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

    Gene ID: 380916, updated on 21-Apr-2024

    Summary

    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, Apr 2022]
    Expression
    Ubiquitous expression in bladder adult (RPKM 4.8), lung adult (RPKM 4.8) and 28 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    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

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Variation

    Alleles

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

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    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 ISO
    Inferred from Sequence Orthology
    more info
     

    General protein information

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

    NCBI Reference Sequences (RefSeq)

    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_001033439.3NP_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:106220
      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:6688
      LRR_RI; leucine-rich repeat [structural motif]
      pfam00307
      Location:591698
      CH; Calponin homology (CH) domain
      pfam13855
      Location:178258
      LRR_8; Leucine rich repeat
    2. NM_001252132.1NP_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:106220
      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:6688
      LRR_RI; leucine-rich repeat [structural motif]
      pfam00307
      Location:564671
      CH; Calponin homology (CH) domain
      pfam13855
      Location:178258
      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_017316067.2XP_017171556.2  leucine-rich repeat and calponin homology domain-containing protein 1 isoform X6

      UniProtKB/TrEMBL
      Q3UP01
      Conserved Domains (4) summary
      PRK15370
      Location:162365
      PRK15370; type III secretion system effector E3 ubiquitin transferase SlrP
      smart00033
      Location:702807
      CH; Calponin homology domain
      sd00031
      Location:376387
      LRR_1; leucine-rich repeat [structural motif]
      sd00033
      Location:167189
      LRR_RI; leucine-rich repeat [structural motif]
    2. XM_006519156.3XP_006519219.3  leucine-rich repeat and calponin homology domain-containing protein 1 isoform X4

      UniProtKB/TrEMBL
      Q3UP01
      Conserved Domains (4) summary
      PRK15370
      Location:162365
      PRK15370; type III secretion system effector E3 ubiquitin transferase SlrP
      smart00033
      Location:729834
      CH; Calponin homology domain
      sd00031
      Location:376387
      LRR_1; leucine-rich repeat [structural motif]
      sd00033
      Location:167189
      LRR_RI; leucine-rich repeat [structural motif]
    3. XM_036158691.1XP_036014584.1  leucine-rich repeat and calponin homology domain-containing protein 1 isoform X8

      UniProtKB/TrEMBL
      Q3UP01
      Conserved Domains (5) summary
      PRK15370
      Location:162365
      PRK15370; type III secretion system effector E3 ubiquitin transferase SlrP
      COG5271
      Location:402655
      MDN1; Midasin, AAA ATPase with vWA domain, involved in ribosome maturation [Translation, ribosomal structure and biogenesis]
      sd00031
      Location:376387
      LRR_1; leucine-rich repeat [structural motif]
      sd00033
      Location:167189
      LRR_RI; leucine-rich repeat [structural motif]
      cd21270
      Location:635746
      CH_LRCH1; calponin homology (CH) domain found in leucine-rich repeat and calponin homology domain-containing protein 1
    4. XM_036158690.1XP_036014583.1  leucine-rich repeat and calponin homology domain-containing protein 1 isoform X3

      UniProtKB/TrEMBL
      Q3UP01
      Conserved Domains (4) summary
      PRK15370
      Location:162365
      PRK15370; type III secretion system effector E3 ubiquitin transferase SlrP
      sd00031
      Location:376387
      LRR_1; leucine-rich repeat [structural motif]
      sd00033
      Location:167189
      LRR_RI; leucine-rich repeat [structural motif]
      cd21270
      Location:697808
      CH_LRCH1; calponin homology (CH) domain found in leucine-rich repeat and calponin homology domain-containing protein 1
    5. XM_006519158.4XP_006519221.3  leucine-rich repeat and calponin homology domain-containing protein 1 isoform X7

      UniProtKB/TrEMBL
      Q3UP01
      Conserved Domains (4) summary
      PRK15370
      Location:162365
      PRK15370; type III secretion system effector E3 ubiquitin transferase SlrP
      smart00033
      Location:667756
      CH; Calponin homology domain
      sd00031
      Location:376387
      LRR_1; leucine-rich repeat [structural motif]
      sd00033
      Location:167189
      LRR_RI; leucine-rich repeat [structural motif]
    6. XM_006519155.4XP_006519218.3  leucine-rich repeat and calponin homology domain-containing protein 1 isoform X2

      UniProtKB/TrEMBL
      Q3UP01
      Conserved Domains (4) summary
      PRK15370
      Location:162365
      PRK15370; type III secretion system effector E3 ubiquitin transferase SlrP
      smart00033
      Location:702791
      CH; Calponin homology domain
      sd00031
      Location:376387
      LRR_1; leucine-rich repeat [structural motif]
      sd00033
      Location:167189
      LRR_RI; leucine-rich repeat [structural motif]
    7. XM_006519157.4XP_006519220.3  leucine-rich repeat and calponin homology domain-containing protein 1 isoform X5

      UniProtKB/TrEMBL
      Q3UP01
      Conserved Domains (4) summary
      PRK15370
      Location:162365
      PRK15370; type III secretion system effector E3 ubiquitin transferase SlrP
      smart00033
      Location:694783
      CH; Calponin homology domain
      sd00031
      Location:376387
      LRR_1; leucine-rich repeat [structural motif]
      sd00033
      Location:167189
      LRR_RI; leucine-rich repeat [structural motif]
    8. XM_006519154.4XP_006519217.3  leucine-rich repeat and calponin homology domain-containing protein 1 isoform X1

      UniProtKB/TrEMBL
      Q3UP01
      Conserved Domains (4) summary
      PRK15370
      Location:162365
      PRK15370; type III secretion system effector E3 ubiquitin transferase SlrP
      smart00033
      Location:729818
      CH; Calponin homology domain
      sd00031
      Location:376387
      LRR_1; leucine-rich repeat [structural motif]
      sd00033
      Location:167189
      LRR_RI; leucine-rich repeat [structural motif]
    9. XM_036158693.1XP_036014586.1  leucine-rich repeat and calponin homology domain-containing protein 1 isoform X10

      Conserved Domains (1) summary
      cd21270
      Location:382493
      CH_LRCH1; calponin homology (CH) domain found in leucine-rich repeat and calponin homology domain-containing protein 1
    10. XM_036158692.1XP_036014585.1  leucine-rich repeat and calponin homology domain-containing protein 1 isoform X9

      Conserved Domains (3) summary
      sd00031
      Location:222
      LRR_1; leucine-rich repeat [structural motif]
      pfam13855
      Location:178
      LRR_8; Leucine rich repeat
      cd21270
      Location:446557
      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