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HMCN2 Gene

protein-coding   GIFtS: 39
GCID: GC09P133029

Hemicentin 2

  Search for HMCN2
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
Hemicentin 21 2
hemicentin-22

External Ids:    HGNC: 212931   Entrez Gene: 2561582   Ensembl: ENSG000001483577   UniProtKB: Q8NDA23   

Export aliases for HMCN2 gene to outside databases

Previous GC identifers: GC09P130263 GC09P132213 GC09P133223 GC09P102707


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for HMCN2 Gene:
HMCN2 (hemicentin 2) is a protein-coding gene. GO annotations related to this gene include calcium ion binding. An important paralog of this gene is LTBP3.


(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 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence:
NC_018920.2  NC_000009.12  NT_008470.20  
Regulatory elements:
   Regulatory transcription factor binding sites in the HMCN2 gene promoter:
         Pax-5   RREB-1   p300   GATA-2   AREB6   CREB   PPAR-gamma1   CP2   PPAR-gamma2   Ik-1   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search Chromatin IP Primers for HMCN2

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat HMCN2


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 9q34.11   Ensembl cytogenetic band:  9q34.11   HGNC cytogenetic band: 9q34.11

HMCN2 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
HMCN2 gene location

GeneLoc information about chromosome 9         GeneLoc Exon Structure

GeneLoc location for GC09P133029:  view genomic region     (about GC identifiers)

Start:
133,046,882 bp from pter      End:
133,309,510 bp from pter
Size:
262,629 bases      Orientation:
plus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: HMCN2_HUMAN, Q8NDA2 (See protein sequence)
Recommended Name: Hemicentin-2 precursor  
Size: 5065 amino acids; 542605 Da
Sequence caution: Sequence=BAB85069.1; Type=Erroneous initiation; Note=Translation N-terminally extended;
Sequence=BAC04201.1; Type=Erroneous initiation; Note=Translation N-terminally extended; Sequence=EAW87931.1;
Type=Erroneous gene model prediction;
Secondary accessions: Q8N225 Q8TCI8
Alternative splicing: 3 isoforms:  Q8NDA2-1   Q8NDA2-2   Q8NDA2-3   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for HMCN2: NX_Q8NDA2

Explore proteomics data for HMCN2 at MOPED

Post-translational modifications: 

  • Glycosylation2 at Asn329, Asn346, Asn379, Asn478, Asn525, Asn547, Asn674, Asn1024, Asn1223, Asn1309,
                                 Asn1507, Asn1533, Asn1641, Asn1900, Asn2000, Asn2079, Asn2085, Asn2243, Asn2281, Asn2361 (see all 39)
  • Modification sites at PhosphoSitePlus

  • See HMCN2 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB


    ENSEMBL proteins: 
     ENSP00000389272   ENSP00000389821   ENSP00000413769   ENSP00000395966   ENSP00000387564  
     ENSP00000305590  

    HMCN2 Human Recombinant Protein Products:

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    Cloud-Clone Corp. CLIAs for HMCN2


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    HGNC Gene Families:
    ISET: Immunoglobulin superfamily / I-set domain containing
    IGD: Immunoglobulin superfamily / Immunoglobulin-like domain containing
    FBLN: Fibulins

    Selected InterPro protein domains (see all 16):
     IPR003598 Ig_sub2
     IPR000742 EG-like_dom
     IPR013098 Ig_I-set
     IPR009017 GFP
     IPR026823 cEGF

    Graphical View of Domain Structure for InterPro Entry Q8NDA2

    ProtoNet protein and cluster: Q8NDA2

    2 Blocks protein domains:
    IPB003598 Immunoglobulin C-2 type
    IPB013098 Immunoglobulin I-set


    UniProtKB/Swiss-Prot: HMCN2_HUMAN, Q8NDA2
    Similarity: Contains 5 EGF-like domains
    Similarity: Contains 42 Ig-like C2-type (immunoglobulin-like) domains
    Similarity: Contains 1 nidogen G2 beta-barrel domain
    Similarity: Contains 1 VWFA domain


    HMCN2 for domains           About GeneDecksing


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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         Gene Ontology (GO): 2 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005509calcium ion binding IEA--
    GO:0005515protein binding ----
         
    HMCN2 for ontologies           About GeneDecksing


    Phenotypes:
         2 GenomeRNAi human phenotypes for HMCN2:
     Decreased POU5F1-GFP protein e  Proliferating cells 

