Right now I'm trying a general blast for everything and then searching for the matches by taxid or the seqid's. I'm tried other approaches using gilists and downloading genomes and have still not obtained the results I need.

These are the results I receive from the online version when I search for Arsb transcript variant 1, for organism Gallus gallus (taxid: 9031), an e value cut off of 0.00005, on database refseq_genomic

Database: NCBI Genomic Reference Sequences
           23,370,420 sequences; 1,019,245,483,979 total letters
Query= NM_005445.3 Homo sapiens structural maintenance of chromosomes 3
(SMC3), mRNA

Length=4131


                                                                                             Score     E
Sequences producing significant alignments:                       (Bits)  Value

NC_006093.4  Gallus gallus isolate RJF #256 breed Red Jungle f...  237     3e-59
NT_455898.1  Gallus gallus isolate RJF #256 breed Red Jungle f...  237     3e-59

I am running a command line blast query which to my understanding should have the two lines of results within the output file. These lines are not in the output however

    blastn -query mRNAfiles/Arsb -db database/refseq_genomic -out "blast_output.txt" -evalue 0.00001 -outfmt '6 qseqid sseqid pident evalue bitscore score qcovs qcovhsp qcovus staxids ssciname'. //This command should show all results for all organisms

When I grep for the organisms taxid and the refseq ids of the output, I do not find anything

grep '9031' blast_ouput.txt  
grep 'NC_006093.4' blast_output.txt 
grep 'NT_455898.1' blast_output.txt