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Slc39a13 solute carrier family 39 (metal ion transporter), member 13 [ Mus musculus (house mouse) ]

Gene ID: 68427, updated on 9-May-2024

Summary

Official Symbol
Slc39a13provided by MGI
Official Full Name
solute carrier family 39 (metal ion transporter), member 13provided by MGI
Primary source
MGI:MGI:1915677
See related
Ensembl:ENSMUSG00000002105 AllianceGenome:MGI:1915677
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
ZIP13; ZIP-13; 1100001L14Rik
Summary
Predicted to enable protein homodimerization activity and zinc ion transmembrane transporter activity. Involved in cellular zinc ion homeostasis; connective tissue development; and zinc ion transmembrane transport. Located in Golgi apparatus 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, Apr 2022]
Expression
Ubiquitous expression in limb E14.5 (RPKM 17.2), lung adult (RPKM 14.9) and 28 other tissues See more
Orthologs
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Genomic context

See Slc39a13 in Genome Data Viewer
Location:
2 E1; 2 50.44 cM
Exon count:
12
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 2 NC_000068.8 (90892136..90900754, complement)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 2 NC_000068.7 (91061781..91070441, complement)

Chromosome 2 - NC_000068.8Genomic Context describing neighboring genes Neighboring gene receptor-associated protein of the synapse Neighboring gene predicted gene 13778 Neighboring gene STARR-positive B cell enhancer ABC_E7840 Neighboring gene proteasome (prosome, macropain) 26S subunit, ATPase 3 Neighboring gene STARR-positive B cell enhancer ABC_E2041 Neighboring gene CapStarr-seq enhancer MGSCv37_chr2:90910894-90911077 Neighboring gene predicted gene, 57833 Neighboring gene predicted gene, 39874 Neighboring gene Spi-1 proto-oncogene Neighboring gene STARR-positive B cell enhancer ABC_E4476 Neighboring gene STARR-positive B cell enhancer ABC_E4477 Neighboring gene STARR-seq mESC enhancer starr_05105 Neighboring gene STARR-seq mESC enhancer starr_05107 Neighboring gene myosin binding protein C, cardiac

Genomic regions, transcripts, and products

Expression

  • Project title: Mouse ENCODE transcriptome data
  • Description: RNA profiling data sets generated by the Mouse ENCODE project.
  • BioProject: PRJNA66167
  • Publication: PMID 25409824
  • Analysis date: n/a

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Variation

Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Endonuclease-mediated (2) 
  • Gene trapped (1) 
  • Targeted (1)  1 citation

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Clone Names

  • MGC118284

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables metal ion transmembrane transporter 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 IC
Inferred by Curator
more info
PubMed 
enables zinc ion transmembrane transporter activity ISO
Inferred from Sequence Orthology
more info
 
Process Evidence Code Pubs
involved_in brown fat cell differentiation IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in connective tissue development IMP
Inferred from Mutant Phenotype
more info
PubMed 
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 IMP
Inferred from Mutant Phenotype
more info
PubMed 
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
 
acts_upstream_of_or_within monoatomic ion transport IEA
Inferred from Electronic Annotation
more info
 
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 IMP
Inferred from Mutant Phenotype
more info
PubMed 
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
 
Component Evidence Code Pubs
located_in Golgi apparatus IDA
Inferred from Direct Assay
more info
PubMed 
located_in Golgi apparatus ISO
Inferred from Sequence Orthology
more info
 
located_in Golgi membrane ISO
Inferred from Sequence Orthology
more info
 
located_in cytoplasmic vesicle IEA
Inferred from Electronic Annotation
more info
 
located_in cytoplasmic vesicle membrane ISO
Inferred from Sequence Orthology
more info
 
located_in endoplasmic reticulum 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 IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
zinc transporter ZIP13
Names
solute carrier family 39 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_001290765.2NP_001277694.1  zinc transporter ZIP13 isoform a precursor

