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TMCO6 Gene

protein-coding   GIFtS: 46
GCID: GC05P140019

Transmembrane And Coiled-Coil Domains 6

  See 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
Transmembrane And Coiled-Coil Domains 61 2
Transmembrane And Coiled-Coil Domain-Containing Protein 62

External Ids:    HGNC: 288141   Entrez Gene: 553742   Ensembl: ENSG000001131197   UniProtKB: Q96DC73   

Export aliases for TMCO6 gene to outside databases

Previous GC identifers: GC05P140000 GC05P140001 GC05P135164


(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 TMCO6 Gene:
TMCO6 (transmembrane and coiled-coil domains 6) is a protein-coding gene. Diseases associated with TMCO6 include childhood leukemia, and meningioma. GO annotations related to this gene include protein transporter activity.


(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_000005.10  NT_029289.12  NC_018916.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the TMCO6 gene promoter:
         CREB   AP-1   ATF-2   deltaCREB   c-Jun   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidTMCO6 promoter sequence
   Search Chromatin IP Primers for TMCO6

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat TMCO6


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

Entrez Gene cytogenetic band: 5q31.3   Ensembl cytogenetic band:  5q31.3   HGNC cytogenetic band: 5q31.3

TMCO6 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
TMCO6 gene location

GeneLoc information about chromosome 5         GeneLoc Exon Structure

GeneLoc location for GC05P140019:  view genomic region     (about GC identifiers)

Start:
140,019,012 bp from pter      End:
140,024,993 bp from pter
Size:
5,982 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: TMCO6_HUMAN, Q96DC7 (See protein sequence)
Recommended Name: Transmembrane and coiled-coil domain-containing protein 6  
Size: 493 amino acids; 54442 Da
Sequence caution: Sequence=AAF69602.1; Type=Miscellaneous discrepancy; Note=Chimeric cDNA; Sequence=AAH01910.1;
Type=Erroneous initiation; Sequence=AAH09618.1; Type=Erroneous initiation; Sequence=EAW62034.1; Type=Erroneous
gene model prediction;
Secondary accessions: Q9BUU0 Q9P198
Alternative splicing: 2 isoforms:  Q96DC7-1   Q96DC7-2   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for TMCO6: NX_Q96DC7

Explore proteomics data for TMCO6 at MOPED


See TMCO6 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

REFSEQ proteins: NP_060972.3  
ENSEMBL proteins: 
 ENSP00000378166   ENSP00000421613   ENSP00000424937   ENSP00000422154   ENSP00000445469  
 ENSP00000443223   ENSP00000423297   ENSP00000426221   ENSP00000252100   ENSP00000444474  

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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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4 InterPro protein domains:
 IPR011989 ARM-like
 IPR000225 Armadillo
 IPR002652 Importin-a_IBB
 IPR016024 ARM-type_fold

Graphical View of Domain Structure for InterPro Entry Q96DC7

ProtoNet protein and cluster: Q96DC7


TMCO6 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): 3 molecular function terms:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0005488binding ----
GO:0005515protein binding ----
GO:0008565protein transporter activity IEA--
     
TMCO6 for ontologies           About GeneDecksing


Animal Models:
   inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for TMCO6
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miRNA
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miRTarBase miRNAs that target TMCO6:
hsa-mir-320a (MIRT044768)

Block miRNA regulation of human, mouse, rat TMCO6 using miScript Target Protectors
3 qRT-PCR Assays for microRNAs that regulate TMCO6:
hsa-miR-3163 hsa-miR-296-5p hsa-miR-548c-3p
SwitchGear 3'UTR luciferase reporter plasmidTMCO6 3' UTR sequence
Inhib. RNA
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OriGene RNAi products in human, mouse, rat for TMCO6
Predesigned siRNA for gene silencing in human, mouse, rat TMCO6

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Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat TMCO6

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Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for TMCO6


(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
TMCO6_HUMAN, Q96DC7: Membrane; Multi-pass membrane protein (Potential)
Subcellular locations from COMPARTMENTS: 

CompartmentConfidence
nucleus2
cytosol1
endoplasmic reticulum1
mitochondrion1
plasma membrane1

Gene Ontology (GO): 3 cellular component terms:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0005634nucleus IEA--
GO:0005737cytoplasm IEA--
GO:0016021integral component of membrane IEA--

TMCO6 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 TMCO6
Interactions:

    Search GeneGlobe Interaction Network for TMCO6

STRING Interaction Network Preview (showing 2 interactants - click image to see more details)

