Aliases &
Descriptions
for HMCN1 gene
(According to
1HGNC,
2Entrez Gene,
3UniProtKB/Swiss-Prot,
4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc
, and/or 7Ensembl,
8miRBase)
About This Section
|
| Aliases & Descriptions |
|---|
| hemicentin 11 2 | | age-related macular degeneration 1 (senile macular degeneration)1 | | FIBL61 2 3 5 | | fibulin-62 | | FIBL-61 2 3 | | hemicentin-12 | | FBLN61 2 5 | | Fibulin-63 | | ARMD12 5 | | |
Export aliases for HMCN1 gene to outside databasesPrevious GC identifers: GC01P182436 GC01P183970 GC01P185703 |
Summaries
for HMCN1 gene(According to Entrez Gene,
Tocris Bioscience,
Wikipedia's
Gene Wiki,
UniProtKB/Swiss-Prot,
and/or
UniProtKB/TrEMBL)
About This Section
|
Entrez Gene summary for HMCN1:
This gene encodes a large extracellular member of the immunoglobulin superfamily. A similar protein in C. elegans formslong, fine tracks at specific extracellular sites that are involved in many processes such as stabilization of thegermline syncytium, anchorage of mechanosensory neurons to the epidermis, and organization of hemidesmosomes in theepidermis. Mutations in this gene may be associated with age-related macular degeneration. (provided by RefSeq)
Gene Wiki entry for HMCN1 |
Genomic Views
for HMCN1 gene
(According to
GeneLoc and/or
HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to
UCSC (hg19) and
Ensembl (release 60),
Regulatory elements and Epigenetics data according to
Qiagen and/or
SABiosciences)
About This Section
|
Regulatory elements:
 SABiosciences Regulatory transcription factor binding sites in the HMCN1 gene promoter:
FOXD1 FOXF2 GATA-3 GATA-1 GATA-2 MEF-2A SRF ISGF-3 FOXJ2 (long isoform) E47
Other transcription factors
Search SABiosciences Chromatin IP Primers for HMCN1
Epigenetics:
|  | QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays  |
Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track
Entrez Gene cytogenetic band: 1q25.3-q31.1 Ensembl cytogenetic band: 1q25.3 HGNC cytogenetic band: 1q25.3-q31.1HMCN1 Gene in genomic location: bands according to Ensembl, locations according to
 (and/or Entrez Gene and/or Ensembl if different)
GeneLoc gene densities for chromosome 1 GeneLoc Exon Structure GeneLoc location for GC01P156939: view genomic region
(about GC identifiers)
Start:
|
156,938,491 bp from pter |
End:
|
157,394,637 bp from pter |
Size:
|
456,147 bases |
Orientation:
|
plus strand |
1 alternative location:
| Chr1+ 185,703,683-186,160,085 |
RefSeq DNA sequence:- NC_000001.10 NT_004487.19
|
Proteins
for HMCN1 gene
(According to
1UniProtKB,
neXtProt,
and/or Ensembl,
Phosphorylation sites according to 2Phosphosite,
RefSeq according to NCBI,
PDB rendering according to OCA and/or Proteopedia,
Recombinant Proteins
from
Millipore,
Sigma-Aldrich,
R&D Systems,
GenScript,
Enzo Life Sciences,
OriGene,
Novus Biologicals,
Sino Biological, and/or
ProSpec,
Biochemical Assays by
Millipore,
Sigma-Aldrich,
R&D Systems,
OriGene,
GenScript,
Cell Signaling Technology,
Enzo Life Sciences, and/or
Uscn,
Ontologies according to Gene
Ontology Consortium 01 Dec 2010 and
Entrez Gene,
Antibodies by
Millipore,
Sigma-Aldrich,
