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

Gene ID: 295928, updated on 2-May-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
Ensembl: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. Located in endoplasmic reticulum. 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, Apr 2022]
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 metal ion transport IEA
Inferred from Electronic Annotation
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 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
    ENSRNOP00000016191.6, ENSRNOT00000016191.6
    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
    ENSRNOP00000096044.1, ENSRNOT00000098235.1
    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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