3 Interacting proteins for TMCO6 (Q96DC72, 3 ENSP000003781664) via UniProtKB, MINT, STRING, and/or I2D
InteractantInteraction Details
GeneCardExternal ID(s)
UBQLN1Q9UMX02, 3, ENSP000003655764MINT-66792 I2D: score=5 STRING: ENSP00000365576
ELOF1P600023I2D: score=1 
UBQLN2ENSP000003451954STRING: ENSP00000345195
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Gene Ontology (GO): 1 biological process term:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0006606protein import into nucleus IEA--

TMCO6 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 TMCO6



(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 TMCO6 gene: 
NM_018502.3  

Unigene Cluster for TMCO6:

Transmembrane and coiled-coil domains 6
Hs.534333  [show with all ESTs]
Unigene Representative Sequence: BC065828
15 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000394671(uc003lgl.3 uc003lgm.3 uc010jft.3) ENST00000513002
ENST00000509217 ENST00000511410(uc011czj.1) ENST00000394669 ENST00000504069
ENST00000515653 ENST00000514449 ENST00000505086 ENST00000252100(uc003lgo.3)
ENST00000510336(uc003lgn.3) ENST00000509605 ENST00000515265 ENST00000509269
ENST00000537378
miRNA
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3 qRT-PCR Assays for microRNAs that regulate TMCO6:
hsa-miR-3163 hsa-miR-296-5p hsa-miR-548c-3p
SwitchGear 3'UTR luciferase reporter plasmidTMCO6 3' UTR sequence
Inhib. RNA
Products:
     
OriGene RNAi products in human, mouse, rat for TMCO6
Predesigned siRNA for gene silencing in human, mouse, rat TMCO6
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GenScript: all cDNA clones in your preferred vector: TMCO6 (NM_018502)
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Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat TMCO6
Primer
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OriGene qPCR primer pairs and template standards for TMCO6
OriGene qSTAR qPCR primer pairs in human, mouse for TMCO6
Pre-validated RT2 qPCR Primer Assay in human, mouse, rat TMCO6
  QuantiTect SYBR Green Assays in human, mouse, rat TMCO6
  QuantiFast Probe-based Assays in human, mouse, rat TMCO6

Additional mRNA sequence: 

AK097088.1 AK289495.1 AK301502.1 AK308722.1 BC001910.1 BC009618.1 BC065828.1 

14 DOTS entries:

DT.92459893  DT.100839141  DT.100839136  DT.120833486  DT.95375434  DT.112834  DT.101980046  DT.100839131 
DT.120833464  DT.100024343  DT.100839133  DT.102825302  DT.95375431  DT.97843997 

Selected AceView cDNA sequences (see all 533):

BQ652981 BQ057575 AA741579 BM423860 BQ069794 BQ650858 BX366187 BQ930303 
BQ072265 BM696337 CR594879 CB107577 NM_018502 BM474961 BM837136 BM789253 
BQ932561 AW263980 NM_017706 BU622009 BU615768 BI860797 CB122404 BM707928 

GeneLoc Exon Structure

4 Alternative Splicing Database (ASD) splice patterns (SP) for TMCO6    About this scheme

ExUns: 1a · 1b ^ 2 ^ 3 ^ 4a · 4b ^ 5 ^ 6 ^ 7
SP1:                                                      
SP2:                                                      
SP3:                          -     -                     
SP4:                                                      


ECgene alternative splicing isoforms for TMCO6

(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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TMCO6 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: --
TMCO6 Expression
About this image

TMCO6 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

TMCO6 Protein Expression

SOURCE GeneReport for Unigene cluster: Hs.534333
    Custom PCR Arrays for TMCO6
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In Situ
Assay Products:
 

 
Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for TMCO6

(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 TMCO6 gene from Selected species (see all 11)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
mouse
(Mus musculus)
Mammalia Tmco61 , 5 transmembrane and coiled-coil domains 61, 5 85.03(n)1
83.67(a)1
  18 (19.46 cM)5
719831  NM_028036.31  NP_082312.31 
 367350705 
chicken
(Gallus gallus)
Aves TMCO61 transmembrane and coiled-coil domains 6 64.91(n)
60.99(a)
  416135  XM_414468.4  XP_414468.4 
lizard
(Anolis carolinensis)
Reptilia TMCO66
transmembrane and coiled-coil domains 6
51(a)
1 ↔ 1
4(77816425-77831707)
tropical clawed frog
(Xenopus tropicalis)
Amphibia tmco61 transmembrane and coiled-coil domains 6 54.7(n)
49.17(a)
  100145543  NM_001126978.1  NP_001120450.1 
zebrafish
(Danio rerio)
Actinopterygii zgc:1622401 zgc:162240 54.61(n)
48.54(a)
  559069  NM_001089537.1  NP_001083006.1 


