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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttattcatgtgtaggaattaaatattccagtgagtttaaccagccatatattttcctataagaacttgttaactttatttagttcatgttctaaatgcagAGGAAGACCCTTCATCGAAGGTAGCCAAAGTGGAAGTGCCATCGCTAAGGCCTCCTGTTATGCCCAATCCAGCGGGCATGGTATATCCTCCACGACCGGC

Basic information

species Oryza sativa
transcript LOC_Os09g38790.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g38790.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G081812_T01 (Zea mays), 3'ss of exon 2
-----ttattcatgtgtaggaattaaatattccagtgagtttaaccagccatatattttcctataagaacttgttaactttatttagttcatgttctaaatgcagAGGAAGACCCTTCATCGAAGGTAGCCAAAGTGGAAGTGCCATCGCTAAGGCCTCCTGTTATGCCCAATCCAGCGGGCATGGTATATCCTCCACGACCGGC
     | | |    | || ||| | ||  || |  |   | || |   ||| | |      |||||    ||    ||||||  |      ||||| |  ||||||||||||||||||| | |||||| ||||||| ||||||||   | ||||||||  | ||||||| ||| |    ||||||| || |||||| ||||| ||
atgcataaattgaatttaagaactgaaacttgctattt-tgtaccattccagaaagagcgttataa----tttcccactttacctgacatttgttccacgtgcagAGGAAGACCCTTCAACAAAGGTACCCAAAGTAGAAGTGCCTCAGGTAAGGCCTGTTATTATGCCTAATTCGCTAGGCATGGCATTTCCTCCGCGACCAGC
















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|29655595|gb|CB651870.1|CB651870
EST:     TGGGATGCAAGGGATTCCTCCAGATGTGTTGGCCGCCCACTATGGAGAAG                         AGGAAGACCCTTCATCGAAGGTAGCCAAAGTGGAAGTGCCATCGCTAAGGC
genomic: TGGGATGCAAGGGATTCCTCCAGATGTGTTGGCCGCCCACTATGGAGAAGgtactgctat ... ctaaatgcagAGGAAGACCCTTCATCGAAGGTAGCCAAAGTGGAAGTGCCATCGCTAAGGC
EST: gi|29624560|gb|CB629571.1|CB629571
EST:     TGGGATGCAAGGGATTCCTCCAGATGTGTTGGCCGCCCACTATGGAGAAG                         AGGAAGACCCTTCATCGAAGGTAGCCAAAGTGGAAGTGCCATCGCTAAGGC
genomic: TGGGATGCAAGGGATTCCTCCAGATGTGTTGGCCGCCCACTATGGAGAAGgtactgctat ... ctaaatgcagAGGAAGACCCTTCATCGAAGGTAGCCAAAGTGGAAGTGCCATCGCTAAGGC
EST: gi|29630516|gb|CB635525.1|CB635525
EST:     TGGGATGCAAGGGATTCCTCCAGATGTGTTGGCCGCCCACTATGGAGAAG                         AGGAAGACCCTTCATCGAAGGTAGCCAAAGTGGAAGTGCCATCGCTAAGGC
genomic: TGGGATGCAAGGGATTCCTCCAGATGTGTTGGCCGCCCACTATGGAGAAGgtactgctat ... ctaaatgcagAGGAAGACCCTTCATCGAAGGTAGCCAAAGTGGAAGTGCCATCGCTAAGGC
EST: gi|58664656|gb|CK053342.1|CK053342
EST:     TGGGATGCAAGGGATTCCTCCAGATGTGTTGGCCGGCCACTATGGAGAAG                         AGGAAGACCCTTCATCGAAGGTAGCCCAAGTGGAAGTGGCATCGCTAAGGC
genomic: TGGGATGCAAGGGATTCCTCCAGATGTGTTGGCCGCCCACTATGGAGAAGgtactgctat ... ctaaatgcagAGGAAGACCCTTCATCGAAGGTAGCCAAAGTGGAAGTGCCATCGCTAAGGC

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), 73 (downstream exon)
Score: 51

GGTTCCCAATGCAAAGCCTGAGAGGGAATCAACAGAGATTGAGATCTTTGGGATGCAAGGGATTCCTCCAGATGTGTTGGCCGCCCACTATGGAGAAGgtactgctat ... ctaaatgcagAGGAAGACCCTTCATCGAAGGTAGCCAAAGTGGAAGTGCCATCGCTAAGGCCTCCTGTTATGCCCAATCCAGCGGGCATGGTATATCCTCCACGACCGGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atatattttcctataagaacttgttaactttatttagttcatgttctaaatgcagAGGAAGACCCTTCATCGAAGGTAGCCAAAGTGGAAGTGCCATCGCTAAGGCCTCCTGTTATGCCCAATCCAGCGGGCATGGTATATCCTCCACGACCGGC
                                           ttctaaa  putative branch site (score: 51)
                    ttgttaactttattta  TA-rich tract