Fetched gene from gff file shows similarity to other organism

Question

[shubhra.bhattacharya]

Dear all, I have extracted gene from reference using gff file. The gene is p53 and the entry is as follows:

AC_000176.1     BestRefSeq%2CGnomon     gene    27985492        27997883        .       -       .       ID=gene22694;Dbxref=BGD:BT10936,GeneID:281542;Name=TP53;description=tumor protein p53;gbkey=Gene;gene=TP53;gene_biotype=protein_coding

I have fetched out this gene using:

bedtools2_2.26/bin/bedtools getfasta -fi sequences.fa -bed p53.bed > p53_from_bed.fa

The bed file (p53.bed) is as follows:

AC_000176.1     27985492        27997883

However when I blast this extracted sequence against Nucleotide db I get the top hit as: Bos mutus isolate yakQH1 chromosome 19 whereas my organism of interest is bos taurus.

Also, identity against Bos taurus TP53 is 99% but query coverage is 17%

Select seq NM_174201.2
    Bos taurus tumor protein p53 (TP53), mRNA
    1729    3975    17%     0.0 99%     NM_174201.2

Is this hit only for mRNA region and hence its coverage is low? Can someone tell me where my understanding is wrong?

[GenoMax]

Are you extracting only the top hit from your search? It is possible that blast is returning an almost identical sequence as top hit from a closely related species which is why you get Bos mutus.

BTW: If you have a known sequence what is the reason to blast it back against nt?

[shubhra.bhattacharya]

I performed online blast and yes that was the top hit ie, the Bos mutus hit. But should I still not get a query coverage of 100% against my gene of interest in Bos taurus from the nt db?

PS: This query was raised by a third party client :)