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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TATCAAGGAGAGCATGGATGGAAGCCACGGAACTACACTGGACTATGTGATAAGATTCTTGCTAAAAGTCAAACTGTGgtatgtgtgatgtaggcattagaccaacctgaacccttttcgttggcatgaagagcacttatttaatatccatttaataatttgatcagtaaacaatgat...

Basic information

species Oryza sativa
transcript LOC_Os09g28570.1
intron # 15
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g28570.2 (Oryza sativa), 5'ss of exon 15
lower sequence: GRMZM2G479068_T01 (Zea mays), 5'ss of exon 3
TATCAAGGAGAGCATGGATGGAAGCCACGGAACTACACTGGACTATGTGATAAGATTCTTGCTAAAAGTCAAACTGTGgtatgt--gtgatgta-ggcattagaccaacctgaacccttttcgttggcatgaag--agcacttatttaatatccat-----ttaataatttgatcagta-aacaatgat----------------------------------------------------------------------------------
||||||||||||   ||||||||||||| ||| ||||||||| |||| || ||||||||||  |||||||| ||||||||||||  ||| || |   ||  | | | |   | || |||||     |   | ||  | |||  | | ||| |  |       |  |   || |  |  | ||| |  |                                                                                   
TATCAAGGAGAGGGAGGATGGAAGCCACAGAATTACACTGGATTATGCGAGAAGATTCTTGGGAAAAGTCAGACTGTGgtatgttcgtgctgaataacaccaaatctaaaaggacgcttttacacagatcgtagttatcacacactgaatctaaaaggacgcttctcgcttaactaccacaaccagaactagaaaaagaagtgcttttaaaagagccactgcaaggacaaatgaagcctaaaattatgagatatcatctttctaatttcag

upper sequence: LOC_Os09g28570.2 (Oryza sativa), 5'ss of exon 15
lower sequence: GRMZM2G147191_T02 (Zea mays), 5'ss of exon 15
TATCAAGGAGAGCATGGATGGAAGCCACGGAACTACACTGGACTATGTGATAAGATTCTTGCTAAAAGTCAAACTGTGgtatgtgtgatgtaggcattagaccaacctgaacccttttcgttggcatgaagagcact--tatttaatatccatttaataatttgatcagtaaacaatg-at----------------
|||||||||||| |||| |||||||||  ||||||||||||||||||||| |||||||| |||||||||||||||||||||||| | |             ||||| |      | || ||| | ||| |  |   |  |||||   || |||| || || ||| | || | |||||| ||                
TATCAAGGAGAGGATGGCTGGAAGCCAAAGAACTACACTGGACTATGTGAGAAGATTCTAGCTAAAAGTCAAACTGTGgtatgtctca-------------ccaactt------tgtttgttagaatgtactgtgatgatatttggcattcattaaacaaattggttaggagacaatgcatgtagtgtatttgatcc
















