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HMCN1 hemicentin 1 [ Homo sapiens (human) ]

Gene ID: 83872, updated on 13-Feb-2019

Summary

Official Symbol
HMCN1provided by HGNC
Official Full Name
hemicentin 1provided by HGNC
Primary source
HGNC:HGNC:19194
See related
Ensembl:ENSG00000143341 MIM:608548
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

Genomic context

See HMCN1 in Genome Data Viewer
Location:
1q25.3-q31.1
Exon count:
107
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 1 NC_000001.11 (185734525..186190953)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (185703683..186160085)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107985239 Neighboring gene long intergenic non-protein coding RNA 1350 Neighboring gene uncharacterized GS1-204I12.4 Neighboring gene uncharacterized LOC105371654 Neighboring gene RNA, U6 small nuclear 1240, pseudogene Neighboring gene proteoglycan 4 Neighboring gene translocated promoter region, nuclear basket protein Neighboring gene odr-4 GPCR localization factor homolog Neighboring gene oculomedin

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 FunctionsWhat's a GeneRIF?

Phenotypes

Associated conditions

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

NHGRI GWAS Catalog

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

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
calcium ion binding IEA
Inferred from Electronic Annotation
more info
 
cell adhesion molecule binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
extracellular matrix structural constituent IEA
Inferred from Electronic Annotation
more info
PubMed 
extracellular matrix structural constituent RCA
inferred from Reviewed Computational Analysis
more info
PubMed 
protein homodimerization activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
signaling receptor activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Process Evidence Code Pubs
cell cycle IEA
Inferred from Electronic Annotation
more info
 
cell division IEA
Inferred from Electronic Annotation
more info
 
heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
homophilic cell adhesion via plasma membrane adhesion molecules IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
response to bacterium IEA
Inferred from Electronic Annotation
more info
 
visual perception IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
basement membrane IEA
Inferred from Electronic Annotation
more info
 
cell cortex IEA
Inferred from Electronic Annotation
more info
 
cell-cell adherens junction IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cleavage furrow IEA
Inferred from Electronic Annotation
more info
 
collagen-containing extracellular matrix HDA PubMed 
colocalizes_with collagen-containing extracellular matrix TAS
Traceable Author Statement
more info
PubMed 
extracellular exosome HDA PubMed 

General protein information

Preferred Names
hemicentin-1
Names
LOC100507250/HMCN1 fusion
fibulin-6

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_011841.1 RefSeqGene

    Range
    5001..461403
    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
    Q96RW7
    Related
    ENSP00000271588.4, ENST00000271588.8
    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: Homo sapiens Annotation Release 109

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p12 Primary Assembly

    Range
    185734525..186190953
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011510041.3XP_011508343.1  hemicentin-1 isoform X4

    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
  2. XM_024450118.1XP_024305886.1  hemicentin-1 isoform X3

    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_011510038.3XP_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
  4. XM_017002437.1XP_016857926.1  hemicentin-1 isoform X2

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