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    SLC39A6 solute carrier family 39 member 6 [ Homo sapiens (human) ]

    Gene ID: 25800, updated on 28-Oct-2024

    Summary

    Official Symbol
    SLC39A6provided by HGNC
    Official Full Name
    solute carrier family 39 member 6provided by HGNC
    Primary source
    HGNC:HGNC:18607
    See related
    Ensembl:ENSG00000141424 MIM:608731; AllianceGenome:HGNC:18607
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    LIV1; ZIP6; LIV-1
    Summary
    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]
    Expression
    Broad expression in prostate (RPKM 62.4), endometrium (RPKM 31.1) and 24 other tissues See more
    Orthologs
    NEW
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    Genomic context

    See SLC39A6 in Genome Data Viewer
    Location:
    18q12.2
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 18 NC_000018.10 (36108531..36129340, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 18 NC_060942.1 (36300097..36320904, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 18 NC_000018.9 (33688494..33709303, complement)

    Chromosome 18 - NC_000018.10Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:33552432-33553324 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr18:33564018-33565217 Neighboring gene chromosome 18 open reading frame 21 Neighboring gene regulation of nuclear pre-mRNA domain containing 1A Neighboring gene Sharpr-MPRA regulatory region 15530 Neighboring gene H3K27ac hESC enhancer GRCh37_chr18:33647245-33647760 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:33664612-33665166 Neighboring gene H3K27ac hESC enhancer GRCh37_chr18:33666275-33666828 Neighboring gene ReSE screen-validated silencer GRCh37_chr18:33678780-33678940 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:33709607-33710112 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:33709101-33709606 Neighboring gene elongator acetyltransferase complex subunit 2 Neighboring gene MPRA-validated peak3116 silencer Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:33765682-33766504 Neighboring gene ReSE screen-validated silencer GRCh37_chr18:33767264-33767527 Neighboring gene uncharacterized LOC124904286 Neighboring gene cell fate and sterol metabolism associated divergent transcript of MOCOS Neighboring gene molybdenum cofactor sulfurase

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    EBI GWAS Catalog

    Description
    Genome-wide association study identifies common variants in SLC39A6 associated with length of survival in esophageal squamous-cell carcinoma.
    EBI GWAS Catalog

    HIV-1 interactions

    Replication interactions

    Interaction Pubs
    HIV-1 infection (VSV-G pseudotyped) of CEMT4 T cells downregulates plasma membrane expression of SLC39A6 PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables monoatomic cation:bicarbonate symporter activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables zinc ion transmembrane transporter activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables zinc ion transmembrane transporter activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables zinc ion transmembrane transporter activity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    enables zinc ion transmembrane transporter activity TAS
    Traceable Author Statement
    more info
     
    Component Evidence Code Pubs
    located_in apical plasma membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in cell surface HDA PubMed 
    located_in endoplasmic reticulum IEA
    Inferred from Electronic Annotation
    more info
     
    located_in lamellipodium membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in membrane raft IDA
    Inferred from Direct Assay
    more info
    PubMed 
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in plasma membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
     

    General protein information

    Preferred Names
    zinc transporter ZIP6
    Names
    LIV-1 protein, estrogen regulated
    ZIP-6
    ZRT/IRT-like protein 6
    estrogen-regulated protein LIV-1
    solute carrier family 39 (metal ion transporter), member 6
    solute carrier family 39 (zinc transporter), member 6
    zinc transporter 6
    zrt- and Irt-like protein 6

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001099406.2NP_001092876.1  zinc transporter ZIP6 isoform 2

      See identical proteins and their annotated locations for NP_001092876.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR and 3' UTR, and lacks exons in the 5' and 3' coding regions (compared to variant 1), resulting in the use of a downstream translation initiation codon. The encoded protein (isoform 2) is shorter at both the N- and C-termini, compared to isoform 1.
      Source sequence(s)
      AC091060, BC039498, DC414741
      Consensus CDS
      CCDS45854.1
      UniProtKB/TrEMBL
      B4DWH6
      Related
      ENSP00000401139.1, ENST00000440549.6
      Conserved Domains (1) summary
      pfam02535
      Location:48431
      Zip; ZIP Zinc transporter
    2. NM_012319.4NP_036451.4  zinc transporter ZIP6 isoform 1 precursor

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AC091060
      Consensus CDS
      CCDS42428.1
      UniProtKB/Swiss-Prot
      B4DR49, B4E224, Q13433, Q8IXR3, Q96HP5
      Related
      ENSP00000269187.4, ENST00000269187.10
      Conserved Domains (1) summary
      pfam02535
      Location:323742
      Zip; ZIP Zinc transporter

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000018.10 Reference GRCh38.p14 Primary Assembly

      Range
      36108531..36129340 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060942.1 Alternate T2T-CHM13v2.0

      Range
      36300097..36320904 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)