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HDHD3 Gene(Protein Coding)

Haloacid Dehalogenase Like Hydrolase Domain Containing 3

GCID:
GC09M113373
GIFtS:
43
Genes Participants
UDN Logo

Aliases for HDHD3 Gene

Aliases for HDHD3 Gene

  • Haloacid Dehalogenase Like Hydrolase Domain Containing 3 2 3 5
  • C9orf158 3 4
  • Haloacid Dehalogenase-Like Hydrolase Domain-Containing Protein 3 3
  • Haloacid Dehalogenase-Like Hydrolase Domain Containing 3 2
  • Chromosome 9 Open Reading Frame 158 2
  • 2810435D12Rik 3

External Ids for HDHD3 Gene

Previous HGNC Symbols for HDHD3 Gene

  • C9orf158

Previous GeneCards Identifiers for HDHD3 Gene

  • GC09M113215
  • GC09M115175
  • GC09M116135
  • GC09M085742

Summaries for HDHD3 Gene

GeneCards Summary for HDHD3 Gene

HDHD3 (Haloacid Dehalogenase Like Hydrolase Domain Containing 3) is a Protein Coding gene. Gene Ontology (GO) annotations related to this gene include hydrolase activity.

Additional gene information for HDHD3 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 HDHD3 Gene

Genomics for HDHD3 Gene

Products:

  1. Regulatory Element

GeneHancer (GH) Regulatory Elements for HDHD3 Gene

Promoters and enhancers for HDHD3 Gene
GeneHancer (GH) Identifier GH Type GH
Score		 GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites		 Gene Targets
GH09I113372 Promoter/Enhancer 2.5 EPDnew Ensembl ENCODE dbSUPER 571.2 -1.0 -991 11.9 HDGF PKNOX1 CLOCK FOXA2 ARNT MLX ARID4B SIN3A DMAP1 YBX1 HDHD3 PRPF4 C9orf43 POLE3 RNF183 ALAD CDC26 BSPRY
GH09I113343 Enhancer 1.2 Ensembl ENCODE dbSUPER 21.4 +33.1 33115 1.2 HDAC1 PKNOX1 ATF1 NFIB ZNF335 ATF7 PHF21A ZBTB11 USF2 REST BSPRY HDHD3 WDR31
GH09I113356 Enhancer 0.6 dbSUPER 20.4 +20.1 20097 0.8 ZFHX2 GLIS1 ZNF629 ZNF398 FEZF1 ZIC2 ATF2 EGR2 HDHD3 WDR31 ALAD RNF183 C9orf43 POLE3 BSPRY
GH09I113339 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 4.8 +36.9 36851 1.7 SMAD1 MLX ARNT ARID4B SIN3A DMAP1 ZNF2 ZBTB7B IRF4 YY1 WDR31 PRPF4 CDC26 BSPRY RNF183 RPL32P22 ALAD C9orf43 POLE3 HDHD3
GH09I113386 Enhancer 1.1 ENCODE dbSUPER 5.2 -11.2 -11153 3.4 FOXA2 MLX ARID4B DMAP1 YY1 RXRA MIER2 REST ZNF623 PPARG ALAD POLE3 C9orf43 RNF183 PRPF4 CDC26 HDHD3
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around HDHD3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the HDHD3 gene promoter:

Genomic Locations for HDHD3 Gene

Genomic Locations for HDHD3 Gene
chr9:113,373,416-113,377,009
(GRCh38/hg38)
Size:
3,594 bases
Orientation:
Minus strand
chr9:116,135,698-116,139,279
(GRCh37/hg19)

Genomic View for HDHD3 Gene

Genes around HDHD3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
HDHD3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for HDHD3 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for HDHD3 Gene

Proteins for HDHD3 Gene

Products:

  1. Antibody
  2. Protein
  3. Assay

  • Protein details for HDHD3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9BSH5-HDHD3_HUMAN
    Recommended name:
    Haloacid dehalogenase-like hydrolase domain-containing protein 3
    Protein Accession:
    Q9BSH5
    Secondary Accessions:
    • B2RD47

    Protein attributes for HDHD3 Gene

    Size:
    251 amino acids
    Molecular mass:
    28000 Da
    Quaternary structure:
    No Data Available

