So, I did some investigating about this.
The rnlA gene is the same as the Ig7 transcript often used as an RNA control, and the rRNA component of the large subunit of the mitochondrial ribosome (not the more general cytoplasmic ribosome). The gene itself is encoded on the mitochondrion, but the NCBI record (D16466) does not explicitly annotate this gene. Consequently, this is likely to be the reason why it isn’t in the RefSeq database. But if you take the raw FASTA sequence, and run blastn against the nr, it will pull up a 100% match with the D. discoideum mitochondrial genome (and a few others).
So, a question for the Dictybase folks - is this worth correcting in the annotation in the NCBI records?
> On Feb 9, 2017, at 9:58 AM, mona saad <[log in to unmask]> wrote:
>
> hello,
> sorry I mean rnla..yes which is a rRNA gene (DDB-G0294034) for gDNA, DDB-0237480 for rRNA seq. when blasting the rRNA of this gene in NCBI with RNA refseq (specifying dictyostelium discoideum AX4), I don't find a result( I don't find the rRNA seq).
>
> On Thu, Feb 9, 2017 at 4:24 PM, Sucgang, Richard S <[log in to unmask]> wrote:
> Hello, Mona,
>
> The first sequenced Dicty genome is from an isolate of AX4. There’s some debate as to the ancestry of the different strains that have evolved in different labs - arguably, AX4 descended from AX3, but even with the same designation, an AX3 from one part of the world is not necessarily genetically identical to that from another. But for the most part, what is in NCBI and Dictybase is assembed from a carefully curated clonal isolate AX4.
>
> Now, what is rlnA? A keyword search in NCBI for that gene name doesn’t turn anything up. Could you mean rnlA? Which is encoded on the mitochondrion.
>
> Note also that rRNA genes are encoded on extrachromosomal palindromic elements in Dicty. Nucleic Acids Res. 2003 May 1;31(9):2361-8.
>
>
>
> > On Feb 9, 2017, at 3:51 AM, mona saad <[log in to unmask]> wrote:
> >
> > Bonjour,
> > I'm wondering if AX3 strain genome of dicty is registered in NCBI, because when trying to blast rRNA sequence of rlna gene with RNArefseq, I don't find the gene sequence, so maybe because AX3 is not registered in NCBI? any idea?
> > thank you
>
>
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