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Aliases for SLC39A6 Gene

Aliases for SLC39A6 Gene

  • Solute Carrier Family 39 Member 6 2 3 4 5
  • Solute Carrier Family 39 (Metal Ion Transporter), Member 6 2 3
  • Solute Carrier Family 39 (Zinc Transporter), Member 6 2 3
  • Estrogen-Regulated Protein LIV-1 3 4
  • Zrt- And Irt-Like Protein 6 3 4
  • ZIP-6 3 4
  • ZIP6 3 4
  • LIV-1 Protein, Estrogen Regulated 3
  • Zinc Transporter ZIP6 3
  • LIV-1 3
  • LIV1 4

External Ids for SLC39A6 Gene

Previous GeneCards Identifiers for SLC39A6 Gene

  • GC18M033576
  • GC18M031941
  • GC18M031940
  • GC18M031943
  • GC18M033688
  • GC18M030547

Summaries for SLC39A6 Gene

Entrez Gene Summary for SLC39A6 Gene

  • Zinc is an essential cofactor for hundreds of enzymes. It is involved in protein, nucleic acid, carbohydrate, and lipid metabolism, as well as in the control of gene transcription, growth, development, and differentiation. SLC39A6 belongs to a subfamily of proteins that show structural characteristics of zinc transporters (Taylor and Nicholson, 2003 [PubMed 12659941]).[supplied by OMIM, Mar 2008]

GeneCards Summary for SLC39A6 Gene

SLC39A6 (Solute Carrier Family 39 Member 6) is a Protein Coding gene. Among its related pathways are Metal ion SLC transporters and Transport of glucose and other sugars, bile salts and organic acids, metal ions and amine compounds. 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 SLC39A10.

UniProtKB/Swiss-Prot for SLC39A6 Gene

  • May act as a zinc-influx transporter.

Gene Wiki entry for SLC39A6 Gene

Additional gene information for SLC39A6 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SLC39A6 Gene

Genomics for SLC39A6 Gene

Regulatory Elements for SLC39A6 Gene

Enhancers for SLC39A6 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH18H035613 1.2 Ensembl ENCODE 4.9 +513.0 512967 7 PKNOX1 FEZF1 FOS ATF7 RUNX3 JUNB REST ZNF518A ZSCAN16 STAT3 ENSG00000268573 GALNT1 ZNF397 SLC39A6 ENSG00000266965 LOC105372065
GH18H035525 1.1 Ensembl ENCODE dbSUPER 5.2 +603.4 603410 1 BHLHE40 CEBPB CEBPG ZNF384 MEF2D ZKSCAN8 IKZF1 CEBPA GLIS1 SLC39A6 INO80C GALNT1
GH18H035155 0.9 Ensembl ENCODE 4.1 +973.9 973877 0 FOXA2 SAP130 FOXA3 HLF ARID4B KAT8 POLR2A SMAD4 RCOR1 RXRB SLC39A6 ENSG00000274400 PIR47170
GH18H035732 0.6 ENCODE 4.3 +397.0 396978 1 ZNF316 MAFG BACH1 NFE2 EMSY MAFK NFE2L2 GALNT1 SLC39A6 ENSG00000267397 NRBF2P1
GH18H035141 0.4 dbSUPER 4.1 +987.4 987398 1 JUNB MAPRE2 ZNF24 SLC39A6 ENSG00000274400 ENSG00000280096
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around SLC39A6 on UCSC Golden Path with GeneCards custom track

Promoters for SLC39A6 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000102278 14 2801 PKNOX1 MLX ARNT ARID4B SIN3A DMAP1 ZNF2 ZBTB7B YY1 SLC30A9

Genomic Location for SLC39A6 Gene

Chromosome:
18
Start:
36,108,531 bp from pter
End:
36,129,814 bp from pter
Size:
21,284 bases
Orientation:
Minus strand

Genomic View for SLC39A6 Gene

Genes around SLC39A6 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SLC39A6 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SLC39A6 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SLC39A6 Gene

Proteins for SLC39A6 Gene

  • Protein details for SLC39A6 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q13433-S39A6_HUMAN
    Recommended name:
    Zinc transporter ZIP6
    Protein Accession:
    Q13433
    Secondary Accessions:
    • B4DR49
    • B4E224
    • Q8IXR3
    • Q96HP5

    Protein attributes for SLC39A6 Gene

    Size:
    755 amino acids
    Molecular mass:
    85047 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=BAG61161.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Alternative splice isoforms for SLC39A6 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SLC39A6 Gene