    Animal Models:
       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for HMCN2
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    Predesigned siRNA for gene silencing in human, mouse, rat HMCN2

    Gene Editing
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    Browse Sino Biological Human cDNA Clones
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for HMCN2
    Search Vector BioLabs for ready-to-use adenovirus/AAV for human, mouse, rat HMCN2

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    In Situ Assay
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for HMCN2


    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    HMCN2_HUMAN, Q8NDA2: Secreted, extracellular space, extracellular matrix (By similarity)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    cytosol2
    extracellular2
    nucleus2
    mitochondrion1
    plasma membrane1

    Gene Ontology (GO): 5 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005576extracellular region ----
    GO:0005578proteinaceous extracellular matrix IEA--
    GO:0005604basement membrane ----
    GO:0005938cell cortex ----
    GO:0030054cell junction ----

    HMCN2 for ontologies           About GeneDecksing


    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for HMCN2
    Interactions:

        Search GeneGlobe Interaction Network for HMCN2

    Gene Ontology (GO): 1 biological process term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0050896response to stimulus IEA--

    HMCN2 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for HMCN2



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, and/or QIAGEN )
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    REFSEQ mRNAs for HMCN2 gene: 
    NM_144655.1  

    Unigene Clusters for HMCN2:

    Hemicentin 2
    Hs.32194  [show with all ESTs], Hs.512559  [show with all ESTs]
    Unigene Representative Sequences: AL834139, AK128020
    9 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000415566 ENST00000420499 ENST00000442930 ENST00000462148 ENST00000455439
    ENST00000487727(uc004bzj.3) ENST00000480829 ENST00000428715 ENST00000302481(uc004bzl.3)

    miRNA
    Products:
         
    Block miRNA regulation of human, mouse, rat HMCN2 using miScript Target Protectors
    Search for qRT-PCR Assays for microRNAs that regulate HMCN2
    Browse SwitchGear 3'UTR luciferase reporter plasmids
    Inhib. RNA
    Products:
         
    Browse OriGene RNAi
    Predesigned siRNA for gene silencing in human, mouse, rat HMCN2
    Clone
    Products:
         
    Browse OriGene untagged/tagged cDNA clones in CMV expression vector
    OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
    GenScript: all cDNA clones in your preferred vector (see all 3): HMCN2 (XM_001715154)
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for HMCN2
    Search Vector BioLabs for ready-to-use adenovirus/AAV for human, mouse, rat HMCN2
    Primer
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    Browse OriGene qPCR
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      QuantiTect SYBR Green Assays in human, mouse, rat HMCN2
      QuantiFast Probe-based Assays in human, mouse, rat HMCN2

    Additional mRNA sequence: 

    AK128020.1 BC146865.1 

    8 DOTS entries:

    DT.40222092  DT.40241368  DT.110474  DT.95132814  DT.91848890  DT.99927682  DT.101971774  DT.121156263 

    1 AceView cDNA sequence:

    T11491 

    GeneLoc Exon Structure


    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    HMCN2 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: CTGGAGCCCG
    HMCN2 Expression
    About this image

    HMCN2 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    HMCN2 Protein Expression

    SOURCE GeneReport for Unigene clusters: Hs.32194 Hs.512559
        Custom PCR Arrays for HMCN2
    Primer
    Products:
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for HMCN2

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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    This gene was present in the common ancestor of animals.

    Orthologs for HMCN2 gene from Selected species (see all 11)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Hmcn21 , 5 hemicentin 21, 5 81.39(n)1
    81.12(a)1
      2 (21.81 cM)5
    6657001  XM_006498501.11  XP_006498564.11 
     313144155 
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia hmcn21 hemicentin 2 57.74(n)
    51.07(a)
      100490941  XM_002936183.2  XP_002936229.2 
    zebrafish
    (Danio rerio)
    Actinopterygii hmcn26
    hemicentin 2
    11(a)
    1 ↔ 1
    8(33554295-33633685) ENSDARG00000079327
    worm
    (Caenorhabditis elegans)
    Secernentea him-46
    Protein HIM-4, isoform a (him-4) mRNA, complete cd...
    3(a)
    1 → many
    X(9717626-9753764) WBGene00001863


