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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

TMEM56 Gene

protein-coding   GIFtS: 44
GCID: GC01P095582

transmembrane protein 56

  Search for TMEM56
in our new
 Human Malady Compendium 
Biological research products
for TMEM56
    

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section

Aliases
Transmembrane Protein 561 2
FLJ318421

External Ids:    HGNC: 264771   Entrez Gene: 1485342   Ensembl: ENSG000001520787   UniProtKB: Q96MV13   

Export aliases for TMEM56 gene to outside databases

Previous GC identifers: GC01P095296 GC01P093704


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

  --

(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 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000001.10  NC_018912.1  NT_032977.9  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the TMEM56 gene promoter:
         Pax-2   Olf-1   Pax-2a   XBP-1   Arnt   Max   Pax-2b   Pax-4a   ATF6   c-Myc   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidTMEM56 promoter sequence
   Search SABiosciences Chromatin IP Primers for TMEM56

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat TMEM56


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

Entrez Gene cytogenetic band: 1p21.3   Ensembl cytogenetic band:  1p21.3   HGNC cytogenetic band: 1p21.3

TMEM56 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
TMEM56 gene location

GeneLoc information about chromosome 1         GeneLoc Exon Structure

GeneLoc location for GC01P095582:  view genomic region     (about GC identifiers)

Start:
95,582,894 bp from pter      End:
95,663,163 bp from pter
Size:
80,270 bases      Orientation:
plus strand

(According to 1UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to 2PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, 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 Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section

UniProtKB/Swiss-Prot: TMM56_HUMAN, Q96MV1 (See protein sequence)
Recommended Name: Transmembrane protein 56  
Size: 263 amino acids; 30041 Da
Subcellular location: Membrane; Multi-pass membrane protein (Potential)
Secondary accessions: B2RPI2 D3DT48

Explore the universe of human proteins at neXtProt for TMEM56: NX_Q96MV1

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q96MV1

  • TMEM56 Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins (2 alternative transcripts): 
    NP_001186608.1  NP_689700.1  

    ENSEMBL proteins: 
     ENSP00000359222   ENSP00000395364   ENSP00000417043  

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    Uscn Proteins for TMEM56

    Gene Ontology (GO): 2 cellular component terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005575cellular_component ND--
    GO:0016021integral to membrane IEA--


    TMEM56 for ontologies           About GeneDecksing



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    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section

    TMEM56 for domains           About GeneDecksing

    1 InterPro domain/family:
     IPR006634 TLC-dom

    Graphical View of Domain Structure for InterPro Entry Q96MV1

    ProtoNet protein and cluster: Q96MV1

    1 Blocks protein family: IPB006634 TRAM

    UniProtKB/Swiss-Prot: TMM56_HUMAN, Q96MV1
    Similarity: Belongs to the TMEM56 family
    Similarity: Contains 1 TLC (TRAM/LAG1/CLN8) domain


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
    About This Section

    miRNA
    Products:
        
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    hsa-miR-124* hsa-miR-3685 hsa-miR-607 hsa-miR-361-5p hsa-miR-300 hsa-miR-200a hsa-miR-30d hsa-miR-507
    SwitchGear 3'UTR luciferase reporter plasmidTMEM56 3' UTR sequence
    Inhib. RNA
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    OriGene 29mer shRNA kits in GFP-retroviral vector in human, mouse, rat for TMEM56 (see all 7)
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    Gene Ontology (GO): 1 molecular function term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003674molecular_function ND--


    TMEM56 for ontologies           About GeneDecksing


    1 GenomeRNAi human phenotype for TMEM56:
     Increased cell number in G2M,  


    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, 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 Mar 2013 via Entrez Gene).
    About This Section



    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for TMEM56

    STRING Interaction Network Preview (showing 1 interactants - click image to see more details)

    1 Interacting protein for TMEM56 (ENSP000003592224) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    ELAVL1ENSP000003852694STRING: ENSP00000385269
    About this table

    Gene Ontology (GO): 1 biological process term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0008150biological_process ND--


    TMEM56 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section
    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for TMEM56
    Search CenterWatch for drugs/clinical trials and news about TMEM56 / TMM56 

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 235 Homo sapiens; Mar 10 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,
    RNAi Products from EMD Millipore,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for TMEM56 gene (2 alternative transcripts): 
    NM_001199679.1  NM_152487.2  

    Unigene Cluster for TMEM56:

