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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacaacagaaatttcttgagtctccttcacccgcttgtatgttgccattggcgccttatatatgttactcaatacatgaaacccaaattctatttccagGAAGCTGTTGACATGGTGAGGCCTATTCAGGATCCCGAACAGGCAGCGAAGAGGCTTCTCCAGGAGGCGTACCAAAGGGGTAGCGCCGATAACATCACCG

Basic information

species Oryza sativa
transcript LOC_Os02g05630.4
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g05630.3 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM5G829894_T03 (Zea mays), 3'ss of exon 2
gtaacaacagaaatttcttgagtctccttcacccgcttgtatgttgccattggcgccttatatatgttactcaatacatgaaacccaaattctatttccagGAAGCTGTTGACATGGTGAGGCCTATTCAGGATCCCGAACAGGCAGCGAAGAGGCTTCTCCAGGAGGCGTACCAAAGGGGTAGCGCCGATAACATCACCG
            |  |   ||   | ||  |     |  |    ||| |||||     | | | ||| ||||  ||| |||  |   |  | | ||||||||||||||||| |||||| | |||||||||||| ||| |  | ||||| || | ||||||| | || |||| || |||||| ||| | |||||||||||||
----------gtacctacagatattgctaaatatattcattcagtgcaattgg-----tctgtctgtcactct-tacctga--cgttatgtatttttccagGAAGCTGTTGCCATGGTCAAGCCTATTCAGGACCCCCAGGAAGCAGCAAACAAGCTTCTCGAAGAAGCGTCCCGAAGGGGAAGCTCTGATAACATCACCG
















