Aliases for SLC39A3 Gene

Aliases for SLC39A3 Gene

  • Solute Carrier Family 39 Member 3 2 3 4 5
  • Solute Carrier Family 39 (Zinc Transporter), Member 3 2 3
  • Zrt- And Irt-Like Protein 3 3 4
  • Zinc Transporter ZIP3 3 4
  • ZIP-3 3 4
  • ZIP3 3 4

External Ids for SLC39A3 Gene

Previous GeneCards Identifiers for SLC39A3 Gene

  • GC19M002795
  • GC19M002672
  • GC19M002683
  • GC19M002502

Summaries for SLC39A3 Gene

GeneCards Summary for SLC39A3 Gene

SLC39A3 (Solute Carrier Family 39 Member 3) is a Protein Coding gene. Among its related pathways are Metal ion SLC transporters and NRF2 pathway. Gene Ontology (GO) annotations related to this gene include metal ion transmembrane transporter activity and zinc ion transmembrane transporter activity. An important paralog of this gene is SLC39A1.

UniProtKB/Swiss-Prot Summary for SLC39A3 Gene

Gene Wiki entry for SLC39A3 Gene

Additional gene information for SLC39A3 Gene

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for SLC39A3 Gene

Genomics for SLC39A3 Gene

GeneHancer (GH) Regulatory Elements for SLC39A3 Gene

Promoters and enhancers for SLC39A3 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
GH19J002738 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE CraniofacialAtlas 512.6 +0.5 549 2.4 RXRA EP300 ZBTB40 ZNF217 SIN3A TCF12 POLR2G USF1 SP1 NCOR1 SLC39A3 ENSG00000267001 lnc-SGTA-1 GNA11 THOP1 ZNF554 ZNF77 TLE2 DIRAS1 ZNF555
GH19J003363 Promoter/Enhancer 2.4 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 13.4 -627.6 -627633 8.1 HNRNPK NRF1 TCF12 USF1 PHB2 ZNF639 ZNF10 ZBTB5 ZIC2 ZBTB10 NFIC CACTIN-AS1 PIAS4 APBA3 C19orf71 ZNF555 LMNB2 CACTIN ZNF77 SLC39A3
GH19J003150 Promoter/Enhancer 2 FANTOM5 Ensembl ENCODE dbSUPER 13.4 -413.3 -413312 6 NRF1 TCF12 SP1 GTF2E2 JUND FOS ZNF639 REST ZBTB10 ZNF263 LOC100996351 ZNF77 CACTIN GNA11 ZNF555 SPPL2B AP3D1 GNA15 TLE2 LMNB2
GH19J003604 Promoter/Enhancer 1.9 EPDnew Ensembl ENCODE dbSUPER 13.4 -867.2 -867179 5.3 NRF1 ZNF300 GTF2E2 ZIC2 ZNF423 ZBTB26 TARDBP KLF4 DNMT1 KLF7 CACTIN-AS1 TBXA2R ZNF77 CACTIN ZNF555 ENSG00000267030 YJU2 GNA11 ZNF554 HDGFL2
GH19J002840 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE CraniofacialAtlas 11 -101.7 -101725 3.2 EP300 CTCF NRF1 POLR2G SP1 PHF8 JUND FOS ZNF639 ZIC2 ZNF555 ZNF77 SF3A2 CACTIN GNA11 ZNF556 ZNF57 ENSG00000253392 SCAMP4 CSNK1G2
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SLC39A3 on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for SLC39A3

Top Transcription factor binding sites by QIAGEN in the SLC39A3 gene promoter:
  • E2F
  • E2F-1
  • E2F-2
  • E2F-3a
  • E2F-4
  • E2F-5
  • E47
  • NF-1
  • NF-1/L
  • Pax-5

Genomic Locations for SLC39A3 Gene

Genomic Locations for SLC39A3 Gene
7,873 bases
Minus strand
7,949 bases
Minus strand

