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    Lrch4 leucine-rich repeats and calponin homology (CH) domain containing 4 [ Mus musculus (house mouse) ]

    Gene ID: 231798, updated on 5-Mar-2024

    Summary

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    Official Symbol
    Lrch4provided by MGI
    Official Full Name
    leucine-rich repeats and calponin homology (CH) domain containing 4provided by MGI
    Primary source
    MGI:MGI:1917193
    See related
    Ensembl:ENSMUSG00000093445 AllianceGenome:MGI:1917193
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    LRN; LRRN4; SAP25; 2810008P14Rik; 2900069C24Rik
    Summary
    Acts upstream of or within negative regulation of transcription, DNA-templated. Located in PML body and cytoplasm. Orthologous to human LRCH4 (leucine rich repeats and calponin homology domain containing 4). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Broad expression in thymus adult (RPKM 109.4), spleen adult (RPKM 73.9) and 25 other tissues See more
    Orthologs
    human all
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    Genomic context

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    Location:
    5 G2; 5 76.59 cM
    Exon count:
    18
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 5 NC_000071.7 (137627385..137639361)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 5 NC_000071.6 (137629123..137641099)

    Chromosome 5 - NC_000071.7Genomic Context describing neighboring genes Neighboring gene predicted gene, 36266 Neighboring gene F-box protein 24 Neighboring gene ubiquinol-cytochrome c reductase binding protein pseudogene Neighboring gene STARR-positive B cell enhancer ABC_E72 Neighboring gene STARR-seq mESC enhancer starr_14649 Neighboring gene predicted gene 20605 Neighboring gene sin3 associated polypeptide Neighboring gene insulin receptor substrate 3

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

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    Related articles in PubMed

    1. Leucine-rich repeats and calponin homology containing 4 (Lrch4) regulates the innate immune response. Aloor JJ, et al. J Biol Chem, 2019 Feb 8. PMID 30523158, Free PMC Article
    2. Molecular cloning of a mouse submaxillary gland renin cDNA fragment. Rougeon F, et al. Proc Natl Acad Sci U S A, 1981 Oct. PMID 6171818, Free PMC Article
    3. Identification and characterization of SAP25, a novel component of the mSin3 corepressor complex. Shiio Y, et al. Mol Cell Biol, 2006 Feb. PMID 16449650, Free PMC Article
    4. The LMO2 oncogene regulates DNA replication in hematopoietic cells. Sincennes MC, et al. Proc Natl Acad Sci U S A, 2016 Feb 2. PMID 26764384, Free PMC Article
    5. Prediction of the coding sequences of mouse homologues of FLJ genes: the complete nucleotide sequences of 110 mouse FLJ-homologous cDnas identified by screening of terminal sequences of cDNA clones randomly sampled from size-fractionated libraries. Okazaki N, et al. DNA Res, 2004 Apr 30. PMID 15449545

    See all (27) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. identify Lrch4 as a broad-spanning regulator of the innate immune response
      Title: Leucine-rich repeats and calponin homology containing 4 (Lrch4) regulates the innate immune response.
    2. SAP25 is a novel core component of the Sin3 corepressor complex whose subcellular location is regulated by PML.
      Title: Identification and characterization of SAP25, a novel component of the mSin3 corepressor complex.
    Submit: New GeneRIF Correction

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Readthrough Gm20605

    Readthrough gene: Gm20605, Included gene: Sap25

    Homology

    Clone Names

    • MGC19364

    Gene Ontology Provided by MGI

    Process Evidence Code Pubs
    involved_in membrane raft assembly IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in positive regulation of toll-like receptor signaling pathway IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in PML body IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in plasma membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    leucine-rich repeat and calponin homology domain-containing protein 4
    Names
    leucine rich repeat protein 4, neuronal

    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_001168652.1 → NP_001162123.1  leucine-rich repeat and calponin homology domain-containing protein 4 isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an internal segment in the 3' region, as compared to variant 1. The resulting isoform (2) is shorter and has a different C-terminus, as compared to isoform 1.
      Source sequence(s)
      BQ924416, BY204138, CA323124, CF729493, CN702489, DV661712
      Consensus CDS
      CCDS57392.1
      UniProtKB/TrEMBL
      Q8C2M4
      Related
      ENSMUSP00000135832.2, ENSMUST00000176667.8
      Conserved Domains (5) summary
      cd00116
      Location:103 → 245
      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 ...
      sd00033
      Location:46 → 69
      LRR_RI; leucine-rich repeat [structural motif]
      pfam00307
      Location:532 → 627
      CH; Calponin homology (CH) domain
      pfam12799
      Location:92 → 131
      LRR_4; Leucine Rich repeats (2 copies)
      pfam13855
      Location:138 → 194
      LRR_8; Leucine rich repeat

    2. NM_146164.2 → NP_666276.1  leucine-rich repeat and calponin homology domain-containing protein 4 isoform 1

      See identical proteins and their annotated locations for NP_666276.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longer isoform (1).
      Source sequence(s)
      AC124730, BQ924416, BY204138, CF729493, CN702489, CV783140, DV650548, DV661712
      Consensus CDS
      CCDS19772.1
      UniProtKB/Swiss-Prot
      H3BLL3, Q921G6
      UniProtKB/TrEMBL
      Q8C2M4
      Related
      ENSMUSP00000031734.10, ENSMUST00000031734.16
      Conserved Domains (6) summary
      cd00116
      Location:103 → 245
      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 ...
      sd00033
      Location:46 → 69
      LRR_RI; leucine-rich repeat [structural motif]
      pfam00307
      Location:532 → 624
      CH; Calponin homology (CH) domain
      pfam02377
      Location:265 → 405
      Dishevelled; Dishevelled specific domain
      pfam12799
      Location:92 → 131
      LRR_4; Leucine Rich repeats (2 copies)
      pfam13855
      Location:138 → 194
      LRR_8; Leucine rich repeat

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000071.7 Reference GRCm39 C57BL/6J

      Range
      137627385..137639361
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q921G6.1 GenPept UniProtKB/Swiss-Prot:Q921G6

    Gene LinkOut

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

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