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    DNAI3 dynein axonemal intermediate chain 3 [ Homo sapiens (human) ]

    Gene ID: 126820, updated on 5-Mar-2024

    Summary

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    Official Symbol
    DNAI3provided by HGNC
    Official Full Name
    dynein axonemal intermediate chain 3provided by HGNC
    Primary source
    HGNC:HGNC:30711
    See related
    Ensembl:ENSG00000162643 MIM:617968; AllianceGenome:HGNC:30711
    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
    DIC3; WDR63; NYD-SP29
    Summary
    Enables Arp2/3 complex binding activity. Involved in negative regulation of Arp2/3 complex-mediated actin nucleation and negative regulation of cell migration. Located in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in testis (RPKM 10.4), adrenal (RPKM 9.4) and 2 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See DNAI3 in Genome Data Viewer
    Location:
    1p22.3
    Exon count:
    24
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (85062327..85133138)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (84902959..84973727)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (85528010..85598821)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory region 13288 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1026 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1260 Neighboring gene mucolipin TRP cation channel 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1261 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1262 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1263 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1264 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1027 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1028 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:85463659-85464530 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1265 Neighboring gene mucolipin TRP cation channel 3 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1029 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1030 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:85527645-85528145 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1266 Neighboring gene microRNA 4423 Neighboring gene NANOG hESC enhancer GRCh37_chr1:85618513-85619014 Neighboring gene synapse defective Rho GTPase homolog 2 Neighboring gene uncharacterized LOC124904207 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:85665814-85666425

    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. Consensus nomenclature for dyneins and associated assembly factors. Braschi B, et al. J Cell Biol, 2022 Feb 7. PMID 35006274, Free PMC Article
    2. Targeted copy number screening highlights an intragenic deletion of WDR63 as the likely cause of human occipital encephalocele and abnormal CNS development in zebrafish. Hofmeister W, et al. Hum Mutat, 2018 Apr. PMID 29285825
    3. Enriched trimethylation of lysine 4 of histone H3 of WDR63 enhanced osteogenic differentiation potentials of stem cells from apical papilla. Diao S, et al. J Endod, 2015 Feb. PMID 25498833
    4. WDR63 inhibits Arp2/3-dependent actin polymerization and mediates the function of p53 in suppressing metastasis. Zhao K, et al. EMBO Rep, 2020 Apr 3. PMID 32128961, Free PMC Article
    5. A unified taxonomy for ciliary dyneins. Hom EF, et al. Cytoskeleton (Hoboken), 2011 Oct. PMID 21953912, Free PMC Article

    See all (15) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. A rare deletion in WDR63 in a case of encephalocele has been characterized. Functional study on zebrafish supports role of WDR63 deletion in abnormal neural development.
      Title: Targeted copy number screening highlights an intragenic deletion of WDR63 as the likely cause of human occipital encephalocele and abnormal CNS development in zebrafish.
    2. These results indicate that WDR63 is a positive enhancer for stem cells from apical papilla osteogenic differentiation and suggest that activation of WDR63 signaling might improve tissue regeneration mediated by MSCs of dental origin.
      Title: Enriched trimethylation of lysine 4 of histone H3 of WDR63 enhanced osteogenic differentiation potentials of stem cells from apical papilla.
    3. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    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
    A genome-wide search for common SNP x SNP interactions on the risk of venous thrombosis.
    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

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ30067, RP11-507C22.2

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables Arp2/3 complex binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables dynein heavy chain binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables dynein light chain binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in cilium movement involved in cell motility IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in inner dynein arm assembly IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in negative regulation of Arp2/3 complex-mediated actin nucleation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in negative regulation of cell migration IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in positive regulation of osteoblast differentiation ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Component Evidence Code Pubs
    part_of axonemal dynein complex ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of inner dynein arm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    dynein axonemal intermediate chain 3
    Names
    WD repeat domain 63
    WD repeat-containing protein 63
    dynein intermediate chain 3, axonemal
    testicular tissue protein Li 225
    testis development protein NYD-SP29 (NYD-SP29)

    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_001288563.2 → NP_001275492.1  dynein axonemal intermediate chain 3 isoform 2

      See identical proteins and their annotated locations for NP_001275492.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an in-frame exon in the central coding region, compared to variant 1. The encoded isoform (2) is shorter, compared to isoform 1.
      Source sequence(s)
      AK054629, BX648851, DB075669
      Consensus CDS
      CCDS72818.1
      UniProtKB/Swiss-Prot
      Q8IWG1
      Related
      ENSP00000317463.8, ENST00000326813.12
      Conserved Domains (2) summary
      COG2319
      Location:331 → 754
      WD40; WD40 repeat [General function prediction only]
      cl20817
      Location:780 → 834
      GBP_C; Guanylate-binding protein, C-terminal domain

    2. NM_145172.5 → NP_660155.2  dynein axonemal intermediate chain 3 isoform 1

      See identical proteins and their annotated locations for NP_660155.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      BC040265, DB075669
      Consensus CDS
      CCDS702.1
      UniProtKB/Swiss-Prot
      A8K988, Q8IWG1, Q96L72, Q96NU4
      UniProtKB/TrEMBL
      A0A140VJZ8
      Related
      ENSP00000294664.6, ENST00000294664.11
      Conserved Domains (1) summary
      COG2319
      Location:370 → 793
      WD40; WD40 repeat [General function prediction only]

    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_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      85062327..85133138
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047444741.1 → XP_047300697.1  dynein axonemal intermediate chain 3 isoform X1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      84902959..84973727
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054334256.1 → XP_054190231.1  dynein axonemal intermediate chain 3 isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8IWG1.1 GenPept UniProtKB/Swiss-Prot:Q8IWG1

    Gene LinkOut

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

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