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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtgttttttcctatccactatatgtcaatatattatgagcacattttatgcagtgtcaagtaatatacaacttagattttctaatatttcagGATGAAGTTGTTGCAAGAGACGAGGGAATAAGGCGAGAGTATAATGAGCTCGACACACTGTGGTTCATGGCAGGTTCATTGTTTCAG

Basic information

species Oryza sativa
transcript LOC_Os12g13460.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g13460.1 (Oryza sativa), 3'ss of exon 3
lower sequence: AC198982.3_FGT006 (Zea mays), 3'ss of exon 1
gttagtgttttt----tcctatccactatatgtcaatatattatgagcacatttta----tgcagtgtcaagtaatatac------aacttagattttctaa-----------tattt-cagGATGAAGTTGTTGCAAGAGACGAGGGAATAAGGCGAGAGTATAATGAGCTCGACACACTGTGGTTCATGGCAGGTTCATTGTTTCAG
||||||| ||||    |  | |     |  | ||||| ||  || |   |  |||     |||||  | |   ||||| |      ||| |  || | ||||           | ||| ||||||||||||||||| ||||| |||| ||||||| |||||||||||||||| |||||| ||||||| |||||||||||| | ||||||
gttagtggttttactcttttgtatctcaattctcaatgtaacattattgccatttgacgttgcaggattattcaatattctgcaaaaacatcaatatcctaacttagatgatatgtttgcagGATGAAGTTGTTGCTAGAGATGAGGCAATAAGGAGAGAGTATAATGAGCTTGACACATTGTGGTTTATGGCAGGTTCACTATTTCAG

upper sequence: LOC_Os12g13460.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G047695_T01 (Zea mays), 3'ss of exon 3
gttagtgttttttcc----tatccactatatgtcaatatattatgagcacatttta----tgcagtgtcaagtaatatac------aacttagattttctaatat------------ttcagGATGAAGTTGTTGCAAGAGACGAGGGAATAAGGCGAGAGTATAATGAGCTCGACACACTGTGGTTCATGGCAGGTTCATTGTTTCAG
||||||| |||| |     |       |  | ||||||||  || |   | ||||     || ||  | |    |||| |      ||| |  || | |||| ||            | ||||||||||||||||| ||||| |||| ||||||| |||||||||||||||| |||||| ||||||| |||||||||||| | ||||||
gttagtggttttactatgttgcatctcaattctcaatataacattattgctttttgatattgaaggattacacgatattctgtaagaacattaatatcctaacatagctgatatatttgcagGATGAAGTTGTTGCTAGAGATGAGGCAATAAGGAGAGAGTATAATGAGCTTGACACATTGTGGTTTATGGCAGGTTCACTATTTCAG
















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|58672789|gb|CK061475.1|CK061475
EST:     TTCTGTGGACCGAAAGTGAACTGAACTACCTGAAGGGTAGCCCCATCAAG                         GATGAAGTTGTTGCAAGAGACGAGGGAATAAGGCGAGAGTATAATGAGCTC
genomic: TTCTGTGGACCGAAAGTGAACTGAACTACCTGAAGGGTAGCCCCATCAAGgttagtgttt ... aatatttcagGATGAAGTTGTTGCAAGAGACGAGGGAATAAGGCGAGAGTATAATGAGCTC
EST: gi|38470357|gb|CF954488.1|CF954488
EST:     TTCTGTGGACCGAAAGTGAACTGAACTACCTGAAGGGTAGCCCCATCAAG                         GATGAAGTTGTTGCAAGAGACGAGGGAATAAGGCGAGAGTATAATGAGCTC
genomic: TTCTGTGGACCGAAAGTGAACTGAACTACCTGAAGGGTAGCCCCATCAAGgttagtgttt ... aatatttcagGATGAAGTTGTTGCAAGAGACGAGGGAATAAGGCGAGAGTATAATGAGCTC
EST: gi|25801429|gb|CA757390.1|CA757390
EST:     TTCTGTGGACCGAAAGTGAACTGAACTACCTGAAGGGTAGCCCCATCAAG                         GATGAAGTTGTTGCAAGAGACGAGGGAATAAGGCGAGAGTATAATGAGCTC
genomic: TTCTGTGGACCGAAAGTGAACTGAACTACCTGAAGGGTAGCCCCATCAAGgttagtgttt ... aatatttcagGATGAAGTTGTTGCAAGAGACGAGGGAATAAGGCGAGAGTATAATGAGCTC
EST: gi|29657714|gb|CB653989.1|CB653989
EST:     TTCTGTGGACCGAAAGTGAACTGAACTACCTGAAGGGTACCCCCATCAAG                         GATGAAGTTGTTGCGAGAGACGAGGGAATAAGGCGAGAGTATAATGAGCTC
genomic: TTCTGTGGACCGAAAGTGAACTGAACTACCTGAAGGGTAGCCCCATCAAGgttagtgttt ... aatatttcagGATGAAGTTGTTGCAAGAGACGAGGGAATAAGGCGAGAGTATAATGAGCTC
EST: gi|33676615|gb|CF304854.1|CF304854
EST:     TTCTGTGGACCGAAAGTGAACTGAACTACCTGAAGGGTAGCCCCATCAAG                         GATGAAGTTGTTGCAAGAGACGAGGGAATAAGGCGAGAGTATAATGAGCTC
genomic: TTCTGTGGACCGAAAGTGAACTGAACTACCTGAAGGGTAGCCCCATCAAGgttagtgttt ... aatatttcagGATGAAGTTGTTGCAAGAGACGAGGGAATAAGGCGAGAGTATAATGAGCTC

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), 72 (downstream exon)
Score: 11

GGAGCTTGATCGCCAGCGAGGAAGGGGGCAATTAGCTGTTGAATCTCCACTTCTGTGGACCGAAAGTGAACTGAACTACCTGAAGGGTAGCCCCATCAAGgttagtgttt ... aatatttcagGATGAAGTTGTTGCAAGAGACGAGGGAATAAGGCGAGAGTATAATGAGCTCGACACACTGTGGTTCATGGCAGGTTCATTGTTTCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agcacattttatgcagtgtcaagtaatatacaacttagattttctaatatttcagGATGAAGTTGTTGCAAGAGACGAGGGAATAAGGCGAGAGTATAATGAGCTCGACACACTGTGGTTCATGGCAGGTTCATTGTTTCAG
                                         ttctaat  putative branch site (score: 11)
                                       ttttcta  CT-rich tract
                       taatatacaacttaga  TA-rich tract