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    SLC39A5 solute carrier family 39 member 5 [ Homo sapiens (human) ]

    Gene ID: 283375, updated on 14-Nov-2024

    Summary

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    Official Symbol
    SLC39A5provided by HGNC
    Official Full Name
    solute carrier family 39 member 5provided by HGNC
    Primary source
    HGNC:HGNC:20502
    See related
    Ensembl:ENSG00000139540 MIM:608730; AllianceGenome:HGNC:20502
    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
    ZIP5; MYP24; LZT-Hs7
    Summary
    The protein encoded by this gene belongs to the ZIP family of zinc transporters that transport zinc into cells from outside, and play a crucial role in controlling intracellular zinc levels. Zinc is an essential cofactor for many enzymes and proteins involved in gene transcription, growth, development and differentiation. Mutations in this gene have been associated with autosomal dominant high myopia (MYP24). Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Sep 2014]
    Expression
    Biased expression in duodenum (RPKM 78.5), small intestine (RPKM 76.3) and 4 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SLC39A5 in Genome Data Viewer
    Location:
    12q13.3
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (56230051..56237846)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (56197676..56205471)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (56623835..56631630)

    Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4550 Neighboring gene ring finger protein 41 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6481 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:56615664-56616598 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:56616599-56617532 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4551 Neighboring gene nucleic acid binding protein 2 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:56630689-56630907 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_29670 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_29671 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_29672 Neighboring gene ankyrin repeat domain 52 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:56650178-56651170 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6484 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4552 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6483 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4553 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4554 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_29674 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_29675 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6485 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:56660797-56661296 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6486 Neighboring gene Sharpr-MPRA regulatory region 15563 Neighboring gene coenzyme Q10A Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_29678 Neighboring gene citrate synthase Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:56693295-56693812 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4556 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4557

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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

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    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Functional characterization of SLC39 family members ZIP5 and ZIP10 in overexpressing HEK293 cells reveals selective copper transport activity.
      Title: Functional characterization of SLC39 family members ZIP5 and ZIP10 in overexpressing HEK293 cells reveals selective copper transport activity.
    2. Genome-wide association study in the Taiwan Biobank identifies four novel genes for human height: NABP2, RASA2, RNF41 and SLC39A5.
      Title: Genome-wide association study in the Taiwan Biobank identifies four novel genes for human height: NABP2, RASA2, RNF41 and SLC39A5.
    3. SLC39A5 dysfunction impairs extracellular matrix synthesis in high myopia pathogenesis.
      Title: SLC39A5 dysfunction impairs extracellular matrix synthesis in high myopia pathogenesis.
    4. SLC39A5 promotes lung adenocarcinoma cell proliferation by activating PI3K/AKT signaling.
      Title: SLC39A5 promotes lung adenocarcinoma cell proliferation by activating PI3K/AKT signaling.
    5. we found that downregulation of ZIP5 by RNA interference inhibited esophageal cancer growth in vivo, reduced the expression of COX2, and promoted the expression of E-cadherin.
      Title: Knockdown of Zinc Transporter ZIP5 by RNA Interference Inhibits Esophageal Cancer Growth In Vivo.
    6. ZIP5 knockdown inhibited the proliferation, migration and invasion of ESCC and suppressed COX2, cyclin D1 and E-cadherin expression, which led to the inhibition of cell progression in esophageal squamous cell carcinoma .
      Title: Knockdown of zinc transporter ZIP5 (SLC39A5) expression significantly inhibits human esophageal cancer progression.
    7. mutation in LRPAP1 is associated with high myopia. Further studies are expected to evaluate the pathogenicity of the variants in CTSH, LEPREL1, ZNF644, SLC39A5, and SCO2.
      Title: Detection of mutations in LRPAP1, CTSH, LEPREL1, ZNF644, SLC39A5, and SCO2 in 298 families with early-onset high myopia by exome sequencing.
    8. Zip5 protein is a zinc transporter that localizes to the basolateral surface of polarized cells
      Title: The mammalian Zip5 protein is a zinc transporter that localizes to the basolateral surface of polarized cells.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Associated conditions

    Description Tests
    Myopia 24, autosomal dominant
    MedGen: C4014762 OMIM: 615946 GeneReviews: Not available
    		Compare labs

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC34778

    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 zinc ion transmembrane transporter activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables zinc ion transmembrane transporter activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Process Evidence Code Pubs
    involved_in BMP signaling pathway IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in G1 to G0 transition involved in cell differentiation ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in bicarbonate transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in cellular response to zinc ion starvation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in eye development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in intracellular monoatomic cation homeostasis IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in neural precursor cell proliferation ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in positive regulation of mRNA splicing, via spliceosome IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in zinc ion import across plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in zinc ion transmembrane transport ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in zinc ion transport ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Component Evidence Code Pubs
    located_in basolateral plasma membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in extracellular exosome HDA PubMed 
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    zinc transporter ZIP5
    Names
    ZRT/IRT-like protein 5
    solute carrier family 39 (metal ion transporter), member 5
    solute carrier family 39 (zinc transporter), member 5
    zinc transporter 5
    zrt- and Irt-like protein 5

    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.

