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    ANKRD13D ankyrin repeat domain 13D [ Homo sapiens (human) ]

    Gene ID: 338692, updated on 2-Nov-2024

    Summary

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    Official Symbol
    ANKRD13Dprovided by HGNC
    Official Full Name
    ankyrin repeat domain 13Dprovided by HGNC
    Primary source
    HGNC:HGNC:27880
    See related
    Ensembl:ENSG00000172932 MIM:615126; AllianceGenome:HGNC:27880
    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
    Summary
    The protein encoded by this gene is a member of the ankyrin repeat domain (ANKRD) 13 family, which currently consists of four proteins containing ubiquitin-interacting motifs. These proteins are integral membrane proteins that bind specifically to Lys-63-linked ubiquitin chains on membrane-bound proteins, targeting those proteins for rapid internalization. [provided by RefSeq, Dec 2016]
    Expression
    Broad expression in bone marrow (RPKM 36.3), spleen (RPKM 13.6) and 23 other tissues See more
    Orthologs
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    Genomic context

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    See ANKRD13D in Genome Data Viewer
    Location:
    11q13.2
    Exon count:
    16
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (67289303..67302484)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (67283279..67296448)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (67056774..67069955)

    Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene lysine demethylase 2A Neighboring gene small nucleolar RNA U13 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr11:66989729-66990608 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5073 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5074 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5075 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr11:67020970-67022169 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3619 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5076 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3620 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5077 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5078 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5079 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:67038522-67039486 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:67039487-67040451 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:67044441-67045054 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:67045055-67045668 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5083 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5084 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3621 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3622 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:67057124-67058048 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:67058049-67058971 Neighboring gene G protein-coupled receptor kinase 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:67070151-67070668 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:67070669-67071188 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5085 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5086 Neighboring gene uncharacterized LOC100130987 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3623 Neighboring gene slingshot protein phosphatase 3 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3624 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:67119697-67120279 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:67120280-67120861 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5087 Neighboring gene DNA polymerase delta 4, accessory subunit

    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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    Related articles in PubMed

    1. Identification of ANKRD13D as a potential target in renal cell carcinomas. Zhou W, et al. Int J Biol Markers, 2024 Jun. PMID 38449090
    2. The Ankrd13 Family of Ubiquitin-interacting Motif-bearing Proteins Regulates Valosin-containing Protein/p97 Protein-mediated Lysosomal Trafficking of Caveolin 1. Burana D, et al. J Biol Chem, 2016 Mar 18. PMID 26797118, Free PMC Article
    3. ENTREP/FAM189A2 encodes a new ITCH ubiquitin ligase activator that is downregulated in breast cancer. Tsunoda T, et al. EMBO Rep, 2022 Feb 3. PMID 34927784, Free PMC Article
    4. The Ankrd 13 family of UIM-bearing proteins regulates EGF receptor endocytosis from the plasma membrane. Tanno H, et al. Mol Biol Cell, 2012 Apr. PMID 22298428, Free PMC Article
    5. Stress-induced NEDDylation promotes cytosolic protein aggregation through HDAC6 in a p62-dependent manner. Kim S, et al. iScience, 2021 Mar 19. PMID 33665565, Free PMC Article

    See all (32) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Identification of ANKRD13D as a potential target in renal cell carcinomas.
      Title: Identification of ANKRD13D as a potential target in renal cell carcinomas.
    2. overexpression of wild-type as well as truncated-mutant Ankrd 13A, 13B and 13D proteins strongly inhibited rapid endocytosis of ubiquitinated EGFR from the surface in EGF-treated cells
      Title: The Ankrd 13 family of UIM-bearing proteins regulates EGF receptor endocytosis from the plasma membrane.
    3. Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
      Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
    4. Observational study of gene-disease association. (HuGE Navigator)
      Title: Gene-centric association signals for lipids and apolipoproteins identified via the HumanCVD BeadChip.
    Submit: New GeneRIF Correction

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See Variation Viewer (GRCh37.p13)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC50828

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables ubiquitin-modified protein reader activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables ubiquitin-modified protein reader activity IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in negative regulation of receptor internalization IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in late endosome IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in perinuclear region of cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in plasma membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    ankyrin repeat domain-containing protein 13D
    Names
    ankyrin repeat domain 13 family, member D

    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_052619.1 RefSeqGene

      Range
      5013..18194
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001347901.2 → NP_001334830.1  ankyrin repeat domain-containing protein 13D isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) contains an alternate exon in the 5' end compared to variant 1. The resulting isoform (2) is shorter at the N-terminus compared to isoform 1.
      Source sequence(s)
      AP001885

    2. NM_207354.3 → NP_997237.2  ankyrin repeat domain-containing protein 13D isoform 1

      See identical proteins and their annotated locations for NP_997237.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longer isoform (1).
      Source sequence(s)
      AP001885, BC044239, BC110419, DB460018
      Consensus CDS
      CCDS31616.2
      UniProtKB/Swiss-Prot
      D6RCN6, Q0VAK0, Q0VGC3, Q6ZTN6, Q6ZVD0, Q86SU1
      Related
      ENSP00000427130.2, ENST00000511455.7
      Conserved Domains (4) summary
      cd00204
      Location:9 → 102
      ANK; ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other ...
      pfam11904
      Location:155 → 469
      GPCR_chapero_1; GPCR-chaperone
      pfam13637
      Location:40 → 93
      Ank_4; Ankyrin repeats (many copies)
      sd00045
      Location:39 → 70
      ANK; ANK repeat [structural motif]

    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_000011.10 Reference GRCh38.p14 Primary Assembly

      Range
      67289303..67302484
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047426873.1 → XP_047282829.1  ankyrin repeat domain-containing protein 13D isoform X1

    2. XM_047426874.1 → XP_047282830.1  ankyrin repeat domain-containing protein 13D isoform X1

    3. XM_047426872.1 → XP_047282828.1  ankyrin repeat domain-containing protein 13D isoform X1

    RNA

    1. XR_428913.3 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060935.1 Alternate T2T-CHM13v2.0

      Range
      67283279..67296448
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054368629.1 → XP_054224604.1  ankyrin repeat domain-containing protein 13D isoform X1

    2. XM_054368630.1 → XP_054224605.1  ankyrin repeat domain-containing protein 13D isoform X1

    3. XM_054368628.1 → XP_054224603.1  ankyrin repeat domain-containing protein 13D isoform X1

    RNA

    1. XR_008488389.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q6ZTN6.3 GenPept UniProtKB/Swiss-Prot:Q6ZTN6

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