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

Gene ID: 27173, updated on 2-Nov-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
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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 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)

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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_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

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