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    Lrch1 leucine-rich repeats and calponin homology (CH) domain containing 1 [ Mus musculus (house mouse) ]

    Gene ID: 380916, updated on 27-Nov-2024

    Summary

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    Official Symbol
    Lrch1provided by MGI
    Official Full Name
    leucine-rich repeats and calponin homology (CH) domain containing 1provided by MGI
    Primary source
    MGI:MGI:2443390
    See related
    Ensembl:ENSMUSG00000068015 AllianceGenome:MGI:2443390
    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
    Chdc1; mKIAA1016; 4832412D13Rik
    Summary
    Involved in cellular response to chemokine; negative regulation of GTPase activity; and negative regulation of T cell migration. Predicted to be active in cytoplasm. Is expressed in several structures, including cardiovascular system; central nervous system; genitourinary system; gut; and hemolymphoid system gland. Used to study multiple sclerosis. Orthologous to human LRCH1 (leucine rich repeats and calponin homology domain containing 1). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in bladder adult (RPKM 4.8), lung adult (RPKM 4.8) and 28 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See Lrch1 in Genome Data Viewer
    Location:
    14 D3; 14 39.39 cM
    Exon count:
    23
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 14 NC_000080.7 (74992113..75185447, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 14 NC_000080.6 (74754673..74948007, complement)

    Chromosome 14 - NC_000080.7Genomic Context describing neighboring genes Neighboring gene STARR-positive B cell enhancer ABC_E5454 Neighboring gene tubulin, alpha 1C pseudogene Neighboring gene esterase D/formylglutathione hydrolase Neighboring gene STARR-positive B cell enhancer ABC_E5455 Neighboring gene predicted gene, 52135 Neighboring gene STARR-positive B cell enhancer ABC_E9901 Neighboring gene STARR-positive B cell enhancer ABC_E8571 Neighboring gene predicted gene 10847 Neighboring gene CapStarr-seq enhancer MGSCv37_chr14:75346402-75346511 Neighboring gene CapStarr-seq enhancer MGSCv37_chr14:75346543-75346730 Neighboring gene STARR-positive B cell enhancer ABC_E5456 Neighboring gene STARR-seq mESC enhancer starr_37134 Neighboring gene predicted gene 4278 Neighboring gene STARR-positive B cell enhancer ABC_E10834 Neighboring gene STARR-positive B cell enhancer ABC_E757 Neighboring gene RUN and cysteine rich domain containing beclin 1 interacting protein like Neighboring gene predicted gene, 57618

    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. LRCH1 deficiency enhances LAT signalosome formation and CD8(+) T cell responses against tumors and pathogens. Liu C, et al. Proc Natl Acad Sci U S A, 2020 Aug 11. PMID 32727906, Free PMC Article
    2. LRCH1 interferes with DOCK8-Cdc42-induced T cell migration and ameliorates experimental autoimmune encephalomyelitis. Xu X, et al. J Exp Med, 2017 Jan. PMID 28028151, Free PMC Article
    3. Microarray analysis of Foxa2 mutant mouse embryos reveals novel gene expression and inductive roles for the gastrula organizer and its derivatives. Tamplin OJ, et al. BMC Genomics, 2008 Oct 30. PMID 18973680, Free PMC Article
    4. Ex vivo Quantitative Proteomic Analysis of Serotonin Transporter Interactome: Network Impact of the SERT Ala56 Coding Variant. Quinlan MA, et al. Front Mol Neurosci, 2020. PMID 32581705, Free PMC Article
    5. Prediction of the coding sequences of mouse homologues of KIAA gene: III. the complete nucleotide sequences of 500 mouse KIAA-homologous cDNAs identified by screening of terminal sequences of cDNA clones randomly sampled from size-fractionated libraries. Okazaki N, et al. DNA Res, 2003 Aug 31. PMID 14621295

    See all (24) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. LRCH1 deficiency enhances LAT signalosome formation and CD8(+) T cell responses against tumors and pathogens.
      Title: LRCH1 deficiency enhances LAT signalosome formation and CD8(+) T cell responses against tumors and pathogens.
    2. LRCH1 as a novel effector to restrain PKCalpha-DOCK8-Cdc42 module-induced T cell migration and ameliorate EAE.
      Title: LRCH1 interferes with DOCK8-Cdc42-induced T cell migration and ameliorates experimental autoimmune encephalomyelitis.
    Submit: New GeneRIF Correction