    Transmembrane protein 56
    Hs.483512  [show with all ESTs]
    Unigene Representative Sequence: NM_001199679
    4 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000370203(uc021oqe.1 uc001drb.3) ENST00000456991 ENST00000455656
    ENST00000463375

    miRNA
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    8/57 QIAGEN miScript miRNA Assays for microRNAs that regulate TMEM56 (see all 57):
    hsa-miR-124* hsa-miR-3685 hsa-miR-607 hsa-miR-361-5p hsa-miR-300 hsa-miR-200a hsa-miR-30d hsa-miR-507
    SwitchGear 3'UTR luciferase reporter plasmidTMEM56 3' UTR sequence
    Inhib. RNA
    Products:
         
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    OriGene 29mer shRNA kits in GFP-retroviral vector in human, mouse, rat for TMEM56 (see all 7)
    OriGene shRNA RFP: TMEM56
    OriGene siRNA: TMEM56
    QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing in human, mouse, rat TMEM56
    Clone
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    OriGene Myc/DDK tagged cDNA clones in CMV expression vector in human, mouse, rat for TMEM56 (see all 3)
    OriGene untagged cDNA clones in CMV expression vector in human, mouse, rat for TMEM56
    OriGene custom cloning services – gene synthesis, subcloning, mutagenesis, variant library, vector shuttling 
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    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat TMEM56 
    Primer
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      QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat TMEM56
      QIAGEN QuantiFast Probe-based Assays in human, mouse, rat TMEM56

    Additional cDNA sequence: 

    AK056404.1 AK126344.1 BC019700.1 BC108263.1 BC137457.1 BC137458.1 BC139737.1 BX537731.1 

    10 DOTS entries:

    DT.210832  DT.95368674  DT.100024370  DT.100787551  DT.212473  DT.100778957  DT.409497  DT.100778956 
    DT.91824373  DT.100024371 

    24/211 AceView cDNA sequences (see all 211):

    AA961117 AA336662 AL598818 AW613686 AA825527 AA328801 BX956929 BQ045393 
    BU782509 AA452629 BX096742 BG566223 BU683936 CD676564 CR613763 AI033315 
    AA699431 BC019700 AK126344 AI033223 AA935999 AI187083 CK430207 N77031 

    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™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    TMEM56 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: AAAACCTTGG

    Microarray
    RNAseq (Illumina Body Map)
    (100×FPKM)½
    SAGE (Serial Analysis of Gene Expression)

    About this image

    TMEM56 expression in embryonic tissues and stem cells
    Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine    About this table
    4 LifeMap In Vivo Development Anatomical Compartments/Cells 
    Tissue Anatomical Compartment CellCategory (developmental path)
    PancreasIslets of LangerhansMature Beta CellsPancreas
    BoneMandibular ProcessBone
    BoneZeugopod Epiphyseal EndBone
    Head MesenchymeFrontonasal ProcessHead Mesenchyme
    Expression: Positive    Negative     Selective marker
    Experimental details: Curated     Microarrays     In-situ hybridization
    Stem Cell Differentiation: 1 LifeMap Cell 
    NameCategory
    Posterior foregut-like cells (A scalable, suspensi...)

    See TMEM56 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for TMEM56

    SOURCE GeneReport for Unigene cluster: Hs.483512
        SABiosciences Custom PCR Arrays for TMEM56
    Primer
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for TMEM56

    (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)
    About This Section

    This gene was present in the common ancestor of eukaryotes.

    Orthologs for TMEM56 gene from 7/21 species (see all 21)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Tmem561 , 5 transmembrane protein 561, 5 80.35(n)1
    77.19(a)1
      3 (52.94 cM)5
    998871  NM_178936.31  NP_849267.11 
     1212017615 
    chicken
    (Gallus gallus)
    Aves TMEM561 transmembrane protein 56 70.93(n)
    62.4(a)
      424483  XM_422325.3  XP_422325.1 
    lizard
    (Anolis carolinensis)
    Reptilia TMEM566
    --
    41(a)
    1 ↔ 1
    2(78565837-78589497)
    African clawed frog
    (Xenopus laevis)
    Amphibia BC056848.12   -- 78.69(n)    BC056848.1 
    zebrafish
    (Danio rerio)
    Actinopterygii tmem56a1 transmembrane protein 56a 61.07(n)
    55.34(a)
      571836  XM_695466.4  XP_700558.3 
    thale cress
    (Arabidopsis thaliana)
    eudicotyledons AT4G103601 TRAM, LAG1 and CLN8 (TLC) lipid-sensing domain containing more 46.81(n)
    30(a)
      826628  NM_001036533.2  NP_001031610.1 
    rice
    (Oryza sativa)
    Liliopsida Os05g04853001 hypothetical protein 46.09(n)
    30.62(a)
      4339138  NM_001062408.1  NP_001055873.1 


