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    LRCH1 leucine rich repeats and calponin homology domain containing 1 [ Homo sapiens (human) ]

    Gene ID: 23143, updated on 7-Oct-2018

    Summary

    Official Symbol
    LRCH1provided by HGNC
    Official Full Name
    leucine rich repeats and calponin homology domain containing 1provided by HGNC
    Primary source
    HGNC:HGNC:20309
    See related
    Ensembl:ENSG00000136141 MIM:610368; Vega:OTTHUMG00000016877
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    NP81; CHDC1
    Summary
    This gene encodes a protein with a leucine-rich repeat and a calponin homology domain. Polymorphism in this gene may be associated with susceptibililty to knee osteoarthritis. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Mar 2010]
    Expression
    Ubiquitous expression in endometrium (RPKM 5.5), placenta (RPKM 5.5) and 25 other tissues See more
    Orthologs

    Genomic context

    See LRCH1 in Genome Data Viewer
    Location:
    13q14.13-q14.2
    Exon count:
    21
    Annotation release Status Assembly Chr Location
    109 current GRCh38.p12 (GCF_000001405.38) 13 NC_000013.11 (46553161..46753041)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 13 NC_000013.10 (47127296..47327176)

    Chromosome 13 - NC_000013.11Genomic Context describing neighboring genes Neighboring gene COX17, cytochrome c oxidase copper chaperone pseudogene 1 Neighboring gene FK506 binding protein 1A pseudogene 3 Neighboring gene uncharacterized LOC107984563 Neighboring gene esterase D

    Genomic regions, transcripts, and products

    Expression

    • 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 Jun 15 11:32:44 2016

    Bibliography

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Clone Names

    • FLJ41660, KIAA1016

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    cellular response to chemokine IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    cellular response to chemokine IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    negative regulation of GTPase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    negative regulation of T cell migration IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    negative regulation of T cell migration IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Component Evidence Code Pubs
    cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    cytoplasm IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 

    General protein information

    Preferred Names
    leucine-rich repeat and calponin homology domain-containing protein 1
    Names
    leucine-rich repeats and calponin homology (CH) domain containing 1
    neuronal protein 81

    NCBI Reference Sequences (RefSeq)

    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.

    Genomic

    1. NG_021335.1 RefSeqGene

      Range
      5001..204881
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001164211.1NP_001157683.1  leucine-rich repeat and calponin homology domain-containing protein 1 isoform 1

      See identical proteins and their annotated locations for NP_001157683.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AL359880, BC117472, BC143883, BM679696, DA231068
      Consensus CDS
      CCDS53865.1
      UniProtKB/Swiss-Prot
      Q9Y2L9
      Related
      ENSP00000374447.3, OTTHUMP00000214856, ENST00000389797.7, OTTHUMT00000354618
      Conserved Domains (4) summary
      smart00033
      Location:615704
      CH; Calponin homology domain
      sd00033
      Location:7698
      LRR_RI; leucine-rich repeat [structural motif]
      cl26018
      Location:71274
      NEL; C-terminal novel E3 ligase, LRR-interacting
      cl26761
      Location:311513
      MDN1; Midasin, AAA ATPase with vWA domain, involved in ribosome maturation [Translation, ribosomal structure and biogenesis]
    2. NM_001164213.1NP_001157685.1  leucine-rich repeat and calponin homology domain-containing protein 1 isoform 3

      See identical proteins and their annotated locations for NP_001157685.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks an alternate in-frame exon and uses an alternate 3' exon, compared to variant 1. These differences result in a distinct 3' UTR, compared to variant 1, and a shorter protein (isoform 3) with a distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      AL530544, AY050631, BC112937, BE018226, BM991796, BM994390, CB529998, CB999464
      Consensus CDS
      CCDS53866.1
      UniProtKB/Swiss-Prot
      Q9Y2L9
      Related
      ENSP00000308493.5, OTTHUMP00000018373, ENST00000311191.10, OTTHUMT00000044825
      Conserved Domains (5) summary
      cd00116
      Location:115226
      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:285296
      LRR_1; leucine-rich repeat [structural motif]
      sd00033
      Location:7698
      LRR_RI; leucine-rich repeat [structural motif]
      pfam00307
      Location:578685
      CH; Calponin homology (CH) domain
      pfam13855
      Location:121177
      LRR_8; Leucine rich repeat
    3. NM_015116.2NP_055931.1  leucine-rich repeat and calponin homology domain-containing protein 1 isoform 2

      See identical proteins and their annotated locations for NP_055931.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon compared to variant 1. The resulting protein (isoform 2) is shorter compared to isoform 1.
      Source sequence(s)
      AL359880, AL530544, AY050632, BC112937, BM679696
      Consensus CDS
      CCDS31972.1
      UniProtKB/Swiss-Prot
      Q9Y2L9
      Related
      ENSP00000374448.3, OTTHUMP00000018372, ENST00000389798.7, OTTHUMT00000044824
      Conserved Domains (5) summary
      smart00033
      Location:580669
      CH; Calponin homology domain
      cd00116
      Location:115226
      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:285296
      LRR_1; leucine-rich repeat [structural motif]
      sd00033
      Location:7698
      LRR_RI; leucine-rich repeat [structural motif]
      pfam13855
      Location:121177
      LRR_8; Leucine rich repeat

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

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

    Reference GRCh38.p12 Primary Assembly

    Genomic

    1. NC_000013.11 Reference GRCh38.p12 Primary Assembly

      Range
      46553161..46753041
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017020483.2XP_016875972.1  leucine-rich repeat and calponin homology domain-containing protein 1 isoform X1

    2. XM_017020484.1XP_016875973.1  leucine-rich repeat and calponin homology domain-containing protein 1 isoform X2

    RNA

    1. XR_001749525.2 RNA Sequence

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