I have searched NCBI for this particular sequence. But I am not getting anything. I think I am making some mistakes in the search. Can anybody please help me?
Try searching on Phytozome.net
search for the protein AcetylCoA carboxylase using ontology search (or directly use the protein/cds sequence if it is available with you) and selecting Oryza sativa as plant. extract the upstream sequence (-1500 to +500) and scan for the promoter using promoter prediction tools.
Not sure how you did the search, but I Agree with Tejas, Phytozome is a good source for genomic sequences, or particularly for rice, you could go to the Rice Genome Browser and get the intergenic region from there. Either case, look for locus LOC_Os10g21910:
http://rice.plantbiology.msu.edu/cgi-bin/ORF_infopage.cgi?orf=LOC_Os10g21910
http://rice.plantbiology.msu.edu/cgi-bin/gbrowse/rice/?name=LOC_Os10g21910
Hi Paromic,
I will suggest that, if you have complete gene or even partial gene sequence of acetyl coA gene from oryza sativa then go for the genome blast or simple nucleotide blast and specify the oryza sativa in organism box. I do find some complete chromosome sequences of no 1, 9 and 10 ncbi. If your getting the blast results for the same match then in genome seq or in chromosome seq u will get the match select the nucleotide match and look for the details about the seq. in genbank format u get the promotor seq. if somebody has annotated it. If not then you may need to predict the promotor in that seq.
All the best...!!
Thanks Tejas, Gustavo Sir, and Sachin. With all your help I am now getting some idea. If I develop any further querries I will deffinitely return to you people.
Thanks once again for all your support.
Please find below the promoter sequence (-1000, +200 relative to tss) for loc_os10g21910
>loc_os10g21910;chr-10;-;1;11202713;-1000;200;11201712;11202913;23134759
aaggaaggaagctgtgtgctgccgcgggcgcatttaaggcgcgtgggtgcggcgaggaggagggaggttggccctcggcgctggatcttgatctggccgtggcgcgccgcggcggcggcattccgtcgaacgggtggcgagcagagcgcgcgcgccggcgtctcgtgcgtacgtttctcttcttcttcttcttcttttttctctctgtctgttcttgcttcttcctcctcctccctgcttcttgcgctcgaattccgccgccggaatcgaggacgctacggccttcggattctcgcacacgcgccgaatctaaaatcccagctctaagagccgcgattttttttcccttttctgttgagctgcagcgcgggatcgggcgaggtgagatcgtagctgatcctgctttgctagggggggggggggagcagagctggcgggctaaaagcctaaagctcttacctttttctcctccttcttcttcgtcttctctagcttcgtttcagcctgtcagattcttgttcgtttttgtttcttggcatgctagagctctgggggtccctcgttcagtgcttatttcgtaatttactaatcttccgtgtctcgactagccactaagattgatgtagcttagccttttgctttggacttttgtgtgatcacacagtcaacctatataaatatatatatatccacctggttaattacaaggggaaatggaaattcacagtctgtgggtcttgctgttctaattctgctggctcttggtttattatttactgttgcggtcaaaaacttttgctgcaaaactgagccgccatggaattcgaggataaattgtactagcgcttatgcgaattttacatttggtactgatggtaaatgggagtagtggtaaattgccggttttcgtttacaccgtttcgtttgtcagaatttgatgtgctgatgatttgttcggtttctttttcgcagcaggtctgaaggttagaggtggttaataatggagggatcttaccaaatgaatggcatactgaacgggatgtctaattcgaggcatccgtcgtcaccctctgaggtcgatgagttctgcaaagcgctcggtggtgattcaccgatacacagtgtgctggttgccaacaatggcatggccgctgtcaagttcatgcgcagcatccgtacatgggcgctggagacctttgg
i hope it is helpful. If you need a longer promoter, then i might be able to help you.
Bijayalaxmi
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