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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgttcttcaacctcattttggttgctacttcttctgaattgtcttattcttccagctaactaccattttcagGCGATAGCACTGCCCAGGAGCTCTTTGGTTTCGGAACGTGTTGGTGATCATGTACTCATCAGCAAAAGTAATGCCTGGCAAATCAAAGTAAACAGTATTT

Basic information

species Oryza sativa
transcript LOC_Os01g72340.1
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g72340.1 (Oryza sativa), 3'ss of exon 15
lower sequence: GRMZM2G032496_T01 (Zea mays), 3'ss of exon 6
------------------------------------------------------------------------------------------------------gtacgttcttcaacctcattttggttgctacttcttctgaattgtcttattcttccagctaactaccattttcagGCGATAGCACTGCCCAGGAGCTCTTTGGTTTCGGAACGTGTTGGTGATCATGTACTCATCAGCAAAAGTAATGCCTGGCAAATCAAAGTAAACAGTATTT
                                                                                                          ||    || | |  | ||  ||  |||| ||  |   |  || |  |||| ||||| | || ||| |||||| ||||||| || |||| ||| ||||||| |  |||||  |||||||| |||||  |||| |||| | |||||||||| |||| ||||||||||||   |
gtatgttttctcagcctgatcttgtttactactatactcctgtttggctgtttcgtcctcatcgtctaacagcttaatactattttactcctgtttcgtcctcattgtctcacagcttagtgttactt--tactcctgtttcttcctcgttgtcttacagcttaatatcatcttcagGTGATAGCATTGTCCAGTAGCCCTTTGGTCTGTGAACGCATTGGTGATAATGTAACCATCTGCAAGAATAATGCCTGGAAAATTAAAGTAAACAGTCAGT
















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|88344079|gb|CI638814.1|CI638814
EST:     TGGCTTCAGCACAAATTTGTTTACCTCCGAAAAAAGGCTTTGTCCCTCAT                         GCGATAGCACTGCCCAGGAGCTCTTTGGTTTCGGAACGTGTTGGTGATCAT
genomic: TGGCTTCAGCACAAATTTGTTTACCTCCGAAAAAAGGCTTTGTCCCTCATgtacgttctt ... ccattttcagGCGATAGCACTGCCCAGGAGCTCTTTGGTTTCGGAACGTGTTGGTGATCAT
EST: gi|58596245|gb|CK006773.1|CK006773
EST:     TGGCTTCAGCACAAATTTGTTTACCTCCGAAAAAAGGCTTGGTCCCTCAT                         GCGATAGCACTGCCCAGGAGCTCTTTGGTTTCGGAACGTGTTGGTGATCAT
genomic: TGGCTTCAGCACAAATTTGTTTACCTCCGAAAAAAGGCTTTGTCCCTCATgtacgttctt ... ccattttcagGCGATAGCACTGCCCAGGAGCTCTTTGGTTTCGGAACGTGTTGGTGATCAT
EST: gi|58681122|gb|CK069809.1|CK069809
EST:     TGGCTTCAGCACAAATTTGTTTACCTCCGAAAAAAGGCTTTGTCCCTCAT                         GCGATAGCACTGCCCAGGAGCTCTTTGGTTTCGGAACGTGTTGGTGATCAT
genomic: TGGCTTCAGCACAAATTTGTTTACCTCCGAAAAAAGGCTTTGTCCCTCATgtacgttctt ... ccattttcagGCGATAGCACTGCCCAGGAGCTCTTTGGTTTCGGAACGTGTTGGTGATCAT
EST: gi|87012504|gb|CI307252.1|CI307252
EST:     TGGCTTCAGCACAAATTTGTTTACCTCCGAAAAAAGGCTTTGTCCCTCAT                         GCGATAGCACTGCCCAGGAGCTCTTTGGTTTCGGAACGTGTTGGTGATCAT
genomic: TGGCTTCAGCACAAATTTGTTTACCTCCGAAAAAAGGCTTTGTCCCTCATgtacgttctt ... ccattttcagGCGATAGCACTGCCCAGGAGCTCTTTGGTTTCGGAACGTGTTGGTGATCAT
EST: gi|86905446|gb|CI285409.1|CI285409
EST:     TGGCTTCAGCACAAATTTGTTTACCTCCGAAAAAAGGCTTTGTCCCTCAT                         GCGATAGCACTGCCCAGGAGCTCTTTGGTTTCGGAACGTGTTGGTGATCAT
genomic: TGGCTTCAGCACAAATTTGTTTACCTCCGAAAAAAGGCTTTGTCCCTCATgtacgttctt ... ccattttcagGCGATAGCACTGCCCAGGAGCTCTTTGGTTTCGGAACGTGTTGGTGATCAT
EST: gi|29677247|gb|CB673522.1|CB673522
EST:     TGGCTTCAGCACAAATTTGTTTACCTCCGAAAAAAGGCTTTGTCCCTCAT                         GCGATAGCACTGCCCAGGAGCTCTTTGGTTTCGGAACGTGTTGGTGATCAT
genomic: TGGCTTCAGCACAAATTTGTTTACCTCCGAAAAAAGGCTTTGTCCCTCATgtacgttctt ... ccattttcagGCGATAGCACTGCCCAGGAGCTCTTTGGTTTCGGAACGTGTTGGTGATCAT

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), 72 (downstream exon)
Score: 35

TAACGTGAAATTGAGGTACCAAACACAATGGGCCAAAGATGGCCATATCTTGGCTTCAGCACAAATTTGTTTACCTCCGAAAAAAGGCTTTGTCCCTCATgtacgttctt ... ccattttcagGCGATAGCACTGCCCAGGAGCTCTTTGGTTTCGGAACGTGTTGGTGATCATGTACTCATCAGCAAAAGTAATGCCTGGCAAATCAAAGTAAACAGTATTT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttggttgctacttcttctgaattgtcttattcttccagctaactaccattttcagGCGATAGCACTGCCCAGGAGCTCTTTGGTTTCGGAACGTGTTGGTGATCATGTACTCATCAGCAAAAGTAATGCCTGGCAAATCAAAGTAAACAGTATTT
                                    agctaac  putative branch site (score: 35)
                                             ccattttc  putative PPT
                          ttattctt  TA-rich tract