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ANKRD13A ankyrin repeat domain 13A [ Homo sapiens (human) ]

Gene ID: 88455, updated on 11-Apr-2024

Summary

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Official Symbol
ANKRD13Aprovided by HGNC
Official Full Name
ankyrin repeat domain 13Aprovided by HGNC
Primary source
HGNC:HGNC:21268
See related
Ensembl:ENSG00000076513 MIM:615123; AllianceGenome:HGNC:21268
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
ANKRD13; NY-REN-25
Summary
Enables ubiquitin-dependent protein binding activity. Involved in negative regulation of protein localization to endosome and negative regulation of receptor internalization. Located in late endosome; perinuclear region of cytoplasm; and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Broad expression in testis (RPKM 37.6), lymph node (RPKM 31.1) and 24 other tissues See more
Orthologs
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Genomic context

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Location:
12q24.11
Exon count:
17
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (109999213..110039763)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (109974902..110015456)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (110437235..110477568)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124903012 Neighboring gene NANOG hESC enhancer GRCh37_chr12:110318928-110319429 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4846 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4847 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:110337802-110338642 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr12:110338643-110339483 Neighboring gene trichoplein keratin filament binding Neighboring gene ReSE screen-validated silencer GRCh37_chr12:110353916-110354160 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:110358257-110358757 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:110361416-110362271 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:110362776-110363756 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:110363757-110364736 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr12:110370433-110371632 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:110384533-110385204 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:110385205-110385876 Neighboring gene GIT ArfGAP 2 Neighboring gene uncharacterized LOC124903013 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6987 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6988 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4849 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6989 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4850 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4851 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6990 Neighboring gene Sharpr-MPRA regulatory region 2512 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6991 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:110460576-110461076 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6992 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr12:110465819-110467018 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:110480304-110480817 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4852 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6993 Neighboring gene chromosome 12 open reading frame 76 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6994 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6995 Neighboring gene CRISPRi-validated cis-regulatory element chr12.3588 Neighboring gene uncharacterized LOC105369976 Neighboring gene Sharpr-MPRA regulatory region 13461

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
  • 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. LncRNA USP30-AS1 promotes the survival of acute myeloid leukemia cells by cis-regulating USP30 and ANKRD13A. Zhou W, et al. Hum Cell, 2022 Jan. PMID 34694569, Free PMC Article
  2. miR-204 targeting of Ankrd13A controls both mesenchymal neural crest and lens cell migration. Avellino R, et al. PLoS One, 2013. PMID 23620728, Free PMC Article
  3. Systems-wide analysis of BCR signalosomes and downstream phosphorylation and ubiquitylation. Satpathy S, et al. Mol Syst Biol, 2015 Jun 2. PMID 26038114, Free PMC Article
  4. 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
  5. 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

See all (48) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. ANKRD13a controls early cell-death checkpoint by interacting with RIP1 independent of NF-kappaB.
    Title: ANKRD13a controls early cell-death checkpoint by interacting with RIP1 independent of NF-κB.
  2. LncRNA USP30-AS1 promotes the survival of acute myeloid leukemia cells by cis-regulating USP30 and ANKRD13A.
    Title: LncRNA USP30-AS1 promotes the survival of acute myeloid leukemia cells by cis-regulating USP30 and ANKRD13A.
  3. The Ankrd13 family of ubiquitin-interacting motif (UIM)-containing proteins are novel VCP-interacting molecules in the endosome.
    Title: The Ankrd13 Family of Ubiquitin-interacting Motif-bearing Proteins Regulates Valosin-containing Protein/p97 Protein-mediated Lysosomal Trafficking of Caveolin 1.
  4. We validated ANKRD13A as a novel constituent of BCR signalosome and showed that BCR-induced phosphorylation of RAB7A at S72 regulates its association with its effector proteins and with endo-lysosomal compartments.
    Title: Systems-wide analysis of BCR signalosomes and downstream phosphorylation and ubiquitylation.
  5. the microRNA miR-204 promotes both mesenchymal neural crest and lens cell migration and elongation by the direct targeting of the Ankrd13A gene.
    Title: miR-204 targeting of Ankrd13A controls both mesenchymal neural crest and lens cell migration.
  6. 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.
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

EBI GWAS Catalog

Description
Genome-wide association study of monoamine metabolite levels in human cerebrospinal fluid.
EBI GWAS Catalog

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

HIV-1 interactions

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Protein interactions

Protein Gene Interaction Pubs
Vpr vpr HIV-1 Vpr is identified to have a physical interaction with ankyrin repeat domain 13A (ANKRD13A) in human HEK293 and/or Jurkat cell lines by using affinity tagging and purification mass spectrometry analyses PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
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 protein localization to endosome IDA
Inferred from Direct Assay
more info
 PubMed 
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 IDA
Inferred from Direct Assay
more info
 PubMed 
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 13A
Names
NY-REN-25 antigen

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_033121.2 → NP_149112.1  ankyrin repeat domain-containing protein 13A

