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    SLC39A13 solute carrier family 39 member 13 [ Homo sapiens (human) ]

    Gene ID: 91252, updated on 23-Nov-2023

    Summary

    Official Symbol
    SLC39A13provided by HGNC
    Official Full Name
    solute carrier family 39 member 13provided by HGNC
    Primary source
    HGNC:HGNC:20859
    See related
    Ensembl:ENSG00000165915 MIM:608735; AllianceGenome:HGNC:20859
    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
    ZIP13; SCDEDS; EDSSPD3; LZT-Hs9
    Summary
    This gene encodes a member of the LIV-1 subfamily of the ZIP transporter family. The encoded transmembrane protein functions as a zinc transporter. Mutations in this gene have been associated with the spondylocheiro dysplastic form of Ehlers-Danlos syndrome. Alternate transcript variants have been found for this gene. [provided by RefSeq, Jan 2016]
    Expression
    Ubiquitous expression in placenta (RPKM 19.2), testis (RPKM 13.3) and 25 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See SLC39A13 in Genome Data Viewer
    Location:
    11p11.2
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (47407276..47416500)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (47566179..47575404)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (47428827..47438051)

    Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene Spi-1 proto-oncogene Neighboring gene ReSE screen-validated silencer GRCh37_chr11:47387327-47387502 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:47395717-47396218 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4696 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4697 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:47399745-47400696 Neighboring gene SLC39A13 antisense RNA 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:47415859-47416416 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3327 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:47421989-47422989 Neighboring gene microRNA 4487 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:47429423-47430245 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:47430534-47431400 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:47431401-47432265 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:47435437-47435936 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:47447617-47447828 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4699 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3329 Neighboring gene proteasome 26S subunit, ATPase 3 Neighboring gene uncharacterized LOC124902673 Neighboring gene uncharacterized LOC124902820 Neighboring gene receptor associated protein of the synapse

    Genomic regions, transcripts, and products

    Expression

    • Project title: 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?

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Clone Names

    • FLJ25785

    Gene Ontology Provided by GOA

    Process Evidence Code Pubs
    involved_in brown fat cell differentiation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in connective tissue development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in intracellular zinc ion homeostasis IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in intracellular zinc ion homeostasis IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in intracellular zinc ion homeostasis ISS
    Inferred from Sequence or Structural Similarity
    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 ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    involved_in zinc ion transport IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Component Evidence Code Pubs
    located_in Golgi apparatus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in Golgi apparatus ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    located_in Golgi membrane IC
    Inferred by Curator
    more info
    PubMed 
    located_in Golgi membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cytoplasmic vesicle membrane IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    located_in endoplasmic reticulum membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in perinuclear region of cytoplasm ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 

    General protein information

    Preferred Names
    zinc transporter ZIP13
    Names
    LIV-1 subfamily of ZIP zinc transporter 9
    LIV-1 subfamily of ZIP zinc transporters human member 9
    ZRT/IRT-like protein 13
    solute carrier family 39 (metal ion transporter), member 13
    solute carrier family 39 (zinc transporter), member 13
    zinc transporter 13
    zrt- and Irt-like protein 13

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_017073.2 RefSeqGene

      Range
      6316..14222
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001128225.3NP_001121697.2  zinc transporter ZIP13 isoform a precursor

      Status: REVIEWED

      Source sequence(s)
      AC090559
      Consensus CDS
      CCDS44592.1
      UniProtKB/Swiss-Prot
      D3DQR6, D3DQR7, E9PLY1, E9PQV3, Q659D9, Q8N7C9, Q8WV10, Q96H72
      Related
      ENSP00000354689.4, ENST00000362021.9
      Conserved Domains (1) summary
      pfam02535
      Location:65365
      Zip; ZIP Zinc transporter
    2. NM_001330245.2NP_001317174.2  zinc transporter ZIP13 isoform c precursor

      Status: REVIEWED

      Source sequence(s)
      AC090559
      Consensus CDS
      CCDS81564.1
      UniProtKB/TrEMBL
      G3V1B2
      Related
      ENSP00000434290.1, ENST00000533076.5
      Conserved Domains (1) summary
      pfam02535
      Location:65298
      Zip; ZIP Zinc transporter
    3. NM_152264.5NP_689477.3  zinc transporter ZIP13 isoform b precursor

      Status: REVIEWED

      Source sequence(s)
      AC090559
      Consensus CDS
      CCDS7934.1
      Related
      ENSP00000346956.4, ENST00000354884.8
      Conserved Domains (1) summary
      pfam02535
      Location:65358
      Zip; ZIP Zinc transporter

    RNA

    1. NR_134854.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AK098651, AL133581

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000011.10 Reference GRCh38.p14 Primary Assembly