R&D Systems,
GenScript,
Cell Signaling Technology,
OriGene,
Novus Biologicals, and/or
Epitomics)
About This Section
|
UniProtKB/Swiss-Prot: HMCN1_HUMAN, Q96RW7 (See
protein sequence)Recommended Name: Hemicentin-1 precursor Size: 5635 amino acids; 613390 Da
Subcellular location: Secreted, extracellular space, extracellular matrix, basement membrane (By similarity)
Sequence caution: Sequence=BAB71154.1; Type=Frameshift; Positions=657; Sequence=BAB71216.1; Type=Erroneous initiation;
Secondary accessions: A6NGE3 Q5TYR7 Q96DN3 Q96DN8 Q96SC3Alternative splicing: 3 isoforms: Q96RW7-1 Q96RW7-2 Q96RW7-3 Explore the universe of human proteins at neXtProt for HMCN1: NX_Q96RW7
Post-translational modifications:
View phosphorylation sites using PhosphoSite2
REFSEQ proteins: NP_114141.2
ENSEMBL proteins: ENSP00000271588 ENSP00000406205 ENSP00000356462
Human Recombinant Proteins
4 Gene Ontology (GO) cellular component terms (GO ID links to tree view): About this table
HMCN1 for ontologies About GeneDecksing
Antibodies for HMCN1:
Assays for HMCN1: |
Protein
Domains/
Families
for HMCN1 gene(According to InterPro, ProtoNet,
UniProtKB, and/or BLOCKS,
Sets of similar genes according to GeneDecks)
About This Section
|
HMCN1 for domains About GeneDecksing
5/17 InterPro domains/families (see all 17):Graphical View of Domain Structure for InterPro Entry Q96RW7ProtoNet protein and cluster: Q96RW7 5/6 Blocks protein families (see all 6): IPB000152 Aspartic acid and asparagine hydroxylation site IPB000875 Cecropin IPB001881 EGF-like calcium-binding IPB002126 Cadherin IPB003598 Immunoglobulin C-2 type
UniProtKB/Swiss-Prot: HMCN1_HUMAN, Q96RW7Similarity: Contains 7 EGF-like domainsSimilarity: Contains 44 Ig-like C2-type (immunoglobulin-like) domainsSimilarity: Contains 1 nidogen G2 beta-barrel domainSimilarity: Contains 6 TSP type-1 domainsSimilarity: Contains 1 VWFA domain |
Gene Function
for HMCN1 gene
(According to UniProtKB,
IUBMB,and/or
Genatlas, Animal models from MGI Dec 24 2010,
shRNA from
OriGene,
Sigma-Aldrich,
RNAi from
Millipore,
siRNAs from
Sigma-Aldrich,
OriGene,
Qiagen,
Super-pooled esiRNAs from Sigma-Aldrich,
microRNA from Sigma-Aldrich,
Qiagen,
SABiosciences,
Clones from Millipore,
Sigma-Aldrich,
OriGene,
GenScript,
Sino Biological,
Cell Lines from GenScript,
Ontologies according to Gene Ontology Consortium 01 Dec 2010 via
Entrez Gene.)
About This Section
|
2 Gene Ontology (GO) molecular function terms (GO ID links to tree view): | GO ID | Qualified GO term | Evidence | PubMed IDs |
|---|
| GO:0004222 | metalloendopeptidase activity |
-- | -- | | GO:0005509 | calcium ion binding |
IEA | -- |
About this table
HMCN1 for ontologies About GeneDecksing
|
Pathways & Interactions
for HMCN1 gene
(Pathways according to
Millipore,
Cell Signaling Technology,
Sigma-Aldrich,
KEGG
and/or UniProtKB,
Sets of similar genes according to GeneDecks,
PCR Arrays from
SABiosciences,
Proteins Network according to
SABiosciences,
Sigma-Aldrich,
Interactions according to 1UniProtKB,
2MINT, and/or
3STRING,
with links to IntAct and
Ensembl,
Ontologies according to Gene Ontology Consortium 01 Dec 2010 via
Entrez Gene).