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Endonuclease-mediated (1)  1 citation
    • Targeted (2) 

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in cellular response to chemokine IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in cellular response to chemokine IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in cellular response to chemokine ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative regulation of GTPase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in negative regulation of GTPase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative regulation of T cell migration IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in negative regulation of T cell migration IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in negative regulation of T cell migration ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    leucine-rich repeat and calponin homology domain-containing protein 1

    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_001033439.3 → NP_001028611.2  leucine-rich repeat and calponin homology domain-containing protein 1 isoform 1

      See identical proteins and their annotated locations for NP_001028611.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AC135083, AC154621, BB612742, BC028469
      Consensus CDS
      CCDS36976.1
      UniProtKB/Swiss-Prot
      E9QLJ4, P62046
      UniProtKB/TrEMBL
      Q3UP01
      Related
      ENSMUSP00000086363.6, ENSMUST00000088970.7
      Conserved Domains (4) summary
      cd00116
      Location:106 → 220
      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:66 → 88
      LRR_RI; leucine-rich repeat [structural motif]
      pfam00307
      Location:591 → 698
      CH; Calponin homology (CH) domain
      pfam13855
      Location:178 → 258
      LRR_8; Leucine rich repeat

    2. NM_001252132.1 → NP_001239061.1  leucine-rich repeat and calponin homology domain-containing protein 1 isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon in the 3' coding region, compared to variant 1, resulting in an isoform (2) that is shorter than isoform 1.
      Source sequence(s)
      AK143909, AK160965, BB612742, BC028469
      Consensus CDS
      CCDS88714.1
      UniProtKB/TrEMBL
      A0A2I3BQ16, Q3UP01
      Related
      ENSMUSP00000154004.2, ENSMUST00000228252.2
      Conserved Domains (4) summary
      cd00116
      Location:106 → 220
      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:66 → 88
      LRR_RI; leucine-rich repeat [structural motif]
      pfam00307
      Location:564 → 671
      CH; Calponin homology (CH) domain
      pfam13855
      Location:178 → 258
      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_000080.7 Reference GRCm39 C57BL/6J

      Range
      74992113..75185447 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017316067.2 → XP_017171556.2  leucine-rich repeat and calponin homology domain-containing protein 1 isoform X6

      UniProtKB/TrEMBL
      Q3UP01
      Conserved Domains (4) summary
      PRK15370
      Location:162 → 365
      PRK15370; type III secretion system effector E3 ubiquitin transferase SlrP
      smart00033
      Location:702 → 807
      CH; Calponin homology domain
      sd00031
      Location:376 → 387
      LRR_1; leucine-rich repeat [structural motif]
      sd00033
      Location:167 → 189
      LRR_RI; leucine-rich repeat [structural motif]

    2. XM_006519156.3 → XP_006519219.3  leucine-rich repeat and calponin homology domain-containing protein 1 isoform X4

      UniProtKB/TrEMBL
      Q3UP01
      Conserved Domains (4) summary
      PRK15370
      Location:162 → 365
      PRK15370; type III secretion system effector E3 ubiquitin transferase SlrP
      smart00033
      Location:729 → 834
      CH; Calponin homology domain
      sd00031
      Location:376 → 387
      LRR_1; leucine-rich repeat [structural motif]
      sd00033
      Location:167 → 189
      LRR_RI; leucine-rich repeat [structural motif]

    3. XM_036158691.1 → XP_036014584.1  leucine-rich repeat and calponin homology domain-containing protein 1 isoform X8

      UniProtKB/TrEMBL
      Q3UP01
      Conserved Domains (5) summary
      PRK15370
      Location:162 → 365
      PRK15370; type III secretion system effector E3 ubiquitin transferase SlrP
      COG5271
      Location:402 → 655
      MDN1; Midasin, AAA ATPase with vWA domain, involved in ribosome maturation [Translation, ribosomal structure and biogenesis]
      sd00031
      Location:376 → 387
      LRR_1; leucine-rich repeat [structural motif]
      sd00033
      Location:167 → 189
      LRR_RI; leucine-rich repeat [structural motif]
      cd21270
      Location:635 → 746
      CH_LRCH1; calponin homology (CH) domain found in leucine-rich repeat and calponin homology domain-containing protein 1