      Range
      47407276..47416500
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011520467.2XP_011518769.1  zinc transporter ZIP13 isoform X13

      See identical proteins and their annotated locations for XP_011518769.1

      UniProtKB/Swiss-Prot
      D3DQR6, D3DQR7, E9PLY1, E9PQV3, Q659D9, Q8N7C9, Q8WV10, Q96H72
      Conserved Domains (1) summary
      pfam02535
      Location:65365
      Zip; ZIP Zinc transporter
    2. XM_017018540.2XP_016874029.1  zinc transporter ZIP13 isoform X3

      UniProtKB/Swiss-Prot
      Q96H72
      Conserved Domains (1) summary
      pfam02535
      Location:65358
      Zip; ZIP Zinc transporter
    3. XM_011520470.2XP_011518772.1  zinc transporter ZIP13 isoform X7

      Conserved Domains (1) summary
      pfam02535
      Location:65329
      Zip; ZIP Zinc transporter
    4. XM_017018541.3XP_016874030.1  zinc transporter ZIP13 isoform X8

    5. XM_047427859.1XP_047283815.1  zinc transporter ZIP13 isoform X11

      UniProtKB/TrEMBL
      K4DIA9
    6. XM_047427860.1XP_047283816.1  zinc transporter ZIP13 isoform X12

      UniProtKB/TrEMBL
      K4DIA9
      Related
      ENSP00000432499.1, ENST00000526614.5
    7. XM_011520466.2XP_011518768.1  zinc transporter ZIP13 isoform X1

      Conserved Domains (1) summary
      pfam02535
      Location:80380
      Zip; ZIP Zinc transporter
    8. XM_006718381.4XP_006718444.1  zinc transporter ZIP13 isoform X2

      Conserved Domains (1) summary
      pfam02535
      Location:80373
      Zip; ZIP Zinc transporter
    9. XM_006718384.3XP_006718447.1  zinc transporter ZIP13 isoform X6

      Conserved Domains (1) summary
      pfam02535
      Location:80313
      Zip; ZIP Zinc transporter
    10. XM_011520469.1XP_011518771.1  zinc transporter ZIP13 isoform X4

      Conserved Domains (1) summary
      pfam02535
      Location:80344
      Zip; ZIP Zinc transporter
    11. XM_006718383.4XP_006718446.1  zinc transporter ZIP13 isoform X5

      Conserved Domains (1) summary
      pfam02535
      Location:80337
      Zip; ZIP Zinc transporter
    12. XM_047427857.1XP_047283813.1  zinc transporter ZIP13 isoform X9

    13. XM_047427858.1XP_047283814.1  zinc transporter ZIP13 isoform X10

      UniProtKB/TrEMBL
      K4DIA9

    RNA

    1. XR_007062524.1 RNA Sequence

    2. XR_007062525.1 RNA Sequence

    3. XR_007062527.1 RNA Sequence

    4. XR_930928.3 RNA Sequence

    5. XR_428862.4 RNA Sequence

    6. XR_007062526.1 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060935.1 Alternate T2T-CHM13v2.0

      Range
      47566179..47575404
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054370479.1XP_054226454.1  zinc transporter ZIP13 isoform X13

    2. XM_054370469.1XP_054226444.1  zinc transporter ZIP13 isoform X3

    3. XM_054370473.1XP_054226448.1  zinc transporter ZIP13 isoform X7

    4. XM_054370474.1XP_054226449.1  zinc transporter ZIP13 isoform X8

    5. XM_054370477.1XP_054226452.1  zinc transporter ZIP13 isoform X11

      UniProtKB/TrEMBL
      K4DIA9
    6. XM_054370478.1XP_054226453.1  zinc transporter ZIP13 isoform X12

      UniProtKB/TrEMBL
      K4DIA9
    7. XM_054370467.1XP_054226442.1  zinc transporter ZIP13 isoform X1

    8. XM_054370468.1XP_054226443.1  zinc transporter ZIP13 isoform X2

    9. XM_054370472.1XP_054226447.1  zinc transporter ZIP13 isoform X6

    10. XM_054370470.1XP_054226445.1  zinc transporter ZIP13 isoform X4

    11. XM_054370471.1XP_054226446.1  zinc transporter ZIP13 isoform X5

    12. XM_054370475.1XP_054226450.1  zinc transporter ZIP13 isoform X9

    13. XM_054370476.1XP_054226451.1  zinc transporter ZIP13 isoform X10

      UniProtKB/TrEMBL
      K4DIA9

    RNA

    1. XR_008488487.1 RNA Sequence

    2. XR_008488488.1 RNA Sequence

    3. XR_008488490.1 RNA Sequence

    4. XR_008488485.1 RNA Sequence

    5. XR_008488486.1 RNA Sequence

    6. XR_008488489.1 RNA Sequence