Geneious Biologics includes a Rabbit IgG (Oryctolagus cuniculus) germline gene reference database, available by default alongside the standard Human, Mouse, and Alpaca databases.
Unlike the other provided databases, a significant number of genes sourced in the Rabbit IgG database were divergent from named IMGT genes. These were named following the IMGT naming conventions, but with Geneious rather than IMGT standard names.
This article describes how these names are assigned and what to be aware of when interpreting results.
Gene sources
Sequences were compiled from publicly available sources, primarily from the NCBI Rabbit genome assembly and other published literature.
However, Rabbit immunoglobulin germline sequences are not as well characterized as those of Human or Mouse, and a significant proportion of V, D, and J genes in public sources were too divergent from named IMGT genes to be assigned a standard IMGT name.
Where publicly sourced genes were not 100% identical to a names IMGT gene, they were named according to the conventions outlined below.
Geneious-curated gene names
Genes that were not identical to an existing named IMGT gene were named by Geneious Biologics as follows:
- Where sequences were sufficiently similar to a named IMGT gene (≥97% identity), an allele was appended as a
Geneioustag, like so:- Example:
IGKV1S9*Geneious-1
- Example:
- Where sequences were less than 97% identical to a named gene, genes were instead grouped into families based on similarity to known IMGT families (e.g.
IGHV1).- Within each family, the gene subtype was numbered in ascending order as they appear along the reference genome, as is the convention outlined by IMGT, with a
Geneioustag inserted to distinguish them from IMGT curated genes. If the genome position of the gene was unknown, this is indicated by an S before the number designation - in this case the number is meaningless. - Example:
IGHV1-Geneious-S1(unknown location)
- Within each family, the gene subtype was numbered in ascending order as they appear along the reference genome, as is the convention outlined by IMGT, with a
This convention is applied consistently across V, D, and J genes.
ORF gene determination
Any gene sequence which contained a frameshift in the FRs or CDRs (excluding CDR3), or a stop codon was flagged as an ORF gene.
What this means for your analysis
- Annotation and V(D)J assignment work the same way as with the other provided databases.
- Germline call outputs will include a mix of IMGT standard names and
Geneioustagged names depending on which gene is the closest match. - When comparing results across tools,
Geneioustagged genes will not have a direct equivalent in IMGT or other databases.
Availability
The Rabbit IgG database is available by default in your organization's reference databases. Contact support if you have questions or do not see it in your account.