    See identical proteins and their annotated locations for NP_149112.1

    Status: VALIDATED

    Source sequence(s)
    AC007546, AF155103, BC032833, BC057817
    Consensus CDS
    CCDS9140.1
    UniProtKB/Swiss-Prot
    O60736, Q8IZ07
    UniProtKB/TrEMBL
    B4DYP5, Q3ZTS7
    Related
    ENSP00000261739.4, ENST00000261739.9
    Conserved Domains (3) summary
    sd00045
    Location:40 → 71
    ANK; ANK repeat [structural motif]
    pfam11904
    Location:156 → 469
    GPCR_chapero_1; GPCR-chaperone
    pfam12796
    Location:13 → 96
    Ank_2; Ankyrin repeats (3 copies)

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_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    109999213..110039763
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005253984.2 → XP_005254041.1  ankyrin repeat domain-containing protein 13A isoform X6

    See identical proteins and their annotated locations for XP_005254041.1

    UniProtKB/TrEMBL
    B4DDL0
    Conserved Domains (1) summary
    pfam11904
    Location:68 → 382
    GPCR_chapero_1; GPCR-chaperone

  2. XM_005253980.4 → XP_005254037.1  ankyrin repeat domain-containing protein 13A isoform X1

    See identical proteins and their annotated locations for XP_005254037.1

    UniProtKB/TrEMBL
    B4DYP5
    Conserved Domains (3) summary
    sd00045
    Location:40 → 71
    ANK; ANK repeat [structural motif]
    pfam11904
    Location:156 → 470
    GPCR_chapero_1; GPCR-chaperone
    pfam12796
    Location:13 → 96
    Ank_2; Ankyrin repeats (3 copies)

  3. XM_005253981.4 → XP_005254038.1  ankyrin repeat domain-containing protein 13A isoform X2

    UniProtKB/TrEMBL
    B4DYP5
    Conserved Domains (4) summary
    cd00204
    Location:4 → 101
    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:156 → 469
    GPCR_chapero_1; GPCR-chaperone
    pfam13637
    Location:41 → 90
    Ank_4; Ankyrin repeats (many copies)
    sd00045
    Location:40 → 71
    ANK; ANK repeat [structural motif]

  4. XM_005253982.4 → XP_005254039.1  ankyrin repeat domain-containing protein 13A isoform X3

    UniProtKB/TrEMBL
    B4DYP5
    Conserved Domains (4) summary
    cd00204
    Location:4 → 101
    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:156 → 468
    GPCR_chapero_1; GPCR-chaperone
    pfam13637
    Location:41 → 90
    Ank_4; Ankyrin repeats (many copies)
    sd00045
    Location:40 → 71
    ANK; ANK repeat [structural motif]

  5. XM_017020162.2 → XP_016875651.1  ankyrin repeat domain-containing protein 13A isoform X7

    Conserved Domains (2) summary
    sd00045
    Location:40 → 71
    ANK; ANK repeat [structural motif]
    pfam13637
    Location:41 → 90
    Ank_4; Ankyrin repeats (many copies)

  6. XM_011538937.2 → XP_011537239.1  ankyrin repeat domain-containing protein 13A isoform X4

    UniProtKB/TrEMBL
    B4DYP5
    Conserved Domains (4) summary
    cd00204
    Location:4 → 101
    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:134 → 422
    GPCR_chapero_1; GPCR-chaperone
    pfam13637
    Location:41 → 90
    Ank_4; Ankyrin repeats (many copies)
    sd00045
    Location:40 → 71
    ANK; ANK repeat [structural motif]

  7. XM_047429810.1 → XP_047285766.1  ankyrin repeat domain-containing protein 13A isoform X5

  8. XM_047429811.1 → XP_047285767.1  ankyrin repeat domain-containing protein 13A isoform X8

RNA

  1. XR_944812.4 RNA Sequence

  2. XR_007063142.1 RNA Sequence

  3. XR_007063141.1 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    109974902..110015456
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054373723.1 → XP_054229698.1  ankyrin repeat domain-containing protein 13A isoform X6

  2. XM_054373718.1 → XP_054229693.1  ankyrin repeat domain-containing protein 13A isoform X1

  3. XM_054373719.1 → XP_054229694.1  ankyrin repeat domain-containing protein 13A isoform X2

  4. XM_054373720.1 → XP_054229695.1  ankyrin repeat domain-containing protein 13A isoform X3

  5. XM_054373724.1 → XP_054229699.1  ankyrin repeat domain-containing protein 13A isoform X7

  6. XM_054373721.1 → XP_054229696.1  ankyrin repeat domain-containing protein 13A isoform X4

  7. XM_054373722.1 → XP_054229697.1  ankyrin repeat domain-containing protein 13A isoform X5

  8. XM_054373725.1 → XP_054229700.1  ankyrin repeat domain-containing protein 13A isoform X8

RNA

  1. XR_008488707.1 RNA Sequence

  2. XR_008488709.1 RNA Sequence

  3. XR_008488708.1 RNA Sequence

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8IZ07.3 GenPept UniProtKB/Swiss-Prot:Q8IZ07

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