Genomic View for SLC39A3 Gene

Genes around SLC39A3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SLC39A3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SLC39A3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SLC39A3 Gene

Proteins for SLC39A3 Gene

  • Protein details for SLC39A3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Zinc transporter ZIP3
    Protein Accession:
    Secondary Accessions:
    • B3KMJ3
    • Q8WUG1

    Protein attributes for SLC39A3 Gene

    314 amino acids
    Molecular mass:
    33601 Da
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for SLC39A3 Gene


neXtProt entry for SLC39A3 Gene

Post-translational modifications for SLC39A3 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for SLC39A3 Gene

No data available for DME Specific Peptides for SLC39A3 Gene

Domains & Families for SLC39A3 Gene

Gene Families for SLC39A3 Gene

Protein Domains for SLC39A3 Gene

  • Zinc transporter ZIP

Suggested Antigen Peptide Sequences for SLC39A3 Gene

GenScript: Design optimal peptide antigens:
  • Zrt- and Irt-like protein 3 (S39A3_HUMAN)

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the ZIP transporter (TC 2.A.5) family.
  • Belongs to the ZIP transporter (TC 2.A.5) family.
genes like me logo Genes that share domains with SLC39A3: view

Function for SLC39A3 Gene

Molecular function for SLC39A3 Gene

UniProtKB/Swiss-Prot Function:
Acts as a zinc-influx transporter.

Phenotypes From GWAS Catalog for SLC39A3 Gene

Gene Ontology (GO) - Molecular Function for SLC39A3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005385 zinc ion transmembrane transporter activity IBA 21873635
GO:0046873 metal ion transmembrane transporter activity IEA --
genes like me logo Genes that share ontologies with SLC39A3: view
genes like me logo Genes that share phenotypes with SLC39A3: view

Animal Models for SLC39A3 Gene

MGI Knock Outs for SLC39A3:

Animal Model Products

  • Taconic Biosciences Mouse Models for SLC39A3

CRISPR Products

miRNA for SLC39A3 Gene

miRTarBase miRNAs that target SLC39A3

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for SLC39A3 Gene

Localization for SLC39A3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SLC39A3 Gene

Membrane; Multi-pass membrane protein.

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 SLC39A3 gene
Compartment Confidence
plasma membrane 4
extracellular 1
mitochondrion 1
nucleus 1
endoplasmic reticulum 1
cytosol 1
lysosome 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for SLC39A3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane IBA,TAS --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with SLC39A3: view

Pathways & Interactions for SLC39A3 Gene

genes like me logo Genes that share pathways with SLC39A3: view

Gene Ontology (GO) - Biological Process for SLC39A3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000902 cell morphogenesis IEA --
GO:0001701 in utero embryonic development IEA --
GO:0006811 ion transport IEA --
GO:0006829 zinc ion transport IEA --
GO:0030001 metal ion transport IEA --
genes like me logo Genes that share ontologies with SLC39A3: view

No data available for SIGNOR curated interactions for SLC39A3 Gene

Drugs & Compounds for SLC39A3 Gene

(1) Drugs for SLC39A3 Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
genes like me logo Genes that share compounds with SLC39A3: view

Transcripts for SLC39A3 Gene

mRNA/cDNA for SLC39A3 Gene

9 NCBI additional mRNA sequence :
6 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 SLC39A3 Gene

No ASD Table

Relevant External Links for SLC39A3 Gene

GeneLoc Exon Structure for

Expression for SLC39A3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for SLC39A3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for SLC39A3 Gene

This gene is overexpressed in Testis (x5.7).

Protein differential expression in normal tissues from HIPED for SLC39A3 Gene

This gene is overexpressed in Ovary (47.7), Testis (14.0), and Platelet (7.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for SLC39A3 Gene

Protein tissue co-expression partners for SLC39A3 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for SLC39A3

SOURCE GeneReport for Unigene cluster for SLC39A3 Gene:


Evidence on tissue expression from TISSUES for SLC39A3 Gene

  • Intestine(4.2)
  • Nervous system(3.6)
genes like me logo Genes that share expression patterns with SLC39A3: view

No data available for mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for SLC39A3 Gene

Orthologs for SLC39A3 Gene

This gene was present in the common ancestor of animals.

