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    Lrch1 leucine rich repeats and calponin homology domain containing 1 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 502020, updated on 5-Mar-2024

    Summary

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    Official Symbol
    Lrch1provided by RGD
    Official Full Name
    leucine rich repeats and calponin homology domain containing 1provided by RGD
    Primary source
    RGD:1595678
    See related
    Ensembl:ENSRNOG00000009412 AllianceGenome:RGD:1595678
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Summary
    Predicted to be involved in cellular response to chemokine; negative regulation of GTPase activity; and negative regulation of T cell migration. Predicted to be active in cytoplasm. Orthologous to human LRCH1 (leucine rich repeats and calponin homology domain containing 1). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in Spleen (RPKM 60.5), Lung (RPKM 60.4) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Lrch1 in Genome Data Viewer
    Location:
    15q11
    Exon count:
    25
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 15 NC_086033.1 (56469403..56659201, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 15 NC_051350.1 (50070605..50249724, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 15 NC_005114.4 (56778738..56970439, complement)

    Chromosome 15 - NC_086033.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC134481990 Neighboring gene 5-hydroxytryptamine receptor 2A Neighboring gene esterase D Neighboring gene uncharacterized LOC134482152 Neighboring gene uncharacterized LOC134482151 Neighboring gene uncharacterized LOC108352942 Neighboring gene rubicon like autophagy enhancer Neighboring gene leucine rich repeat containing 63 Neighboring gene lymphocyte cytosolic protein 1

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

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    Related articles in PubMed

    1. Inhibition of leucine-rich repeats and calponin homology domain containing 1 accelerates microglia-mediated neuroinflammation in a rat traumatic spinal cord injury model. Chen WK, et al. J Neuroinflammation, 2020 Jul 6. PMID 32631435, 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. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, et al. Proc Natl Acad Sci U S A, 2002 Dec 24. PMID 12477932, Free PMC Article
    4. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Inhibition of leucine-rich repeats and calponin homology domain containing 1 accelerates microglia-mediated neuroinflammation in a rat traumatic spinal cord injury model.
      Title: Inhibition of leucine-rich repeats and calponin homology domain containing 1 accelerates microglia-mediated neuroinflammation in a rat traumatic spinal cord injury model.
    Submit: New GeneRIF Correction

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    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 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 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
    		  
    located_in membrane IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    leucine-rich repeat and calponin homology domain-containing protein 1
    Names
    leucine-rich repeats and calponin homology (CH) domain containing 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_001134727.1 → NP_001128199.1  leucine-rich repeat and calponin homology domain-containing protein 1

      See identical proteins and their annotated locations for NP_001128199.1

      Status: PROVISIONAL

      Source sequence(s)
      BC166585
      UniProtKB/TrEMBL
      A6HTS0, B2GV98
      Related
      ENSRNOP00000047801.3, ENSRNOT00000047192.4
      Conserved Domains (5) summary
      smart00033
      Location:561 → 666
      CH; Calponin homology domain
      cd00116
      Location:99 → 214
      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 ...
      sd00031
      Location:269 → 280
      LRR_1; leucine-rich repeat [structural motif]
      sd00033
      Location:60 → 82
      LRR_RI; leucine-rich repeat [structural motif]
      pfam13855
      Location:172 → 252
      LRR_8; Leucine rich repeat

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086033.1 Reference GRCr8

      Range
      56469403..56659201 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_063274585.1 → XP_063130655.1  leucine-rich repeat and calponin homology domain-containing protein 1 isoform X7

    2. XM_006252312.5 → XP_006252374.1  leucine-rich repeat and calponin homology domain-containing protein 1 isoform X3

      UniProtKB/TrEMBL
      A0A8I6AAA9, A6HTS0
      Related
      ENSRNOP00000090771.1
      Conserved Domains (5) summary
      smart00033
      Location:596 → 701
      CH; Calponin homology domain
      cd00116
      Location:99 → 214
      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 ...
      sd00031
      Location:269 → 280
      LRR_1; leucine-rich repeat [structural motif]
      sd00033
      Location:60 → 82
      LRR_RI; leucine-rich repeat [structural motif]
      pfam13855
      Location:172 → 252
      LRR_8; Leucine rich repeat

    3. XM_006252315.5 → XP_006252377.1  leucine-rich repeat and calponin homology domain-containing protein 1 isoform X10

      UniProtKB/TrEMBL
      A0A8I5Y080, A6HTS0
      Related
      ENSRNOP00000076612.1
      Conserved Domains (5) summary
      smart00033
      Location:588 → 693
      CH; Calponin homology domain
      cd00116
      Location:99 → 214
      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 ...
      sd00031
      Location:269 → 280
      LRR_1; leucine-rich repeat [structural motif]
      sd00033
      Location:60 → 82
      LRR_RI; leucine-rich repeat [structural motif]
      pfam13855
      Location:172 → 252
      LRR_8; Leucine rich repeat

    4. XM_008770896.4 → XP_008769118.1  leucine-rich repeat and calponin homology domain-containing protein 1 isoform X2

      UniProtKB/TrEMBL
      A6HTS0
      Conserved Domains (4) summary
      smart00033
      Location:567 → 656
      CH; Calponin homology domain
      cd00116
      Location:99 → 214
      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:60 → 82
      LRR_RI; leucine-rich repeat [structural motif]
      pfam13855
      Location:172 → 252
      LRR_8; Leucine rich repeat

    5. XM_006252311.5 → XP_006252373.1  leucine-rich repeat and calponin homology domain-containing protein 1 isoform X1

      UniProtKB/TrEMBL
      A6HTS0
      Conserved Domains (4) summary
      smart00033
      Location:596 → 685
      CH; Calponin homology domain
      cd00116
      Location:99 → 214
      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:60 → 82
      LRR_RI; leucine-rich repeat [structural motif]
      pfam13855
      Location:172 → 252
      LRR_8; Leucine rich repeat

    6. XM_006252313.5 → XP_006252375.1  leucine-rich repeat and calponin homology domain-containing protein 1 isoform X5

      UniProtKB/TrEMBL
      A0A8I6ABL3, A6HTS0
      Related
      ENSRNOP00000089380.1
      Conserved Domains (4) summary
      smart00033
      Location:561 → 650
      CH; Calponin homology domain
      cd00116
      Location:99 → 214
      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:60 → 82
      LRR_RI; leucine-rich repeat [structural motif]
      pfam13855
      Location:172 → 252
      LRR_8; Leucine rich repeat

    7. XM_063274586.1 → XP_063130656.1  leucine-rich repeat and calponin homology domain-containing protein 1 isoform X8

    8. XM_039093606.2 → XP_038949534.1  leucine-rich repeat and calponin homology domain-containing protein 1 isoform X9

      Conserved Domains (2) summary
      COG5271
      Location:57 → 188
      MDN1; Midasin, AAA ATPase with vWA domain, involved in ribosome maturation [Translation, ribosomal structure and biogenesis]
      cd21270
      Location:356 → 467
      CH_LRCH1; calponin homology (CH) domain found in leucine-rich repeat and calponin homology domain-containing protein 1

    9. XM_017599784.3 → XP_017455273.1  leucine-rich repeat and calponin homology domain-containing protein 1 isoform X4

      UniProtKB/TrEMBL
      A6HTS0

    10. XM_063274584.1 → XP_063130654.1  leucine-rich repeat and calponin homology domain-containing protein 1 isoform X6

    Nucleotide Protein Strain
    Heading Accession and Version

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