    Three dimensional structures from OCA and Proteopedia for HDHD3 Gene

neXtProt entry for HDHD3 Gene

Protein Expression for HDHD3 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for HDHD3 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for HDHD3 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for HDHD3 Gene

Domains & Families for HDHD3 Gene

Gene Families for HDHD3 Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for HDHD3 Gene

InterPro:
Blocks:
ProtoNet:

Suggested Antigen Peptide Sequences for HDHD3 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q9BSH5

UniProtKB/Swiss-Prot:

HDHD3_HUMAN :
  • Belongs to the HAD-like hydrolase superfamily.
Family:
  • Belongs to the HAD-like hydrolase superfamily.
genes like me logo Genes that share domains with HDHD3: view

Function for HDHD3 Gene

Products:

  1. Animal Model
  2. CRISPR
  3. miRNA
  4. Inhibitory RNA
  5. Clone
  6. Cell Line

Phenotypes From GWAS Catalog for HDHD3 Gene

Gene Ontology (GO) - Molecular Function for HDHD3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 16189514
GO:0016787 hydrolase activity IEA --
genes like me logo Genes that share ontologies with HDHD3: view
genes like me logo Genes that share phenotypes with HDHD3: view

Animal Model Products

miRNA for HDHD3 Gene

miRTarBase miRNAs that target HDHD3

Clone Products

  • Addgene plasmids for HDHD3

No data available for Molecular function , Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for HDHD3 Gene

Localization for HDHD3 Gene

Subcellular locations from

COMPARTMENTS
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 HDHD3 gene
Compartment Confidence
mitochondrion 3
nucleus 3
extracellular 1
peroxisome 1
cytosol 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoli (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for HDHD3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005739 mitochondrion IEA --
genes like me logo Genes that share ontologies with HDHD3: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot for HDHD3 Gene

Pathways & Interactions for HDHD3 Gene

SuperPathways for HDHD3 Gene

PathCards logo More details on SuperPathways for HDHD3
No Data Available

Gene Ontology (GO) - Biological Process for HDHD3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0008152 metabolic process IEA --
genes like me logo Genes that share ontologies with HDHD3: view

No data available for Pathways by source and SIGNOR curated interactions for HDHD3 Gene

Drugs & Compounds for HDHD3 Gene

Products:

  1. Drug
No Compound Related Data Available

Transcripts for HDHD3 Gene

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone

mRNA/cDNA for HDHD3 Gene

(4) REFSEQ mRNAs :
(5) Additional mRNA sequences :
(241) Selected AceView cDNA sequences:
(3) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for HDHD3 Gene

Haloacid dehalogenase-like hydrolase domain containing 3:
Representative Sequences:

Clone Products

  • Addgene plasmids for HDHD3

Alternative Splicing Database (ASD) splice patterns (SP) for HDHD3 Gene

ExUns: 1a · 1b ^ 2a · 2b · 2c ^ 3a · 3b
SP1: -
SP2: - -
SP3:

Relevant External Links for HDHD3 Gene

GeneLoc Exon Structure for
HDHD3
ECgene alternative splicing isoforms for
HDHD3

Expression for HDHD3 Gene

Products:

  1. Primer
  2. Gene Expression Assay

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for HDHD3 Gene

mRNA expression in normal human tissues for HDHD3 Gene
mRNA expression by BioGPS for HDHD3 GenemRNA expression by GTEx for HDHD3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for HDHD3 Gene

This gene is overexpressed in Adrenal Gland (x6.8).

Protein differential expression in normal tissues from HIPED for HDHD3 Gene

This gene is overexpressed in Adrenal (10.5), Salivary gland (9.0), and Skin (8.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for HDHD3 Gene



Protein tissue co-expression partners for HDHD3 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of HDHD3 Gene:

HDHD3

SOURCE GeneReport for Unigene cluster for HDHD3 Gene:

Hs.7739

Evidence on tissue expression from TISSUES for HDHD3 Gene

  • Intestine(4.4)
  • Liver(4.3)
  • Skin(4.2)
genes like me logo Genes that share expression patterns with HDHD3: view

No data available for mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for HDHD3 Gene