About This Section
|
SABiosciences Custom Pathway-Focused PCR Arrays for HMCN1
SABiosciences Gene Network CentralTM Interacting Genes and Proteins Network for HMCN1
5 Gene Ontology (GO) biological process terms (GO ID links to tree view): About this table
HMCN1 for ontologies About GeneDecksing
|
Drugs & Compounds
for HMCN1 gene(Chemical Compounds according to UniProtKB, Enzo Life Sciences,
Sigma-Aldrich, Tocris Bioscience, and/or
Novoseek and Drugs according to
Enzo Life Sciences and/or
PharmGKB)
About This Section
|
 Browse Tocris compounds for HMCN1
|
Transcripts
for HMCN1 gene(GenBank/EMBL/DDBJ Accessions according to
Unigene
(Build 228 Homo sapiens; Dec 8 2010) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or
AceView,
transcript ids from Ensembl
with links to UCSC,
non coding RNAs according to
RNAdb,
ESTs according to GeneTide,
exon structure from GeneLoc,
alternative splicing isoforms according to ASD and/or
ECgene,
RNAi Products from
Millipore,
siRNAs from
Sigma-Aldrich,
OriGene,
Qiagen,
Super-pooled esiRNAs from Sigma-Aldrich,
shRNA from
Sigma-Aldrich,
OriGene,
microRNA from Sigma-Aldrich,
Qiagen,
SABiosciences,
Tagged/untagged cDNA clones from
OriGene,
Sigma-Aldrich,
GenScript,
Primers from
OriGene and/or
SABiosciences)
About This Section
|
REFSEQ mRNAs for HMCN1 gene: NM_031935.2 Additional cDNA sequence: AF156100.1 AJ306906.1 AK027344.1 AK056336.1 AK056557.1 AK096452.1 AL833232.1 BC139908.1 6 DOTS entries: DT.426313 DT.121423978 DT.95113331 DT.100681143 DT.91664556 DT.97825451 24/49 AceView cDNA sequences (see all 49): BQ722715 AK096452 BQ425569 AK056336 BU622124 AL833232 AJ306906 AK027344 NM_031935 D62730 CB999578 CA420501 CD511728 BG149239 BX503106 AI298034 AI679767 AK056557 BE328248 BF356611 AF156100 AI681770 BQ006694 BE043096
 highest scoring ESTs for HMCN1:AI681770 AA135903 AA379823 AF156100 AI298034 AI679767 AJ306906 AK027344 AK096452 AL833232 Unigene Cluster for HMCN1: Hemicentin 1 Hs.58877 [show with all ESTs]Unigene Representative Sequence: NM_031935
GeneLoc Exon Structure
2 Alternative Splicing Database (ASD) splice patterns (SP) for HMCN1
| ExUns: | 1 | ^ | 2 | ^ | 3 | ^ | 4 | ^ | 5 | ^ | 6 | ^ | 7 | ^ | 8 | ^ | 9 | ^ | 10 | ^ | 11 | ^ | 12 | ^ | 13 | ^ | 14 | ^ | 15 | ^ | 16 | ^ | 17 | ^ | 18 | ^ | 19 | ^ | 20 | ^ | 21 | ^ | 22 | ^ | 23 | ^ | 24 | ^ | 25 | ^ | 26 | ^ |
|---|
|
| SP1: | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
| SP2: | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
| ExUns: | 27 | ^ | 28 | ^ | 29 | ^ | 30 | ^ | 31 | ^ | 32 | ^ | 33a | · | 33b | ^ | 34 | ^ | 35 | ^ | 36 | ^ | 37 | ^ | 38 | ^ | 39 | ^ | 40 | ^ | 41 | ^ | 42 | ^ | 43 | ^ | 44 | ^ | 45 | ^ | 46 | ^ | 47 | ^ | 48 | ^ | 49a | · | 49b |
|---|
|
| SP1: | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
| SP2: | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - | | | | | | | | | |
About this scheme
ECgene alternative splicing isoforms for HMCN1
6 Ensembl transcripts including schematic representations, and UCSC links where relevant: ENST00000271588(uc001grq.1) ENST00000485744(uc001grr.1) ENST00000493413
ENST00000475585 ENST00000414277 ENST00000367492(uc001grs.1)
|
Expression
for HMCN1 gene
(Experimental results according to
1GeneNote
and GNF BioGPS,
probe sets-to-genes annotations according to
2GeneAnnot ,
3GeneTide ,
Sets of similar genes according to GeneDecks,
Electronic Northern calculations according to data from
UniGene (Build 228 Homo sapiens),
SAGE tags according to
CGAP,
plus additional links to
SOURCE, and/or
GNF
BioGPS, and/or
EXPOLDB, and/or
UniProtKB,
Primers from
OriGene and/or
SABiosciences
)
About This Section
