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    LRRC40 leucine rich repeat containing 40 [ Homo sapiens (human) ]

    Gene ID: 55631, updated on 5-Mar-2024

    Summary

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    Official Symbol
    LRRC40provided by HGNC
    Official Full Name
    leucine rich repeat containing 40provided by HGNC
    Primary source
    HGNC:HGNC:26004
    See related
    Ensembl:ENSG00000066557 AllianceGenome:HGNC:26004
    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
    dJ677H15.1
    Summary
    Predicted to enable protein serine/threonine phosphatase activity. Predicted to be involved in signal transduction. Located in membrane. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Ubiquitous expression in brain (RPKM 8.0), testis (RPKM 8.0) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See LRRC40 in Genome Data Viewer
    Location:
    1p31.1
    Exon count:
    16
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (70144805..70205579, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (70023294..70084095, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (70610488..70671262, complement)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene leucine rich repeat containing 7 Neighboring gene peptidylprolyl cis/trans isomerase, NIMA-interacting 1 pseudogene 1 Neighboring gene NANOG hESC enhancer GRCh37_chr1:70503542-70504181 Neighboring gene LRRC7 antisense RNA 1 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:70534982-70535190 Neighboring gene Sharpr-MPRA regulatory region 9273 Neighboring gene NANOG hESC enhancer GRCh37_chr1:70606447-70606948 Neighboring gene Sharpr-MPRA regulatory region 3760 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:70626481-70626982 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1186 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1187 Neighboring gene RNA, 7SL, cytoplasmic 242, pseudogene Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:70686957-70687502 Neighboring gene MPRA-validated peak281 silencer Neighboring gene serine and arginine rich splicing factor 11 Neighboring gene ankyrin repeat domain 13C Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr1:70818812-70820011 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:70820190-70821107

    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. PLXNA2 and LRRC40 as candidate genes in autism spectrum disorder. Pijuan J, et al. Autism Res, 2021 Jun. PMID 33749153
    2. Mass spectrometry-based proteomic analysis of FSCN1-interacting proteins in laryngeal squamous cell carcinoma cells. Liu H, et al. IUBMB Life, 2019 Nov. PMID 31298480
    3. STUB1 is targeted by the SUMO-interacting motif of EBNA1 to maintain Epstein-Barr Virus latency. Wang Y, et al. PLoS Pathog, 2020 Mar. PMID 32176739, Free PMC Article
    4. Human Immunodeficiency Virus Type 1 Vpr Mediates Degradation of APC1, a Scaffolding Component of the Anaphase-Promoting Complex/Cyclosome. Barbosa JAF, et al. J Virol, 2021 Jul 12. PMID 34011540, Free PMC Article
    5. UM171 Preserves Epigenetic Marks that Are Reduced in Ex Vivo Culture of Human HSCs via Potentiation of the CLR3-KBTBD4 Complex. Chagraoui J, et al. Cell Stem Cell, 2021 Jan 7. PMID 33417871

    See all (48) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. PLXNA2 and LRRC40 as candidate genes in autism spectrum disorder.
      Title: PLXNA2 and LRRC40 as candidate genes in autism spectrum disorder.
    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

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ20331

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in signal transduction IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    located_in membrane HDA PubMed 

    General protein information

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    Preferred Names
    leucine-rich repeat-containing protein 40
    Names
    testicular tissue protein Li 109

    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_017768.5 → NP_060238.3  leucine-rich repeat-containing protein 40

      See identical proteins and their annotated locations for NP_060238.3

      Status: VALIDATED

      Source sequence(s)
      AI015897, BC008586, DA310461
      Consensus CDS
      CCDS646.1
      UniProtKB/Swiss-Prot
      Q9BTR7, Q9H9A6, Q9NSK1, Q9NXC1
      UniProtKB/TrEMBL
      A0A140VJN3
      Related
      ENSP00000359990.3, ENST00000370952.4
      Conserved Domains (3) summary
      sd00033
      Location:107 → 129
      LRR_RI; leucine-rich repeat [structural motif]
      pfam13855
      Location:84 → 140
      LRR_8; Leucine rich repeat
      cl26793
      Location:120 → 577
      PLN00113; leucine-rich repeat receptor-like protein kinase; Provisional

    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_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      70144805..70205579 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011541763.2 → XP_011540065.1  leucine-rich repeat-containing protein 40 isoform X2

      See identical proteins and their annotated locations for XP_011540065.1

      Conserved Domains (3) summary
      PLN00113
      Location:1 → 359
      PLN00113; leucine-rich repeat receptor-like protein kinase; Provisional
      sd00031
      Location:302 → 325
      LRR_1; leucine-rich repeat [structural motif]
      sd00033
      Location:27 → 48
      LRR_RI; leucine-rich repeat [structural motif]

    2. XM_047424520.1 → XP_047280476.1  leucine-rich repeat-containing protein 40 isoform X2

    3. XM_047424519.1 → XP_047280475.1  leucine-rich repeat-containing protein 40 isoform X1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      70023294..70084095 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054337542.1 → XP_054193517.1  leucine-rich repeat-containing protein 40 isoform X2

    2. XM_054337541.1 → XP_054193516.1  leucine-rich repeat-containing protein 40 isoform X2

    3. XM_054337540.1 → XP_054193515.1  leucine-rich repeat-containing protein 40 isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9H9A6.1 GenPept UniProtKB/Swiss-Prot:Q9H9A6

    Gene LinkOut

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

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