Orthologs for HDHD3 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for HDHD3 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
 Mammalia HDHD3 33 34
  • 98.8 (n)
cow
(Bos Taurus)
 Mammalia HDHD3 33 34
  • 85.39 (n)
dog
(Canis familiaris)
 Mammalia HDHD3 33 34
  • 84.68 (n)
mouse
(Mus musculus)
 Mammalia Hdhd3 33 16 34
  • 80.72 (n)
rat
(Rattus norvegicus)
 Mammalia Hdhd3 33
  • 79.38 (n)
oppossum
(Monodelphis domestica)
 Mammalia HDHD3 34
  • 68 (a)
 OneToOne
platypus
(Ornithorhynchus anatinus)
 Mammalia HDHD3 34
  • 57 (a)
 OneToOne
chicken
(Gallus gallus)
 Aves LOC101747936 33
  • 64.96 (n)
HDHD3 34
  • 55 (a)
 OneToOne
tropical clawed frog
(Silurana tropicalis)
 Amphibia hdhd3 33
  • 60.74 (n)
zebrafish
(Danio rerio)
 Actinopterygii hdhd3 33 34
  • 52.16 (n)
fruit fly
(Drosophila melanogaster)
 Insecta CG15912 33 34
  • 47.39 (n)
Reg-2 34
  • 26 (a)
 OneToMany
worm
(Caenorhabditis elegans)
 Secernentea K01G5.10 33 34
  • 42.41 (n)
baker's yeast
(Saccharomyces cerevisiae)
 Saccharomycetes -- 34
  • 19 (a)
 OneToOne
-- 36
thale cress
(Arabidopsis thaliana)
 eudicotyledons AT5G44730 33
  • 39.97 (n)
rice
(Oryza sativa)
 Liliopsida Os06g0665100 33
  • 43.69 (n)
sea squirt
(Ciona savignyi)
 Ascidiacea -- 34
  • 25 (a)
 OneToOne
Species where no ortholog for HDHD3 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)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • 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)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for HDHD3 Gene

ENSEMBL:
Gene Tree for HDHD3 (if available)
TreeFam:
Gene Tree for HDHD3 (if available)

Paralogs for HDHD3 Gene

No data available for Paralogs for HDHD3 Gene

Variants for HDHD3 Gene

Products:

  1. SNP Genotyping and Copy Number Assay

Sequence variations from dbSNP and Humsavar for HDHD3 Gene

SNP ID Clin Chr 09 pos Variation AA Info Type
rs1000132984 -- 113,378,062(-) C/G upstream_transcript_variant
rs1000673165 -- 113,375,383(-) T/C intron_variant
rs1001221457 -- 113,378,351(-) G/A upstream_transcript_variant
rs1001260328 -- 113,377,684(-) C/G upstream_transcript_variant
rs1001296433 -- 113,372,978(-) G/A downstream_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for HDHD3 Gene

Variant ID Type Subtype PubMed ID
esv3576690 CNV gain 25503493
esv3621540 CNV gain 21293372
nsv1036586 CNV gain 25217958
nsv519849 CNV gain 19592680
nsv615214 CNV gain 21841781

Variation tolerance for HDHD3 Gene

Residual Variation Intolerance Score: 67.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.57; 30.27% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for HDHD3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
HDHD3

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for HDHD3 Gene

Disorders for HDHD3 Gene

Additional Disease Information for HDHD3

ATLAS of Genetics and Cytogenetics in Oncology and Haematology

No disorders were found for HDHD3 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for HDHD3 Gene

Publications for HDHD3 Gene

  1. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58
  2. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PMID: 12477932) Strausberg RL … Mammalian Gene Collection Program Team (Proceedings of the National Academy of Sciences of the United States of America 2002) 2 3 58
  3. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 58
  4. Panorama of ancient metazoan macromolecular complexes. (PMID: 26344197) Wan C … Emili A (Nature 2015) 3 58
  5. An enzyme assisted RP-RPLC approach for in-depth analysis of human liver phosphoproteome. (PMID: 24275569) Bian Y … Zou H (Journal of proteomics 2014) 4 58

Products for HDHD3 Gene

  • Addgene plasmids for HDHD3

Sources for HDHD3 Gene

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