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TNMD Gene

protein-coding   GIFtS: 50
GCID: GC0XP099839

Tenomodulin

  See TNMD-related diseases
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
tenomodulin1 2     BRICD42
CHM1L2 3 5     chondromodulin-IB2
BRICHOS Domain Containing 41 2     myodulin2
Chondromodulin-1-Like Protein2 3     tendin2
Chondromodulin-I-Like Protein2 3     ChM1L3
hChM1L2 3     Myodulin3
hTeM2 3     TeM3
TEM2 5     Tendin3

External Ids:    HGNC: 177571   Entrez Gene: 641022   Ensembl: ENSG000000000057   OMIM: 3004595   UniProtKB: Q9H2S63   

Export aliases for TNMD gene to outside databases

Previous GC identifers: GC0XP095121 GC0XP096800 GC0XP097875 GC0XP098611 GC0XP099645 GC0XP089639


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for TNMD Gene:
This gene encodes a protein that is related to chondromodulin-I, which is a cartilage-specific glycoprotein that
functions to stimulate chondrocyte growth and to inhibit tube formation of endothelial cells. This protein is
also an angiogenesis inhibitor. Genetic variation in this gene is associated with a risk for type 2 diabetes,
central obesity and serum levels of systemic immune mediators in a body size-dependent manner. This gene is also
a candidate gene for age-related macular degeneration, though a direct link has yet to be demonstrated. (provided
by RefSeq, Sep 2009)

GeneCards Summary for TNMD Gene:
TNMD (tenomodulin) is a protein-coding gene. Diseases associated with TNMD include mitral valve insufficiency, and obesity. An important paralog of this gene is LECT1.

UniProtKB/Swiss-Prot: TNMD_HUMAN, Q9H2S6
Function: May be an angiogenesis inhibitor

Gene Wiki entry for TNMD 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 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:
NC_000023.10  NT_011651.18  NC_018934.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the TNMD gene promoter:
         TBP   GR-beta   Nkx2-5   Tal-1beta   E47   HNF-1A   HNF-1   TFIID   c-Myb   GR-alpha   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidTNMD promoter sequence
   Search Chromatin IP Primers for TNMD

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


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

Entrez Gene cytogenetic band: Xq21.33-q23   Ensembl cytogenetic band:  Xq22.1   HGNC cytogenetic band: Xq21.33-q23

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

GeneLoc information about chromosome X         GeneLoc Exon Structure

GeneLoc location for GC0XP099839:  view genomic region     (about GC identifiers)

Start:
99,839,790 bp from pter      End:
99,854,882 bp from pter
Size:
15,093 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, Cloud-Clone Corp., eBioscience, and/or antibodies-online,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., eBioscience, and/or antibodies-online, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, Cloud-Clone Corp, antibodies-online, and/or others.)
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UniProtKB/Swiss-Prot: TNMD_HUMAN, Q9H2S6 (See protein sequence)
Recommended Name: Tenomodulin  
Size: 317 amino acids; 37130 Da
Secondary accessions: Q9HBX0 Q9UJG0

Explore the universe of human proteins at neXtProt for TNMD: NX_Q9H2S6

Explore proteomics data for TNMD at MOPED

Post-translational modifications: 

  • Glycosylation2 at Asn94, Asn180

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

    REFSEQ proteins: NP_071427.2  
    ENSEMBL proteins: 
     ENSP00000362122  

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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    HGNC Gene Families:
    BRICD: BRICHOS domain containing

    1 InterPro protein domain:
     IPR007084 BRICHOS_dom

    Graphical View of Domain Structure for InterPro Entry Q9H2S6

    ProtoNet protein and cluster: Q9H2S6

    1 Blocks protein domain: IPB007084 BRICHOS domain

    UniProtKB/Swiss-Prot: TNMD_HUMAN, Q9H2S6
    Similarity: Belongs to the chondromodulin-1 family
    Similarity: Contains 1 BRICHOS domain


    Find genes that share domains with TNMD           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, 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, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: TNMD_HUMAN, Q9H2S6
    Function: May be an angiogenesis inhibitor

         Gene Ontology (GO): 1 molecular function term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0008061chitin binding ----
         
    Find genes that share ontologies with TNMD           About GenesLikeMe


    Phenotypes:
         3 MGI mutant phenotypes (inferred from 1 allele(MGI details for Tnmd):
     muscle  skeleton  vision/eye 

