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    Slc39a13 solute carrier family 39 member 13 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 295928, updated on 27-Nov-2024

    Summary

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    Official Symbol
    Slc39a13provided by RGD
    Official Full Name
    solute carrier family 39 member 13provided by RGD
    Primary source
    RGD:1304695
    See related
    EnsemblRapid:ENSRNOG00000011981 AllianceGenome:RGD:1304695
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Summary
    Predicted to enable protein homodimerization activity and zinc ion transmembrane transporter activity. Involved in response to zinc ion. Predicted to be located in several cellular components, including Golgi membrane; endoplasmic reticulum membrane; and perinuclear region of cytoplasm. Human ortholog(s) of this gene implicated in Ehlers-Danlos syndrome and Ehlers-Danlos syndrome spondylodysplastic type 3. Orthologous to human SLC39A13 (solute carrier family 39 member 13). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in Kidney (RPKM 97.9), Muscle (RPKM 96.8) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Slc39a13 in Genome Data Viewer
    Location:
    3q24
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 3 NC_086021.1 (97495229..97504279, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 3 NC_051338.1 (77039411..77047528, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 3 NC_005102.4 (79884524..79892664, complement)

    Chromosome 3 - NC_086021.1Genomic Context describing neighboring genes Neighboring gene receptor-associated protein of the synapse Neighboring gene proteasome 26S subunit, ATPase 3 Neighboring gene uncharacterized LOC134486120 Neighboring gene uncharacterized LOC120101909 Neighboring gene Spi-1 proto-oncogene

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

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    Related articles in PubMed

    1. Zinc deficiency mediates alcohol-induced apoptotic cell death in the liver of rats through activating ER and mitochondrial cell death pathways. Sun Q, et al. Am J Physiol Gastrointest Liver Physiol, 2015 May 1. PMID 25767260, Free PMC Article
    2. Over-expression of Zip-13 mRNA in kidney and lung during dietary zinc deficiency in Wistar rats. Guo L, et al. Mol Biol Rep, 2011 Mar. PMID 20859692
    3. Spondylocheiro dysplastic form of the Ehlers-Danlos syndrome--an autosomal-recessive entity caused by mutations in the zinc transporter gene SLC39A13. Giunta C, et al. Am J Hum Genet, 2008 Jun. PMID 18513683, Free PMC Article
    4. Biochemical characterization of human ZIP13 protein: a homo-dimerized zinc transporter involved in the spondylocheiro dysplastic Ehlers-Danlos syndrome. Bin BH, et al. J Biol Chem, 2011 Nov 18. PMID 21917916, Free PMC Article
    5. The zinc transporter SLC39A13/ZIP13 is required for connective tissue development; its involvement in BMP/TGF-beta signaling pathways. Fukada T, et al. PLoS One, 2008. PMID 18985159, Free PMC Article

    See all (7) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Zip-13 shows an up-regulation (P < 0.05) in zinc-deficiency group both in kidney and lung.
      Title: Over-expression of Zip-13 mRNA in kidney and lung during dietary zinc deficiency in Wistar rats.
    Submit: New GeneRIF Correction

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC124816

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables metal ion transmembrane transporter activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein homodimerization activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein homodimerization activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables zinc ion transmembrane transporter activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables zinc ion transmembrane transporter activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables zinc ion transmembrane transporter activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables zinc ion transmembrane transporter activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Process Evidence Code Pubs
    involved_in brown fat cell differentiation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in brown fat cell differentiation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in brown fat cell differentiation ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in connective tissue development IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in connective tissue development ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in intracellular zinc ion homeostasis IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in intracellular zinc ion homeostasis IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in intracellular zinc ion homeostasis ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in response to zinc ion IEP
    Inferred from Expression Pattern
    more info
    		 PubMed 
    involved_in transmembrane transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in zinc ion transmembrane transport IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in zinc ion transmembrane transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in zinc ion transmembrane transport ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in zinc ion transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in zinc ion transport ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in zinc ion transport ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Component Evidence Code Pubs
    located_in Golgi apparatus ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in Golgi membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in Golgi membrane ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in cytoplasmic vesicle membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytoplasmic vesicle membrane ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in cytoplasmic vesicle membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in endoplasmic reticulum membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in endoplasmic reticulum membrane ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in membrane ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in perinuclear region of cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in perinuclear region of cytoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    zinc transporter ZIP13
    Names
    ZIP-13
    solute carrier family 39 (metal ion transporter), member 13
    solute carrier family 39 (zinc transporter), member 13
    zrt- and Irt-like protein 13

    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_001399258.1 → NP_001386187.1  zinc transporter ZIP13 isoform 1 precursor

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000003
      UniProtKB/TrEMBL
      A6HNA4
      Related
      ENSRNOP00000016191.7, ENSRNOT00000016191.7
      Conserved Domains (1) summary
      pfam02535
      Location:65 → 357
      Zip; ZIP Zinc transporter

    2. NM_001399259.1 → NP_001386188.1  zinc transporter ZIP13 isoform 2 precursor

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000003
      UniProtKB/TrEMBL
      A0A8I6GLF4
      Related
      ENSRNOP00000078410.2, ENSRNOT00000112322.2
      Conserved Domains (1) summary
      pfam02535
      Location:65 → 323
      Zip; ZIP Zinc transporter

    3. NM_001429906.1 → NP_001416835.1  zinc transporter ZIP13 isoform 3 precursor

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000003

    RNA

    1. NR_174175.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000003

    2. NR_174176.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000003

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086021.1 Reference GRCr8

      Range
      97495229..97504279 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_063283289.1 → XP_063139359.1  zinc transporter ZIP13 isoform X2

    2. XM_063283288.1 → XP_063139358.1  zinc transporter ZIP13 isoform X1

    3. XM_039104519.1 → XP_038960447.1  zinc transporter ZIP13 isoform X6

      UniProtKB/TrEMBL
      A6HNA5
      Conserved Domains (1) summary
      pfam02535
      Location:45 → 190
      Zip; ZIP Zinc transporter

    4. XM_063283292.1 → XP_063139362.1  zinc transporter ZIP13 isoform X5

    5. XM_063283291.1 → XP_063139361.1  zinc transporter ZIP13 isoform X4

    6. XM_063283290.1 → XP_063139360.1  zinc transporter ZIP13 isoform X3

    RNA

    1. XR_010064578.1 RNA Sequence

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001039196.1: Suppressed sequence

      Description
      NM_001039196.1: This RefSeq was removed because currently there is insufficient support for the transcript and the protein.
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q2M1K6.1 GenPept UniProtKB/Swiss-Prot:Q2M1K6

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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