Human Gene DBC1 (uc004bkc.2) Description and Page Index
  Description: Homo sapiens deleted in bladder cancer 1 (DBC1), mRNA.
RefSeq Summary (NM_014618): This gene is located within a chromosomal region that shows loss of heterozygosity in some bladder cancers. It contains a 5' CpG island that may be a frequent target of hypermethylation, and it may undergo hypermethylation-based silencing in some bladder cancers. [provided by RefSeq, Jul 2008]. Publication Note: This RefSeq record includes a subset of the publications that are available for this gene. Please see the Gene record to access additional publications. ##Evidence-Data-START## Transcript exon combination :: SRR1660805.100445.1, SRR1803617.54931.1 [ECO:0000332] RNAseq introns :: single sample supports all introns SAMEA2145544, SAMEA2145743 [ECO:0000348] ##Evidence-Data-END## ##RefSeq-Attributes-START## MANE Ensembl match :: ENST00000265922.8/ ENSP00000265922.2 RefSeq Select criteria :: based on single protein-coding transcript ##RefSeq-Attributes-END##
Transcript (Including UTRs)
   Position: hg19 chr9:121,928,908-122,131,739 Size: 202,832 Total Exon Count: 8 Strand: -
Coding Region
   Position: hg19 chr9:121,929,362-122,075,633 Size: 146,272 Coding Exon Count: 7 

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 (chr9:121,928,908-122,131,739)mRNA (may differ from genome)Protein (761 aa)
Gene SorterGenome BrowserOther Species FASTATable SchemaBioGPSCGAP
EnsemblEntrez GeneExonPrimerGeneCardsGeneNetworkHGNC
HPRDLynxMGIneXtProtOMIMPubMed
Stanford SOURCETreefamUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: DBC1_HUMAN
DESCRIPTION: RecName: Full=Deleted in bladder cancer protein 1; AltName: Full=Protein FAM5A; Flags: Precursor;
FUNCTION: Inhibits cell proliferation by negative regulation of the G1/S transition. Mediates cell death which is not of the classical apoptotic type and regulates expression of components of the plasminogen pathway.
INTERACTION: Q5BKZ1:ZNF326; NbExp=5; IntAct=EBI-3904864, EBI-2560158;
SUBCELLULAR LOCATION: Cytoplasm.
TISSUE SPECIFICITY: Highly expressed in brain. Weakly expressed in heart, lung, skeletal muscle, kidney, thymus, prostate, testis and small intestine.
MISCELLANEOUS: DBC1 is silenced by methylation in 50% of bladder cancer cell lines.
SIMILARITY: Belongs to the FAM5 family.
SIMILARITY: Contains 1 MACPF domain.

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): DBC1
CDC HuGE Published Literature: DBC1
Positive Disease Associations: Asthma , Cholesterol , Cornea , Echocardiography , Exercise Test , Glucose , Heart Failure , multiple sclerosis , Myocardial Infarction , Parkinson Disease , Parkinson's disease , Triglycerides
Related Studies:
  1. Asthma
    Medea Imboden et al. The Journal of allergy and clinical immunology 2012, Genome-wide association study of lung function decline in adults with and without asthma., The Journal of allergy and clinical immunology. [PubMed 22424883]
    Genetic heterogeneity of lung function might be extensive. Our results suggest that genetic determinants of longitudinal and cross-sectional lung function differ and vary by asthma status.
  2. Cholesterol
    , , . [PubMed 0]
  3. Cornea
    Karolina Aberg et al. Biological psychiatry 2010, Genomewide association study of movement-related adverse antipsychotic effects., Biological psychiatry. [PubMed 19875103]
    Although our findings require replication and validation, this study demonstrates the potential of genomewide association studies to discover genes and pathways that mediate adverse effects of antipsychotics.
           more ... click here to view the complete list