    ENSEMBL Gene Tree for HMCN2 (if available)
    TreeFam Gene Tree for HMCN2 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for HMCN2 gene
    LTBP32  HMCN12  SCUBE32  FBLN52  MEGF62  EFEMP12  LTBP42  SCUBE12  
    EFEMP22  LTBP22  LTBP12  FBLN22  FBLN12  SCUBE22  
    Selected SIMAP similar genes for HMCN2 using alignment to 6 protein entries:     HMCN2_HUMAN (see all proteins) (see all similar genes):
    LOC392395    FBLN1    FGFR1    KIAA0992    MUSK    CRELD1
    SDK1    DKFZp762L185    DCC    ROBO3    FGFR3    IGDCC3
    LRIG3(NM_001136051)-ROS1    LRIG3(NM_153377)-ROS1    NCAM2    PRTG    ROBO2    LSAMP

    HMCN2 for paralogs           About GeneDecksing



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for HMCN2 (see all 2008)    About this table    
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 9 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs10066151,2
    C,F,Auntested1133320064(+) GGCCCA/C/TTCTAC 2 P syn18MN NA WA EA 550
    rs1513279661,2
    C--102711447(+) TTAGA-/GT    
       GCAGT
    AGTGC
    1 -- int10--------
    rs1480535221,2
    C--102718504(+) AAGGG-/AGGAT 
     GGATGGA
    TGGAT
    1 -- int10--------
    rs617489161,2
    C,F--102721989(+) TTGAGC/AAAGCC 2 /K /Q mis15Minor allele frequency- A:0.11NS CSA WA NA EU 869
    rs617488971,2
    C,F--102722015(+) GGGAGC/TTACCG 2 S syn16Minor allele frequency- T:0.12NS NA CSA WA EU 870
    rs112438751,2
    C,F,H--102732764(+) GGACCC/TGCTGA 2 P L mis120Minor allele frequency- T:0.11NS EA NA 2562
    rs342107731,2
    C--102785354(+) GTCCA-/ATTATAT 1 -- int10--------
    rs713873401,2
    C--133225336(+) CAGTG-/GTGCAG
    T
    /TGCAGTG
    GAACG
    1 -- int11NA 2
    rs1450433491,2
    C--133226117(+) AAAAA-/AAATATAT 1 -- cds10--------
    rs585223201,2
    C--133231452(+) CCCCCC/-TCCCT 1 -- int11Minor allele frequency- -:0.50CSA 2

    HapMap Linkage Disequilibrium report for HMCN2 (133046882 - 133296882 bp, first 250kb of HMCN2)

    Structural Variations
          Database of Genomic Variants (DGV) variations for HMCN2: --
    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing HMCN2
    DNA2.0 Custom Variant and Variant Library Synthesis for HMCN2

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    HMCN2 for disorders           About GeneDecksing

    Genetic Association Database (GAD): HMCN2
    Human Genome Epidemiology (HuGE) Navigator: HMCN2 (1 document)

    Export disorders for HMCN2 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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    PubMed articles for HMCN2 gene integrated from 10 sources:
    (articles sorted by number of sources associating them with HMCN2)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PubMed id 20379614)1, 4 Rose J.E....Uhl G.R. (Mol. Med. 2010)
    2. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (Nat. Genet. 2004)
    3. Genome-scale RNAi screen for host factors required for HIV replication. (PubMed id 18976975)1 Zhou H....Espeseth A.S. (amp 2008)
    4. Global analysis of host-pathogen interactions that regulate early-stage HIV-1 replication. (PubMed id 18854154)1 KAPnig R....Chanda S.K. (Cell 2008)
    5. The full-ORF clone resource of the German cDNA consortium. (PubMed id 17974005)2 Bechtel S.... Schupp I. (BMC Genomics 2007)
    6. DNA sequence and analysis of human chromosome 9. (PubMed id 15164053)2 Humphray S.J.... Dunham I. (Nature 2004)
    7. Distribution and evolution of von Willebrand/integrin A domains: widely dispersed domains with roles in cell adhesion and elsewhere. (PubMed id 12388743)1 Whittaker C.A. and Hynes R.O. (Mol. Biol. Cell 2002)
    8. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (Proc. Natl. Acad. Sci. U.S.A. 2002)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 256158 HGNC: 21293 AceView: DKFZp434P0216.1 Ensembl:ENSG00000148357 euGenes: HUgn256158
    ECgene: HMCN2 H-InvDB: HMCN2

    (According to HUGE)
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      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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    NameDescription
    PharmGKB entry for HMCN2 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for HMCN2 gene:
    Search GeneIP for patents involving HMCN2

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript, and ESI BIO, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
    Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
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