Orthologs for SLC39A3 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia SLC39A3 31 30
  • 99.36 (n)
(Canis familiaris)
Mammalia SLC39A3 31 30
  • 89.38 (n)
(Bos Taurus)
Mammalia SLC39A3 31 30
  • 88.85 (n)
(Mus musculus)
Mammalia Slc39a3 17 31 30
  • 81.74 (n)
(Rattus norvegicus)
Mammalia Slc39a3 30
  • 81.74 (n)
(Monodelphis domestica)
Mammalia SLC39A3 31
  • 80 (a)
(Ornithorhynchus anatinus)
Mammalia SLC39A3 31
  • 75 (a)
(Gallus gallus)
Aves SLC39A3 31 30
  • 76.78 (n)
tropical clawed frog
(Silurana tropicalis)
Amphibia slc39a3 30
  • 62.83 (n)
Str.17341 30
fruit fly
(Drosophila melanogaster)
Insecta Zip3 31 30
  • 49.83 (n)
ZIP1 31
  • 26 (a)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP011178 30
  • 46.38 (n)
(Caenorhabditis elegans)
Secernentea C18A3.2 31
  • 20 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 30 (a)
Species where no ortholog for SLC39A3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • 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)
  • 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 (Oryza sativa)
  • 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)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • zebrafish (Danio rerio)

Evolution for SLC39A3 Gene

Gene Tree for SLC39A3 (if available)
Gene Tree for SLC39A3 (if available)
Evolutionary constrained regions (ECRs) for SLC39A3: view image

Paralogs for SLC39A3 Gene

Paralogs for SLC39A3 Gene

(2) SIMAP similar genes for SLC39A3 Gene using alignment to 4 proteins:

  • S39A3_HUMAN
  • F5H385_HUMAN
genes like me logo Genes that share paralogs with SLC39A3: view

Variants for SLC39A3 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for SLC39A3 Gene

SNP ID Clinical significance and condition Chr 19 pos Variation AA Info Type
770650 Benign: not provided 2,733,190(-) C/T MISSENSE_VARIANT
rs11539244 - p.Phe100Leu
rs35594294 - p.Pro257Leu

Additional dbSNP identifiers (rs#s) for SLC39A3 Gene

Structural Variations from Database of Genomic Variants (DGV) for SLC39A3 Gene

Variant ID Type Subtype PubMed ID
esv3643437 CNV gain 21293372
nsv509714 CNV insertion 20534489
nsv828397 CNV gain 20364138

Variation tolerance for SLC39A3 Gene

Residual Variation Intolerance Score: 20.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.87; 34.97% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SLC39A3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SLC39A3 Gene

Disorders for SLC39A3 Gene

Additional Disease Information for SLC39A3

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology

No disorders were found for SLC39A3 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for SLC39A3 Gene

Publications for SLC39A3 Gene

  1. Findings from bipolar disorder genome-wide association studies replicate in a Finnish bipolar family-cohort. (PMID: 19308021) Ollila HM … Paunio T (Molecular psychiatry 2009) 3 41 54
  2. hZip2 and hZip3 zinc transporters are down regulated in human prostate adenocarcinomatous glands. (PMID: 17550612) Desouki MM … Costello LC (Molecular cancer 2007) 3 23 54
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 54
  4. Structure, function, and regulation of a subfamily of mouse zinc transporter genes. (PMID: 14525987) Dufner-Beattie J … Andrews GK (The Journal of biological chemistry 2003) 3 23 54
  5. Functional expression of the human hZIP2 zinc transporter. (PMID: 10681536) Gaither LA … Eide DJ (The Journal of biological chemistry 2000) 2 3 54

Products for SLC39A3 Gene

Sources for SLC39A3 Gene