Human Gene C6orf1 (uc003ojh.3) Description and Page Index
  Description: Homo sapiens chromosome 6 open reading frame 1 (C6orf1), transcript variant 3, mRNA.
Transcript (Including UTRs)
   Position: hg19 chr6:34,214,157-34,216,904 Size: 2,748 Total Exon Count: 5 Strand: -
Coding Region
   Position: hg19 chr6:34,214,291-34,215,262 Size: 972 Coding Exon Count: 3 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr6:34,214,157-34,216,904)mRNA (may differ from genome)Protein (159 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneTable SchemaBioGPS
CGAPEnsemblEntrez GeneExonPrimerGeneCardsGeneNetwork
H-INVHGNCHPRDLynxMGIneXtProt
OMIMPubMedStanford SOURCEUniProtKB

-  Comments and Description Text from UniProtKB
  ID: CF001_HUMAN
DESCRIPTION: RecName: Full=Uncharacterized protein C6orf1; AltName: Full=Protein LBH; Flags: Precursor;
SUBCELLULAR LOCATION: Secreted (Potential).
TISSUE SPECIFICITY: Expressed in spleen, thymus, prostate, testis, uterus, small intestine, colon and peripheral blood leukocytes.

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): C6orf1
CDC HuGE Published Literature: C6orf1
Positive Disease Associations: Body Height , height
Related Studies:
  1. Body Height
    Amidou N'Diaye et al. PLoS genetics 2011, Identification, replication, and fine-mapping of Loci associated with adult height in individuals of african ancestry., PLoS genetics. [PubMed 21998595]
  2. height
    Kim ,et al. 2009, Identification of 15 loci influencing height in a Korean population, Journal of human genetics 2010 55- 1 : 27-31. [PubMed 19893584]

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  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: 42.66 RPKM in Brain - Hypothalamus
Total median expression: 850.87 RPKM



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

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -124.50280-0.445 Picture PostScript Text
3' UTR -39.10134-0.292 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
  ModBase Predicted Comparative 3D Structure on Q86T20
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 orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
      
      
      
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Cellular Component:
GO:0005576 extracellular region


-  Descriptions from all associated GenBank mRNAs
  AK290164 - Homo sapiens cDNA FLJ76010 complete cds.
BC047919 - Homo sapiens chromosome 6 open reading frame 1, mRNA (cDNA clone MGC:57858 IMAGE:6190218), complete cds.
BC023627 - Homo sapiens chromosome 6 open reading frame 1, mRNA (cDNA clone MGC:23478 IMAGE:4764944), complete cds.
BC009526 - Homo sapiens chromosome 6 open reading frame 1, mRNA (cDNA clone IMAGE:3890372), with apparent retained intron.
JD235146 - Sequence 216170 from Patent EP1572962.
DL491604 - Novel nucleic acids.
DL490199 - Novel nucleic acids.
JD391892 - Sequence 372916 from Patent EP1572962.
JD404011 - Sequence 385035 from Patent EP1572962.
JD100157 - Sequence 81181 from Patent EP1572962.
KJ900479 - Synthetic construct Homo sapiens clone ccsbBroadEn_09873 C6orf1 gene, encodes complete protein.

-  Other Names for This Gene
  Alternate Gene Symbols: A8K299, CF001_HUMAN, LBH, NM_001008704, NP_848603, Q86T20
UCSC ID: uc003ojh.3
RefSeq Accession: NM_001008704
Protein: Q86T20 (aka CF001_HUMAN)
CCDS: CCDS4790.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001008704.1
exon count: 5CDS single in 3' UTR: no RNA size: 932
ORF size: 480CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 969.00frame shift in genome: no % Coverage: 95.92
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.