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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtatgctcaagtatatagttgtacagtttccaactggagcaattagacattatttgttacacattctaggtgtgatctatactttaagcatatggttatattttacttcacctgttttgataacatacacatgggatggtttgtgtgtgatgtgtgtagGTGATGGCAAAGAAGTTTGGTGCGGCAGTGGTCTCCCCTGAGCATCGGTACTACGGAAAGAGTTCCCCTTTTGAGAGTTTGACAACGGAAAATCTAAGGT

Basic information

species Oryza sativa
transcript LOC_Os10g36760.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g36760.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G031572_T01 (Zea mays), 3'ss of exon 2
gtgagtatgctcaagtatatagttgtacagt------ttccaactggagcaattagacattatttgttacacattctaggtgtgatctatactttaagcatatggttatattttacttcacctgttttgataacatacacatgggatggtttgtgtgtgatgtgtg---tagGTGATGGCAAAGAAGTTTGGTGCGGCAGTGGTCTCCCCTGAGCATCGGTACTACGGAAAGAGTTCCCCTTTTGAGAGTTTGACAACGGAAAATCTAAGGT
|| ||| |  |  |||||||||   | ||||      ||   | |  |   ||| |||||  | |  | |  | ||||  | |   | ||  || |     ||  || || |  ||      |||      |   |     |  |||    | |   | |||  ||   |||||| |||||||||| |||||||| ||| |||| || ||||||||||| ||||| ||||||||||| |||||| | ||||||||||| |||||||||  ||
gtaagtttaat-gagtatatagacatgcagtcacatatttttagttaaatgattggacatcttatactgcttactctaactctagac-atgattcatattcataatt-tactcaaccatttgtgtgcaacaactttggctgttagataacatatacat-atggatggattagGTGGTGGCAAAGAAATTTGGTGCTGCATTGGTTTCTCCTGAGCATCGATACTATGGAAAGAGTTCTCCTTTTAACAGTTTGACAACAGAAAATCTACAGT

upper sequence: LOC_Os10g36760.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv04s0023g03020.t01 (Vitis vinifera), 3'ss of exon 2
gtgagtatgctcaagtatatagttgtacagtttccaactggagcaattagacattatttgttacacattctaggtgtgatctatactttaagcatatggttatatttta-cttcacctgttttgataacatacacatgggatggtttgtgt-gtgatgt-gtgtagGTGATGGCAAAGAAGTTTGGTGCGGCAGTGGTCTCCCCTGAGCATCGGTACTACGGAAAGAGTTCCCCTTTTGAGAGTTTGACAACGGAAAATCTAAGGT
                                                                   |   |  |   ||| || ||   |   || |   |      |  || || ||| |    ||| | |  |    ||  |     | || |||| |   ||||  |||||||||| ||||| || || ||||| || | ||||||||| ||||| |||||||||||||| |||  |  | ||| ||| |||||||| |  |
------------------------------------------------------------------ctcaaaactaaaatccatcctcagattgtaggagcaaggaggagttttacttgtataacaaacttgctgaaaaaattctgaaccttgtaatgttggacagGTTTTGGCAAAGAAATTTGGAGCAGCTGTGGTTTCTCTTGAGCATCGCTACTATGGAAAGAGTTCCCCCTTTCGGTCTCTGAGAACAGAAAATCTGAAAT
















