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INO80D INO80 complex subunit D [ Homo sapiens (human) ]

Gene ID: 54891, updated on 2-Nov-2024

Summary

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Official Symbol
INO80Dprovided by HGNC
Official Full Name
INO80 complex subunit Dprovided by HGNC
Primary source
HGNC:HGNC:25997
See related
Ensembl:ENSG00000114933 MIM:619207; AllianceGenome:HGNC:25997
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
Summary
Involved in several processes, including chromatin remodeling; regulation of chromosome organization; and regulation of nucleobase-containing compound metabolic process. Part of Ino80 complex. [provided by Alliance of Genome Resources, Nov 2024]
Expression
Ubiquitous expression in bone marrow (RPKM 2.7), thyroid (RPKM 1.0) and 25 other tissues See more
Orthologs
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Genomic context

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See INO80D in Genome Data Viewer
Location:
2q33.3
Exon count:
15
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (205993721..206086174, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (206475671..206568063, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (206858445..206950898, complement)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene RN7SK pseudogene 178 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:206809315-206809815 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:206811287-206811786 Neighboring gene peptidylprolyl isomerase A pseudogene 68 Neighboring gene MPRA-validated peak4024 silencer Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:206868888-206869466 Neighboring gene ribosomal protein L27 pseudogene 8 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:206946709-206947498 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr2:206948195-206949016 Neighboring gene Sharpr-MPRA regulatory region 7917 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12263 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12264 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12265 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:206950661-206951480 Neighboring gene INO80D antisense RNA 1 Neighboring gene NADH:ubiquinone oxidoreductase core subunit S1 Neighboring gene GCSH pseudogene 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17025 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17026 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12266 Neighboring gene small nucleolar RNA, C/D box 51 Neighboring gene eukaryotic translation elongation factor 1 beta 2

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. Whole exome sequencing implicates an INO80D mutation in a syndrome of aortic hypoplasia, premature atherosclerosis, and arterial stiffness. Shameer K, et al. Circ Cardiovasc Genet, 2014 Oct. PMID 25122053
  2. Genome-wide analysis of lncRNAs in 3'-untranslated regions: CR933609 acts as a decoy to protect the INO80D gene. Chang CC, et al. Int J Oncol, 2018 Jul. PMID 29750421
  3. INO80 is required for oncogenic transcription and tumor growth in non-small cell lung cancer. Zhang S, et al. Oncogene, 2017 Mar. PMID 27641337, Free PMC Article
  4. The mammalian INO80 chromatin remodeling complex is required for replication stress recovery. Vassileva I, et al. Nucleic Acids Res, 2014 Aug. PMID 25016522, Free PMC Article
  5. Common body mass index-associated variants confer risk of extreme obesity. Cotsapas C, et al. Hum Mol Genet, 2009 Sep 15. PMID 19553259, Free PMC Article

See all (30) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. expression levels of CR933609 and INO80D were decreased in CR933609-knockdown NSCLC cells, but only expression levels of INO80D decreased in INO80D knockdown cells. It was shown that there are independent promoters in CR933609 and INO80D
    Title: Genome-wide analysis of lncRNAs in 3'-untranslated regions: CR933609 acts as a decoy to protect the INO80D gene.
  2. INO80D is a subunit of the human INO80 chromatin remodeling complex; its Ser818Cys mutation has a role in accelerated arterial aging
    Title: Whole exome sequencing implicates an INO80D mutation in a syndrome of aortic hypoplasia, premature atherosclerosis, and arterial stiffness.
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
Common body mass index-associated variants confer risk of extreme obesity.
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)

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ20309

Gene Ontology Provided by GOA

Process Evidence Code Pubs
involved_in DNA recombination IEA
Inferred from Electronic Annotation
more info
  
involved_in DNA repair IEA
Inferred from Electronic Annotation
more info
  
involved_in chromatin remodeling IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in positive regulation of DNA repair ISO
Inferred from Sequence Orthology
more info
  
involved_in positive regulation of DNA-templated transcription IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of telomere maintenance in response to DNA damage ISO
Inferred from Sequence Orthology
more info
  
involved_in regulation of DNA repair ISO
Inferred from Sequence Orthology
more info
  
involved_in regulation of DNA replication IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in regulation of DNA strand elongation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in regulation of cell cycle IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in regulation of chromosome organization IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in regulation of embryonic development ISO
Inferred from Sequence Orthology
more info
  
involved_in telomere maintenance ISO
Inferred from Sequence Orthology
more info
  
Component Evidence Code Pubs
part_of Ino80 complex IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nucleoplasm TAS
Traceable Author Statement
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
INO80 complex subunit 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.

