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    Hmcn1 hemicentin 1 [ Mus musculus (house mouse) ]

    Gene ID: 545370, updated on 9-Dec-2024

    Summary

    Official Symbol
    Hmcn1provided by MGI
    Official Full Name
    hemicentin 1provided by MGI
    Primary source
    MGI:MGI:2685047
    See related
    Ensembl:ENSMUSG00000066842 AllianceGenome:MGI:2685047
    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
    Gm201; FIBL-6; EG545370
    Summary
    Predicted to enable calcium ion binding activity. Predicted to be an extracellular matrix structural constituent. Involved in basement membrane organization. Acts upstream of or within response to bacterium. Located in several cellular components, including basement membrane; cell cortex; and muscle tendon junction. Is expressed in several structures, including early embryo; extracellular matrix; limb; metanephros; and skin. 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
    Broad expression in lung adult (RPKM 6.3), limb E14.5 (RPKM 5.8) and 16 other tissues See more
    Orthologs
    NEW
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    Try the new Transcript table

    Genomic context

    See Hmcn1 in Genome Data Viewer
    Location:
    1 G1; 1 63.84 cM
    Exon count:
    108
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 1 NC_000067.7 (150438251..150869568, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 1 NC_000067.6 (150562500..150993652, complement)

    Chromosome 1 - NC_000067.7Genomic Context describing neighboring genes Neighboring gene spindle and kinetochore associated complex subunit 2-like, pseudogene Neighboring gene predicted gene, 33818 Neighboring gene STARR-positive B cell enhancer mm9_chr1:152856440-152856740 Neighboring gene CapStarr-seq enhancer MGSCv37_chr1:152872392-152872545 Neighboring gene predicted gene, 36297 Neighboring gene predicted gene, 22756 Neighboring gene predicted gene, 36139 Neighboring gene predicted gene, 36077

    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

    Variation

    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)

    General gene information

    Markers

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables calcium ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables extracellular matrix structural constituent RCA
    inferred from Reviewed Computational Analysis
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in actin cytoskeleton organization ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in actin cytoskeleton organization ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in basement membrane organization IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in cell division IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules IBA
    Inferred from Biological aspect of Ancestor
    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 IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    Component Evidence Code Pubs
    is_active_in adherens junction IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in basement membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cell cortex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cell junction IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cleavage furrow IEA
    Inferred from Electronic Annotation
    more info
     
    located_in collagen-containing extracellular matrix HDA PubMed 
    is_active_in collagen-containing extracellular matrix IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in extracellular region IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in muscle tendon junction IDA
    Inferred from Direct Assay
    more info
    PubMed 

    General protein information

    Preferred Names
    hemicentin-1
    Names
    fibulin-6

    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_001024720.4NP_001019891.2  hemicentin-1 precursor

      Status: VALIDATED

      Source sequence(s)
      AC111145, AC113326, AC115051, AC124120
      Consensus CDS
      CCDS15357.2
      UniProtKB/Swiss-Prot
      D3YXG0, D3Z2Q7
      Related
      ENSMUSP00000074340.6, ENSMUST00000074783.12
      Conserved Domains (13) summary
      cd00096
      Location:11881254
      Ig; Immunoglobulin domain
      smart00408
      Location:24922556
      IGc2; Immunoglobulin C-2 Type
      smart00179
      Location:54315470
      EGF_CA; Calcium-binding EGF-like domain
      smart00209
      Location:45884640
      TSP1; Thrombospondin type 1 repeats
      smart00409
      Location:14591541
      IG; Immunoglobulin
      smart00410
      Location:18331914
      IG_like; Immunoglobulin like
      smart00682
      Location:48675091
      G2F; G2 nidogen domain and fibulin
      cd00054
      Location:52295262
      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:24772566
      I-set; Immunoglobulin I-set domain
      pfam00047
      Location:528606
      ig; Immunoglobulin domain
      pfam07645
      Location:52715312
      EGF_CA; Calcium-binding EGF domain
      pfam13519
      Location:42212
      VWA_2; von Willebrand factor type A domain
      cl11960
      Location:32433337
      Ig; Immunoglobulin domain

    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_000067.7 Reference GRCm39 C57BL/6J

      Range
      150438251..150869568 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006529758.5XP_006529821.1  hemicentin-1 isoform X2

      Related
      ENSMUSP00000121500.3, ENSMUST00000137197.9
      Conserved Domains (12) summary
      smart00179
      Location:53385377
      EGF_CA; Calcium-binding EGF-like domain
      smart00209
      Location:46124664
      TSP1; Thrombospondin type 1 repeats
      smart00409
      Location:35583639
      IG; Immunoglobulin
      smart00410
      Location:14591541
      IG_like; Immunoglobulin like
      smart00682
      Location:48915115
      G2F; G2 nidogen domain and fibulin
      cd00054
      Location:52535286
      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 ...
      cd00198
      Location:42198
      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 ...
      pfam07645
      Location:52955336
      EGF_CA; Calcium-binding EGF domain
      cd00096
      Location:31923260
      Ig; Immunoglobulin domain
      pfam07679
      Location:25012590
      I-set; Immunoglobulin I-set domain
      pfam13927
      Location:23132390
      Ig_3; Immunoglobulin domain
      cl11960
      Location:32673361
      Ig; Immunoglobulin domain
    2. XM_006529757.5XP_006529820.1  hemicentin-1 isoform X1

      Conserved Domains (11) summary
      smart00179
      Location:54555494
      EGF_CA; Calcium-binding EGF-like domain
      smart00209
      Location:46124664
      TSP1; Thrombospondin type 1 repeats
      smart00410
      Location:14591541
      IG_like; Immunoglobulin like
      smart00682
      Location:48915115
      G2F; G2 nidogen domain and fibulin
      cd00054
      Location:52535286
      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 ...
      cd00198
      Location:42198
      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 ...
      pfam07645
      Location:52955336
      EGF_CA; Calcium-binding EGF domain
      cd00096
      Location:31923260
      Ig; Immunoglobulin domain
      pfam07679
      Location:25012590
      I-set; Immunoglobulin I-set domain
      pfam13927
      Location:23132390
      Ig_3; Immunoglobulin domain
      cl11960
      Location:32673361
      Ig; Immunoglobulin domain
    3. XM_011248051.3XP_011246353.1  hemicentin-1 isoform X3

      Conserved Domains (11) summary
      smart00179
      Location:48104849
      EGF_CA; Calcium-binding EGF-like domain
      smart00209
      Location:39674019
      TSP1; Thrombospondin type 1 repeats
      smart00409
      Location:29132994
      IG; Immunoglobulin
      smart00410
      Location:814896
      IG_like; Immunoglobulin like
      smart00682
      Location:42464470
      G2F; G2 nidogen domain and fibulin
      cd00054
      Location:46084641
      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 ...
      pfam07645
      Location:46504691
      EGF_CA; Calcium-binding EGF domain
      cd00096
      Location:25472615
      Ig; Immunoglobulin domain
      pfam07679
      Location:18561945
      I-set; Immunoglobulin I-set domain
      pfam13927
      Location:16681745
      Ig_3; Immunoglobulin domain
      cl11960
      Location:26222716
      Ig; Immunoglobulin domain

    RNA

    1. XR_387184.5 RNA Sequence