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    KLHL42 kelch like family member 42 [ Homo sapiens (human) ]

    Gene ID: 57542, updated on 10-Dec-2024

    Summary

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    Official Symbol
    KLHL42provided by HGNC
    Official Full Name
    kelch like family member 42provided by HGNC
    Primary source
    HGNC:HGNC:29252
    See related
    Ensembl:ENSG00000087448 MIM:618919; AllianceGenome:HGNC:29252
    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
    Ctb9; KLHDC5
    Summary
    Contributes to ubiquitin-protein transferase activity. Involved in proteasome-mediated ubiquitin-dependent protein catabolic process; protein polyubiquitination; and regulation of microtubule-based process. Part of Cul3-RING ubiquitin ligase complex. [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Ubiquitous expression in brain (RPKM 7.6), endometrium (RPKM 5.0) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See KLHL42 in Genome Data Viewer
    Location:
    12p11.22
    Exon count:
    4
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (27780233..27803040)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (27651947..27674765)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (27933166..27955973)

    Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene MRPS35 divergent transcript Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:27857921-27858432 Neighboring gene high mobility group box 1 pseudogene 49 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6147 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6148 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6149 Neighboring gene mitochondrial ribosomal protein S35 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:27904053-27904827 Neighboring gene MANSC domain containing 4 Neighboring gene MPRA-validated peak1632 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4313 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:27933183-27933682 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_27127 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_27159 Neighboring gene uncharacterized LOC105369709 Neighboring gene RN7SK pseudogene 15 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr12:27974511-27975710

    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. Kelch-like protein 42 is a profibrotic ubiquitin E3 ligase involved in systemic sclerosis. Lear TB, et al. J Biol Chem, 2020 Mar 27. PMID 32071084, Free PMC Article
    2. The Cul3/Klhdc5 E3 ligase regulates p60/katanin and is required for normal mitosis in mammalian cells. Cummings CM, et al. J Biol Chem, 2009 Apr 24. PMID 19261606, Free PMC Article
    3. The ubiquitin conjugating enzyme, UbcM2, engages in novel interactions with components of cullin-3 based E3 ligases. Plafker KS, et al. Biochemistry, 2009 Apr 21. PMID 19256485, Free PMC Article
    4. A novel missense variant in CUL3 shows altered binding ability to BTB-adaptor proteins leading to diverse phenotypes of CUL3-related disorders. Kato K, et al. J Hum Genet, 2021 May. PMID 33130828
    5. Novel Cul3 binding proteins function to remodel E3 ligase complexes. Wimuttisuk W, et al. BMC Cell Biol, 2014 Jul 10. PMID 25011449, Free PMC Article

    See all (34) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Kelch-like protein 42 is a profibrotic ubiquitin E3 ligase involved in systemic sclerosis.
      Title: Kelch-like protein 42 is a profibrotic ubiquitin E3 ligase involved in systemic sclerosis.
    2. Cul3-deficient cells or Ctb9/KLHDC5-deficient cells show an increase in p60/katanin levels, indicating that Cul3/Ctb9/KLHDC5 is required for efficient p60/katanin removal
      Title: The Cul3/Klhdc5 E3 ligase regulates p60/katanin and is required for normal mitosis in mammalian cells.
    Submit: New GeneRIF Correction

    Phenotypes

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    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)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • KIAA1340, MGC131714

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    contributes_to ubiquitin-protein transferase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in cell division IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in proteasome-mediated ubiquitin-dependent protein catabolic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in proteasome-mediated ubiquitin-dependent protein catabolic process IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in protein polyubiquitination IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in protein polyubiquitination IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in regulation of microtubule-based process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of microtubule-based process IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of Cul3-RING ubiquitin ligase complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of Cul3-RING ubiquitin ligase complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  
    located_in spindle IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    kelch-like protein 42
    Names
    cullin-3-binding protein 9
    kelch domain containing 5
    kelch domain-containing protein 5

    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_020782.2 → NP_065833.1  kelch-like protein 42

      See identical proteins and their annotated locations for NP_065833.1

      Status: VALIDATED

      Source sequence(s)
      AC009511
      Consensus CDS
      CCDS31763.1
      UniProtKB/Swiss-Prot
      Q2VPK1, Q8N334, Q9P2K6
      UniProtKB/TrEMBL
      B2RNT7
      Related
      ENSP00000370671.2, ENST00000381271.7
      Conserved Domains (4) summary
      PHA03098
      Location:210 → 497
      PHA03098; kelch-like protein; Provisional
      sd00038
      Location:244 → 287
      Kelch; KELCH repeat [structural motif]
      cd18319
      Location:4 → 111
      BTB_POZ_KLHL42; BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in Kelch-like protein 42 (KLHL42)
      cd18478
      Location:128 → 237
      BACK_KLHL42_KLHDC5; BACK (BTB and C-terminal Kelch) domain found in Kelch-like protein 42 (KLHL42)

    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_000012.12 Reference GRCh38.p14 Primary Assembly

      Range
      27780233..27803040
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017019698.3 → XP_016875187.1  kelch-like protein 42 isoform X1

      UniProtKB/TrEMBL
      F5H523
      Related
      ENSP00000444748.1, ENST00000539176.1
      Conserved Domains (4) summary
      cd14735
      Location:129 → 169
      BACK_Kelch; BTB-And-C-terminal-Kelch (BACK) domain of Kelch-like proteins
      sd00038
      Location:244 → 287
      Kelch; KELCH repeat [structural motif]
      cl02518
      Location:7 → 69
      BTB; BTB/POZ domain
      cl28614
      Location:217 → 353
      BTB; Broad-Complex, Tramtrack and Bric a brac

    RNA

    1. XR_931315.4 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060936.1 Alternate T2T-CHM13v2.0

      Range
      27651947..27674765
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054372646.1 → XP_054228621.1  kelch-like protein 42 isoform X1

      UniProtKB/TrEMBL
      F5H523

    RNA

    1. XR_008488645.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9P2K6.2 GenPept UniProtKB/Swiss-Prot:Q9P2K6

    Gene LinkOut

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

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