Underscore in Gene symbols

Question

[Space_Life]

Hi, I have a gene list and their counts in a group of microbes. Some of the genes are named with underscore. For example: rnfC, rnfC_1, rnfC_2, Should I consider them as one gene or should I treat them differently? I need to count the number of genes present in a particular bacteria. Can I take the one with highest number? I want to know whats the standard practice.

Here it says, Alternative transcripts that originate from the same gene are not normally given different gene symbols and names. To refer to specific splice forms of a gene, the following format should be used (gene symbol, followed by underscore, followed by sequence accession ID): Genesymbol_accID Link: http://www.informatics.jax.org/mgihome/nomen/gene.shtml

Thank you.

Answer 1

[GenoMax]

Outside of some model organisms that have gene nomenclature committees ( e.g. https://www.genenames.org/ ) gene names can be confusing. If you search NCBI Gene database for rnfC_1 or rnfC_2 you will come up with several gene records that appear to have been discontinued. rnfC seems to be a valid bacterial gene name.

See if you can trace the names back to some origin (or least a genome build) and then decide if those warrant separate handling.

Bacterial genes are named following: https://en.wikipedia.org/wiki/Gene_nomenclature#Bacterial_genetic_nomenclature

[Space_Life]

Thank you.