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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAAAAGAATCCGGAGACGGCGTTCTCAAACAAGAAATCAGCACTTGTAAAGATAATCGAGGAATCTCCTGTCCGTAAAACAATTATTTTCTGCAACAAGgtagttcctctccagtattccagcatacgatctgcaaccaaaaagagtttgcagtgtatctgacagatggattttttttttgtggtggtgttag

Basic information

species Oryza sativa
transcript LOC_Os03g01830.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g01830.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G113267_T02 (Zea mays), 5'ss of exon 6
GGAAAAGAATCCGGAGACGGCGTTCTCAAACAAGAAATCAGCACTTGTAAAGATAATCGAGGAATCTCCTGTCCGTAAAACAATTATTTTCTGCAACAAGgtagttcctctcc--agtattcca---gcatacgatctgcaaccaaaaagagtttgcagtgtatctgacagatggattttttttttgtggtggtgttag
 ||||||||||| || || || || || ||||||||| |||| ||| | ||||| |||||||| ||||||||||| ||||||||| |||||||||||||||||  |||  |||  |  |  ||    ||| ||      ||  || | ||||    ||   |  |   | |||| ||||| |||   || | |      
AGAAAAGAATCCAGAAACCGCCTTTTCGAACAAGAAAACAGCGCTTTTGAAGATTATCGAGGAGTCTCCTGTCCGCAAAACAATTGTTTTCTGCAACAAGgtaagtcccttccctaacaccccctgtgcacactgatgacaggcagacagagaaatcacactgcccc-ctgatg-attttatttccttgctag------
















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|29646792|gb|CB651799.1|CB651799
EST:     AGATAATCGAGGAATCTCCTGTCCGTAAAACAATTATTTTCTGCAACAAG                         ATTGAGACATGCAGAAAGGTTGAGAATGCGCTGAGGCGGGTGGACAGGAAG
genomic: AGATAATCGAGGAATCTCCTGTCCGTAAAACAATTATTTTCTGCAACAAGgtagttcctc ... gtggtgttagATTGAGACATGCAGAAAGGTTGAGAATGCGCTGAGGCGGGTGGACAGGAAG
EST: gi|29625765|gb|CB630776.1|CB630776
EST:     AGATAATCGAGGAATCTCCTGTCCGTAAAACAATTATTTTCTGCAACAAG                         ATTGAGACATGCAGAAAGGTTGAGAATGCGCTGAGGCGGGTGGACAGGAAG
genomic: AGATAATCGAGGAATCTCCTGTCCGTAAAACAATTATTTTCTGCAACAAGgtagttcctc ... gtggtgttagATTGAGACATGCAGAAAGGTTGAGAATGCGCTGAGGCGGGTGGACAGGAAG
EST: gi|29641693|gb|CB646700.1|CB646700
EST:     TGTCCGTAAAACAATTATTTTCTGCAACAAG                         ATTGAGACATGCAGAAAGGTTGAGAATGCGCTGAGGCGGGTGGACAGGAAG
genomic: TGTCCGTAAAACAATTATTTTCTGCAACAAGgtagttcctc ... gtggtgttagATTGAGACATGCAGAAAGGTTGAGAATGCGCTGAGGCGGGTGGACAGGAAG
EST: gi|313081075|gb|HO213661.1|HO213661
EST:     AGATAATCGAGGAATCTCCTGTCCGTAAAACAATTATTTTCTGCAACAAG                         ATTGAGACATGCAGAAAGGTTGAGAATGCGCTGAGGCGGGTGGACAGGAAG
genomic: AGATAATCGAGGAATCTCCTGTCCGTAAAACAATTATTTTCTGCAACAAGgtagttcctc ... gtggtgttagATTGAGACATGCAGAAAGGTTGAGAATGCGCTGAGGCGGGTGGACAGGAAG
EST: gi|313079579|gb|HO213137.1|HO213137
EST:     AGATAATCGAGGAATCTCCTGTCCGTAAAACAATTATTTTCTGCAACAAG                         ATTGAGACATGCAGAAAGGTTGAGAATGCGCTGAGGCGGGTGGACAGGAAG
genomic: AGATAATCGAGGAATCTCCTGTCCGTAAAACAATTATTTTCTGCAACAAGgtagttcctc ... gtggtgttagATTGAGACATGCAGAAAGGTTGAGAATGCGCTGAGGCGGGTGGACAGGAAG
EST: gi|29628634|gb|CB633645.1|CB633645
EST:     AGATAATCGAGGAATCTCCTGTCCGTAAAACAATTATTTTCTGCAACAAG                         ATTGAGACATGCAGAAAGGTTGAGAATGCGCTGAGGCGGGTGGACAGGAAG
genomic: AGATAATCGAGGAATCTCCTGTCCGTAAAACAATTATTTTCTGCAACAAGgtagttcctc ... gtggtgttagATTGAGACATGCAGAAAGGTTGAGAATGCGCTGAGGCGGGTGGACAGGAAG
EST: gi|58688877|gb|CK077564.1|CK077564
EST:     AGATAATCGAGGAATCTCCTGTCCGTAAAACAATTATTTTCTGCAACAAG                         ATTGAGACATGCAGAAAGGTTGAGAATGCGCTGAGGCGGGTGGACAGGAAG
genomic: AGATAATCGAGGAATCTCCTGTCCGTAAAACAATTATTTTCTGCAACAAGgtagttcctc ... gtggtgttagATTGAGACATGCAGAAAGGTTGAGAATGCGCTGAGGCGGGTGGACAGGAAG
EST: gi|14571286|gb|BI118654.1|BI118654
EST:     AGATAATCGAGGAATCTCCTGTCCGTAAAACAATTATTTTCTGCAACAAG                         ATTGAGACATGCAGAAAGGTTGAGAATGCGCTGAGGCGGGTGGACAGGAAG
genomic: AGATAATCGAGGAATCTCCTGTCCGTAAAACAATTATTTTCTGCAACAAGgtagttcctc ... gtggtgttagATTGAGACATGCAGAAAGGTTGAGAATGCGCTGAGGCGGGTGGACAGGAAG
EST: gi|88211803|gb|CI211443.1|CI211443
EST:     TCTGCAACAAG                         ATTGAGACATGCAGAAAGGTTGAGAATGCGCTGAGGCGGGTGGACAGGAAG
genomic: TCTGCAACAAGgtagttcctc ... gtggtgttagATTGAGACATGCAGAAAGGTTGAGAATGCGCTGAGGCGGGTGGACAGGAAG
EST: gi|218481605|gb|FG958669.1|FG958669
EST:     AGATAATCGAGGAATCTCCTGTCCGTAAAACAATTATTTTCTGCAACAAG                         ATTGAGACATGCAGAAAGGTTGAGAATGCGCTGAGGCGGGTGGACAGGAAG
genomic: AGATAATCGAGGAATCTCCTGTCCGTAAAACAATTATTTTCTGCAACAAGgtagttcctc ... gtggtgttagATTGAGACATGCAGAAAGGTTGAGAATGCGCTGAGGCGGGTGGACAGGAAG

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), 67 (downstream exon)
Score: 29

GGAAAAGAATCCGGAGACGGCGTTCTCAAACAAGAAATCAGCACTTGTAAAGATAATCGAGGAATCTCCTGTCCGTAAAACAATTATTTTCTGCAACAAGgtagttcctc ... gtggtgttagATTGAGACATGCAGAAAGGTTGAGAATGCGCTGAGGCGGGTGGACAGGAAGGCTTCGCAGATCAAAGTGCTCCCCTTCCATGCTGCATTGGATCAACAAC




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