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

Gene ID: 116138, updated on 11-Apr-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_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (43014249..43021294)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (42843347..42850393)
105.20220307 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: 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. 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. 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
  3. 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
  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 (37) 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)

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

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 
part_of 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_2023_10

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

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

    UniProtKB/Swiss-Prot
    A8K2W9, Q9BQ90

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

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

    UniProtKB/Swiss-Prot
    A8K2W9, Q9BQ90

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

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