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    SLC39A1 solute carrier family 39 member 1 [ Homo sapiens (human) ]

    Gene ID: 27173, updated on 3-Dec-2024

    Summary

    Official Symbol
    SLC39A1provided by HGNC
    Official Full Name
    solute carrier family 39 member 1provided by HGNC
    Primary source
    HGNC:HGNC:12876
    See related
    Ensembl:ENSG00000143570 MIM:604740; AllianceGenome:HGNC:12876
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    ZIP1; ZIRTL
    Summary
    This gene encodes a member of the zinc-iron permease family. The encoded protein is localized to the cell membrane and acts as a zinc uptake transporter. This gene has been linked to prostate cancer, breast cancer, and Alzheimer's disease. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2012]
    Expression
    Ubiquitous expression in placenta (RPKM 41.2), lung (RPKM 24.3) and 25 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See SLC39A1 in Genome Data Viewer
    Location:
    1q21.3
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (153959110..153968184, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (153096371..153105445, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (153931586..153940660, complement)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC101928059 Neighboring gene DENN domain containing 4B Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1756 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1757 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:153918384-153918884 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1758 Neighboring gene CREB regulated transcription coactivator 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1759 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1760 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1761 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1347 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1762 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr1:153935601-153936800 Neighboring gene microRNA 6737 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:153939664-153940520 Neighboring gene cAMP responsive element binding protein 3 like 4 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:153948322-153948971 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:153949621-153950269 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1770 Neighboring gene Sharpr-MPRA regulatory region 11874 Neighboring gene jumping translocation breakpoint Neighboring gene JTB divergent transcript

    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

    EBI GWAS Catalog

    Description
    Genome-wide association identifies genetic variants associated with lentiform nucleus volume in N = 1345 young and elderly subjects.
    EBI GWAS Catalog

    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 inorganic cation transmembrane transporter activity TAS
    Traceable Author Statement
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables signaling receptor binding IEA
    Inferred from Electronic Annotation
    more info
     
    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 TAS
    Traceable Author Statement
    more info
     
    Process Evidence Code Pubs
    involved_in embryonic cranial skeleton morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in in utero embryonic development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in limb development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in monoatomic cation transport TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in zinc ion transmembrane transport IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in zinc ion transmembrane transport 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 endoplasmic reticulum membrane IEA
    Inferred from Electronic Annotation
    more info
     
    located_in membrane TAS
    Traceable Author Statement
    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 ZIP1
    Names
    ZRT/IRT-like protein 1
    solute carrier family 39 (zinc transporter), member 1
    solute carrier family 39 (zinc transporter), member 3
    zinc transporter 1
    zrt- and Irt-like protein 1

    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_001271957.2NP_001258886.1  zinc transporter ZIP1 isoform a

      See identical proteins and their annotated locations for NP_001258886.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1, 2, 3, 4 and 5 encode the same protein (isoform a).
      Source sequence(s)
      AF132942, AK074943, AL358472, BG704399, DA354647
      Consensus CDS
      CCDS1055.1
      UniProtKB/Swiss-Prot
      B4DDY7, Q5T4K1, Q8N2H7, Q9BTV0, Q9NY26, Q9UBI7, Q9Y2Z7, Q9Y380
      UniProtKB/TrEMBL
      Q6IAD8
      Related
      ENSP00000357610.1, ENST00000368621.5
      Conserved Domains (1) summary
      pfam02535
      Location:48319
      Zip; ZIP Zinc transporter
    2. NM_001271958.2NP_001258887.1  zinc transporter ZIP1 isoform a

      See identical proteins and their annotated locations for NP_001258887.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. Variants 1, 2, 3, 4 and 5 encode the same protein (isoform a).
      Source sequence(s)
      AF132942, AK075257, BC014303
      Consensus CDS
      CCDS1055.1
      UniProtKB/Swiss-Prot
      B4DDY7, Q5T4K1, Q8N2H7, Q9BTV0, Q9NY26, Q9UBI7, Q9Y2Z7, Q9Y380
      UniProtKB/TrEMBL
      Q6IAD8
      Related
      ENSP00000348535.4, ENST00000356205.9
      Conserved Domains (1) summary
      pfam02535
      Location:48319
      Zip; ZIP Zinc transporter
    3. NM_001271959.2NP_001258888.1  zinc transporter ZIP1 isoform a

