Human Gene CBWD1 (uc003zgc.4)
  Description: Homo sapiens COBW domain containing 1 (CBWD1), transcript variant 3, mRNA.
Transcript (Including UTRs)
   Position: hg19 chr9:121,038-179,075 Size: 58,038 Total Exon Count: 14 Strand: -
Coding Region
   Position: hg19 chr9:121,467-178,969 Size: 57,503 Coding Exon Count: 14 

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 (chr9:121,038-179,075)mRNA (may differ from genome)Protein (376 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsH-INV
HGNCLynxMGIOMIMPubMedTreefam
UniProtKBWikipediaBioGrid 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: 1.69 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 54.13 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 -51.00106-0.481 Picture PostScript Text
3' UTR -80.12429-0.187 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:
PF02492 - CobW/HypB/UreG, nucleotide-binding domain
PF07683 - Cobalamin synthesis protein cobW C-terminal domain

SCOP Domains:
52540 - P-loop containing nucleoside triphosphate hydrolases
90002 - Hypothetical protein YjiA, C-terminal domain

ModBase Predicted Comparative 3D Structure on Q9BRT8-3
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 Details     
Gene Sorter     
      
      
      

-  Descriptions from all associated GenBank mRNAs
  AF257330 - Homo sapiens dopamine-responsive protein mRNA, complete cds.
AY343911 - Homo sapiens COBW domain containing protein 1 (CBWD1) mRNA, complete cds.
AK290648 - Homo sapiens cDNA FLJ75442 complete cds, highly similar to Homo sapiens COBW domain containing 1, mRNA.
BC132759 - Homo sapiens COBW domain containing 1, mRNA (cDNA clone MGC:164390 IMAGE:40146781), complete cds.
AF212253 - Homo sapiens HCOBP mRNA, complete cds.
BC013432 - Homo sapiens COBW domain containing 1, mRNA (cDNA clone MGC:14814 IMAGE:4133722), complete cds.
BC009573 - Homo sapiens COBW domain containing 1, mRNA (cDNA clone MGC:14547 IMAGE:4133536), complete cds.
AK315855 - Homo sapiens cDNA, FLJ79504 complete cds, highly similar to COBW domain-containing protein 1.
BC005996 - Homo sapiens COBW domain containing 1, mRNA (cDNA clone MGC:14800 IMAGE:4069589), complete cds.
BC037212 - Homo sapiens COBW domain containing 1, mRNA (cDNA clone IMAGE:4838356), with apparent retained intron.
HQ447613 - Synthetic construct Homo sapiens clone IMAGE:100070959; CCSB013253_01 COBW domain containing 1 (CBWD1) gene, encodes complete protein.
KJ899209 - Synthetic construct Homo sapiens clone ccsbBroadEn_08603 CBWD1 gene, encodes complete protein.
JF432127 - Synthetic construct Homo sapiens clone IMAGE:100073266 COBW domain containing 1 (CBWD1) gene, encodes complete protein.
KJ894280 - Synthetic construct Homo sapiens clone ccsbBroadEn_03674 CBWD1 gene, encodes complete protein.
HQ258394 - Synthetic construct Homo sapiens clone IMAGE:100072823 COBW domain containing 1 (CBWD1) gene, encodes complete protein.
KJ899210 - Synthetic construct Homo sapiens clone ccsbBroadEn_08604 CBWD1 gene, encodes complete protein.
AK297292 - Homo sapiens cDNA FLJ50730 complete cds, highly similar to COBW domain-containing protein 1.
CU679405 - Synthetic construct Homo sapiens gateway clone IMAGE:100022199 5' read CBWD1 mRNA.
JD566734 - Sequence 547758 from Patent EP1572962.
CU675219 - Synthetic construct Homo sapiens gateway clone IMAGE:100019222 5' read CBWD1 mRNA.
AY295766 - Homo sapiens COBW protein-like mRNA, partial sequence.
AY320414 - Homo sapiens nasopharyngeal carcinoma-associated antigen NPC-A-6 mRNA, complete cds.

-  Other Names for This Gene
  Alternate Gene Symbols: NM_001145356, NP_001138828, Q9BRT8-3
UCSC ID: uc003zgc.4
RefSeq Accession: NM_001145356
Protein: Q9BRT8-3, splice isoform of Q9BRT8 CCDS: CCDS6438.1, CCDS47947.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001145356.1
exon count: 14CDS single in 3' UTR: no RNA size: 1683
ORF size: 1131CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2462.00frame shift in genome: no % Coverage: 98.99
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.