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

Gene ID: 25800, updated on 6-May-2021

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
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
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
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Genomic context

See SLC39A6 in Genome Data Viewer
Location:
18q12.2
Exon count:
11
Annotation release Status Assembly Chr Location
109.20210226 current GRCh38.p13 (GCF_000001405.39) 18 NC_000018.10 (36108531..36129868, complement)
105.20201022 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 uncharacterized LOC105372066 Neighboring gene Sharpr-MPRA regulatory region 2053 Neighboring gene chromosome 18 open reading frame 21 Neighboring gene regulation of nuclear pre-mRNA domain containing 1A Neighboring gene elongator acetyltransferase complex subunit 2 Neighboring gene cell fate and sterol metabolism associated divergent transcript of MOCOS Neighboring gene molybdenum cofactor sulfurase Neighboring gene RNA, U4 small nuclear 3, pseudogene

Genomic regions, transcripts, and products

Expression

  • Project title: 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

Associated conditions

Description Tests
Genome-wide association study identifies common variants in SLC39A6 associated with length of survival in esophageal squamous-cell carcinoma.
GeneReviews: Not available

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

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables zinc ion transmembrane transporter activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables zinc ion transmembrane transporter activity IDA
Inferred from Direct Assay
more info
PubMed 
Process Evidence Code Pubs
involved_in cellular zinc ion homeostasis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in cellular zinc ion homeostasis IDA
Inferred from Direct Assay
more info
PubMed 
involved_in zinc ion import across plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in zinc ion import across plasma membrane IDA
Inferred from Direct Assay
more info
PubMed 
involved_in zinc ion transmembrane transport IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in zinc ion transmembrane transport TAS
Traceable Author Statement
more info
 
Component Evidence Code Pubs
located_in cell surface HDA PubMed 
located_in endoplasmic reticulum IEA
Inferred from Electronic Annotation
more info
 
is_active_in integral component of plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
located_in integral component of plasma membrane IDA
Inferred from Direct Assay
more info
PubMed 
located_in lamellipodium membrane IDA
Inferred from Direct Assay
more info
PubMed 
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
estrogen-regulated protein LIV-1
solute carrier family 39 (metal ion transporter), member 6
solute carrier family 39 (zinc transporter), member 6
zrt- and Irt-like protein 6

NCBI Reference Sequences (RefSeq)

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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/Swiss-Prot
    Q13433
    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
    Related
    ENSP00000269187.4, ENST00000269187.10
    Conserved Domains (1) summary
    pfam02535
    Location:323742
    Zip; ZIP Zinc transporter

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20210226

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000018.10 Reference GRCh38.p13 Primary Assembly

    Range
    36108531..36129868 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011525901.2XP_011524203.1  zinc transporter ZIP6 isoform X1

    See identical proteins and their annotated locations for XP_011524203.1

    UniProtKB/Swiss-Prot
    Q13433
    Conserved Domains (1) summary
    pfam02535
    Location:323742
    Zip; ZIP Zinc transporter
  2. XM_011525900.2XP_011524202.1  zinc transporter ZIP6 isoform X1

    See identical proteins and their annotated locations for XP_011524202.1

    UniProtKB/Swiss-Prot
    Q13433
    Related
    ENSP00000465915.1, ENST00000590986.5
    Conserved Domains (1) summary
    pfam02535
    Location:323742
    Zip; ZIP Zinc transporter
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