ENSEMBL Gene Tree for TMCO6 (if available)
TreeFam Gene Tree for TMCO6 (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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  --

(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 TMCO6 (see all 223)    About this table    
Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 5 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs1816935701,2
--140017071(+) AAAGCA/TAAAAT 1 -- us2k10--------
rs1447529071,2
--140017151(+) AAACCC/TGAGTG 1 -- us2k10--------
rs1482579511,2
--140017152(+) AACCCA/GAGTGA 1 -- us2k10--------
rs1115038001,2
C--140017460(+) GTCCCGCTT/-  
        
GCCTT
1 -- us2k11Minor allele frequency- -:0.50CSA 2
rs2012531321,2
C--140017462(+) CCCGC-/TTGC  
        
CTTTC
1 -- us2k10--------
rs1413069571,2
--140017523(+) CCTTCC/TTCCTT 1 -- us2k10--------
rs1451682331,2
--140017555(+) TCTTT-/TCTCC 
        
CTTTC
1 -- us2k10--------
rs3767036221,2
C--140017559(+) TCTCC-/CTTT  
        
CTTTC
1 -- us2k10--------
rs68645801,2
C,A--140017583(+) ttcttC/Tcttcc 1 -- us2k1 trp31Minor allele frequency- T:0.50CSA 2
rs68645831,2
A--140017587(+) tccttC/Tctttc 1 -- us2k1 trp30--------

HapMap Linkage Disequilibrium report for TMCO6 (140019012 - 140024993 bp)

Structural Variations
      Database of Genomic Variants (DGV) variations for TMCO6: --
Site Specific Mutation Identification with PCR Assays
SeqTarget long-range PCR primers for resequencing TMCO6
DNA2.0 Custom Variant and Variant Library Synthesis for TMCO6

(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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3 diseases for TMCO6:    
About MalaCards
childhood leukemia    meningioma    leukemia


TMCO6 for disorders           About GeneDecksing

Genetic Association Database (GAD): TMCO6
Human Genome Epidemiology (HuGE) Navigator: TMCO6 (5 documents)

Export disorders for TMCO6 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 TMCO6 gene integrated from 10 sources:
(articles sorted by number of sources associating them with TMCO6)
    Utopia: connect your pdf to the dynamic
world of online information

  1. Polymorphisms in innate immunity genes and risk of childhood leukemia. (PubMed id 20438785)1, 4 Han S....Kang D. (Hum. Immunol. 2010)
  2. Risk of meningioma and common variation in genes related to innate immunity. (PubMed id 20406964)1, 4 Rajaraman P....Inskip P.D. (amp 2010)
  3. Candidate gene polymorphisms for ischemic stroke. (PubMed id 19729601)1, 4 Matarin M....Meschia J.F. ( a journal of cerebral circulation 2009)
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (Nat. Genet. 2004)
  5. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1, 3 Strausberg R.L....Marra M.A. (Proc. Natl. Acad. Sci. U.S.A. 2002)
  6. Pathway Analysis of ChIP-Seq-Based NRF1 Target Genes Suggests a Logical Hypothesis of their Involvement in the Pathogenesis of Neurodegenerative Diseases. (PubMed id 24250222)1 Satoh J....Yamamoto Y. (Gene Regul Syst Bio 2013)
  7. Common variation in genes related to innate immunity and risk of adult glioma. (PubMed id 19423540)1 Rajaraman P....Chanock S.J. (amp 2009)
  8. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. (PubMed id 16344560)1 Kimura K.... Sugano S. (Genome Res. 2006)
  9. Towards a proteome-scale map of the human protein-protein interaction network. (PubMed id 16189514)1 Rual J.F....Vidal M. (Nature 2005)
  10. 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. (Genome Res. 2004)

(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: 55374 HGNC: 28814 AceView: IK Ensembl:ENSG00000113119 euGenes: HUgn55374
ECgene: TMCO6 H-InvDB: TMCO6

(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 TMCO6 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 TMCO6 gene:
Search GeneIP for patents involving TMCO6

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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 Search www.enzolifesciences.com for proteins, assays, substrates, inhibitors & antibodies

 Novus Tissue Slides
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 inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for TMCO6
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GeneCards Homepage - Last full update: 7 May 2014 - Incrementals: 9 May 2014 , 2 Jun 2014 , 26 Jun 2014 , 30 Jun 2014

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