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

+  Common Gene Haplotype Alleles
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-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 24.26 RPKM in Brain - Cortex
Total median expression: 211.61 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 -189.10456-0.415 Picture PostScript Text
3' UTR -102.70454-0.226 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
IPR020864 - MACPF

Pfam Domains:
PF01823 - MAC/Perforin domain

ModBase Predicted Comparative 3D Structure on O60477
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 BrowserNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGDEnsembl   
 Protein SequenceProtein Sequence   
 AlignmentAlignment   

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding

Biological Process:
GO:0001662 behavioral fear response
GO:0007049 cell cycle
GO:0007050 cell cycle arrest
GO:0007614 short-term memory
GO:0008219 cell death
GO:0035176 social behavior
GO:0035640 exploration behavior
GO:0042711 maternal behavior
GO:0045666 positive regulation of neuron differentiation
GO:0045786 negative regulation of cell cycle
GO:0045930 negative regulation of mitotic cell cycle
GO:0050768 negative regulation of neurogenesis
GO:0071300 cellular response to retinoic acid
GO:0071625 vocalization behavior

Cellular Component:
GO:0005737 cytoplasm
GO:0005783 endoplasmic reticulum
GO:0030425 dendrite
GO:0043025 neuronal cell body


-  Descriptions from all associated GenBank mRNAs
  BC071702 - Homo sapiens deleted in bladder cancer 1, mRNA (cDNA clone MGC:87969 IMAGE:5244680), complete cds.
AF027734 - Homo sapiens IB3089A (IB3089A) mRNA, complete cds.
AK293649 - Homo sapiens cDNA FLJ56532 complete cds, highly similar to Protein FAM5A precursor.
BC065196 - Homo sapiens deleted in bladder cancer 1, mRNA (cDNA clone MGC:75035 IMAGE:5245480), complete cds.
BC021560 - Homo sapiens deleted in bladder cancer 1, mRNA (cDNA clone IMAGE:4591607), complete cds.
KJ901374 - Synthetic construct Homo sapiens clone ccsbBroadEn_10768 DBC1 gene, encodes complete protein.
JD419966 - Sequence 400990 from Patent EP1572962.
JD314179 - Sequence 295203 from Patent EP1572962.
JD147771 - Sequence 128795 from Patent EP1572962.
JD282612 - Sequence 263636 from Patent EP1572962.
JD327831 - Sequence 308855 from Patent EP1572962.
JD204323 - Sequence 185347 from Patent EP1572962.
AK293501 - Homo sapiens cDNA FLJ56953 complete cds, highly similar to Protein FAM5A precursor.
JD114919 - Sequence 95943 from Patent EP1572962.
JD057056 - Sequence 38080 from Patent EP1572962.
JD455475 - Sequence 436499 from Patent EP1572962.
JD069370 - Sequence 50394 from Patent EP1572962.
JD443524 - Sequence 424548 from Patent EP1572962.
JD065077 - Sequence 46101 from Patent EP1572962.
JD442318 - Sequence 423342 from Patent EP1572962.
JD442151 - Sequence 423175 from Patent EP1572962.
JD395407 - Sequence 376431 from Patent EP1572962.
JD443863 - Sequence 424887 from Patent EP1572962.
JD460700 - Sequence 441724 from Patent EP1572962.
JD443866 - Sequence 424890 from Patent EP1572962.
JD064274 - Sequence 45298 from Patent EP1572962.
JD129387 - Sequence 110411 from Patent EP1572962.
JD399271 - Sequence 380295 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: DBC1_HUMAN, DBCCR1, FAM5A, IB3089A, NM_014618, NP_055433, O60477, Q6IPV6, Q6P1A0, Q8WU22
UCSC ID: uc004bkc.2
RefSeq Accession: NM_014618
Protein: O60477 (aka DBC1_HUMAN)
CCDS: CCDS6822.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_014618.2
exon count: 8CDS single in 3' UTR: no RNA size: 3196
ORF size: 2286CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 4561.50frame shift in genome: no % Coverage: 100.00
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
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