| HMCN1 expression in normal and diseased human tissues
1 / 2 / 3 3 probe-sets matching HMCN1 gene
Affymetrix
probe-set |
Array |
GeneAnnot data |
GeneNote data |
GeneTide data |
| # genes |
Sensitivity |
Specificity |
Correlation |
Length |
Gb_Accession |
Consensus |
Uniqueness |
Score |
Rank |
| 83173_at2, 3
|
U95-E |
1 |
0.50 |
1.00 |
1.00 |
1.00 |
AI681770 |
1.00 |
1.00 |
1.00 |
1 |
| 235944_at2, 3
|
U133-B |
1 |
0.64 |
1.00 |
-- |
-- |
BF446673 |
0.80 |
1.00 |
0.91 |
1 |
| 235944_at2
|
U133Plus2 |
1 |
0.64 |
1.00 |
-- |
-- |
-- |
-- |
-- |
-- |
-- |
About this table
HMCN1 for expression About GeneDecksing
Data from
Genenote
(Publications) and GNF BioGPS
About these images
About these images
CGAP SAGE TAG: GTGGTAATAG
SOURCE GeneReport for Unigene cluster: Hs.58877
UniProtKB/Swiss-Prot: HMCN1_HUMAN, Q96RW7Tissue specificity: Isoform 1 and isoform 2 are expressed in skin fibroblasts and retinal pigment epithelium (RPE)cells
SABiosciences Custom PCR Arrays for HMCN1
|
Orthologs
for HMCN1 gene
(Orthologs according to
1,2HomoloGene (2older version, for species not in 1newer version),
3euGenes,
4SGD
and/or
5MGI Dec 24 2010,
with possible further links to
Flybase
and/or
WormBase,
Gene Trees according to Ensembl)
About This Section
|
Orthologs for HMCN1 gene from 5/8 species (see all 8)
About this table Species with no ortholog for HMCN1
ENSEMBL Gene Tree for HMCN1 (if available) |
Paralogs
for HMCN1 gene(Paralogs according to 1HomoloGene
and 2Ensembl, Pseudogenes according to 3Pseudogene.org)
About This Section
| Paralogs for HMCN1 gene
- VCAM12 IGSF102 HMCN22 HSPG22 MXRA52 LOC1002892002
HMCN1 for paralogs About GeneDecksing
|
Genomic Variants
for HMCN1 gene(SNPs according to the
1NCBI SNP Database,
2Ensembl,
3PupaSUITE, and
UniProtKB,
Linkage Disequilibrium by HapMap,
Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Resequencing Primers from Qiagen)
About This Section
|
| Genomic Data | Transcription Related Data | Allele Frequencies | | SNP ID | Valid | Chr 1 pos | Sequence | Recs | AA
Chg | Type | More | Recs | Allele
freq | Pop | Total
sample | More |
|---|
About this tableHapMap Linkage Disequilibrium images for HMCN1 (up to first 250kb)
Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
Database of Genomic Variants (DGV): 12 variations for HMCN1
9 CNVs: 97584 97583 65402 74814 74811 97585 84708 43748 84709
3 Indels: 74813 74812 44478 | | QIAGEN SeqTarget long-range PCR primers for resequencing HMCN1 |
|
Disorders & Mutations
for HMCN1 gene
(in which this Gene is Involved, According to
OMIM, UniProtKB,
PharmGKB,
Genatlas, GeneTests,
Blood group antigen gene mutations by BGMUT,
LSDB, HGMD, GAD,
HuGE Navigator,
and/or TGDB.)
About This Section
|
HMCN1 for disorders About GeneDecksing
OMIM: 608548 disorders: 603075 UniProtKB/Swiss-Prot: HMCN1_HUMAN, Q96RW7
Defects in HMCN1 are a cause of age-related macular degeneration type 1 (ARMD1) [MIM:603075]. ARMD is amultifactorial eye disease and the most common cause of irreversible vision loss in the developed world. In mostpatients, the disease is manifest as ophthalmoscopically visible yellowish accumulations of protein and lipid (knownas drusen) that lie beneath the retinal pigment epithelium and within an elastin-containing structure known as BruchmembraneHuman Gene Mutation Database (HGMD): HMCN1
Genetic Association Database (GAD): HMCN1
Human Genome Epidemiology (HuGE) Navigator: HMCN1 (9 documents)
Export disorders and mutations for HMCN1 gene to outside databases
|
Medical News
for HMCN1 gene(Possibly Related Articles in
Doctor's Guide)
About This Section
| -- |
Publications
for HMCN1 gene (in
PubMed.