    Genomic

    1. NG_034265.2 RefSeqGene

      Range
      5002..12797
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001135195.1 → NP_001128667.1  zinc transporter ZIP5 precursor

      See identical proteins and their annotated locations for NP_001128667.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Both variants 1 and 2 encode the same protein.
      Source sequence(s)
      AK172768, DA640935
      Consensus CDS
      CCDS8912.2
      UniProtKB/Swiss-Prot
      B2R808, Q6ZMH5, Q8N6Y3
      Related
      ENSP00000266980.4, ENST00000266980.8
      Conserved Domains (1) summary
      pfam02535
      Location:248 → 504
      Zip; ZIP Zinc transporter

    2. NM_173596.3 → NP_775867.2  zinc transporter ZIP5 precursor

      See identical proteins and their annotated locations for NP_775867.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript. Both variants 1 and 2 encode the same protein.
      Source sequence(s)
      AC073896
      Consensus CDS
      CCDS8912.2
      UniProtKB/Swiss-Prot
      B2R808, Q6ZMH5, Q8N6Y3
      Related
      ENSP00000405360.2, ENST00000454355.7
      Conserved Domains (1) summary
      pfam02535
      Location:248 → 504
      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_000012.12 Reference GRCh38.p14 Primary Assembly

      Range
      56230051..56237846
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047428714.1 → XP_047284670.1  zinc transporter ZIP5 isoform X1

      UniProtKB/Swiss-Prot
      B2R808, Q6ZMH5, Q8N6Y3

    2. XM_047428713.1 → XP_047284669.1  zinc transporter ZIP5 isoform X1

      UniProtKB/Swiss-Prot
      B2R808, Q6ZMH5, Q8N6Y3

    3. XM_047428716.1 → XP_047284672.1  zinc transporter ZIP5 isoform X2

    4. XM_011538199.3 → XP_011536501.1  zinc transporter ZIP5 isoform X1

      See identical proteins and their annotated locations for XP_011536501.1

      UniProtKB/Swiss-Prot
      B2R808, Q6ZMH5, Q8N6Y3
      Conserved Domains (1) summary
      pfam02535
      Location:248 → 504
      Zip; ZIP Zinc transporter

    5. XM_011538200.3 → XP_011536502.1  zinc transporter ZIP5 isoform X1

      See identical proteins and their annotated locations for XP_011536502.1

      UniProtKB/Swiss-Prot
      B2R808, Q6ZMH5, Q8N6Y3
      Conserved Domains (1) summary
      pfam02535
      Location:248 → 504
      Zip; ZIP Zinc transporter

    6. XM_047428715.1 → XP_047284671.1  zinc transporter ZIP5 isoform X1

      UniProtKB/Swiss-Prot
      B2R808, Q6ZMH5, Q8N6Y3

    7. XM_011538201.3 → XP_011536503.1  zinc transporter ZIP5 isoform X1

      See identical proteins and their annotated locations for XP_011536503.1

      UniProtKB/Swiss-Prot
      B2R808, Q6ZMH5, Q8N6Y3
      Conserved Domains (1) summary
      pfam02535
      Location:248 → 504
      Zip; ZIP Zinc transporter

    8. XM_005268803.3 → XP_005268860.1  zinc transporter ZIP5 isoform X1

      See identical proteins and their annotated locations for XP_005268860.1

      UniProtKB/Swiss-Prot
      B2R808, Q6ZMH5, Q8N6Y3
      Conserved Domains (1) summary
      pfam02535
      Location:248 → 504
      Zip; ZIP Zinc transporter

    RNA

    1. XR_007063069.1 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060936.1 Alternate T2T-CHM13v2.0

      Range
      56197676..56205471
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054371782.1 → XP_054227757.1  zinc transporter ZIP5 isoform X1

      UniProtKB/Swiss-Prot
      B2R808, Q6ZMH5, Q8N6Y3

    2. XM_054371780.1 → XP_054227755.1  zinc transporter ZIP5 isoform X1

      UniProtKB/Swiss-Prot
      B2R808, Q6ZMH5, Q8N6Y3

    3. XM_054371787.1 → XP_054227762.1  zinc transporter ZIP5 isoform X2

    4. XM_054371785.1 → XP_054227760.1  zinc transporter ZIP5 isoform X1

      UniProtKB/Swiss-Prot
      B2R808, Q6ZMH5, Q8N6Y3

    5. XM_054371783.1 → XP_054227758.1  zinc transporter ZIP5 isoform X1

      UniProtKB/Swiss-Prot
      B2R808, Q6ZMH5, Q8N6Y3

    6. XM_054371786.1 → XP_054227761.1  zinc transporter ZIP5 isoform X1

      UniProtKB/Swiss-Prot
      B2R808, Q6ZMH5, Q8N6Y3

    7. XM_054371784.1 → XP_054227759.1  zinc transporter ZIP5 isoform X1

      UniProtKB/Swiss-Prot
      B2R808, Q6ZMH5, Q8N6Y3

    8. XM_054371781.1 → XP_054227756.1  zinc transporter ZIP5 isoform X1

      UniProtKB/Swiss-Prot
      B2R808, Q6ZMH5, Q8N6Y3

    RNA

    1. XR_008488567.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q6ZMH5.3 GenPept UniProtKB/Swiss-Prot:Q6ZMH5

    Gene LinkOut

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