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Aliases for HHLA3 Gene

Aliases for HHLA3 Gene

  • HERV-H LTR-Associating 3 2 3 5
  • Human Endogenous Retrovirus-H Long Terminal Repeat-Associating Protein 3 4

External Ids for HHLA3 Gene

Previous GeneCards Identifiers for HHLA3 Gene

  • GC01P070944
  • GC01P069743
  • GC01P070205
  • GC01P070190
  • GC01P070532
  • GC01P070820
  • GC01P068931

Summaries for HHLA3 Gene

GeneCards Summary for HHLA3 Gene

HHLA3 (HERV-H LTR-Associating 3) is a Protein Coding gene.

Additional gene information for HHLA3 Gene

No data available for Entrez Gene Summary , CIViC summary , UniProtKB/Swiss-Prot , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for HHLA3 Gene

Genomics for HHLA3 Gene

GeneHancer (GH) Regulatory Elements for HHLA3 Gene

Promoters and enhancers for HHLA3 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH01I070352 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 570.2 -0.6 -608 3.6 CLOCK MLX YY1 ZNF213 E2F8 ZNF143 SP3 MEF2D ZNF610 GLIS1 HHLA3 ANKRD13C LRRC40 LOC102724548 GC01M070275
GH01I070409 Promoter/Enhancer 2.3 EPDnew FANTOM5 Ensembl ENCODE 21.1 +56.4 56435 3.5 HDGF PKNOX1 SMAD1 FOXA2 MLX ARNT ARID4B SIN3A FEZF1 DMAP1 CTH SRSF11 HHLA3 ZRANB2 ANKRD13C ENSG00000278636
GH01I070319 Enhancer 0.4 ENCODE 10.8 -34.7 -34690 2 JUND FOSL2 ZBTB33 HHLA3 GC01M070275 ANKRD13C
GH01I070460 Enhancer 0.8 ENCODE 4.2 +106.5 106450 0.8 HDAC1 TCF12 CAVIN1 ZEB2 HDAC8 ZNF592 MEF2D NFIC SMARCA4 IKZF1 HHLA3 LOC105378793 GC01M070473
GH01I070284 Enhancer 0.3 ENCODE 6.2 -70.2 -70152 1.1 ZNF121 HHLA3 GC01M070275 GC01P070230 ANKRD13C
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around HHLA3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the HHLA3 gene promoter:

Genomic Locations for HHLA3 Gene

Genomic Locations for HHLA3 Gene
30,543 bases
Plus strand

Genomic View for HHLA3 Gene

Genes around HHLA3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
HHLA3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for HHLA3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for HHLA3 Gene

Proteins for HHLA3 Gene

  • Protein details for HHLA3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    HERV-H LTR-associating protein 3
    Protein Accession:
    Secondary Accessions:
    • D3DQ74
    • Q5VZP2
    • Q96FH5
    • Q9XRX4

    Protein attributes for HHLA3 Gene

    114 amino acids
    Molecular mass:
    12913 Da
    Quaternary structure:
    No Data Available
    • Sequence=AAD33288.1; Type=Frameshift; Positions=72; Evidence={ECO:0000305};

    Alternative splice isoforms for HHLA3 Gene


neXtProt entry for HHLA3 Gene

Post-translational modifications for HHLA3 Gene

No Post-translational modifications

No data available for DME Specific Peptides for HHLA3 Gene

Domains & Families for HHLA3 Gene

Gene Families for HHLA3 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for HHLA3 Gene


Suggested Antigen Peptide Sequences for HHLA3 Gene

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with HHLA3: view

No data available for UniProtKB/Swiss-Prot for HHLA3 Gene

Function for HHLA3 Gene

Gene Ontology (GO) - Molecular Function for HHLA3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 16189514
genes like me logo Genes that share ontologies with HHLA3: view
genes like me logo Genes that share phenotypes with HHLA3: view

Animal Model Products

Clone Products

No data available for Molecular function , Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for HHLA3 Gene

Localization for HHLA3 Gene

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for HHLA3 gene
Compartment Confidence
nucleus 3
extracellular 2
cytosol 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoplasm (2)
  • Vesicles (2)
See all subcellular structures

No data available for Subcellular locations from UniProtKB/Swiss-Prot and Gene Ontology (GO) - Cellular Components for HHLA3 Gene

