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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
    mouse all
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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)

    Genotypes

    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

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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