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    HMCN1 hemicentin 1 [ Homo sapiens (human) ]

    Gene ID: 83872, updated on 2-May-2024

    Summary

    Official Symbol
    HMCN1provided by HGNC
    Official Full Name
    hemicentin 1provided by HGNC
    Primary source
    HGNC:HGNC:19194
    See related
    Ensembl:ENSG00000143341 MIM:608548; AllianceGenome:HGNC:19194
    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
    ARMD1; FBLN6; FIBL6; FIBL-6
    Summary
    This gene encodes a large extracellular member of the immunoglobulin superfamily. A similar protein in C. elegans forms long, fine tracks at specific extracellular sites that are involved in many processes such as stabilization of the germline syncytium, anchorage of mechanosensory neurons to the epidermis, and organization of hemidesmosomes in the epidermis. Mutations in this gene may be associated with age-related macular degeneration. [provided by RefSeq, Jul 2008]
    Expression
    Broad expression in lung (RPKM 3.2), gall bladder (RPKM 2.4) and 21 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Location:
    1q25.3-q31.1
    Exon count:
    108
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (185734391..186190949)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (185089079..185545614)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (185703523..186160081)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107985239 Neighboring gene MPRA-validated peak505 silencer Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:185554623-185555822 Neighboring gene long intergenic non-protein coding RNA 1350 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2245 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr1:185615105-185616018 Neighboring gene uncharacterized GS1-204I12.4 Neighboring gene NANOG hESC enhancer GRCh37_chr1:185663280-185663781 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr1:185668941-185669602 Neighboring gene MPRA-validated peak509 silencer Neighboring gene MPRA-validated peak510 silencer Neighboring gene MPRA-validated peak511 silencer Neighboring gene Sharpr-MPRA regulatory region 5860 Neighboring gene MPRA-validated peak512 silencer Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr1:185917425-185918340 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr1:185922788-185923626 Neighboring gene MPRA-validated peak513 silencer Neighboring gene uncharacterized LOC105371654 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr1:186156636-186157835 Neighboring gene MPRA-validated peak514 silencer Neighboring gene uncharacterized LOC124904471 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:186214031-186214197 Neighboring gene RNA, U6 small nuclear 1240, pseudogene Neighboring gene proteoglycan 4 Neighboring gene translocated promoter region, nuclear basket protein

    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 Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    Associated conditions

    Description Tests
    Age related macular degeneration 1
    MedGen: C1864205 OMIM: 603075 GeneReviews: Not available
    Compare labs

    EBI GWAS Catalog

    Description
    Generalization of variants identified by genome-wide association studies for electrocardiographic traits in African Americans.
    EBI GWAS Catalog

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables calcium ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables extracellular matrix structural constituent HDA PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in actin cytoskeleton organization IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in basement membrane organization ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    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
     
    involved_in response to bacterium IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in visual perception IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    is_active_in adherens junction IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in basement membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in cell cortex IEA
    Inferred from Electronic Annotation
    more info
     
    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
     
    colocalizes_with collagen-containing extracellular matrix TAS
    Traceable Author Statement
    more info
    PubMed 
    located_in cytoplasm ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in extracellular exosome HDA PubMed 
    located_in muscle tendon junction ISS
    Inferred from Sequence or Structural Similarity
    more info
     

    General protein information

    Preferred Names
    hemicentin-1
    Names
    LOC100507250/HMCN1 fusion
    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.

    Genomic

    1. NG_011841.2 RefSeqGene

      Range
      5002..461560
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_031935.3NP_114141.2  hemicentin-1 precursor