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|66916002|gb|CX102850.1|CX102850
EST:     AGTTCCTCATCCTTGCTAGCGATGGACTTTGGGATGTTGTAAGTAACAAG                         GAAGCTGTTGACATGGTGAGGCCTATTCAGGATCCCGAACAGGCAGCGAAG
genomic: AGTTCCTCATCCTTGCTAGCGATGGACTTTGGGATGTTGTAAGTAACAAGgtaacaacag ... ctatttccagGAAGCTGTTGACATGGTGAGGCCTATTCAGGATCCCGAACAGGCAGCGAAG
EST: gi|29677669|gb|CB673944.1|CB673944
EST:     AGTTCCTCATCCTTGCTAGCGATGGACTTTGGGATGTTGTAAGTAACAAG                         GAAGCTGTTGACATGGTGAGGCCTATTCAGGATCCCGAACAGGCAGCGAAG
genomic: AGTTCCTCATCCTTGCTAGCGATGGACTTTGGGATGTTGTAAGTAACAAGgtaacaacag ... ctatttccagGAAGCTGTTGACATGGTGAGGCCTATTCAGGATCCCGAACAGGCAGCGAAG
EST: gi|163926798|gb|EG715086.1|EG715086
EST:     AGTTCCTCATCCTTGCTAGCGATGGACTTTGGGATGTTGTAAGTAACAAG                         GAAGCTGTTGACATGGTGAGGCCTATTCAGGATCCCGAACAGGCAGCGAAG
genomic: AGTTCCTCATCCTTGCTAGCGATGGACTTTGGGATGTTGTAAGTAACAAGgtaacaacag ... ctatttccagGAAGCTGTTGACATGGTGAGGCCTATTCAGGATCCCGAACAGGCAGCGAAG
EST: gi|3767442|gb|AU031552.1|AU031552
EST:     AGTTCCTCATCCTTGCTAGCGATGGACTTTGGGATGTTGTAAGTAACAAG                         GAAGCTGTTGACATGGTGAGGCCTATTCAGGATCCCGAACAGGCAGCGAAG
genomic: AGTTCCTCATCCTTGCTAGCGATGGACTTTGGGATGTTGTAAGTAACAAGgtaacaacag ... ctatttccagGAAGCTGTTGACATGGTGAGGCCTATTCAGGATCCCGAACAGGCAGCGAAG
EST: gi|29662048|gb|CB658323.1|CB658323
EST:     AGTTCCTCATCCTTGCTAGCGATGGACTTTGGGATGTTGTAAGTAACAAG                         GAAGCTGTTGACATGGTGAGGCCTATTCAGGATCCCGAACAGGCAGCGAAG
genomic: AGTTCCTCATCCTTGCTAGCGATGGACTTTGGGATGTTGTAAGTAACAAGgtaacaacag ... ctatttccagGAAGCTGTTGACATGGTGAGGCCTATTCAGGATCCCGAACAGGCAGCGAAG
EST: gi|29615476|gb|CB620488.1|CB620488
EST:     AGTTCCTCATCCTTGCTAGCGATGGACTTTGGGATGTTGTAAGTAACAAG                         GAAGCTGTTGACATGGTGAGGCCTATTCAGGATCCCGAACAGGCAGCGAAG
genomic: AGTTCCTCATCCTTGCTAGCGATGGACTTTGGGATGTTGTAAGTAACAAGgtaacaacag ... ctatttccagGAAGCTGTTGACATGGTGAGGCCTATTCAGGATCCCGAACAGGCAGCGAAG
EST: gi|29666985|gb|CB663260.1|CB663260
EST:     AGTTCCTCATCCTTGCTAGCGATGGACTTTGGGATGTTGTAAGTAACAAG                         GAAGCTGTTGACATGGTGAGGCCTATTCAGGATCCCGAACAGGCAGCGAAG
genomic: AGTTCCTCATCCTTGCTAGCGATGGACTTTGGGATGTTGTAAGTAACAAGgtaacaacag ... ctatttccagGAAGCTGTTGACATGGTGAGGCCTATTCAGGATCCCGAACAGGCAGCGAAG
EST: gi|163920197|gb|EG714431.1|EG714431
EST:     AGTTCCTCATCCTTGCTAGCGATGGACTTTGGGATGTTGTAAGTAACAAG                         GAAGCTGTTGACATGGTGAGGCCTATTCAGGATCCCGAACAGGCAGCGAAG
genomic: AGTTCCTCATCCTTGCTAGCGATGGACTTTGGGATGTTGTAAGTAACAAGgtaacaacag ... ctatttccagGAAGCTGTTGACATGGTGAGGCCTATTCAGGATCCCGAACAGGCAGCGAAG
EST: gi|29666852|gb|CB663127.1|CB663127
EST:     AGTTCCTCATCCTTGCTAGCGATGGACTTTGGGATGTTGTAAGTAACAAG                         GAAGCTGTTGACATGGTGAGGCCTATTCAGGATCCCGAACAGGCAGCGAAG
genomic: AGTTCCTCATCCTTGCTAGCGATGGACTTTGGGATGTTGTAAGTAACAAGgtaacaacag ... ctatttccagGAAGCTGTTGACATGGTGAGGCCTATTCAGGATCCCGAACAGGCAGCGAAG
EST: gi|33681625|gb|CF309864.1|CF309864
EST:     AGTTCCTCATCCTTGCTAGCGATGGACTTTGGGATGTTGTAAGTAACAAG                         GAAGCTGTTGACATGGTGAGGCCTATTCAGGATCCCGAACAGGCAGCGAAG
genomic: AGTTCCTCATCCTTGCTAGCGATGGACTTTGGGATGTTGTAAGTAACAAGgtaacaacag ... ctatttccagGAAGCTGTTGACATGGTGAGGCCTATTCAGGATCCCGAACAGGCAGCGAAG
EST: gi|568785|gb|D39634.1|D39634
EST:     AGTTCCTCATCCTTGCTAGCGATGGACTTTGGGATGTTGTAAGTAACAAG                         GAAGCTGTTGACATGGTGAGGCCTATTCAGGATCCCGAACAGGCAGCGAAG
genomic: AGTTCCTCATCCTTGCTAGCGATGGACTTTGGGATGTTGTAAGTAACAAGgtaacaacag ... ctatttccagGAAGCTGTTGACATGGTGAGGCCTATTCAGGATCCCGAACAGGCAGCGAAG
EST: gi|87019102|gb|CI297303.1|CI297303
EST:     CGTTCCTCATCCTTGCTAGCGATGGACTTTGGGATGTTGTAAGTAACAAG                         GAAGCTGTTGACATGGTGAGGCCTATTCAGGATCCCGAACAGGCAGCGAAG
genomic: -GTTCCTCATCCTTGCTAGCGATGGACTTTGGGATGTTGTAAGTAACAAGgtaacaacag ... ctatttccagGAAGCTGTTGACATGGTGAGGCCTATTCAGGATCCCGAACAGGCAGCGAAG

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: 59

GAGGAGATTGTCGATAGCTCCCTTGAGTTCCTCATCCTTGCTAGCGATGGACTTTGGGATGTTGTAAGTAACAAGgtaacaacag ... ctatttccagGAAGCTGTTGACATGGTGAGGCCTATTCAGGATCCCGAACAGGCAGCGAAGAGGCTTCTCCAGGAGGCGTACCAAAGGGGTAGCGCCGATAACATCACCG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccattggcgccttatatatgttactcaatacatgaaacccaaattctatttccagGAAGCTGTTGACATGGTGAGGCCTATTCAGGATCCCGAACAGGCAGCGAAGAGGCTTCTCCAGGAGGCGTACCAAAGGGGTAGCGCCGATAACATCACCG
                                           ttctatttcc  CT-rich tract
           ttatatatgttact  TA-rich tract