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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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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

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

Gene LinkOut

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