TL;DR: the status of your gene of interest is predicted, so trust, but verify. For example, check if RNAseq mapping confirms the gene annotation - there is plenty of bovine RNAseq data available.
Longer explanation:
The genome data and its annotation are two different, but inter-related, entities. The sequence of the genome will depend on coverage, sequencing technologies, assembler used, heterozygosity rate and / or number of individuals sequenced, and so on. Usually, the paper describing the genome in question, and the NCBI genome page, have information about its sequencing and assembly, and are good sources of information about its quality.
The annotation is performed over a certain genome assembly of choice, and thus depends in part on the quality of the assembled genome. Thus, if an assembly i fragmented, its gene predictions will be also incomplete and fragmented. However, as Emily_Ensembl said, annotations rely a lot on mapping genes and proteins from other species, so genomes from poorly studied taxa will have poorer annotations, because there are less experimental data validating good gene models. Availability of good sequencing RNAseq data, from several tissues, help in annotation as well.
A further point is most genomes are assembled from a single individual. While this is good to get a better quality assembly, it also means the reference genome sequence may be different from your sample of interest.
Your text talks about a bovin gene, your title about goat or dog. Can you clarify?