    ENSEMBL Gene Tree for TMEM56 (if available)
    TreeFam Gene Tree for TMEM56 (if available) 

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for TMEM56 gene

    TMEM56 for paralogs           About GeneDecksing


    2 Pseudogenes.org Pseudogenes for TMEM56
    PGOHUM00000245091 PGOHUM00000245488


    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, UniProtKB, 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) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    10/1215 NCBI SNPs in TMEM56 are shown (see all 1215    About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 1 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs675785511,2
    C,--93780277(+) TAAGA-/TTTTTT 1 -- ut312Minor allele frequency- T:0.00NA CSA 4
    rs1500617471,2
    --95581046(+) TCCTAA/GGGTCA 1 -- us2k10--------
    rs1453455801,2
    --95581112(+) TCTCAC/TAGCTC 1 -- us2k10--------
    rs1492023671,2
    --95581249(+) TTCTGG/TGGGTT 1 -- us2k10--------
    rs1432523441,2
    --95581342(+) GAGCTA/GCTATC 1 -- us2k10--------
    rs42456701,2
    C,F,A,--95581348(+) CTATCA/GGCCAC 1 -- us2k16Minor allele frequency- G:0.21NA WA EA 364
    rs1467029011,2
    --95581398(+) TGATAC/TAGACT 1 -- us2k10--------
    rs1818852821,2
    --95581469(+) ACCATC/TCTGCC 1 -- us2k10--------
    rs1143252851,2
    --95581508(+) GTGCAC/GAAGGT 2 -- us2k11Minor allele frequency- G:0.01NA 120
    rs1402978741,2
    --95581549(+) CTGCAC/TATATT 2 -- us2k10--------

    HapMap Linkage Disequilibrium report for TMEM56 (95582894 - 95663163 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
    Database of Genomic Variants (DGV): 1 variation for TMEM56
         1 CNV: 4235

    SABiosciences Cancer Mutation PCR Assays
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    (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.)
    About This Section

    TMEM56 for disorders           About MalaCards

    TMEM56 for disorders           About GeneDecksing

    Human Genome Epidemiology (HuGE) Navigator: TMEM56 (1 document)

    Export disorders for TMEM56 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)
    About This Section

    PubMed articles for TMEM56 gene integrated from 9 sources:
    (articles sorted by number of sources associating them with TMEM56)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (2004)
    2. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PubMed id 20379614)1 Rose J.E....Uhl G.R. (2010)
    3. Lysine acetylation targets protein complexes and co-regulates major cellular functions. (PubMed id 19608861)2 Choudhary C.... Mann M. (2009)
    4. Ubiquitin-mediated proteolysis of HuR by heat shock. (PubMed id 19322201)1 Abdelmohsen K....Gorospe M. (2009)
    5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)2 Gerhard D.S....Malek J. (2004)
    6. 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. (2002)
    7. Normalization and subtraction: two approaches to facilitate gene discovery. (PubMed id 8889548)1 Bonaldo M.F.... Soares M.B. (1996)

    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section
     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)
    About This Section
    Entrez Gene: 148534 HGNC: 26477 AceView: RWDD3andFLJ31842 Ensembl:ENSG00000152078 euGenes: HUgn148534
    ECgene: TMEM56 H-InvDB: TMEM56

    (According to HUGE)
    About This Section
      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    NameDescription
    PharmGKB entry for TMEM56 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    Patent Information for TMEM56 gene:
    Search GeneIP for patents involving TMEM56

    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, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Uscn, Thermo Fisher Scientific, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript and LifeMap BioReagents, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or Enzo Life Sciences),
    In Situ Hybridization Assays from
    Advanced Cell Diagnostics
    About This Section

     
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    GeneCards Homepage - Last full update: 18 Mar 2013 - Incrementals: 21 Mar 2013 , 15 Apr 2013 , 26 Apr 2013

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    von Willebrand factor
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