Gene family annotation
H-InvDB_9.0 released on May 27, 2015.
Search by for Advanced Search
Home Quick guide Navi BLAST Site map Download Contact us Help

H-InvDB Gene Families/Groups

HIF0000001 Ig: immunoglobulin [Download]

Description: Immunoglobulin (Ig) is essential for the immune responses, and expressed at the surface of the B cells or secreted by the plasma cells. Ig is composed of the polypeptide chains with two different characters: heavy and light chains (κ,λ).
H-InvDB Ig annotation dataset was intended to include the genes of heavy and light chains (κ,λ). Ig-like genes and non-Ig genes (ex. VpreB, T-cell receptor) were excluded. The H-InvDB Ig dataset was defined by genomic location obtained from literature, sequence similarity search using a standard protein dataset, keyword search against sequence description and manual curation.

HIF0000002 MHC: major histocompatibility complex [Download]

Description: The human major histocompatibility complex (MHC), or human leukocyte antigen (HLA), is a gene family located on 6p21.3 containing the most polymorphic genes in the human genome. The HLA molecules play a key role in immune responses by presenting peptides to T-lymphocytes.
We manually annotated functional class I and class II MHC loci by carefully examining human MHC transcripts, using the extended-MHC gene map (http://www.sanger.ac.uk/HGP/Chr6/XMHC/xlist.shtml) as a reference.The dataset of MHC transcripts were collected based on sequence similarity search and keyword search.

HIF0000003 TCR: T-cell receptor [Download]

Description: T-cell receptors (TCRs) are antigen-specific receptors found on the cell surface of T-lymphocytes and are essential for the immune responses. TCRs are heterodimers consisting of alpha and beta, or gamma and delta chains that recognize specific antigens presented by MHC molecules on antigen-presenting cells.
The H-InvDB TCR dataset was defined by sequence homology search against standard TCR proteins, genomic location obtained from literature, keyword search against sequence description and manual curation.

HIF0000004 OR: olfactory receptor [Download ORs in H-InvDB] [Download ORs of Niimura & Nei(2003) (nucleotide_seq, amino_acid_seq)]

Description: Olfaction, the sense of smell, is important for animals to find food, identify mates and offspring, and avoid danger. The olfactory perception begins when odorous ligands activate olfactory receptors (OR) expressed in olfactory sensory neurons of the olfactory epithelium located in the posterior upper part of the nasal cavity. ORs are encoded by the largest gene family including pseudogenes.
H-InvDB OR gene family is predicted based on the method of modified Niimura and Nei (2003, PMID: 14507991) and keyword search using sequence description. The dataset include the following information; intact gene or pseudogene, protein evidence, expressional evidence, ID of Niimura and Nei (2003).

Predicted human gene family/group (HIF0000005 to HIF0003438) [Download]

Description: We defined predicted human gene families/groups based on the sequence similarities and assigned an HIF ID for each H-Inv gene family/group. A unique HIF ID is assigned to each group of H-Inv cluster entries identifying the groupings of the human gene in a context of sequence similarity and conservation of functional motif.