Orthologues, paralogues and gene families

A gene-tree label can identify a sequence or gene from a particular organism. Find the starting record, then inspect the relation the source identifies as orthology or paralogy. Ensembl reconciles gene and species trees to distinguish events. The inference depends on the gene set, alignment and method; similar names do not replace that analysis.

Families and domains answer different questions. InterPro distinguishes families, domains, repeats, sites and homologous superfamilies. A domain can occupy part of a protein. Sharing a domain does not automatically make two whole proteins orthologues or functionally identical. Check the entry type and the sequence region it describes.

Choose the molecular query

Try it. Search for BRCA2 and choose a specific starting record with its organism. Open that record first, then request source-supported orthologues. For one result, record the relationship type, both gene identifiers, source version and available evidence. If the source fails or provides no relationship, retain that state rather than completing the list using similar names.

A map and a sample

Next, follow a result to its organism and map. A map marker represents a published observation of an organism linked to a molecular record. It does not by itself show that the selected gene was sequenced from that particular field sample. That requires an explicit connection to the sample and its molecular data.

Check coverage

Check your understanding. Switching from an exact record to a family changes the inclusion criterion. Read the resulting list with the evidence for membership. An organism missing from EcoGenesis's current molecular index has unknown coverage here; the missing link does not prove the organism lacks the gene.

Three query scopes

Three ways to define a molecular query; the results depend on verified source relationships.

Teaching case: an ancestral gene is inherited by species A and B after their separation; those copies are orthologues in the stated model. If the gene then duplicates within A, the two A copies are paralogues. The answer follows the events in this supplied history, not a rule that similar names or sequences always imply one relationship. For real genes, inspect the inferred gene tree and its evidence.