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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTATCAAGAATACAGGACAGAGTACATCACTACTCAAAAACGTGCTTATTTTGACCTTAACAAGAATGATGATCGgtaagtcaaaatgatttagctgtacacaactaggaacaaaaatggtccacttgctttaactgacatttcatttgctttcacttgcag

Basic information

species Oryza sativa
transcript LOC_Os06g48530.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g48530.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G156099_T01 (Zea mays), 5'ss of exon 5
GTATCAAGAATACAGGACAGAGTACATCACTACTCAAAAACGTGCTTATTTTGACCTTAACAAGAATGATGATCGgtaagtc----aaaatgatttagctgtaca--caactaggaacaaaa-atggtccacttgctttaactgacatttc-atttgctttcacttgcag
||| |||||||| || || ||||| ||||| ||||| ||||||||||||||||| ||  |||| || || ||| |||| ||     | | | |||  ||| | ||   |   ||||   | | ||||| || |  ||| || || | ||||  ||||||| |||||||||
GTACCAAGAATATAGAACTGAGTATATCACAACTCAGAAACGTGCTTATTTTGATCTCCACAAAAACGAAGATTGgtacgtttcagacactaattgtgctcttcaggtatgcaggagttacatatggtgcattcactt-aattgtcttttctgtttgcttacacttgcag

upper sequence: LOC_Os06g48530.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM5G817439_T01 (Zea mays), 5'ss of exon 5
GTATCAAGAATACAGGACAGAGTACATCACTACTCAAAAACGTGCTTATTTTGACCTTAACAAGAATGATGATCGgtaagt--caaaatgatttagctgtacacaa----------ctaggaacaaaa---------atggtccacttgctttaactgacatttcatttgctttcacttgcag
||| ||||| || || || ||||| ||||||||||| ||||||||||||||||| ||  |||||||||| ||| |||| ||  ||| |   ||||     |||| |           |||| |   |          ||||| || |  ||| |  || | |||  ||||||| |||||||||
GTACCAAGAGTATAGAACTGAGTATATCACTACTCAGAAACGTGCTTATTTTGATCTCCACAAGAATGAAGATTGgtacgttccaagagattttattcagacactaattgtgctctttaggtatgcaggagttgcatatggttcattcactt-atttgtctttttgtttgcttacacttgcag
















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|29680659|gb|CB676934.1|CB676934
EST:     ATCACTACTCAAAAACGTGCTTATTTTGACCTTAACAAGAATGATGATCG                         GTTGAAAGACAAGTACCATCCGACCAACTTGTCATCTGTTATTGACAG
genomic: ATCACTACTCAAAAACGTGCTTATTTTGACCTTAACAAGAATGATGATCGgtaagtcaaa ... tcacttgcagGTTGAAAGACAAGTACCATCCGACCAACTTGTCATCTGTTATTGACAG
EST: gi|58679286|gb|CK067973.1|CK067973
EST:     ATCACTACTCAAAAACGTGCTTATTTTGACCTTAACAAGAATGATGATCG                         GTTGAAAGACAAGTACCATCCGACCAACTTGTCATCTGTTATTGACAG
genomic: ATCACTACTCAAAAACGTGCTTATTTTGACCTTAACAAGAATGATGATCGgtaagtcaaa ... tcacttgcagGTTGAAAGACAAGTACCATCCGACCAACTTGTCATCTGTTATTGACAG
EST: gi|88344921|gb|CI625767.1|CI625767
EST:     ATCACTACTCAAAAACGTGCTTATTTTGACCTTAACAAGAATGATGATCG                         GTTGAAAGACAAGTACCATCCGACCAACTTGTCATCTGTTATTGACAG
genomic: ATCACTACTCAAAAACGTGCTTATTTTGACCTTAACAAGAATGATGATCGgtaagtcaaa ... tcacttgcagGTTGAAAGACAAGTACCATCCGACCAACTTGTCATCTGTTATTGACAG

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: 62 (upstream exon), 69 (downstream exon)
Score: 9

GTATCAAGAATACAGGACAGAGTACATCACTACTCAAAAACGTGCTTATTTTGACCTTAACAAGAATGATGATCGgtaagtcaaa ... tcacttgcagGTTGAAAGACAAGTACCATCCGACCAACTTGTCATCTGTTATTGACAG




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