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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTTGCTGTCCTTGCATCACGAATGGAGCAATATATTCAAGGGCAATCCAGAGATTTAATTGATAAAGCATACACAAAGCTAgtgagtaccccccccccccccccccccctagctatttatactactagctgtataaattcgacctatttttcctttgtgaataaatggctcttggtatgatttatag

Basic information

species Oryza sativa
transcript LOC_Os03g42750.2
intron # 19
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g42750.1 (Oryza sativa), 5'ss of exon 19
lower sequence: GRMZM2G099056_T01 (Zea mays), 5'ss of exon 19
ATTTGCTGTCCTTGCATCACGAATGGAGCAATATATTCAAGGGCAATCCAGAGATTTAATTGATAAAGCATACACAAAGCTAgtgagtaccccccccccccccccccccctagctatttatactactagctgtataaattcgacctatttttcctttgtgaataaatg---gctcttggtatgatttatag
||||||||||||||||||||| ||||| |||||||| ||||| |||||||| ||||||||||||||||||||||||||||||||||||    |   |||   |   |    |  | |||  | |  | | | || | |||   || ||||    ||  | |||   ||   |  ||| |||  | |     
ATTTGCTGTCCTTGCATCACGTATGGAACAATATATCCAAGGACAATCCAGGGATTTAATTGATAAAGCATACACAAAGCTAgtgagt--ttcattcccttgcaatcttgcacttgtttgcattcttgg-tatacatattttgccgatttag--ttcataaatttgtgttagtacttagtagtactg----
















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|58665096|gb|CK053782.1|CK053782
EST:     ATATTCAAGGGCAATCCAGAGATTTAATTGATAAAGCATACACAAAGCTA                         GTCAGCACAATGTTCACAACTTTGGACAAAATTG
genomic: ATATTCAAGGGCAATCCAGAGATTTAATTGATAAAGCATACACAAAGCTAgtgagtaccc ... tgatttatagGTCAGCACAATGTTCACAACTTTGGACAAAATTG
EST: gi|58680504|gb|CK069191.1|CK069191
EST:     ATATTCAAGGGCAATCCAGAGATTTAATTGATAAAGCATACACAAAGCTA                         GTCAGCACAATGTTCACAACTTTGGACAAAATTGCACATAGTGACCCCAAA
genomic: ATATTCAAGGGCAATCCAGAGATTTAATTGATAAAGCATACACAAAGCTAgtgagtaccc ... tgatttatagGTCAGCACAATGTTCACAACTTTGGACAAAATTGCACATAGTGACCCCAAA
EST: gi|58604329|gb|CK014857.1|CK014857
EST:     ATATTCAAGGGCAATCCAGAGATTTAATTGATAAAGCATACACAAAGCTA                         GTCAGCACAATGTTCACAACTTTGGACAAAATTGCACATAGTGACCCCAAA
genomic: ATATTCAAGGGCAATCCAGAGATTTAATTGATAAAGCATACACAAAGCTAgtgagtaccc ... tgatttatagGTCAGCACAATGTTCACAACTTTGGACAAAATTGCACATAGTGACCCCAAA
EST: gi|29627167|gb|CB632178.1|CB632178
EST:     ATATTCAAGGGCAATCCAGAGATTTAATTGATAAAGCATACACAAAGCTA                         GTCAGCACAATGTTCACAACTTTGGACAAAATTGCACATAGTGACCCCAAA
genomic: ATATTCAAGGGCAATCCAGAGATTTAATTGATAAAGCATACACAAAGCTAgtgagtaccc ... tgatttatagGTCAGCACAATGTTCACAACTTTGGACAAAATTGCACATAGTGACCCCAAA

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), 71 (downstream exon)
Score: 23

ATTTGCTGTCCTTGCATCACGAATGGAGCAATATATTCAAGGGCAATCCAGAGATTTAATTGATAAAGCATACACAAAGCTAgtgagtaccc ... tgatttatagGTCAGCACAATGTTCACAACTTTGGACAAAATTGCACATAGTGACCCCAAAACTGCAGACATTGTATTGATAGAGAATTATGCTGCCTTCCAGAACAG




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