      See identical proteins and their annotated locations for NP_114141.2

      Status: REVIEWED

      Source sequence(s)
      AL118512, AL121996, AL133515, AL133553, AL135796, AL135797, AL391824, BX928748
      Consensus CDS
      CCDS30956.1
      UniProtKB/Swiss-Prot
      A6NGE3, Q5TYR7, Q96DN3, Q96DN8, Q96RW7, Q96SC3
      Related
      ENSP00000271588.4, ENST00000271588.9
      Conserved Domains (12) summary
      cd00096
      Location:720786
      Ig; Immunoglobulin domain
      smart00408
      Location:24932557
      IGc2; Immunoglobulin C-2 Type
      smart00179
      Location:54325471
      EGF_CA; Calcium-binding EGF-like domain
      smart00209
      Location:46464698
      TSP1; Thrombospondin type 1 repeats
      smart00409
      Location:10861167
      IG; Immunoglobulin
      smart00410
      Location:22992380
      IG_like; Immunoglobulin like
      smart00682
      Location:48685092
      G2F; G2 nidogen domain and fibulin
      cd00054
      Location:52305263
      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:11711258
      I-set; Immunoglobulin I-set domain
      pfam07645
      Location:52725313
      EGF_CA; Calcium-binding EGF domain
      pfam13519
      Location:42212
      VWA_2; von Willebrand factor type A domain
      cl11960
      Location:32443338
      Ig; Immunoglobulin domain

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      185734391..186190949
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011510038.4XP_011508340.1  hemicentin-1 isoform X1

      UniProtKB/Swiss-Prot
      Q96RW7
      Conserved Domains (12) summary
      cd00096
      Location:720786
      Ig; Immunoglobulin domain
      smart00408
      Location:24932557
      IGc2; Immunoglobulin C-2 Type
      smart00179
      Location:53155354
      EGF_CA; Calcium-binding EGF-like domain
      smart00209
      Location:46464698
      TSP1; Thrombospondin type 1 repeats
      smart00409
      Location:22992380
      IG; Immunoglobulin
      smart00410
      Location:10861167
      IG_like; Immunoglobulin like
      smart00682
      Location:48685092
      G2F; G2 nidogen domain and fibulin
      cd00054
      Location:52305263
      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:11711258
      I-set; Immunoglobulin I-set domain
      pfam07645
      Location:52725313
      EGF_CA; Calcium-binding EGF domain
      pfam13519
      Location:42212
      VWA_2; von Willebrand factor type A domain
      cl11960
      Location:32443338
      Ig; Immunoglobulin domain
    2. XM_024450118.2XP_024305886.1  hemicentin-1 isoform X4

      Conserved Domains (9) summary
      smart00408
      Location:18431905
      IGc2; Immunoglobulin C-2 Type
      smart00409
      Location:10861167
      IG; Immunoglobulin
      smart00410
      Location:526608
      IG_like; Immunoglobulin like
      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 ...
      pfam07679
      Location:11711258
      I-set; Immunoglobulin I-set domain
      pfam13927
      Location:23832461
      Ig_3; Immunoglobulin domain
      cd00096
      Location:31693235
      Ig; Immunoglobulin domain
      cl11960
      Location:792875
      Ig; Immunoglobulin domain
      cl28434
      Location:17461822
      I-set; Immunoglobulin I-set domain
    3. XM_011510041.4XP_011508343.1  hemicentin-1 isoform X5

      Conserved Domains (7) summary
      cd00096
      Location:720786
      Ig; Immunoglobulin domain
      smart00408
      Location:24932557
      IGc2; Immunoglobulin C-2 Type
      smart00409
      Location:10861167
      IG; Immunoglobulin
      smart00410
      Location:799884
      IG_like; Immunoglobulin like
      pfam07679
      Location:11711258
      I-set; Immunoglobulin I-set domain
      pfam13519
      Location:42212
      VWA_2; von Willebrand factor type A domain
      cl11960
      Location:792884
      Ig; Immunoglobulin domain
    4. XM_017002437.2XP_016857926.1  hemicentin-1 isoform X2

    5. XM_047431608.1XP_047287564.1  hemicentin-1 isoform X3

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      185089079..185545614
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054339006.1XP_054194981.1  hemicentin-1 isoform X1

    2. XM_054339009.1XP_054194984.1  hemicentin-1 isoform X4

    3. XM_054339010.1XP_054194985.1  hemicentin-1 isoform X5

    4. XM_054339007.1XP_054194982.1  hemicentin-1 isoform X2

    5. XM_054339008.1XP_054194983.1  hemicentin-1 isoform X3