGATCCTCTAGTTGCAAGGATCATATGGGAATGCTGGCAGAAgtgagtgttt ... taaacctcagGGATCCAAATTTGCGGCCCTCGTTTGCACAGTTAACCAGTGCTTTGAAGAC
EST: gi|86861852|gb|CI329572.1|CI329572
EST:     AGGAAATTGATCCTCTAGGTTGCAAGGATCATATGGGAATGCTGGCAGAA                         GGATCCAAATTTGCGGCCCTCGTTTGCACAGTTAACCAGTGCTTTGAAGAC
genomic: AGGAAATTGATCCTCTA-GTTGCAAGGATCATATGGGAATGCTGGCAGAAgtgagtgttt ... taaacctcagGGATCCAAATTTGCGGCCCTCGTTTGCACAGTTAACCAGTGCTTTGAAGAC
EST: gi|88388580|gb|CI683361.1|CI683361
EST:     AAGGAAATTGATCCTCTAGTTGCAAGGATCATATGGGAATGCTGGCAGAA                         GGATCCAAATTTGCGGCCCTCGTTTGCACAGTTAACCAGTGCTTTGAAGAC
genomic: AAGGAAATTGATCCTCTAGTTGCAAGGATCATATGGGAATGCTGGCAGAAgtgagtgttt ... taaacctcagGGATCCAAATTTGCGGCCCTCGTTTGCACAGTTAACCAGTGCTTTGAAGAC
EST: gi|86482006|gb|CI124639.1|CI124639
EST:     AAGGAAATTGATCCTCTAGTTGCAAGGATCATATGGGAATGCTGGCAGAA                         GGATCCAAATTTGCGGCCCTCGTTTGCACAGTTAACCAGTGCTTTGAAGAC
genomic: AAGGAAATTGATCCTCTAGTTGCAAGGATCATATGGGAATGCTGGCAGAAgtgagtgttt ... taaacctcagGGATCCAAATTTGCGGCCCTCGTTTGCACAGTTAACCAGTGCTTTGAAGAC
EST: gi|25803481|gb|CA759450.1|CA759450
EST:     AAGGAAATTGATCCTCTAGTTGCAAGGATCATATGGGAATGCTGGCAGAA                         GGATCCAAATTTGCGGCCCTCGTTTGCACAGTTAACCAGTGCTTTGAAGAC
genomic: AAGGAAATTGATCCTCTAGTTGCAAGGATCATATGGGAATGCTGGCAGAAgtgagtgttt ... taaacctcagGGATCCAAATTTGCGGCCCTCGTTTGCACAGTTAACCAGTGCTTTGAAGAC
EST: gi|86826649|gb|CI364201.1|CI364201
EST:     AAGGAAATTGATCCTCTAGTTGCAAGGATCATATGGGAATGCTGGCAGAA                         GGATCCAAATTTGCGGCCCTCATTTGCACAGTTAACCAGTGCTTTGAAGAC
genomic: AAGGAAATTGATCCTCTAGTTGCAAGGATCATATGGGAATGCTGGCAGAAgtgagtgttt ... taaacctcagGGATCCAAATTTGCGGCCCTCGTTTGCACAGTTAACCAGTGCTTTGAAGAC
EST: gi|88506904|gb|CI434410.1|CI434410
EST:     AAGGAAATTGATCCTCTAGTTGCAAGGATCATATGGGAATGCTGGCAGAA                         GGATCCAAATTTGCGGCCCTCGTTTGCACAGTTAACCAGTGCTTTGAAGAC
genomic: AAGGAAATTGATCCTCTAGTTGCAAGGATCATATGGGAATGCTGGCAGAAgtgagtgttt ... taaacctcagGGATCCAAATTTGCGGCCCTCGTTTGCACAGTTAACCAGTGCTTTGAAGAC
EST: gi|29621961|gb|CB626972.1|CB626972
EST:     AAGGAAATTGATCCTCTAGTTGCAAGGATCATATGGGAATGCTGGCAGAA                         GGATCCAAATTTGCGGCCCTCGTTTGCACAGTTAACCAGTGCTTTGAAGAC
genomic: AAGGAAATTGATCCTCTAGTTGCAAGGATCATATGGGAATGCTGGCAGAAgtgagtgttt ... taaacctcagGGATCCAAATTTGCGGCCCTCGTTTGCACAGTTAACCAGTGCTTTGAAGAC
EST: gi|86427747|gb|CI072844.1|CI072844
EST:     TGGGAATGCTGGCAGAA                         GGATCCAAATTTGCGGCCCTCGTTTGCACAGTTAACCAGTGCTTTGAAGAC
genomic: TGGGAATGCTGGCAGAAgtgagtgttt ... taaacctcagGGATCCAAATTTGCGGCCCTCGTTTGCACAGTTAACCAGTGCTTTGAAGAC
EST: gi|86437095|gb|CI118817.1|CI118817
EST:     AAGGAAATTGATCCTCTAGTTGCAAGGATCATATGGGAATGCTGGCAGAA                         GGATCCAAATTTGCGGCCCTCGTTTGCACAGTTAACCAGTGCTTTGAAGAC
genomic: AAGGAAATTGATCCTCTAGTTGCAAGGATCATATGGGAATGCTGGCAGAAgtgagtgttt ... taaacctcagGGATCCAAATTTGCGGCCCTCGTTTGCACAGTTAACCAGTGCTTTGAAGAC

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: 75 (upstream exon), 73 (downstream exon)
Score: 46

TGCAAGTTGTTGGGGCAGTCGGCTTCCAGGACAAGCGGCTCGATATTCCCAAGGAAATTGATCCTCTAGTTGCAAGGATCATATGGGAATGCTGGCAGAAgtgagtgttt ... taaacctcagGGATCCAAATTTGCGGCCCTCGTTTGCACAGTTAACCAGTGCTTTGAAGACTGTCCAAAGGCTAGTAACCCCTTCTCACCAGGAGTCCCAGAGCCCTCCT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccaactatcaattgtgttgctagatccgagctaatatttggtttttaaacctcagGGATCCAAATTTGCGGCCCTCGTTTGCACAGTTAACCAGTGCTTTGAAGACTGTCCAAAGGCTAGTAACCCCTTCTCACCAGGAGTCCCAGAGCCCTCCT
                            agctaat  putative branch site (score: 46)
                                         ttttt  putative PPT
                               taatatttggttttta  TA-rich tract