Genes with multiple chromosome locations

Question

[Pac314]

Hi, I am trying to annotate my list of gene IDs, some of which have multiple loci, e.g.:

   refseq_mrna hgnc_symbol   gene_biotype chromosome_name start_position end_position
7    NM_000076      CDKN1C protein_coding  HSCHR11_1_CTG7         115392       118091
8    NM_000076      CDKN1C protein_coding              11        2883213      2885775

What is the recommended practice for collapsing gene annotation with multiple entries of genes with alternative loci for a given gene?

[GenoMax]

Where did this annotation originate from?

CDKN1C seems to be annotated only at one location. https://www.ncbi.nlm.nih.gov/gene/1028/ and https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:1786

[Pac314]

Thanks for your reply. I obtained this annotation using the biomaRt R library:

library(biomaRt)

ensembl <- useMart("ensembl", dataset = "hsapiens_gene_ensembl")

attrs <- c('refseq_mrna', 'hgnc_symbol', 'gene_biotype', 'chromosome_name', 
           'start_position', 'end_position')

annot_mrna <- getBM(attributes = attrs,
                     filters = 'refseq_mrna',
                     values = rownames(cts_mat),
                     mart = ensembl)

I have multiple gene IDs with different chromosome names like the above example.

[Alex Reynolds]

You might look for a canonical gene isoform. UCSC may have some useful advice: https://genome.ucsc.edu/FAQ/FAQgenes.html#singledownload