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|29667887|gb|CB664162.1|CB664162
EST:     ATATCTGTGGAGAATCTTCGTGCAACGGGATTCCTAACAGCTACTTAGCT                         GTGATGGCAAAGAAGTTTGGTGCGGCAGTGGTCTCCCCTGAGCATCGGTAC
genomic: ATATCTGTGGAGAATCTTCGTGCAACGGGATTCCTAACAGCTACTTAGCTgtgagtatgc ... atgtgtgtagGTGATGGCAAAGAAGTTTGGTGCGGCAGTGGTCTCCCCTGAGCATCGGTAC
EST: gi|33795268|gb|CF323506.1|CF323506
EST:     ATATCTGTGGAGAATCTTCGTGCAACGGGATTCCTAACAGCTACTTAGCT                         GTGATGGCAAAGAAGTTTGGTGCGGCAGTGGTCTCCCCTGAGCATCGGTAC
genomic: ATATCTGTGGAGAATCTTCGTGCAACGGGATTCCTAACAGCTACTTAGCTgtgagtatgc ... atgtgtgtagGTGATGGCAAAGAAGTTTGGTGCGGCAGTGGTCTCCCCTGAGCATCGGTAC
EST: gi|29635606|gb|CB640615.1|CB640615
EST:     ATATCTGTGGAGAATCTTCGTGCAACGGGATTCCTAACAGCTACTTAACT                         GTGATGGCAAAGAAGTTTGGTGCGGCAGTGGTCTCCCCTGAG
genomic: ATATCTGTGGAGAATCTTCGTGCAACGGGATTCCTAACAGCTACTTAGCTgtgagtatgc ... atgtgtgtagGTGATGGCAAAGAAGTTTGGTGCGGCAGTGGTCTCCCCTGAG
EST: gi|33797174|gb|CF324451.1|CF324451
EST:     ATATCTGTGGAGAATCTTCGTGCAACGGGATTCCTAACAGCTACTTAGCT                         GTGATGGCAAAGAAGTTTGGTGCGGCAGTGGTCTCCCCTGAGCATCGGTAC
genomic: ATATCTGTGGAGAATCTTCGTGCAACGGGATTCCTAACAGCTACTTAGCTgtgagtatgc ... atgtgtgtagGTGATGGCAAAGAAGTTTGGTGCGGCAGTGGTCTCCCCTGAGCATCGGTAC
EST: gi|29678499|gb|CB674774.1|CB674774
EST:     ATATCTGTGGAGAATCTTCGTGCAACGGGATTCCTAACAGCTACTTAGCT                         GTGATGGCAAAGAAGTTTGGTGCGGCAGTGGTCTCCCCTGAGCATCGGTAC
genomic: ATATCTGTGGAGAATCTTCGTGCAACGGGATTCCTAACAGCTACTTAGCTgtgagtatgc ... atgtgtgtagGTGATGGCAAAGAAGTTTGGTGCGGCAGTGGTCTCCCCTGAGCATCGGTAC
EST: gi|88315058|gb|CI610117.1|CI610117
EST:     ATATCTGTGGAGAATCTTCGTGCAACGGGATTCCTAACAGCTACTTAGCT                         GTGATGGCAAAGAAGTTTGGTGCGGCAG
genomic: ATATCTGTGGAGAATCTTCGTGCAACGGGATTCCTAACAGCTACTTAGCTgtgagtatgc ... atgtgtgtagGTGATGGCAAAGAAGTTTGGTGCGGCAG
EST: gi|33794179|gb|CF322980.1|CF322980
EST:     ATATCTGTGGAGAATCTTCGTGCAACGGGATTCCTAACAGCTACTTAGCT                         GTGATGGCAAAGAAGTTTGGTGCGGCAGTGGTCTCCCCTGAGCATCGGTAC
genomic: ATATCTGTGGAGAATCTTCGTGCAACGGGATTCCTAACAGCTACTTAGCTgtgagtatgc ... atgtgtgtagGTGATGGCAAAGAAGTTTGGTGCGGCAGTGGTCTCCCCTGAGCATCGGTAC

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: 71 (upstream exon), 74 (downstream exon)
Score: 27

CTATGAATTCCTTGATTACTACCGAGCTCCAAAAGGGCCAATTTTCTTATATATCTGTGGAGAATCTTCGTGCAACGGGATTCCTAACAGCTACTTAGCTgtgagtatgc ... atgtgtgtagGTGATGGCAAAGAAGTTTGGTGCGGCAGTGGTCTCCCCTGAGCATCGGTACTACGGAAAGAGTTCCCCTTTTGAGAGTTTGACAACGGAAAATCTAAGGT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acttcacctgttttgataacatacacatgggatggtttgtgtgtgatgtgtgtagGTGATGGCAAAGAAGTTTGGTGCGGCAGTGGTCTCCCCTGAGCATCGGTACTACGGAAAGAGTTCCCCTTTTGAGAGTTTGACAACGGAAAATCTAAGGT
             tgataac  putative branch site (score: 27)
          ttttgataa  TA-rich tract