Human Gene C6orf136 (uc011dmn.2)
  Description: Homo sapiens chromosome 6 open reading frame 136 (C6orf136), transcript variant 2, mRNA.
Transcript (Including UTRs)
   Position: hg19 chr6:30,614,816-30,620,987 Size: 6,172 Total Exon Count: 5 Strand: +
Coding Region
   Position: hg19 chr6:30,615,009-30,620,692 Size: 5,684 Coding Exon Count: 5 

Page IndexSequence and LinksPrimersCTDGene AllelesRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesmRNA DescriptionsOther Names
Model InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr6:30,614,816-30,620,987)mRNA (may differ from genome)Protein (181 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCLynxMGIPubMed
TreefamUniProtKBBioGrid 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


-  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: 25.45 RPKM in Brain - Cerebellum
Total median expression: 521.97 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 -67.00193-0.347 Picture PostScript Text
3' UTR -70.14295-0.238 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
  Pfam Domains:
PF10184 - Uncharacterized conserved protein (DUF2358)

ModBase Predicted Comparative 3D Structure on Q5SQH8-3
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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 BrowserNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
 Protein Sequence    
 Alignment    

-  Descriptions from all associated GenBank mRNAs
  BC073975 - Homo sapiens chromosome 6 open reading frame 136, mRNA (cDNA clone IMAGE:5764635), partial cds.
AK127564 - Homo sapiens cDNA FLJ45657 fis, clone CTONG2014959.
BC064397 - Homo sapiens chromosome 6 open reading frame 136, mRNA (cDNA clone IMAGE:5762716), partial cds.
BC016167 - Homo sapiens chromosome 6 open reading frame 136, mRNA (cDNA clone MGC:15854 IMAGE:3509511), complete cds.
CU677581 - Synthetic construct Homo sapiens gateway clone IMAGE:100021854 5' read C6orf136 mRNA.
HQ447672 - Synthetic construct Homo sapiens clone IMAGE:100071113; CCSB012468_01 chromosome 6 open reading frame 136 (C6orf136) gene, encodes complete protein.
KJ904035 - Synthetic construct Homo sapiens clone ccsbBroadEn_13429 C6orf136 gene, encodes complete protein.
JD161475 - Sequence 142499 from Patent EP1572962.
JD240348 - Sequence 221372 from Patent EP1572962.
JD330642 - Sequence 311666 from Patent EP1572962.
JD164036 - Sequence 145060 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: NM_145029, NP_659466, Q5SQH8-3
UCSC ID: uc011dmn.2
RefSeq Accession: NM_145029
Protein: Q5SQH8-3, splice isoform of Q5SQH8 CCDS: CCDS4684.2

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_145029.3
exon count: 5CDS single in 3' UTR: no RNA size: 1039
ORF size: 546CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 1220.00frame shift in genome: no % Coverage: 99.52
has start codon: yes stop codon in genome: no # of Alignments: 7
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.