mRNA and Protein(s)

  1. NM_017759.5 → NP_060229.3  INO80 complex subunit D

    See identical proteins and their annotated locations for NP_060229.3

    Status: VALIDATED

    Source sequence(s)
    AC007679, AK000316, AK096585, BC004193, CR746991, DB233201
    Consensus CDS
    CCDS46500.1
    UniProtKB/Swiss-Prot
    B3KU68, B9EG77, Q53TQ3, Q6PJC6, Q6PJU1, Q6PKA1, Q9NXD5
    Related
    ENSP00000384198.1, ENST00000403263.6
    Conserved Domains (3) summary
    PRK14971
    Location:211 → 290
    PRK14971; DNA polymerase III subunit gamma/tau
    pfam05109
    Location:914 → 1025
    Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)
    pfam13891
    Location:18 → 79
    zf-C3Hc3H; Potential DNA-binding domain

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_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    205993721..206086174 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047444830.1 → XP_047300786.1  INO80 complex subunit D isoform X2

  2. XM_011511375.3 → XP_011509677.1  INO80 complex subunit D isoform X2

    See identical proteins and their annotated locations for XP_011509677.1

    UniProtKB/Swiss-Prot
    Q53TQ3
    Conserved Domains (1) summary
    pfam13891
    Location:342 → 406
    zf-C3Hc3H; Potential DNA-binding domain

  3. XM_011511371.3 → XP_011509673.1  INO80 complex subunit D isoform X3

    See identical proteins and their annotated locations for XP_011509673.1

    UniProtKB/Swiss-Prot
    B3KU68, B9EG77, Q53TQ3, Q6PJC6, Q6PJU1, Q6PKA1, Q9NXD5
    Conserved Domains (3) summary
    PRK14971
    Location:211 → 290
    PRK14971; DNA polymerase III subunit gamma/tau
    pfam05109
    Location:914 → 1025
    Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)
    pfam13891
    Location:18 → 79
    zf-C3Hc3H; Potential DNA-binding domain

  4. XM_011511369.4 → XP_011509671.1  INO80 complex subunit D isoform X1

    Conserved Domains (1) summary
    pfam13891
    Location:50 → 108
    zf-C3Hc3H; Potential DNA-binding domain

  5. XM_011511370.3 → XP_011509672.1  INO80 complex subunit D isoform X3

    See identical proteins and their annotated locations for XP_011509672.1

    UniProtKB/Swiss-Prot
    B3KU68, B9EG77, Q53TQ3, Q6PJC6, Q6PJU1, Q6PKA1, Q9NXD5
    Conserved Domains (3) summary
    PRK14971
    Location:211 → 290
    PRK14971; DNA polymerase III subunit gamma/tau
    pfam05109
    Location:914 → 1025
    Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)
    pfam13891
    Location:18 → 79
    zf-C3Hc3H; Potential DNA-binding domain

  6. XM_011511376.2 → XP_011509678.1  INO80 complex subunit D isoform X2

    See identical proteins and their annotated locations for XP_011509678.1

    UniProtKB/Swiss-Prot
    Q53TQ3
    Conserved Domains (1) summary
    pfam13891
    Location:342 → 406
    zf-C3Hc3H; Potential DNA-binding domain

  7. XM_047444829.1 → XP_047300785.1  INO80 complex subunit D isoform X2

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_015495299.1 Reference GRCh38.p14 PATCHES

    Range
    102739..195192 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054331985.1 → XP_054187960.1  INO80 complex subunit D isoform X2

  2. XM_054331983.1 → XP_054187958.1  INO80 complex subunit D isoform X2

  3. XM_054331982.1 → XP_054187957.1  INO80 complex subunit D isoform X1

  4. XM_054331986.1 → XP_054187961.1  INO80 complex subunit D isoform X2

  5. XM_054331984.1 → XP_054187959.1  INO80 complex subunit D isoform X2

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    206475671..206568063 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054342668.1 → XP_054198643.1  INO80 complex subunit D isoform X2

  2. XM_054342666.1 → XP_054198641.1  INO80 complex subunit D isoform X2

  3. XM_054342665.1 → XP_054198640.1  INO80 complex subunit D isoform X1

  4. XM_054342669.1 → XP_054198644.1  INO80 complex subunit D isoform X2

  5. XM_054342667.1 → XP_054198642.1  INO80 complex subunit D isoform X2

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q53TQ3.3 GenPept UniProtKB/Swiss-Prot:Q53TQ3

Gene LinkOut

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