    Find genes that share phenotypes with TNMD           About GenesLikeMe

    Animal Models:
         MGI mouse knock-out Tnmdtm1Ref for TNMD

       genOway: Develop your customized and physiologically relevant rodent model for TNMD

    miRNA
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    2 qRT-PCR Assays for microRNAs that regulate TNMD:
    hsa-miR-3668 hsa-miR-664
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    Inhib. RNA
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    (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
    TNMD_HUMAN, Q9H2S6: Membrane; Single-pass type II membrane protein (Potential)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    plasma membrane3
    extracellular2
    cytosol1
    mitochondrion1
    nucleus1
    peroxisome1

    Gene Ontology (GO): 1 cellular component term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0016021integral component of membrane IEA--

    Find genes that share ontologies with TNMD           About GenesLikeMe


    (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 TNMD
    Interactions:

        Search GeneGlobe Interaction Network for TNMD

    Gene Ontology (GO): 5 biological process terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0001886endothelial cell morphogenesis IEA--
    GO:0001937negative regulation of endothelial cell proliferation IEA--
    GO:0016525negative regulation of angiogenesis IEA--
    GO:0035990tendon cell differentiation IEA--
    GO:0071773cellular response to BMP stimulus IEA--

    Find genes that share ontologies with TNMD           About GenesLikeMe



    (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 TNMD



    (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, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    REFSEQ mRNAs for TNMD gene: 
    NM_022144.2  

    Unigene Cluster for TNMD:

    Tenomodulin
    Hs.132957  [show with all ESTs]
    Unigene Representative Sequence: NM_022144
    2 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000373031(uc004efy.4 uc004efz.2) ENST00000485971
    miRNA
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    2 qRT-PCR Assays for microRNAs that regulate TNMD:
    hsa-miR-3668 hsa-miR-664
    SwitchGear 3'UTR luciferase reporter plasmidTNMD 3' UTR sequence
    Inhib. RNA
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    Additional mRNA sequence: 

    AB055421.1 AF191770.1 AF234259.1 AF291656.1 AY358706.1 

    3 DOTS entries:

    DT.405245  DT.99997264  DT.40129518 

    24 AceView cDNA sequences:

    BX104255 AF291656 BC034030 AY358706 BQ934226 AB055421 AI146280 AF234259 
    CD103859 AI039039 BF439260 CB114632 AI147044 AF191770 NM_022144 AI123839 
    AA297231 CD512100 AA236166 T12180 AA236692 AW962409 AA453695 BF679243 

    GeneLoc Exon Structure

    3 Alternative Splicing Database (ASD) splice patterns (SP) for TNMD    About this scheme

    ExUns: 1a · 1b ^ 2 ^ 3a · 3b ^ 4 ^ 5 ^ 6a · 6b
    SP1:                    -                                 
    SP2:                    -                                 
    SP3:                                                      


    ECgene alternative splicing isoforms for TNMD

    (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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    TNMD expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: CTATTCAATG
    TNMD Expression
    About this image


    TNMD expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 9) fully expand
     
     Tendon & Ligament (Muscoskeletal System)    fully expand to see all 4 entries
             Early Tenocyte Cells Limb Tendon Primordia
     
     Bone (Muscoskeletal System)    fully expand to see all 5 entries
             Endochondral Facial Bones
     
     Tendon & Ligament
             Cranial Tendons Cells Branchial Arch 1
     
     Head Mesenchyme (Muscoskeletal System)
             Cranial Tendons Cells Branchial Arch 1
     
     Inner Cell Mass (Early Embryonic Tissues)    fully expand to see all 2 entries
             Human embryonic stem cells (family)
    TNMD Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    TNMD Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.132957
        Custom PCR Arrays for TNMD
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    In Situ
    Assay Products:
     

     
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    (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 chordates.

    Orthologs for TNMD gene from Selected species (see all 10)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Tnmd1 , 5 tenomodulin1, 5 91.59(n)1
    96.21(a)1
      X (55.47 cM)5
    641031  NM_022322.21  NP_071717.11 
     1338509805 
    chicken
    (Gallus gallus)
    Aves TNMD1 tenomodulin 62.99(n)
    62.15(a)
      404530  NM_206985.2  NP_996868.1 
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia LOC1017313751 tenomodulin-like 64.36(n)
    57.57(a)
      101731375  XM_004919194.1  XP_004919251.1 
    zebrafish
    (Danio rerio)
    Actinopterygii tnmd1 tenomodulin 55.17(n)
    44.6(a)
      556984  NM_001114413.1  NP_001107885.1 


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

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for TNMD gene
    LECT12  
    1 SIMAP similar gene for TNMD using alignment to 1 protein entry:     TNMD_HUMAN:
    LECT1

