For GeneLossDB Users

Gene loss information available in this database is sourced exclusively from peer-reviewed articles containing valuable confirmed biological data regarding gene loss in multiple species.

Each gene loss annotation is linked to an orthologous reference gene in the human genome, when this is not applicable, an alternative reference gene from another species is selected. Alternative reference genes are used when gene structure is not conserved between target species and humans.

Gene loss information available in this database is sourced exclusively from peer-reviewed articles containing valuable confirmed biological data regarding

Gene loss database integrates information from external sources and databases to enrich information of reference genes.

1. NCBI Gene: provides descriptive information about reference gene loci, information collected: Gene symbol, Alias, Summary EC number, OMIM number, GO gene ontology information.
2. NCBI taxonomy: taxid, species name, common name and lineage information
3. PantherDB – collects paralog information

Gene loss annotation fields:

LOSS TYPE:

• Full : gene loss is expected to be observed in all individuals of the species in question.
• Polymorphic : gene loss is observed in some individuals of the species in question.
• Undetermined : insufficient information to determine the extent of gene loss in this species.

GENE LOSS MECHANISM:

• LOF : gene inactivation occurs by one or more loss of function mutations, this includes frameshift mutations, premature stop codons, and ablation of canonical splice sites.
• Gene deletion : the gene in question is not found in the genome possibly due to large deletions.
• Exon(s) deletion : portions of the gene are missing from the genome.
• Regulatory region mutation : mutations that disrupt the transcription of the genes.
• Other : chromosome rearrangements, inversions, or other phenomena that can be described in curator observations or in the publication excerpt section.

EVIDENCE:

Biological evidence provided in the analysed publication to support gene loss, can be of several types:

• Multiple individual SRA : Validated for more than one individual using SRA data of independent samples.
• Single individual SRA : Validated for one individual using SRA data.
• Sanger seq Multiple : Validated for more than one individual using Sanger sequencing of independent samples.
• Sanger seq Single : Validated for one individual using Sanger sequencing.
• Transcriptomic : Gene loss verified using transcriptomic reads.
• Genomic : Gene loss verified using genomic data or assembled genome.
• Genomic and Transcriptomic : Gene loss verified using transcriptomic reads and genomic data.
• Synteny maps : Gene loss validated using conserved synteny maps.

LINEAGE SPECIFIC:

• YES : the gene in question is lost in all individuals of this specific lineage, evidence is provided as conserved mutations shared by all species analysed.
• Species rank : indicates which lineage is affected by gene loss.
• NO : No evidence is provided supporting that this gene loss event is extended to other species in the same lineage.

CURATOR OBSERVATIONS:

Gene loss curators can use this field to provide information regarding mutation conservation or other details relevant to the annotation process.

STATEMENTS:

Publication excerpts – Small quotation taken from reference manuscript describing specific aspects of gene loss. To facilitate data interpretation excerpts are classified into several types depending on the information quoted. Types of excerpts: Mutational description, Timing of Loss, Phenotypic, Functional, Other