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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagcactctgtagttaccacttagtccagtatcatcttgctgtgaaggcaaatgttcaccttgttaattttttttttctgttggcagGTTACTGCGGTGAAGCTAAAGAATGGAAACGTGCTGGAAGCTGACATTGTTATTGTCGGTGTCGGTGGCAGGCCACTGACTCATCTCTTCAAGGGTCAAG

Basic information

species Oryza sativa
transcript LOC_Os08g44340.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g44340.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G134708_T01 (Zea mays), 3'ss of exon 7
-------gtgagcactctgtagttaccacttagtccagt--atcatct-tgctgtgaaggcaaatgttcaccttgttaattttttttttctgttggcagGTTACTGCGGTGAAGCTAAAGAATGGAAACGTGCTGGAAGCTGACATTGTTATTGTCGGTGTCGGTGGCAGGCCACTGACTCATCTCTTCAAGGGTCAAG
        ||| ||||||| || |  || ||| || | |  || || | |||| |||| |  | ||||||||||  |              | || ||||| ||| | |||||| | ||||||||||  || || |||||||| ||||||||||| || ||||| ||||||||| |||| | ||||||||  || ||||
gtgagcactgaacactctgcagat-tcagttaatcaattttataatgtgtgctctgaatgttattgttcaccttaatg-------------gatgccagGTCACTACAGTGAAGTTGAAGAATGGAAGTGTTCTCGAAGCTGATATTGTTATTGTTGGCGTCGGCGGCAGGCCATTGACGCGTCTCTTCATAGGCCAAG

upper sequence: LOC_Os08g44340.1 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv08s0007g03610.t01 (Vitis vinifera), 3'ss of exon 7
gtgagcactctgtagttaccacttagtccagtatcatcttgctgtgaaggcaaatgttcaccttgttaattttttttttctgttgg-cagGTTACTGCGGTGAAGCTAAAGAATGGAAACGTGCTGGAAGCTGACATTGTTATTGTCGGTGTCGGTGGCAGGCCACTGACTCATCTCTTCAAGGGTCAAG
|| |   ||  |   |  |   |  ||  | | |  | ||  | ||   ||||| |       |||     |||   |  | |    ||||| |  |  ||||| || ||| |||| |  ||||||||||||||||||||| |||| ||||| ||||| || || || ||     | ||||| || || |
gtaatttcttggacat--ctgatatgttaattttagtatttatttgggagcaaaagccttttatgtagcaatttgagtcttatcattcagGTAAAGGAAGTGAAACTTAAGGATGGTAGGGTGCTGGAAGCTGACATTGTTGTTGTTGGTGTTGGTGGAAGACCCCTTACAACATTATTCAAAGGACAGG
















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|29662249|gb|CB658524.1|CB658524
EST:     GTGGCTGTTGGTTTTGATGCTGATGCCAATGGAGAT                         GTTACTGCGGTGAAGCTAAAGAATGGAAACGTGCTGGAAGCTGACATTGTT
genomic: GTGGCTGTTGGTTTTGATGCTGATGCCAATGGAGATgtgagcactc ... ctgttggcagGTTACTGCGGTGAAGCTAAAGAATGGAAACGTGCTGGAAGCTGACATTGTT
EST: gi|33691642|gb|CF319881.1|CF319881
EST:     TCATAAAGGGAACCGTGGCTGTTGGTTTTGATGCTGATGCCAATGGAGAT                         GTTACTGCGGTGAAGCTAAAGAATGGAAACGTGCTGGAAGCTGACATTGTC
genomic: TCATAAAGGGAACCGTGGCTGTTGGTTTTGATGCTGATGCCAATGGAGATgtgagcactc ... ctgttggcagGTTACTGCGGTGAAGCTAAAGAATGGAAACGTGCTGGAAGCTGACATTGTT
EST: gi|38568445|gb|CD670660.1|CD670660
EST:     TCATAAANGGAACCGTGGCTGTTGGTTTTGATGCTGATGCCAATGGAGAT                         GTTACTGCNGTGAAGCTAAAGAATGGAAACGTGCTGGAAGCTGA
genomic: TCATAAAGGGAACCGTGGCTGTTGGTTTTGATGCTGATGCCAATGGAGATgtgagcactc ... ctgttggcagGTTACTGCGGTGAAGCTAAAGAATGGAAACGTGCTGGAAGCTGA
EST: gi|33681535|gb|CF309774.1|CF309774
EST:     TCATAAAGGGAACCGTGGCTGTTGGTTTTGATGCTGATGCCAATGGAGAT                         GTTACTGCGGTGAAGCTAAAGAATGGAAACGTGCTGGAAGCTGACATTGTT
genomic: TCATAAAGGGAACCGTGGCTGTTGGTTTTGATGCTGATGCCAATGGAGATgtgagcactc ... ctgttggcagGTTACTGCGGTGAAGCTAAAGAATGGAAACGTGCTGGAAGCTGACATTGTT
EST: gi|29636698|gb|CB641707.1|CB641707
EST:     TCATAAAGGGAACCGTGGCTGTTGGTTTTGATGCTGATGCCAATGGAGAT                         GTTACTGCGGTGAAGCTAAAGAATGGAAACGTGCT
genomic: TCATAAAGGGAACCGTGGCTGTTGGTTTTGATGCTGATGCCAATGGAGATgtgagcactc ... ctgttggcagGTTACTGCGGTGAAGCTAAAGAATGGAAACGTGCT
EST: gi|66912833|gb|CX099681.1|CX099681
EST:     TCATAAAGGGAACCGTGGCTGTTGGTTTTGATGCTGATGCCAATGGAGAT                         GTTACTGCGGTGAAGCTAAAGAATGGAAACGTGCTGGAAGCTGACATTGTT
genomic: TCATAAAGGGAACCGTGGCTGTTGGTTTTGATGCTGATGCCAATGGAGATgtgagcactc ... ctgttggcagGTTACTGCGGTGAAGCTAAAGAATGGAAACGTGCTGGAAGCTGACATTGTT

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: 70 (upstream exon), 71 (downstream exon)
Score: 59

TGGCCTTGCTGCTTTCTACGAGGGATACTACGCTAACAAAGGAATCCATATCATAAAGGGAACCGTGGCTGTTGGTTTTGATGCTGATGCCAATGGAGATgtgagcactc ... ctgttggcagGTTACTGCGGTGAAGCTAAAGAATGGAAACGTGCTGGAAGCTGACATTGTTATTGTCGGTGTCGGTGGCAGGCCACTGACTCATCTCTTCAAGGGTCAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catcttgctgtgaaggcaaatgttcaccttgttaattttttttttctgttggcagGTTACTGCGGTGAAGCTAAAGAATGGAAACGTGCTGGAAGCTGACATTGTTATTGTCGGTGTCGGTGGCAGGCCACTGACTCATCTCTTCAAGGGTCAAG
                             tgttaat  putative branch site (score: 59)
                          ccttgttaattttttt  CT-rich tract
                            ttgttaattttttttt  TA-rich tract