Human Gene TMCO1 (uc001gdj.5)
  Description: Homo sapiens transmembrane and coiled-coil domains 1 (TMCO1), transcript variant 1, mRNA.
RefSeq Summary (NM_019026): This locus encodes a transmembrane protein. Mutations at this locus have been associated with craniofacial dysmorphism, skeletal anomalies, and cognitive disability. Mutations at this locus have also been associated with open angle glaucoma blindness. Alternatively spliced transcript variants have been described. [provided by RefSeq, Jan 2012].
Transcript (Including UTRs)
   Position: hg19 chr1:165,693,528-165,738,159 Size: 44,632 Total Exon Count: 7 Strand: -
Coding Region
   Position: hg19 chr1:165,697,260-165,738,141 Size: 40,882 Coding Exon Count: 7 

Page IndexSequence and LinksPrimersGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:165,693,528-165,738,159)mRNA (may differ from genome)Protein (239 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMalacards
MGIOMIMPubMedUniProtKBWikipediaBioGrid CRISPR DB

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): TMCO1
CDC HuGE Published Literature: TMCO1
Positive Disease Associations: Blood Pressure Determination
Related Studies:
  1. Blood Pressure Determination
    , , . [PubMed 0]

-  MalaCards Disease Associations
  MalaCards Gene Search: TMCO1
Diseases sorted by gene-association score: craniofacial dysmorphism, skeletal anomalies, and mental retardation syndrome* (1019), sprengel deformity (19), open-angle glaucoma (16), ocular hypertension (8), glaucoma 1, open angle, e (5)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 32.07 RPKM in Adrenal Gland
Total median expression: 869.65 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -2.1018-0.117 Picture PostScript Text
3' UTR -943.603732-0.253 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR002809 - DUF106_TM
IPR008559 - UCP023322_TM_euk

Pfam Domains:
PF01956 - Integral membrane protein DUF106

ModBase Predicted Comparative 3D Structure on J9JIE6
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologGenome BrowserGenome BrowserGenome BrowserGenome BrowserNo ortholog
Gene DetailsGene Details Gene DetailsGene Details 
Gene SorterGene Sorter Gene SorterGene Sorter 
 RGDEnsemblFlyBaseWormBase 
 Protein SequenceProtein SequenceProtein SequenceProtein Sequence 
 AlignmentAlignmentAlignmentAlignment 

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005262 calcium channel activity

Biological Process:
GO:0032469 endoplasmic reticulum calcium ion homeostasis
GO:0070588 calcium ion transmembrane transport

Cellular Component:
GO:0005783 endoplasmic reticulum
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0030176 integral component of endoplasmic reticulum membrane


-  Descriptions from all associated GenBank mRNAs
  LF383658 - JP 2014500723-A/191161: Polycomb-Associated Non-Coding RNAs.
JD121083 - Sequence 102107 from Patent EP1572962.
AY763589 - Homo sapiens xenogeneic cross-immune protein (PCIA3) mRNA, complete cds.
AK093302 - Homo sapiens cDNA FLJ35983 fis, clone TESTI2014007, highly similar to Homo sapiens mRNA for putative membrane protein.
AY359027 - Homo sapiens clone DNA16438 STMF151 (UNQ151) mRNA, complete cds.
AF274935 - Homo sapiens PNAS-10 mRNA, complete cds.
BC000104 - Homo sapiens transmembrane and coiled-coil domains 1, mRNA (cDNA clone MGC:1176 IMAGE:3504808), complete cds.
AF070626 - Homo sapiens clone 24483 unknown mRNA, parital cds.
AB020980 - Homo sapiens mRNA for putative membrane protein, complete cds.
AK316080 - Homo sapiens cDNA, FLJ78979 complete cds, highly similar to Transmembrane and coiled-coil domains protein 1.
LF320569 - JP 2014500723-A/128072: Polycomb-Associated Non-Coding RNAs.
AK298614 - Homo sapiens cDNA FLJ50833 complete cds, highly similar to Transmembrane and coiled-coil domains protein 1.
JD192612 - Sequence 173636 from Patent EP1572962.
LF320568 - JP 2014500723-A/128071: Polycomb-Associated Non-Coding RNAs.
AF277194 - Homo sapiens PNAS-136 mRNA, complete cds.
AK316610 - Homo sapiens cDNA, FLJ96894, Homo sapiens putative membrane protein (LOC54499), mRNA.
CU674038 - Synthetic construct Homo sapiens gateway clone IMAGE:100018000 5' read TMCO1 mRNA.
LF320566 - JP 2014500723-A/128069: Polycomb-Associated Non-Coding RNAs.
LF320565 - JP 2014500723-A/128068: Polycomb-Associated Non-Coding RNAs.
JD066560 - Sequence 47584 from Patent EP1572962.
JD401235 - Sequence 382259 from Patent EP1572962.
JD289225 - Sequence 270249 from Patent EP1572962.
MA619235 - JP 2018138019-A/191161: Polycomb-Associated Non-Coding RNAs.
MA556146 - JP 2018138019-A/128072: Polycomb-Associated Non-Coding RNAs.
MA556145 - JP 2018138019-A/128071: Polycomb-Associated Non-Coding RNAs.
MA556143 - JP 2018138019-A/128069: Polycomb-Associated Non-Coding RNAs.
MA556142 - JP 2018138019-A/128068: Polycomb-Associated Non-Coding RNAs.

-  Other Names for This Gene
  Alternate Gene Symbols: hCG_1766418, J9JIE6, J9JIE6_HUMAN, NM_019026, NP_061899, uc001gdj.4
UCSC ID: uc001gdj.5
RefSeq Accession: NM_019026
Protein: J9JIE6 CCDS: CCDS1251.2

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_019026.4
exon count: 7CDS single in 3' UTR: no RNA size: 4478
ORF size: 720CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 1640.00frame shift in genome: no % Coverage: 99.82
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.