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

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 Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification 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
GH01J070352 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE CraniofacialAtlas 520.1 -0.8 -796 4.8 ZBTB40 ZNF217 EP300 TCF12 SIN3A NRF1 POLR2G GTF2E2 PHF8 TEAD4 HHLA3 ANKRD13C SRSF11 ZRANB2 MIR186 LRRC40 HHLA3-AS1 lnc-LRRC40-5
GH01J070409 Promoter/Enhancer 2.2 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas 21.1 +57.2 57152 4.9 ZNF217 EP300 SIN3A NRF1 POLR2G SP1 PHF8 TEAD4 ZNF639 ZNF10 CTH lnc-ANKRD13C-4 HHLA3 ZRANB2 ANKRD13C SRSF11 ENSG00000278636
GH01J070441 Enhancer 0.5 Ensembl 22.3 +87.7 87704 3.8 RBM22 SPI1 FOS STAT1 POLR2A CEBPB ZBTB40 NR4A1 CAVIN1 HHLA3 ENSG00000271992 ENSG00000278636
GH01J070361 Enhancer 0.5 Ensembl 14.3 +7.4 7404 0.8 EP300 ATF2 MAFF MAFK GATA2 ZNF629 PRDM1 ENSG00000226088 HHLA3-AS1 HHLA3 lnc-ANKRD13C-4
GH01J070319 Enhancer 0.6 Ensembl ENCODE 10.8 -34.7 -34697 2.2 FOSL2 ZBTB33 JUND HHLA3 lnc-LRRC40-5 ANKRD13C lnc-LRRC40-3
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around HHLA3 on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for HHLA3

Top Transcription factor binding sites by QIAGEN in the HHLA3 gene promoter:
  • AML1a
  • COUP
  • COUP-TF1
  • GATA-1
  • GATA-2
  • GATA-3
  • HEN1
  • HNF-4alpha1
  • HNF-4alpha2

Genomic Locations for HHLA3 Gene

Genomic Locations for HHLA3 Gene
30,543 bases
Plus strand
30,535 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; Evidence={ECO:0000305};

    Alternative splice isoforms for HHLA3 Gene


neXtProt entry for HHLA3 Gene

Post-translational modifications for HHLA3 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

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

GenScript: Design optimal peptide antigens:
  • Human endogenous retrovirus-H long terminal repeat-associating protein 3 (HHLA3_HUMAN)
  • HERV-H LTR-associating 3, isoform CRA_b (Q5VZP2_HUMAN)
genes like me logo Genes that share domains with HHLA3: view

No data available for Graphical View of Domain Structure and 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

CRISPR 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
extracellular 2
nucleus 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

PathCards logo

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

mRNA/cDNA for HHLA3 Gene

6 NCBI additional mRNA sequence :
7 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

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

Expression for HHLA3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and 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

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for HHLA3

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 31
  • 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)
Evolutionary constrained regions (ECRs) for HHLA3: view image

Paralogs for HHLA3 Gene

No data available for Paralogs for HHLA3 Gene

Variants for HHLA3 Gene

Additional dbSNP identifiers (rs#s) for HHLA3 Gene

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

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP 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 23 54
  2. The DNA sequence and biological annotation of human chromosome 1. (PMID: 16710414) Gregory SG … Prigmore E (Nature 2006) 3 4 54
  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 54
  4. A proteome-scale map of the human interactome network. (PMID: 25416956) Rolland T … Vidal M (Cell 2014) 3 54
  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 54

Products for HHLA3 Gene

Sources for HHLA3 Gene