Associations of this gene to articles via
1Entrez Gene,
2UniProtKB/Swiss-Prot,
3HGNC,
4GAD,
5PharmGKB,
6UniProtKB/TrEMBL, and/or
7Novoseek)
About This Section
|
10/26 PubMed articles for HMCN1 gene, integrated from 7 sources (see all 26):
(articles sorted by number of sources associating them with HMCN1)- Analysis of the ARMD1 locus: evidence that a mutation in hemicentin-1 is associated with age-related macular degeneration in a large family. (PubMed id 14570714)1, 2, 7 Schultz D.W.... Acott T.S. (2003)
- Evaluation of the ARMD1 locus on 1q25-31 in patients with age-related maculopathy: genetic variation in laminin genes and in exon 104 of HEMICENTIN-1. (PubMed id 15370542)1, 4, 7 Hayashi M....Allikmets R. (2004)
- The DNA sequence and biological annotation of human chromosome 1. (PubMed id 16710414)1, 2 Gregory S.G.... Bentley D.R. (2006)
- Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (2004)
- A novel diagnostic test detects a low frequency of the hemicentin Gln5345Arg variant among Northern Irish age related macular degeneration patients. (PubMed id 15467524)1, 4 McKay G.J....Simpson D.A. (2004)
- Hemicentin, a conserved extracellular member of the immunoglobulin superfamily, organizes epithelial and other cell attachments into oriented line-shaped junctions. (PubMed id 11222143)1, 3 Vogel B.E. and Hedgecock E.M. (2001)
- Case-control genetic association study of fibulin-6 (FBLN6 or HMCN1) variants in age-related macular degeneration (AMD). (PubMed id 17216616)1, 7 Fisher S.A....Weber B.H. (2007)
- Fibulin-6 expression and anoikis in human salivary gland epithelial cells: implications in Sjogren's syndrome. (PubMed id 19190085)1, 7 Sisto M....Lisi S. (2009)
- Analysis of variants in the complement factor H, the elongation of very long chain fatty acids-like 4 and the hemicentin 1 genes of age-related macular degeneration in the Finnish population. (PubMed id 16885922)1, 7 Seitsonen S....Jarvela I. (2006)
- Analysis of Hemicentin-1, hOgg1, and E-selectin single nucleotide polymorphisms in age-related macular degeneration. (PubMed id 17057786)1, 7 Bojanowski C.M....Chan C.C. (2005)
|
External Searches for HMCN1 gene
(in PubMed,
OMIM, and NCBI Bookshelf)
About This Section
|
|
Genome Databases showing HMCN1 gene
(According to
Entrez Gene,
HGNC,
AceView,
euGenes,
Ensembl,
miRBase,
ECgene,
Kegg,
and/or
H-InvDB)
About This Section
|
|
Other Databases showing HMCN1 gene
(According to HUGE)
About This Section
| -- |
Specialized Databases showing HMCN1 gene(According to ATLAS, HORDE, IMGT, MTDB, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
About This Section
|
| Name | Description |
| GeneReviews | http://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/HMCN1 |
|
| | |
About This Section
| Patent Information for HMCN1 gene:
Search GeneIP for patents involving HMCN1
GeneCards and IP:
Japan Patent Office Licenses GeneCards European Patent Office Licenses GeneCards Improving the IP Search
|
Products
for HMCN1 gene(Antibodies, recombinant proteins, and assays by Millipore, Sigma-Aldrich, R&D Systems, Qiagen, GenScript, Cell Signaling Technology, SABiosciences, Novus Biologicals, Epitomics, ProSpec, Uscn,
Clones available from Millipore, Sigma-Aldrich, OriGene, GenScript, Sino Biological, PCR Arrays from SABiosciences, Drugs and/or compounds by Sigma-Aldrich, Tocris Bioscience, and/or
Enzo Life Sciences)
About This Section
|
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 |  |  |  | |
| |  | Search Tocris compounds for HMCN1 |
| |  |  |  |  | | | | |
 | | | ELISAs and CLIAs for HMCN1 |
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