    4. XM_036158690.1 → XP_036014583.1  leucine-rich repeat and calponin homology domain-containing protein 1 isoform X3

      UniProtKB/TrEMBL
      Q3UP01
      Conserved Domains (4) summary
      PRK15370
      Location:162 → 365
      PRK15370; type III secretion system effector E3 ubiquitin transferase SlrP
      sd00031
      Location:376 → 387
      LRR_1; leucine-rich repeat [structural motif]
      sd00033
      Location:167 → 189
      LRR_RI; leucine-rich repeat [structural motif]
      cd21270
      Location:697 → 808
      CH_LRCH1; calponin homology (CH) domain found in leucine-rich repeat and calponin homology domain-containing protein 1

    5. XM_006519158.4 → XP_006519221.3  leucine-rich repeat and calponin homology domain-containing protein 1 isoform X7

      UniProtKB/TrEMBL
      Q3UP01
      Conserved Domains (4) summary
      PRK15370
      Location:162 → 365
      PRK15370; type III secretion system effector E3 ubiquitin transferase SlrP
      smart00033
      Location:667 → 756
      CH; Calponin homology domain
      sd00031
      Location:376 → 387
      LRR_1; leucine-rich repeat [structural motif]
      sd00033
      Location:167 → 189
      LRR_RI; leucine-rich repeat [structural motif]

    6. XM_006519155.4 → XP_006519218.3  leucine-rich repeat and calponin homology domain-containing protein 1 isoform X2

      UniProtKB/TrEMBL
      Q3UP01
      Conserved Domains (4) summary
      PRK15370
      Location:162 → 365
      PRK15370; type III secretion system effector E3 ubiquitin transferase SlrP
      smart00033
      Location:702 → 791
      CH; Calponin homology domain
      sd00031
      Location:376 → 387
      LRR_1; leucine-rich repeat [structural motif]
      sd00033
      Location:167 → 189
      LRR_RI; leucine-rich repeat [structural motif]

    7. XM_006519157.4 → XP_006519220.3  leucine-rich repeat and calponin homology domain-containing protein 1 isoform X5

      UniProtKB/TrEMBL
      Q3UP01
      Conserved Domains (4) summary
      PRK15370
      Location:162 → 365
      PRK15370; type III secretion system effector E3 ubiquitin transferase SlrP
      smart00033
      Location:694 → 783
      CH; Calponin homology domain
      sd00031
      Location:376 → 387
      LRR_1; leucine-rich repeat [structural motif]
      sd00033
      Location:167 → 189
      LRR_RI; leucine-rich repeat [structural motif]

    8. XM_006519154.4 → XP_006519217.3  leucine-rich repeat and calponin homology domain-containing protein 1 isoform X1

      UniProtKB/TrEMBL
      Q3UP01
      Conserved Domains (4) summary
      PRK15370
      Location:162 → 365
      PRK15370; type III secretion system effector E3 ubiquitin transferase SlrP
      smart00033
      Location:729 → 818
      CH; Calponin homology domain
      sd00031
      Location:376 → 387
      LRR_1; leucine-rich repeat [structural motif]
      sd00033
      Location:167 → 189
      LRR_RI; leucine-rich repeat [structural motif]

    9. XM_036158693.1 → XP_036014586.1  leucine-rich repeat and calponin homology domain-containing protein 1 isoform X10

      Conserved Domains (1) summary
      cd21270
      Location:382 → 493
      CH_LRCH1; calponin homology (CH) domain found in leucine-rich repeat and calponin homology domain-containing protein 1

    10. XM_036158692.1 → XP_036014585.1  leucine-rich repeat and calponin homology domain-containing protein 1 isoform X9

      Conserved Domains (3) summary
      sd00031
      Location:2 → 22
      LRR_1; leucine-rich repeat [structural motif]
      pfam13855
      Location:1 → 78
      LRR_8; Leucine rich repeat
      cd21270
      Location:446 → 557
      CH_LRCH1; calponin homology (CH) domain found in leucine-rich repeat and calponin homology domain-containing protein 1

    RNA

    1. XR_001781129.2 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P62046.2 GenPept UniProtKB/Swiss-Prot:P62046

    Gene LinkOut

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

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