    Find genes that share paralogs with TNMD           About GenesLikeMe



    (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 TNMD (see all 254)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr X posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs78905861,2
    C,F,A,H--99803848(+) CCATCA/GCTGTA 1 -- us2k125Minor allele frequency- G:0.70NS EA NA WA CSA 2539
    rs9324371,2
    C,F,A,H--99803898(+) AAGTCG/CAGATC 1 -- us2k120Minor allele frequency- C:0.49NS EA NA WA CSA 2156
    rs1900625221,2
    --99804010(+) TCTTAA/GAAAGA 1 -- us2k10--------
    rs1383711881,2
    C--99804092(+) CTCAAC/TTTAAA 1 -- us2k10--------
    rs1827118431,2
    --99804309(+) ATAACG/TAATTC 1 -- us2k10--------
    rs1428585881,2
    C--99804323(+) TCGGGA/TTATAT 1 -- us2k10--------
    rs1460802691,2
    C--99804635(+) CCTCAC/TATTTT 1 -- us2k10--------
    rs1852777591,2
    --99805217(+) GGCCTG/TGAAAT 1 -- us2k10--------
    rs1484596921,2
    C--99805320(+) GTCTGC/TGTAAA 1 -- us2k10--------
    rs1908892151,2
    --99805430(+) ATGAAA/GAGAGA 1 -- us2k10--------

    HapMap Linkage Disequilibrium report for TNMD (99839790 - 99854882 bp)

    Structural Variations
          Database of Genomic Variants (DGV) variations for TNMD: --
    Locus Specific Mutation Databases (LSDB): TNMD

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing TNMD
    DNA2.0 Custom Variant and Variant Library Synthesis for TNMD

    (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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    OMIM gene information: 300459    OMIM disorders: --

    2 diseases for TNMD:    
    About MalaCards
    mitral valve insufficiency    obesity

    1 disease from the University of Copenhagen DISEASES database for TNMD:
    Mitral valve insufficiency

    Find genes that share disorders with TNMD           About GenesLikeMe

    Genetic Association Database (GAD): TNMD
    Human Genome Epidemiology (HuGE) Navigator: TNMD (4 documents)

    Export disorders for TNMD 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 TNMD gene, integrated from 10 sources (see all 31):
    (articles sorted by number of sources associating them with TNMD)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Single nucleotide polymorphisms of the tenomodulin gene (TNMD) in age-related macular degeneration. (PubMed id 19381347)1, 4, 9 Tolppanen A.M....Pulkkinen L. (Mol. Vis. 2009)
    2. The genetic variation of the tenomodulin gene (TNMD) is associated with serum levels of systemic immune mediators--the Finnish Diabetes Prevention Study. (PubMed id 18580688)1, 4, 9 Tolppanen A.M....Uusitupa M. (Genet. Med. 2008)
    3. A novel gene, tendin, is strongly expressed in tendons and ligaments and shows high homology with chondromodulin-I. (PubMed id 11357195)1, 2, 9 Brandau O.... Aszodi A. (Dev. Dyn. 2001)
    4. The genetic variation in the tenomodulin gene is associated with serum total and LDL cholesterol in a body size-dependent manner. (PubMed id 18982016)1, 4, 9 Tolppanen A.M....Kuusisto J. (Int J Obes (Lond) 2008)
    5. Tenomodulin variants, APOE and Alzheimer's disease in a Finnish case-control cohort. (PubMed id 19524323)1, 4 Tolppanen A.M....Soininen H. (Neurobiol. Aging 2011)
    6. The DNA sequence of the human X chromosome. (PubMed id 15772651)1, 2 Ross M.T.... Bentley D.R. (Nature 2005)
    7. The secreted protein discovery initiative (SPDI), a large-scale effort to identify novel human secreted and transmembrane proteins: a bioinformatics assessment. (PubMed id 12975309)1, 2 Clark H.F.... Gray A.M. (Genome Res. 2003)
    8. Molecular cloning and characterization of ChM1L, a novel membrane molecule similar to chondromodulin-I. (PubMed id 11162640)1, 2 Yamana K.... Kiyoki M. (Biochem. Biophys. Res. Commun. 2001)
    9. Molecular cloning of tenomodulin, a novel chondromodulin-I related gene. (PubMed id 11162673)1, 2 Shukunami C.... Hiraki Y. (Biochem. Biophys. Res. Commun. 2001)
    10. Tenomodulin is highly expressed in adipose tissue, increased in obesity, and down-regulated during diet-induced weight loss. (PubMed id 19602561)1, 9 Saiki A....Carlsson L.M. (J. Clin. Endocrinol. Metab. 2009)

    (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: 64102 HGNC: 17757 AceView: TNMD Ensembl:ENSG00000000005 euGenes: HUgn64102
    ECgene: TNMD H-InvDB: TNMD

    (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 TNMD 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 TNMD gene:
    Search GeneIP for patents involving TNMD

    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, eBioscience, antibodies-online, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, 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 genOway)
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