      See identical proteins and their annotated locations for NP_001258888.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) differs in the 5' UTR compared to variant 1. Variants 1, 2, 3, 4 and 5 encode the same protein (isoform a).
      Source sequence(s)
      AF151829, AL358472, DA711655, HY042960
      Consensus CDS
      CCDS1055.1
      UniProtKB/Swiss-Prot
      B4DDY7, Q5T4K1, Q8N2H7, Q9BTV0, Q9NY26, Q9UBI7, Q9Y2Z7, Q9Y380
      UniProtKB/TrEMBL
      Q6IAD8
      Related
      ENSP00000484182.1, ENST00000621013.4
      Conserved Domains (1) summary
      pfam02535
      Location:48319
      Zip; ZIP Zinc transporter
    4. NM_001271960.2NP_001258889.1  zinc transporter ZIP1 isoform a

      See identical proteins and their annotated locations for NP_001258889.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) differs in the 5' UTR compared to variant 1. Variants 1, 2, 3, 4 and 5 encode the same protein (isoform a).
      Source sequence(s)
      AW571711, BC014303, DB001496
      Consensus CDS
      CCDS1055.1
      UniProtKB/Swiss-Prot
      B4DDY7, Q5T4K1, Q8N2H7, Q9BTV0, Q9NY26, Q9UBI7, Q9Y2Z7, Q9Y380
      UniProtKB/TrEMBL
      Q6IAD8
      Related
      ENSP00000479421.1, ENST00000617697.4
      Conserved Domains (1) summary
      pfam02535
      Location:48319
      Zip; ZIP Zinc transporter
    5. NM_001271961.2NP_001258890.1  zinc transporter ZIP1 isoform b

      Status: REVIEWED

      Description
      Transcript Variant: This variant (6) differs in the 5' UTR and lacks an exon in the 3' coding region which results in a frameshift, compared to variant 1. The encoded isoform (b) is shorter and has a distinct C-terminus, compared to isoform a.
      Source sequence(s)
      AK293389, BM807264
      Consensus CDS
      CCDS72920.1
      UniProtKB/TrEMBL
      A0A0A0MTL8
      Related
      ENSP00000443632.2, ENST00000537590.5
    6. NM_014437.5NP_055252.2  zinc transporter ZIP1 isoform a

      See identical proteins and their annotated locations for NP_055252.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes isoform a. Variants 1, 2, 3, 4 and 5 encode the same protein (isoform a).
      Source sequence(s)
      AL358472, AW571711, BC014303
      Consensus CDS
      CCDS1055.1
      UniProtKB/Swiss-Prot
      B4DDY7, Q5T4K1, Q8N2H7, Q9BTV0, Q9NY26, Q9UBI7, Q9Y2Z7, Q9Y380
      UniProtKB/TrEMBL
      Q6IAD8
      Related
      ENSP00000309710.6, ENST00000310483.10
      Conserved Domains (1) summary
      pfam02535
      Location:48319
      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_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      153959110..153968184 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047418008.1XP_047273964.1  zinc transporter ZIP1 isoform X1

      UniProtKB/Swiss-Prot
      B4DDY7, Q5T4K1, Q8N2H7, Q9BTV0, Q9NY26, Q9UBI7, Q9Y2Z7, Q9Y380
      UniProtKB/TrEMBL
      Q6IAD8

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      153096371..153105445 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054336011.1XP_054191986.1  zinc transporter ZIP1 isoform X1

      UniProtKB/Swiss-Prot
      B4DDY7, Q5T4K1, Q8N2H7, Q9BTV0, Q9NY26, Q9UBI7, Q9Y2Z7, Q9Y380
      UniProtKB/TrEMBL
      Q6IAD8