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    KLHDC3 kelch domain containing 3 [ Homo sapiens (human) ]

    Gene ID: 116138, updated on 10-Dec-2024

    Summary

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    Official Symbol
    KLHDC3provided by HGNC
    Official Full Name
    kelch domain containing 3provided by HGNC
    Primary source
    HGNC:HGNC:20704
    See related
    Ensembl:ENSG00000124702 MIM:611248; AllianceGenome:HGNC:20704
    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
    Also known as
    PEAS; dJ20C7.3
    Summary
    The protein encoded by this gene contains six repeated kelch motifs that are structurally similar to recombination activating gene 2, a protein involved in the activation of the V(D)J recombination. In mouse, this gene is found to be expressed specifically in testis. Its expression in pachytene spermatocytes is localized to cytoplasma and meiotic chromatin, suggesting that this gene may be involved in meiotic recombination. [provided by RefSeq, Jun 2012]
    Expression
    Broad expression in testis (RPKM 98.0), brain (RPKM 70.2) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See KLHDC3 in Genome Data Viewer
    Location:
    6p21.1
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (43014249..43021294)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (42843347..42850393)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (42981987..42989032)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124900215 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:42948960-42949178 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24583 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17211 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17212 Neighboring gene protein phosphatase 2 regulatory subunit B'delta Neighboring gene Sharpr-MPRA regulatory region 14905 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:42979352-42979852 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17213 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24584 Neighboring gene male-enhanced antigen 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:42988913-42989644 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:42989645-42990376 Neighboring gene ribosomal RNA processing 36 Neighboring gene RNA, 7SL, cytoplasmic 403, pseudogene

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    1. Peas-Mea1-Ppp2r5d overlapping gene complex: a transposon mediated-gene formation in mammals. Ohinata Y, et al. DNA Res, 2003 Apr 30. PMID 12755172
    2. Characterization of sorCS1, an alternatively spliced receptor with completely different cytoplasmic domains that mediate different trafficking in cells. Hermey G, et al. J Biol Chem, 2003 Feb 28. PMID 12482870
    3. A novel testis-specific RAG2-like protein, Peas: its expression in pachytene spermatocyte cytoplasm and meiotic chromatin. Ohinata Y, et al. FEBS Lett, 2003 Feb 27. PMID 12606021
    4. Male-enhanced antigen-1 gene flanked by two overlapping genes is expressed in late spermatogenesis. Ohinata Y, et al. Biol Reprod, 2002 Dec. PMID 12444059
    5. CRL2(KLHDC3) mediates p14ARF N-terminal ubiquitylation degradation to promote non-small cell lung carcinoma progression. Liu Y, et al. Oncogene, 2022 May. PMID 35468939

    See all (38) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. CRL2(KLHDC3) mediates p14ARF N-terminal ubiquitylation degradation to promote non-small cell lung carcinoma progression.
      Title: CRL2(KLHDC3) mediates p14ARF N-terminal ubiquitylation degradation to promote non-small cell lung carcinoma progression.
    2. cloned human and mouse Peas cDNAs (hPEAS/mPeas) and analyzed their tissue and stage-specific expressions; may be involved in meiotic recombination process
      Title: A novel testis-specific RAG2-like protein, Peas: its expression in pachytene spermatocyte cytoplasm and meiotic chromatin.
    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)

    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

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables chromatin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables chromatin binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables ubiquitin-like ligase-substrate adaptor activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in proteasome-mediated ubiquitin-dependent protein catabolic process IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in protein ubiquitination IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in reciprocal meiotic recombination NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in ubiquitin-dependent protein catabolic process via the C-end degron rule pathway IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of Cul2-RING ubiquitin ligase complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in chromatin IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    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 cytosol TAS
    Traceable Author Statement
    more info
    		  
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  

    General protein information

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    Preferred Names
    kelch domain-containing protein 3
    Names
    testis intracellular mediator protein

    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_057161.4 → NP_476502.1  kelch domain-containing protein 3

      See identical proteins and their annotated locations for NP_476502.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the functional protein.
      Source sequence(s)
      BC001789, DC395338
      Consensus CDS
      CCDS4880.1
      UniProtKB/Swiss-Prot
      A8K2W9, Q9BQ90
      UniProtKB/TrEMBL
      Q96GH7
      Related
      ENSP00000313995.4, ENST00000326974.9
      Conserved Domains (3) summary
      sd00038
      Location:128 → 173
      Kelch; KELCH repeat [structural motif]
      pfam13964
      Location:14 → 61
      Kelch_6; Kelch motif
      cl26061
      Location:74 → 318
      PLN02193; nitrile-specifier protein

    RNA

    1. NR_040101.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks an internal exon compared to variant 1 that results in premature translation termination. This variant is represented as non-coding because the use of the 5'-most expected translational start codon used in variant 1 renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AB055925, BC041793, CN269587
      Related
      ENST00000244670.12

    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_000006.12 Reference GRCh38.p14 Primary Assembly

      Range
      43014249..43021294
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047418163.1 → XP_047274119.1  kelch domain-containing protein 3 isoform X1

      UniProtKB/Swiss-Prot
      A8K2W9, Q9BQ90
      UniProtKB/TrEMBL
      Q96GH7

    2. XM_047418164.1 → XP_047274120.1  kelch domain-containing protein 3 isoform X1

      UniProtKB/Swiss-Prot
      A8K2W9, Q9BQ90
      UniProtKB/TrEMBL
      Q96GH7

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      42843347..42850393
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054354188.1 → XP_054210163.1  kelch domain-containing protein 3 isoform X1

      UniProtKB/Swiss-Prot
      A8K2W9, Q9BQ90
      UniProtKB/TrEMBL
      Q96GH7

    2. XM_054354189.1 → XP_054210164.1  kelch domain-containing protein 3 isoform X1

      UniProtKB/Swiss-Prot
      A8K2W9, Q9BQ90
      UniProtKB/TrEMBL
      Q96GH7

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001242872.1: Suppressed sequence

      Description
      NM_001242872.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9BQ90.1 GenPept UniProtKB/Swiss-Prot:Q9BQ90

    Gene LinkOut

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

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