Post-translational modifications for SLC39A6 Gene

  • N-glycosylated.
  • Ubiquitination at isoforms=77
  • Glycosylation at Asn67, Asn68, isoforms=196, Ser219, Ser221, isoforms=222, isoforms=225, isoforms=227, isoforms=228, Asn241, isoforms=266, Asn283, and isoforms=2684
  • Modification sites at PhosphoSitePlus

Other Protein References for SLC39A6 Gene

No data available for DME Specific Peptides for SLC39A6 Gene

Domains & Families for SLC39A6 Gene

Gene Families for SLC39A6 Gene

HGNC:
IUPHAR :
Human Protein Atlas (HPA):
  • Predicted membrane proteins
  • Transporters

Protein Domains for SLC39A6 Gene

InterPro:
Blocks:
ProtoNet:

Suggested Antigen Peptide Sequences for SLC39A6 Gene

Graphical View of Domain Structure for InterPro Entry

Q13433

UniProtKB/Swiss-Prot:

S39A6_HUMAN :
  • Belongs to the ZIP transporter (TC 2.A.5) family.
Family:
  • Belongs to the ZIP transporter (TC 2.A.5) family.
genes like me logo Genes that share domains with SLC39A6: view

Function for SLC39A6 Gene

Molecular function for SLC39A6 Gene

UniProtKB/Swiss-Prot Function:
May act as a zinc-influx transporter.
UniProtKB/Swiss-Prot Induction:
Up-regulated by estrogen in breast cancer cells lines.

Phenotypes From GWAS Catalog for SLC39A6 Gene

Gene Ontology (GO) - Molecular Function for SLC39A6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005385 zinc ion transmembrane transporter activity TAS --
GO:0046873 metal ion transmembrane transporter activity IEA --
genes like me logo Genes that share ontologies with SLC39A6: view
genes like me logo Genes that share phenotypes with SLC39A6: view

Animal Model Products

  • Taconic Biosciences Mouse Models for SLC39A6

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for SLC39A6
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for SLC39A6 Gene

Localization for SLC39A6 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SLC39A6 Gene

Cell membrane; Multi-pass membrane protein.

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 SLC39A6 gene
Compartment Confidence
plasma membrane 5
endoplasmic reticulum 2
cytosol 1

Gene Ontology (GO) - Cellular Components for SLC39A6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005783 endoplasmic reticulum IEA --
GO:0005886 plasma membrane TAS --
GO:0005887 integral component of plasma membrane IDA 15642354
GO:0009986 cell surface IDA 19581412
GO:0016020 membrane IEA --
genes like me logo Genes that share ontologies with SLC39A6: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for SLC39A6 Gene

Pathways & Interactions for SLC39A6 Gene

genes like me logo Genes that share pathways with SLC39A6: view

Interacting Proteins for SLC39A6 Gene

Gene Ontology (GO) - Biological Process for SLC39A6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006810 transport IEA --
GO:0006811 ion transport IEA --
GO:0006829 zinc II ion transport IEA --
GO:0006882 cellular zinc ion homeostasis IDA 15642354
GO:0030001 metal ion transport IEA --
genes like me logo Genes that share ontologies with SLC39A6: view

No data available for SIGNOR curated interactions for SLC39A6 Gene

Drugs & Compounds for SLC39A6 Gene

No Compound Related Data Available

Transcripts for SLC39A6 Gene

Unigene Clusters for SLC39A6 Gene

Solute carrier family 39 (zinc transporter), member 6:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for SLC39A6
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

Alternative Splicing Database (ASD) splice patterns (SP) for SLC39A6 Gene

ExUns: 1a · 1b · 1c · 1d ^ 2a · 2b ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8a · 8b ^ 9 ^ 10a · 10b ^ 11
SP1: - - - -
SP2:
SP3: -
SP4:
SP5: -

Relevant External Links for SLC39A6 Gene

GeneLoc Exon Structure for
SLC39A6
ECgene alternative splicing isoforms for
SLC39A6

Expression for SLC39A6 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SLC39A6 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for SLC39A6 Gene

This gene is overexpressed in Fetal Brain (33.9) and Frontal cortex (25.8).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for SLC39A6 Gene



Protein tissue co-expression partners for SLC39A6 Gene

NURSA nuclear receptor signaling pathways regulating expression of SLC39A6 Gene:

SLC39A6

SOURCE GeneReport for Unigene cluster for SLC39A6 Gene:

Hs.79136

mRNA Expression by UniProt/SwissProt for SLC39A6 Gene:

Q13433-S39A6_HUMAN
Tissue specificity: Highly expressed in the breast, prostate, placenta, kidney, pituitary and corpus callosum. Weakly expressed in heart and intestine. Also highly expressed in cells derived from an adenocarcinoma of the cervix and lung carcinoma.