    See identical proteins and their annotated locations for NP_001277694.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (a).
    Source sequence(s)
    AL691439
    Consensus CDS
    CCDS71095.1
    UniProtKB/Swiss-Prot
    Q8BZH0
    Related
    ENSMUSP00000107063.3, ENSMUST00000111436.3
    Conserved Domains (1) summary
    pfam02535
    Location:65369
    Zip; ZIP Zinc transporter
  2. NM_026721.4NP_080997.1  zinc transporter ZIP13 isoform b precursor

    See identical proteins and their annotated locations for NP_080997.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 5' coding region, compared to variant 1, resulting in an isoform (b) that is shorter than isoform a.
    Source sequence(s)
    AL691439
    Consensus CDS
    CCDS16424.1
    UniProtKB/Swiss-Prot
    B7ZCF2, Q497M5, Q8BZH0, Q8VDX1, Q9D1R4
    UniProtKB/TrEMBL
    B2RQ45
    Related
    ENSMUSP00000073263.6, ENSMUST00000073575.12
    Conserved Domains (1) summary
    pfam02535
    Location:65356
    Zip; ZIP Zinc transporter

RNA

  1. NR_110981.2 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) lacks two internal exons and uses an alternate splice site, compared to variant 1. This variant is represented as non-coding becuase the predicted protein does not meet RefSeq quality criteria.
    Source sequence(s)
    AL691439
    Related
    ENSMUST00000079976.10

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000068.8 Reference GRCm39 C57BL/6J

    Range
    90892136..90900754 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006500101.4XP_006500164.1  zinc transporter ZIP13 isoform X4

    Conserved Domains (1) summary
    pfam02535
    Location:65322
    Zip; ZIP Zinc transporter
  2. XM_030252030.2XP_030107890.1  zinc transporter ZIP13 isoform X5

    Conserved Domains (1) summary
    pfam02535
    Location:44189
    Zip; ZIP Zinc transporter
  3. XM_030252029.2XP_030107889.1  zinc transporter ZIP13 isoform X5

    Conserved Domains (1) summary
    pfam02535
    Location:44189
    Zip; ZIP Zinc transporter
  4. XM_006500100.4XP_006500163.1  zinc transporter ZIP13 isoform X3

    Conserved Domains (1) summary
    pfam02535
    Location:65335
    Zip; ZIP Zinc transporter
  5. XM_017319236.3XP_017174725.1  zinc transporter ZIP13 isoform X2

    UniProtKB/Swiss-Prot
    B7ZCF2, Q497M5, Q8BZH0, Q8VDX1, Q9D1R4
    UniProtKB/TrEMBL
    B2RQ45
    Conserved Domains (1) summary
    pfam02535
    Location:65356
    Zip; ZIP Zinc transporter
  6. XM_006500099.5XP_006500162.1  zinc transporter ZIP13 isoform X1

    See identical proteins and their annotated locations for XP_006500162.1

    UniProtKB/Swiss-Prot
    Q8BZH0
    Conserved Domains (1) summary
    pfam02535
    Location:65369
    Zip; ZIP Zinc transporter
  7. XM_036162524.1XP_036018417.1  zinc transporter ZIP13 isoform X1

    Conserved Domains (1) summary
    pfam02535
    Location:65369
    Zip; ZIP Zinc transporter
  8. XM_030252031.2XP_030107891.1  zinc transporter ZIP13 isoform X6

    Conserved Domains (1) summary
    pfam02535
    Location:65295
    Zip; ZIP Zinc transporter

RNA

  1. XR_003953709.2 RNA Sequence

  2. XR_003953711.2 RNA Sequence

  3. XR_003953712.2 RNA Sequence

  4. XR_004940715.1 RNA Sequence

  5. XR_374515.4 RNA Sequence

  6. XR_003953710.2 RNA Sequence

  7. XR_004940716.1 RNA Sequence

  8. XR_004940717.1 RNA Sequence