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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAATTGCCAAAGATGCTGTATTATCTAGATGTAAGATCATTGCTGAACCTTGGGATTGCGGCGGCCTTTATCTCGTAGGGCGTTTCCCTAACTGGGACAGgtgatttgaacacttctatatttctataaaaagaatttggtggtatagatgttttatccttgcttcttttaggactaaagatttggtgatacagtaacac...

Basic information

species Oryza sativa
transcript LOC_Os09g29404.1
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g29404.1 (Oryza sativa), 5'ss of exon 13
lower sequence: GRMZM2G150796_T02 (Zea mays), 5'ss of exon 13
AAATTGCCAAAGATGCTGTATTATCTAGATGTAAGATCATTGCTGAACCTTGGGATTGCGGCGGCCTTTATCTCGTAGGGCGTTTCCCTAACTGGGACAGgtgatttga--acacttctatatttctataaaaagaatttggtggtatagatgttttatccttgcttcttttaggactaaagatttggtgatacagtaacac
|||||||||||||  ||||||| |||||||||||||||||||||||||||||||| || || ||||||||||| |||||| | |||||||| |||||||||| ||||||    | || | |     ||  ||    |     ||    | ||||   | |    |   ||| ||   | |  | ||  |   | |||    |
AAATTGCCAAAGACTCTGTATTGTCTAGATGTAAGATCATTGCTGAACCTTGGGACTGTGGTGGCCTTTATCTAGTAGGGAGGTTCCCTAATTGGGACAGgtaatttgatagtaattttttgaacttactaatttgacaatatgacg-aaatgtacgaacga-acgaatttaagtgtttattactttatttcatagtttttc

upper sequence: LOC_Os09g29404.1 (Oryza sativa), 5'ss of exon 13
lower sequence: GLYMA06G10540.1 (Glycine max), 5'ss of exon 11
AAATTGCCAAAGATGCTGTATTATCTAGATGTAAGATCATTGCTGAACCTTGGGATTGCGGCGGCCTTTATCTCGTAGGGCGTTTCCCTAACTGGGACAGgtgat----ttg-----aacacttctatatttctataaaaagaatttggt--ggtatagatgttttatccttgcttcttttaggactaaagatttggtgatacagtaacac
  ||||| |||||||| |||||||| |||||||| || ||||| || ||||||||||| || || || ||||| || ||| |||| ||||| |||||  ||| ||    |||     ||   |||| ||||| | ||   |  ||||  |     |   || ||  | ||| || |        | |      |||||||           
CTATTGCTAAAGATGCAGTATTATCAAGATGTAAAATTATTGCAGAGCCTTGGGATTGTGGAGGTCTCTATCTTGTTGGGAGTTTTCCTAATTGGGATCGgtaatatttttgttgttaatgtttct-tatttttttagtgaatatttattttatgaataatattgaaccctagcgtagcagtaaagttgcaccttggtgac----------

upper sequence: LOC_Os09g29404.1 (Oryza sativa), 5'ss of exon 13
lower sequence: EFJ06781 (Selaginella moellendorffii), 5'ss of exon 14
AAATTGCCAAAGATGCTGTATTATCTAGATGTAAGATCATTGCTGAACCTTGGGATTGCGGCGGCCTTTATCTCGTAGGGCGTTTCCCTAACTGGGACAGgtgatttgaacacttctatatttctataaaaagaatttggtggtatagatgttttatccttg-cttcttttaggactaaagatttggtgatacagtaacac
 |||    || ||||  ||  | || |  || ||| | ||||| |||||||||||||| || ||||| ||| | |||||    || |||||||||||||||||       | | | | |||||||  || |     | | |  | ||    ||  |     | |||  |||   |                          
CAATATGTAAGGATGAAGTGCTGTCCAAGTGCAAGCTTATTGCCGAACCTTGGGATTGTGGAGGCCTGTATTTAGTAGGCGCGTTTCCTAACTGGGACAGgtg-------cgcctttctatttct-caagattggctcgctt-tgtaagccttccacttccgacttgatttttcag-------------------------

upper sequence: LOC_Os09g29404.1 (Oryza sativa), 5'ss of exon 13
lower sequence: EFJ21739 (Selaginella moellendorffii), 5'ss of exon 11
AAATTGCCAAAGATGCTGTATTATCTAGATGTAAGATCATTGCTGAACCTTGGGATTGCGGCGGCCTTTATCTCGTAGGGCGTTTCCCTAACTGGGACAGgtgatttgaacacttctatatttctataaaaagaatttggtggtatagatgttttatccttg-cttcttttaggactaaagatttggtgatacagtaacac
 |||    || ||||  ||  | || |  || ||| | ||||| |||||||||||||| || ||||| ||| | |||||    || |||||||||||||||     ||  || |||||| | ||    || |     | |   | ||    ||  |     | |||  |||   |                          
CAATATGTAAGGATGAAGTGCTGTCCAAGTGCAAGCTTATTGCCGAACCTTGGGATTGTGGAGGCCTGTATTTAGTAGGCGCGTTTCCTAACTGGGACAGg-----tgcgcatttctatttctc----aagattggctcgctttgtaagccttccacttccgacttgatttttcag-------------------------

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|218500325|gb|FG953825.1|FG953825
EST:     TGGGATTGCGGCGGCCTTTATCTCGTAGGGCGTTTCCCTAACTGGGACAG                         GTGGGCTGAATGGAACGGCAAATACAGAGATGATCTTCGAAGATTTATTAA
genomic: TGGGATTGCGGCGGCCTTTATCTCGTAGGGCGTTTCCCTAACTGGGACAGgtgatttgaa ... cctcttgcagGTGGGCTGAATGGAACGGCAAATACAGAGATGATCTTCGAAGATTTATTAA
EST: gi|58587143|gb|CF985451.1|CF985451
EST:     TGGGATTGCGGCGGCCTTTATCTCGTAGGGCGTTTCCCTAACTGGGACAG                         GTGGGCTGAATGGAACGGCAAATACAGAGATGATCTTCGAAGATTTATTAA
genomic: TGGGATTGCGGCGGCCTTTATCTCGTAGGGCGTTTCCCTAACTGGGACAGgtgatttgaa ... cctcttgcagGTGGGCTGAATGGAACGGCAAATACAGAGATGATCTTCGAAGATTTATTAA

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: 59 (upstream exon), 70 (downstream exon)
Score: 19

AAATTGCCAAAGATGCTGTATTATCTAGATGTAAGATCATTGCTGAACCTTGGGATTGCGGCGGCCTTTATCTCGTAGGGCGTTTCCCTAACTGGGACAGgtgatttgaa ... cctcttgcagGTGGGCTGAATGGAACGGCAAATACAGAGATGATCTTCGAAGATTTATTAAG




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