Human Gene FAM5B (uc001glf.3) Description and Page Index
  Description: Homo sapiens family with sequence similarity 5, member B (FAM5B), mRNA.
Transcript (Including UTRs)
   Position: hg19 chr1:177,140,633-177,251,558 Size: 110,926 Total Exon Count: 8 Strand: +
Coding Region
   Position: hg19 chr1:177,199,013-177,250,664 Size: 51,652 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 (chr1:177,140,633-177,251,558)mRNA (may differ from genome)Protein (783 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneTable SchemaBioGPS
CGAPEnsemblEntrez GeneExonPrimerGeneCardsGeneNetwork
H-INVHGNCHPRDLynxMGIneXtProt
PubMedStanford SOURCETreefamUniProtKB

-  Comments and Description Text from UniProtKB
  ID: FAM5B_HUMAN
DESCRIPTION: RecName: Full=Protein FAM5B; AltName: Full=BMP/retinoic acid-inducible neural-specific protein 2; AltName: Full=DBCCR1-like protein 2; Flags: Precursor;
SUBCELLULAR LOCATION: Secreted (Potential).
SIMILARITY: Belongs to the FAM5 family.
SIMILARITY: Contains 1 MACPF domain.
SEQUENCE CAUTION: Sequence=BAB21838.1; Type=Erroneous initiation;

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): FAM5B
CDC HuGE Published Literature: FAM5B
Positive Disease Associations: Alcohol Drinking , Blood Pressure , Body Mass Index , Body Weight , Cholesterol , Cholesterol, LDL , Forced Vital Capacity , Menarche
Related Studies:
  1. Alcohol Drinking
    , , . [PubMed 0]
  2. Blood Pressure
    Daniel Levy et al. BMC medical genetics 2007, Framingham Heart Study 100K Project: genome-wide associations for blood pressure and arterial stiffness., BMC medical genetics. [PubMed 17903302]
    These results of genome-wide association testing for blood pressure and arterial stiffness phenotypes in an unselected community-based sample of adults may aid in the identification of the genetic basis of hypertension and arterial disease, help identify high risk individuals, and guide novel therapies for hypertension. Additional studies are needed to replicate any associations identified in these analyses.
  3. Body Mass Index
    Caroline S Fox et al. BMC medical genetics 2007, Genome-wide association to body mass index and waist circumference: the Framingham Heart Study 100K project., BMC medical genetics. [PubMed 17903300]
    Adiposity traits are associated with SNPs on the Affymetrix 100K SNP GeneChip. Replication of these initial findings is necessary. These data will serve as a resource for replication as more genes become identified with BMI and WC.
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-  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: 21.32 RPKM in Brain - Cortex
Total median expression: 125.76 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 -98.10312-0.314 Picture PostScript Text
3' UTR -274.51894-0.307 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
IPR000742 - EG-like_dom
IPR020864 - MACPF

Pfam Domains:
PF01823 - MAC/Perforin domain

ModBase Predicted Comparative 3D Structure on Q9C0B6
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 BrowserNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
 Protein Sequence    
 Alignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Biological Process:
GO:0007049 cell cycle
GO:0007050 cell cycle arrest
GO:0045666 positive regulation of neuron differentiation
GO:0045930 negative regulation of mitotic cell cycle
GO:0071300 cellular response to retinoic acid

Cellular Component:
GO:0005576 extracellular region
GO:0005783 endoplasmic reticulum
GO:0030425 dendrite
GO:0043025 neuronal cell body


-  Descriptions from all associated GenBank mRNAs
  AK296524 - Homo sapiens cDNA FLJ60628 complete cds, highly similar to Protein FAM5B precursor.
AB051534 - Homo sapiens KIAA1747 mRNA for KIAA1747 protein.
AB161694 - Homo sapiens DBCCR1L2 mRNA for DBCCR1-like2, complete cds.
BC028036 - Homo sapiens family with sequence similarity 5, member B, mRNA (cDNA clone MGC:40127 IMAGE:5242899), complete cds.
CU688376 - Synthetic construct Homo sapiens gateway clone IMAGE:100017816 5' read FAM5B mRNA.
KJ894457 - Synthetic construct Homo sapiens clone ccsbBroadEn_03851 FAM5B gene, encodes complete protein.
AB385502 - Synthetic construct DNA, clone: pF1KA1747, Homo sapiens FAM5B gene for FAM5B protein, complete cds, without stop codon, in Flexi system.
AL035289 - H.sapiens gene from PAC 1026E2, partial.
JD438558 - Sequence 419582 from Patent EP1572962.
JD485376 - Sequence 466400 from Patent EP1572962.
JD416971 - Sequence 397995 from Patent EP1572962.
JD471350 - Sequence 452374 from Patent EP1572962.
JD067800 - Sequence 48824 from Patent EP1572962.
AK123336 - Homo sapiens cDNA FLJ41342 fis, clone BRAWH2001940.
AK098386 - Homo sapiens cDNA FLJ25520 fis, clone CBR06831.
AF131833 - Homo sapiens clone 24828 mRNA sequence, partial cds.
JD436730 - Sequence 417754 from Patent EP1572962.
JD211956 - Sequence 192980 from Patent EP1572962.
JD042420 - Sequence 23444 from Patent EP1572962.
JD167787 - Sequence 148811 from Patent EP1572962.
JD061779 - Sequence 42803 from Patent EP1572962.
JD227795 - Sequence 208819 from Patent EP1572962.
JD206088 - Sequence 187112 from Patent EP1572962.
JD193107 - Sequence 174131 from Patent EP1572962.
JD151487 - Sequence 132511 from Patent EP1572962.
JD559238 - Sequence 540262 from Patent EP1572962.
JD393859 - Sequence 374883 from Patent EP1572962.
JD124399 - Sequence 105423 from Patent EP1572962.
JD403732 - Sequence 384756 from Patent EP1572962.
JD281288 - Sequence 262312 from Patent EP1572962.
JD300142 - Sequence 281166 from Patent EP1572962.
JD168878 - Sequence 149902 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: BRINP2, DBCCR1L2, FAM5B_HUMAN, KIAA1747, NM_021165, NP_066988, O95560, Q6ZWC1, Q7LCZ9, Q8N360, Q9C0B6
UCSC ID: uc001glf.3
RefSeq Accession: NM_021165
Protein: Q9C0B6 (aka FAM5B_HUMAN)
CCDS: CCDS1320.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_021165.2
exon count: 8CDS single in 3' UTR: no RNA size: 3617
ORF size: 2352CDS single in intron: no Alignment % ID: 99.97
txCdsPredict score: 4786.50frame shift in genome: no % Coverage: 98.37
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.