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    LRRC42 leucine rich repeat containing 42 [ Homo sapiens (human) ]

    Gene ID: 115353, updated on 27-Nov-2024

    Summary

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    Official Symbol
    LRRC42provided by HGNC
    Official Full Name
    leucine rich repeat containing 42provided by HGNC
    Primary source
    HGNC:HGNC:28792
    See related
    Ensembl:ENSG00000116212 MIM:620896; AllianceGenome:HGNC:28792
    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
    dJ167A19.4
    Expression
    Ubiquitous expression in thyroid (RPKM 11.3), testis (RPKM 10.8) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See LRRC42 in Genome Data Viewer
    Location:
    1p32.3
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (53946350..53968168)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (53829258..53851077)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (54412023..54433841)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124904180 Neighboring gene iodothyronine deiodinase 1 Neighboring gene uncharacterized LOC124904181 Neighboring gene intraflagellar transport 25 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 913 Neighboring gene Sharpr-MPRA regulatory region 3629 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr1:54422389-54423588 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:54424449-54425155 Neighboring gene heterogeneous nuclear ribonucleoprotein A3 pseudogene 12 Neighboring gene low density lipoprotein receptor class A domain containing 1

    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. Identification of a nuclear protein, LRRC42, involved in lung carcinogenesis. Fujitomo T, et al. Int J Oncol, 2014 Jul. PMID 24806090
    2. The Eyes Absent family members EYA4 and EYA1 promote PLK1 activation and successful mitosis through tyrosine dephosphorylation. Nelson CB, et al. Nat Commun, 2024 Feb 15. PMID 38360978, Free PMC Article
    3. Systematic identification of cancer cell vulnerabilities to natural killer cell-mediated immune surveillance. Pech MF, et al. Elife, 2019 Aug 27. PMID 31452512, Free PMC Article
    4. ARIH2 Is a Vif-Dependent Regulator of CUL5-Mediated APOBEC3G Degradation in HIV Infection. Hüttenhain R, et al. Cell Host Microbe, 2019 Jul 10. PMID 31253590, Free PMC Article
    5. Signal sequence and keyword trap in silico for selection of full-length human cDNAs encoding secretion or membrane proteins from oligo-capped cDNA libraries. Otsuki T, et al. DNA Res, 2005. PMID 16303743

    See all (20) citations in PubMed

    GeneRIFs: Gene References Into Functions

    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)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC8974

    General protein information

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    Preferred Names
    leucine-rich repeat-containing protein 42

    NCBI Reference Sequences (RefSeq)

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    NEW Try the new Transcript table

    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_001256409.2 → NP_001243338.1  leucine-rich repeat-containing protein 42

      See identical proteins and their annotated locations for NP_001243338.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript. Variants 1 and 2 encode the same protein.
      Source sequence(s)
      AK095767, CB851494, CX783955
      Consensus CDS
      CCDS585.1
      UniProtKB/Swiss-Prot
      D3DQ46, Q8N2Q8, Q9Y546
      Related
      ENSP00000360421.3, ENST00000371370.8
      Conserved Domains (2) summary
      sd00034
      Location:175 → 202
      LRR_AMN1; leucine-rich repeat [structural motif]
      cl26161
      Location:167 → 272
      LRR_RI; Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond ...

    2. NM_052940.5 → NP_443172.1  leucine-rich repeat-containing protein 42

      See identical proteins and their annotated locations for NP_443172.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an alternate exon in the 5' UTR, compared to variant 1. Variants 1 and 2 encode the same protein.
      Source sequence(s)
      AK075201, CB851494, CX783955
      Consensus CDS
      CCDS585.1
      UniProtKB/Swiss-Prot
      D3DQ46, Q8N2Q8, Q9Y546
      Related
      ENSP00000318185.4, ENST00000319223.8
      Conserved Domains (2) summary
      sd00034
      Location:175 → 202
      LRR_AMN1; leucine-rich repeat [structural motif]
      cl26161
      Location:167 → 272
      LRR_RI; Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond ...

    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_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      53946350..53968168
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006710328.5 → XP_006710391.1  leucine-rich repeat-containing protein 42 isoform X1

      See identical proteins and their annotated locations for XP_006710391.1

      UniProtKB/Swiss-Prot
      D3DQ46, Q8N2Q8, Q9Y546
      Conserved Domains (2) summary
      sd00034
      Location:175 → 202
      LRR_AMN1; leucine-rich repeat [structural motif]
      cl26161
      Location:167 → 272
      LRR_RI; Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond ...

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      53829258..53851077
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054334161.1 → XP_054190136.1  leucine-rich repeat-containing protein 42 isoform X1

      UniProtKB/Swiss-Prot
      D3DQ46, Q8N2Q8, Q9Y546

    2. XM_054334162.1 → XP_054190137.1  leucine-rich repeat-containing protein 42 isoform X1

      UniProtKB/Swiss-Prot
      D3DQ46, Q8N2Q8, Q9Y546
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9Y546.1 GenPept UniProtKB/Swiss-Prot:Q9Y546

    Gene LinkOut

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

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