Evidence on tissue expression from TISSUES for SLC39A6 Gene

  • Eye(4.2)
  • Nervous system(3)
genes like me logo Genes that share expression patterns with SLC39A6: view

Primer Products

No data available for mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for SLC39A6 Gene

Orthologs for SLC39A6 Gene

This gene was present in the common ancestor of animals.

Orthologs for SLC39A6 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SLC39A6 33 34
  • 99.43 (n)
cow
(Bos Taurus)
Mammalia SLC39A6 33 34
  • 92.88 (n)
dog
(Canis familiaris)
Mammalia SLC39A6 33 34
  • 91.97 (n)
rat
(Rattus norvegicus)
Mammalia Slc39a6 33
  • 85.46 (n)
mouse
(Mus musculus)
Mammalia Slc39a6 33 16 34
  • 84.53 (n)
oppossum
(Monodelphis domestica)
Mammalia SLC39A6 34
  • 79 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia SLC39A6 34
  • 72 (a)
OneToOne
chicken
(Gallus gallus)
Aves SLC39A6 33 34
  • 70.4 (n)
lizard
(Anolis carolinensis)
Reptilia SLC39A6 34
  • 69 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC100487349 33
  • 67.12 (n)
zebrafish
(Danio rerio)
Actinopterygii slc39a6 33 34
  • 62.58 (n)
fruit fly
(Drosophila melanogaster)
Insecta foi 34
  • 26 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 45 (a)
OneToMany
Species where no ortholog for SLC39A6 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)
  • 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)
  • 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)
  • worm (Caenorhabditis elegans)

Evolution for SLC39A6 Gene

ENSEMBL:
Gene Tree for SLC39A6 (if available)
TreeFam:
Gene Tree for SLC39A6 (if available)

Paralogs for SLC39A6 Gene

(1) SIMAP similar genes for SLC39A6 Gene using alignment to 2 proteins:

genes like me logo Genes that share paralogs with SLC39A6: view

Variants for SLC39A6 Gene

Sequence variations from dbSNP and Humsavar for SLC39A6 Gene

SNP ID Clin Chr 18 pos Sequence Context AA Info Type
rs1000097196 -- 36,121,737(+) GTATC(C/T)ATGTA intron-variant
rs1000101292 -- 36,112,244(+) ACACA(A/G)CTCAT intron-variant
rs1000312054 -- 36,118,011(+) GGGCG(A/T)CAGAG intron-variant
rs1000317584 -- 36,108,908(+) TGATA(C/T)ATTGC utr-variant-3-prime
rs1000343919 -- 36,124,852(+) TGCCT(C/T)CAGCT intron-variant

Structural Variations from Database of Genomic Variants (DGV) for SLC39A6 Gene

Variant ID Type Subtype PubMed ID
nsv576651 CNV loss 21841781
nsv576652 CNV loss 21841781

Variation tolerance for SLC39A6 Gene

Residual Variation Intolerance Score: 9.02% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.42; 27.87% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for SLC39A6 Gene

Human Gene Mutation Database (HGMD)
SLC39A6
SNPedia medical, phenotypic, and genealogical associations of SNPs for
SLC39A6

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SLC39A6 Gene

Disorders for SLC39A6 Gene

Relevant External Links for SLC39A6

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
SLC39A6

No disorders were found for SLC39A6 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for SLC39A6 Gene

Publications for SLC39A6 Gene

  1. Structure-function analysis of LIV-1, the breast cancer-associated protein that belongs to a new subfamily of zinc transporters. (PMID: 12839489) Taylor KM … Nicholson RI (The Biochemical journal 2003) 2 3 4 22 60
  2. The LZT proteins; the LIV-1 subfamily of zinc transporters. (PMID: 12659941) Taylor KM … Nicholson RI (Biochimica et biophysica acta 2003) 2 3 22 60
  3. Concordant correlation of LIV-1 and E-cadherin expression in human breast cancer cell MCF-7. (PMID: 18330719) Shen H … Guo J (Molecular biology reports 2009) 3 22 60
  4. LIV-1 suppression inhibits HeLa cell invasion by targeting ERK1/2-Snail/Slug pathway. (PMID: 17825787) Zhao L … Li X (Biochemical and biophysical research communications 2007) 3 22 60
  5. Signal peptide prediction based on analysis of experimentally verified cleavage sites. (PMID: 15340161) Zhang Z … Henzel WJ (Protein science : a publication of the Protein Society 2004) 3 4 60

Products for SLC39A6 Gene

Sources for SLC39A6 Gene

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