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

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

Summary

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
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Genomic context

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

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

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 
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

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_057161.4NP_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:128173
    Kelch; KELCH repeat [structural motif]
    pfam13964
    Location:1461
    Kelch_6; Kelch motif
    cl26061
    Location:74318
    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_047418163.1XP_047274119.1  kelch domain-containing protein 3 isoform X1

    UniProtKB/Swiss-Prot
    A8K2W9, Q9BQ90
  2. XM_047418164.1XP_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_054354188.1XP_054210163.1  kelch domain-containing protein 3 isoform X1

    UniProtKB/Swiss-Prot
    A8K2W9, Q9BQ90
  2. XM_054354189.1XP_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.