Pathways & Interactions for HHLA3 Gene

SuperPathways for HHLA3 Gene

No Data Available

Interacting Proteins for HHLA3 Gene

Gene Ontology (GO) - Biological Process for HHLA3 Gene


No data available for Pathways by source and SIGNOR curated interactions for HHLA3 Gene

Drugs & Compounds for HHLA3 Gene

No Compound Related Data Available

Transcripts for HHLA3 Gene

Unigene Clusters for HHLA3 Gene

HERV-H LTR-associating 3:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for HHLA3 Gene

ExUns: 1a · 1b · 1c · 1d · 1e ^ 2a · 2b ^ 3 ^ 4 ^ 5a · 5b · 5c · 5d
SP1: -
SP2: - - -
SP3: - - -
SP4: - - - -
SP5: - - -
SP6: - - - -

Relevant External Links for HHLA3 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for HHLA3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for HHLA3 Gene

Protein differential expression in normal tissues from HIPED for HHLA3 Gene

This gene is overexpressed in Plasma (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for HHLA3 Gene

Protein tissue co-expression partners for HHLA3 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of HHLA3 Gene:


SOURCE GeneReport for Unigene cluster for HHLA3 Gene:


mRNA Expression by UniProt/SwissProt for HHLA3 Gene:

Tissue specificity: Expressed in kidney and liver.
genes like me logo Genes that share expression patterns with HHLA3: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for HHLA3 Gene

Orthologs for HHLA3 Gene

This gene was present in the common ancestor of human and chimp.

Orthologs for HHLA3 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia HHLA3 34
  • 97 (a)
Species where no ortholog for HHLA3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • cow (Bos Taurus)
  • dog (Canis familiaris)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • lizard (Anolis carolinensis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • mouse (Mus musculus)
  • oppossum (Monodelphis domestica)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rat (Rattus norvegicus)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)
  • zebrafish (Danio rerio)

Evolution for HHLA3 Gene

Gene Tree for HHLA3 (if available)
Gene Tree for HHLA3 (if available)

Paralogs for HHLA3 Gene

No data available for Paralogs for HHLA3 Gene

Variants for HHLA3 Gene

Sequence variations from dbSNP and Humsavar for HHLA3 Gene

SNP ID Clin Chr 01 pos Variation AA Info Type
rs1000030676 -- 70,365,032(+) T/G intron_variant
rs1000208440 -- 70,353,957(+) G/A 5_prime_UTR_variant, genic_upstream_transcript_variant, upstream_transcript_variant
rs1000226569 -- 70,354,228(+) G/A/C 5_prime_UTR_variant, genic_upstream_transcript_variant, upstream_transcript_variant
rs1000288398 -- 70,353,860(+) G/A 5_prime_UTR_variant, genic_upstream_transcript_variant, upstream_transcript_variant
rs1000536887 -- 70,357,474(+) A/G intron_variant

Structural Variations from Database of Genomic Variants (DGV) for HHLA3 Gene

Variant ID Type Subtype PubMed ID
esv27106 CNV loss 19812545
esv3586353 CNV loss 21293372
nsv1012563 CNV gain 25217958
nsv830137 CNV loss 17160897

Variation tolerance for HHLA3 Gene

Residual Variation Intolerance Score: 61.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.72; 46.54% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for HHLA3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for HHLA3 Gene

Disorders for HHLA3 Gene

Additional Disease Information for HHLA3

No disorders were found for HHLA3 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for HHLA3 Gene

Publications for HHLA3 Gene

  1. Endogenous retroviruses provide the primary polyadenylation signal for two new human genes (HHLA2 and HHLA3). (PMID: 10444326) Mager DL … Freeman JD (Genomics 1999) 2 3 4 22 58
  2. The DNA sequence and biological annotation of human chromosome 1. (PMID: 16710414) Gregory SG … Prigmore E (Nature 2006) 3 4 58
  3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58
  4. A proteome-scale map of the human interactome network. (PMID: 25416956) Rolland T … Vidal M (Cell 2014) 3 58
  5. hORFeome v3.1: a resource of human open reading frames representing over 10,000 human genes. (PMID: 17207965) Lamesch P … Vidal M (Genomics 2007) 3 58

Products for HHLA3 Gene

Sources for HHLA3 Gene

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