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    Hmcn1 hemicentin 1 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 289094, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Hmcn1provided by RGD
    Official Full Name
    hemicentin 1provided by RGD
    Primary source
    RGD:1564772
    See related
    EnsemblRapid:ENSRNOG00000028627 AllianceGenome:RGD:1564772
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    RGD1564772
    Summary
    Predicted to enable axon guidance receptor activity. Predicted to be involved in several processes, including actin cytoskeleton organization; basement membrane organization; and homophilic cell adhesion via plasma membrane adhesion molecules. Predicted to act upstream of or within response to bacterium. Predicted to be located in several cellular components, including basement membrane; cell cortex; and muscle tendon junction. Predicted to be active in axon; neuronal cell body; and plasma membrane. Human ortholog(s) of this gene implicated in age related macular degeneration 1. Orthologous to human HMCN1 (hemicentin 1). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Lung (RPKM 255.6), Spleen (RPKM 214.8) and 8 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Hmcn1 in Genome Data Viewer
    Location:
    13q21
    Exon count:
    108
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 13 NC_086031.1 (65165532..65634681, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 13 NC_051348.1 (62615461..63084524, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 13 NC_005112.4 (67799791..68360664, complement)

    Chromosome 13 - NC_086031.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC134481514 Neighboring gene uncharacterized LOC134481513 Neighboring gene odr-4 GPCR localization factor homolog Neighboring gene translocated promoter region, nuclear basket protein Neighboring gene proteoglycan 4 Neighboring gene small nucleolar RNA U13 Neighboring gene U4 spliceosomal RNA Neighboring gene Glyceraldehyde-3-phosphate dehydrogenase, pseudogene 93

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. Hemicentin 1 influences podocyte dynamic changes in glomerular diseases. Toffoli B, et al. Am J Physiol Renal Physiol, 2018 Jun 1. PMID 29488390
    2. Hemicentins assemble on diverse epithelia in the mouse. Xu X, et al. J Histochem Cytochem, 2007 Feb. PMID 17015624
    3. FMRP recruitment of β-catenin to the translation pre-initiation complex represses translation. Ehyai S, et al. EMBO Rep, 2018 Dec. PMID 30361391, Free PMC Article
    4. Impact of lactobacilli on orally acquired listeriosis. Archambaud C, et al. Proc Natl Acad Sci U S A, 2012 Oct 9. PMID 23012479, Free PMC Article
    5. In-depth proteomic analyses of exosomes isolated from expressed prostatic secretions in urine. Principe S, et al. Proteomics, 2013 May. PMID 23533145, Free PMC Article

    See all (7) citations in PubMed

    GeneRIFs: Gene References Into Functions

    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 RGD

    Function Evidence Code Pubs
    enables axon guidance receptor activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables calcium ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in actin cytoskeleton organization ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in axon guidance IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in basement membrane organization ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in homophilic cell adhesion via plasma membrane adhesion molecules IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within response to bacterium ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in synapse organization IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    is_active_in axon IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in basement membrane ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in cell cortex ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in cell junction ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in cytoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in extracellular region ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in muscle tendon junction ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in neuronal cell body IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    hemicentin-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_001271292.2 → NP_001258221.1  hemicentin-1 precursor

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000013
      UniProtKB/TrEMBL
      F1M4Q3
      Related
      ENSRNOP00000033710.8, ENSRNOT00000030971.9
      Conserved Domains (13) summary
      cd00096
      Location:1188 → 1255
      Ig; Immunoglobulin domain
      smart00408
      Location:2493 → 2557
      IGc2; Immunoglobulin C-2 Type
      smart00179
      Location:5432 → 5471
      EGF_CA; Calcium-binding EGF-like domain
      smart00209
      Location:4589 → 4641
      TSP1; Thrombospondin type 1 repeats
      smart00409
      Location:1834 → 1915
      IG; Immunoglobulin
      smart00410
      Location:799 → 884
      IG_like; Immunoglobulin like
      smart00682
      Location:4868 → 5092
      G2F; G2 nidogen domain and fibulin
      cd00054
      Location:5230 → 5263
      EGF_CA; Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the ...
      pfam07679
      Location:2478 → 2567
      I-set; Immunoglobulin I-set domain
      pfam00047
      Location:524 → 606
      ig; Immunoglobulin domain
      pfam07645
      Location:5272 → 5313
      EGF_CA; Calcium-binding EGF domain
      pfam13519
      Location:42 → 212
      VWA_2; von Willebrand factor type A domain
      cl11960
      Location:3244 → 3338
      Ig; Immunoglobulin domain

    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_086031.1 Reference GRCr8

      Range
      65165532..65634681 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_039090457.2 → XP_038946385.2  hemicentin-1 isoform X2

      UniProtKB/TrEMBL
      F1M4Q3

    2. XM_039090458.2 → XP_038946386.2  hemicentin-1 isoform X3

      UniProtKB/TrEMBL
      F1M4Q3
      Related
      ENSRNOP00000094032.2, ENSRNOT00000093469.3

    3. XM_039090459.2 → XP_038946387.2  hemicentin-1 isoform X4

      UniProtKB/TrEMBL
      F1M4Q3

    4. XM_039090456.2 → XP_038946384.2  hemicentin-1 isoform X1

      UniProtKB/TrEMBL
      F1M4Q3
      Related
      ENSRNOP00000067981.4, ENSRNOT00000076776.4

    5. XM_039090460.2 → XP_038946388.2  hemicentin-1 isoform X5

      UniProtKB/TrEMBL
      F1M4Q3

    6. XM_039090461.2 → XP_038946389.1  hemicentin-1 isoform X6

      Conserved Domains (6) summary
      smart00408
      Location:1843 → 1905
      IGc2; Immunoglobulin C-2 Type
      cd00198
      Location:42 → 198
      vWFA; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...
      pfam07679
      Location:2478 → 2567
      I-set; Immunoglobulin I-set domain
      pfam13927
      Location:3150 → 3228
      Ig_3; Immunoglobulin domain
      cd00096
      Location:451 → 513
      Ig; Immunoglobulin domain
      cl11960
      Location:1262 → 1355
      Ig; Immunoglobulin domain
    Nucleotide Protein Strain
    Heading Accession and Version

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