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|86876432|gb|CI318417.1|CI318417
EST:     GATTCTTTCTAAAAGTCAAACTGTG                         GCTGGTTTTTTCCTAATCCAGTATGCTCACTTGTGGCAAGATCATCTTGAC
genomic: GATTCTTGCTAAAAGTCAAACTGTGgtatgtgtga ... tcaacttcagGCTGGTTTTTTCCTAATCCAGTATGCTCACTTGTGGCAAGATCATCTTGAC
EST: gi|29670808|gb|CB667083.1|CB667083
EST:     GGAACTACACTGGACTATGTGATAAGATTCTTGCTAAAAGTCAAACTGTG                         GCTGGTTTTTTCCTAATCCAGTATGCTCACTTGTGGCAAGATCATCTTGAC
genomic: GGAACTACACTGGACTATGTGATAAGATTCTTGCTAAAAGTCAAACTGTGgtatgtgtga ... tcaacttcagGCTGGTTTTTTCCTAATCCAGTATGCTCACTTGTGGCAAGATCATCTTGAC
EST: gi|88834245|gb|CI000609.1|CI000609
EST:     GGAACTACACTGGACTATGTGATAAGATTCTTGCTATAAGTCAAACTGTG                         GCTGGTTTTTTCCTAATCCAGTATGCTCACTTGTGGCAAGATCATCTTGAC
genomic: GGAACTACACTGGACTATGTGATAAGATTCTTGCTAAAAGTCAAACTGTGgtatgtgtga ... tcaacttcagGCTGGTTTTTTCCTAATCCAGTATGCTCACTTGTGGCAAGATCATCTTGAC
EST: gi|66913912|gb|CX100760.1|CX100760
EST:     GGAACTACACTGGACTATGTGATAAGATTCTTGCTAAAAGTCAAACTGTG                         GCTGGTTTTTTCCTAATCCAGTATGCTCACTTGTGGCAAGATCATCTTGAC
genomic: GGAACTACACTGGACTATGTGATAAGATTCTTGCTAAAAGTCAAACTGTGgtatgtgtga ... tcaacttcagGCTGGTTTTTTCCTAATCCAGTATGCTCACTTGTGGCAAGATCATCTTGAC
EST: gi|86907581|gb|CI296578.1|CI296578
EST:     GGAACTACACTGGACTATGTGATAAGATTCTTGCTAAAAGTCAAACTGTG                         GCTGGTTTTTTCCTAATCCAGTATGCTCACTTGTGGCAAGATCATCTTGAC
genomic: GGAACTACACTGGACTATGTGATAAGATTCTTGCTAAAAGTCAAACTGTGgtatgtgtga ... tcaacttcagGCTGGTTTTTTCCTAATCCAGTATGCTCACTTGTGGCAAGATCATCTTGAC
EST: gi|33800750|gb|CF326245.1|CF326245
EST:     GCTAAAAGTCAAACTGTG                         GCTGGTTTTTTCCTAATCCAGTATGCTCACTTGTGGCAAGATCATCTTGAC
genomic: GCTAAAAGTCAAACTGTGgtatgtgtga ... tcaacttcagGCTGGTTTTTTCCTAATCCAGTATGCTCACTTGTGGCAAGATCATCTTGAC
EST: gi|3766964|gb|AU031074.1|AU031074
EST:     GGAACTACACTGGACTATGTGATAAGATTCTTGCTAAAAGTCAAACTGTG                         GCTGGTTTTTTCCTAATCCAGTATGGCTCACTTGTGGCAAGATCATCTTGG
genomic: GGAACTACACTGGACTATGTGATAAGATTCTTGCTAAAAGTCAAACTGTGgtatgtgtga ... tcaacttcagGCTGGTTTTTTCCTAATCCAGTATG-CTCACTTGTGGCAAGATCATCTTG-
EST: gi|29675620|gb|CB671895.1|CB671895
EST:     GGAACTACACTGGACTATGTGATAAGATTCTTGCTAAAAGTCAAACTGTG                         GCTGGTTTTTTCCTAATCCAGTATGCTCACTTGTGGCAAGATCATCTTGAC
genomic: GGAACTACACTGGACTATGTGATAAGATTCTTGCTAAAAGTCAAACTGTGgtatgtgtga ... tcaacttcagGCTGGTTTTTTCCTAATCCAGTATGCTCACTTGTGGCAAGATCATCTTGAC
EST: gi|87009274|gb|CI313747.1|CI313747
EST:     TTGCTAAAAGTCAAACTG-G                         GCCTGGTTTTTGTCCTAATCCAGTATGCTCACTTG-GGCAAGATCATCTTG
genomic: TTGCTAAAAGTCAAACTGTGgtatgtgtga ... tcaacttcagG-CTGGTTTTT-TCCTAATCCAGTATGCTCACTTGTGGCAAGATCATCTTG

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), 61 (downstream exon)
Score: 18

TATCAAGGAGAGCATGGATGGAAGCCACGGAACTACACTGGACTATGTGATAAGATTCTTGCTAAAAGTCAAACTGTGgtatgtgtga ... tcaacttcagGCTGGTTTTTTCCTAATCCAGTATGCTCACTTGTGGCAAGATCATCTTGACAAACTTTTTGACCTGTATGCCTCTGGAAAGCTAAAG




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