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FAM78B Gene

protein-coding   GIFtS: 41
GCID: GC01M166027

Family With Sequence Similarity 78, Member B

  Search for FAM78B
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
Family With Sequence Similarity 78, Member B1 2
Protein FAM78B2

External Ids:    HGNC: 134951   Entrez Gene: 1492972   Ensembl: ENSG000001888597   UniProtKB: Q5VT403   

Export aliases for FAM78B gene to outside databases

Previous GC identifers: GC01M162772 GC01M164293 GC01M164305 GC01M137286


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for FAM78B Gene:
FAM78B (family with sequence similarity 78, member B) is a protein-coding gene. An important paralog of this gene is FAM78A.


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:
NC_000001.10  NC_018912.2  NT_004487.20  
Regulatory elements:
   Regulatory transcription factor binding sites in the FAM78B gene promoter:
         Elk-1   STAT1   Pax-5   GATA-3   Pax-2   STAT1beta   CUTL1   STAT1alpha   N-Myc   Pax-4a   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
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Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat FAM78B


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 1q24.1   Ensembl cytogenetic band:  1q24.1   HGNC cytogenetic band: 1q24.1

FAM78B Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
FAM78B gene location

GeneLoc information about chromosome 1         GeneLoc Exon Structure

GeneLoc location for GC01M166027:  view genomic region     (about GC identifiers)

Start:
166,026,674 bp from pter      End:
166,136,206 bp from pter
Size:
109,533 bases      Orientation:
minus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, Cloud-Clone Corp., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: FA78B_HUMAN, Q5VT40 (See protein sequence)
Recommended Name: Protein FAM78B  
Size: 261 amino acids; 29835 Da
Secondary accessions: B7Z693

Explore the universe of human proteins at neXtProt for FAM78B: NX_Q5VT40

Explore proteomics data for FAM78B at MOPED


See FAM78B Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

REFSEQ proteins: NP_001017961.1  
ENSEMBL proteins: 
 ENSP00000412766   ENSP00000389945   ENSP00000393329   ENSP00000346404   ENSP00000339681  

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(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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ProtoNet protein and cluster: Q5VT40

UniProtKB/Swiss-Prot: FA78B_HUMAN, Q5VT40
Similarity: Belongs to the FAM78 family


(According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Phenotypes:
     1 GenomeRNAi human phenotype for FAM78B:
 Increased S DNA content 

Animal Models:
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SwitchGear 3'UTR luciferase reporter plasmidFAM78B 3' UTR sequence
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(According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Subcellular locations from COMPARTMENTS: 

CompartmentConfidence
mitochondrion2
cytosol1
endoplasmic reticulum1
nucleus1
peroxisome1

(SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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    Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for FAM78B
Interactions:

    Search GeneGlobe Interaction Network for FAM78B

(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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Browse Small Molecules at EMD Millipore
   Browse drugs & compounds from Enzo Life Sciences
  Browse compounds at ApexBio 

Browse Tocris compounds for FAM78B (FA78B)



(Secondary structures according to fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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REFSEQ mRNAs for FAM78B gene: 
NM_001017961.3  

Unigene Cluster for FAM78B:

Family with sequence similarity 78, member B
Hs.133029  [show with all ESTs]
Unigene Representative Sequence: AB593134
5 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000435676(uc001gdq.3 uc010plc.2 uc021pee.1) ENST00000456900
ENST00000441649 ENST00000354422 ENST00000338353(uc021pef.1)
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SwitchGear 3'UTR luciferase reporter plasmidFAM78B 3' UTR sequence
Inhib. RNA
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Additional mRNA sequence: 

AB593134.1 AK055347.1 BC032900.2 BC114214.1 

3 DOTS entries:

DT.304305  DT.40130519  DT.97807854 

Selected AceView cDNA sequences (see all 26):

BM682606 BM719916 CD672898 BM676774 BF510140 BM714792 BM726180 CR613414 
BE388915 AL558619 AI440068 BG218787 BM663586 BU738951 BF510138 BC032900 
BX387125 AL526678 BF919367 BF919237 AL580399 AL526712 BM691105 N73628 

GeneLoc Exon Structure


(RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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FAM78B expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: CAGTGAGGGT
FAM78B Expression
About this image


FAM78B expression in embryonic tissues and stem cells    About this table
Data from LifeMap, the Embryonic Development and Stem Cells Database
 selected tissues (see all 2) fully expand
 
 NULL (Uncategorized)
         Neural rosettes
 
 Stomach (Gastrointestinal Tract)
FAM78B Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

FAM78B Protein Expression

SOURCE GeneReport for Unigene cluster: Hs.133029
    Custom PCR Arrays for FAM78B
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In Situ
Assay Products:
 

 
Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for FAM78B

(Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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This gene was present in the common ancestor of chordates.

Orthologs for FAM78B gene from Selected species (see all 11)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
mouse
(Mus musculus)
Mammalia Fam78b1 , 5 family with sequence similarity 78, member B1, 5 96.04(n)1
100(a)1
  1 (74.38 cM)5
2266101  NM_001160262.11  NP_001153734.11 
 1670014325 
chicken
(Gallus gallus)
Aves FAM78B1 family with sequence similarity 78, member B 83.14(n)
89.66(a)
  769830  XM_001232253.2  XP_001232254.1 
lizard
(Anolis carolinensis)
Reptilia FAM78B6
family with sequence similarity 78, member B
90(a)
1 ↔ 1
4(73878753-73890364)
tropical clawed frog
(Xenopus tropicalis)
Amphibia fam78b1 family with sequence similarity 78, member B 82.38(n)
92.72(a)
  100496935  XM_002933772.2  XP_002933818.1 
zebrafish
(Danio rerio)
Actinopterygii fam78bb1 family with sequence similarity 78, member B b 75.35(n)
82.76(a)
  796762  NM_001123313.1  NP_001116785.1 


ENSEMBL Gene Tree for FAM78B (if available)
TreeFam Gene Tree for FAM78B (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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Paralogs for FAM78B gene
FAM78A2  
1 SIMAP similar gene for FAM78B using alignment to 4 protein entries:     FA78B_HUMAN (see all proteins):
FAM78A

Find genes that share paralogs with FAM78B           About GenesLikeMe



(SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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Selected SNPs for FAM78B (see all 2046)    About this table                                 

Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 1 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs1436510891,2
Cuntested1166039754(+) CAGGTC/TGTGAA 2 T syn10--------
rs1461897931,2
--166038791(+) AAAGAA/GGTGGG 1 -- ds50010--------
rs45280971,2
C,F,H--166038795(+) AGGTGG/CGTAGA 1 -- ds50019Minor allele frequency- C:0.03NS EA NA 960
rs1454504721,2
--166038799(+) GGGTAA/GACGGA 1 -- ds50010--------
rs1488369961,2
--166038801(+) GTAGAC/TGGAAC 1 -- ds50010--------
rs1434946461,2
--166038802(+) TAGACA/GGAACT 1 -- ds50010--------
rs618350881,2
C,F--166038842(+) CACCTT/CGGACA 1 -- ds50015Minor allele frequency- C:0.15NA WA EA 362
rs1479975231,2
--166038860(+) GGAGGC/TTTTCT 1 -- ds50010--------
rs745860871,2
C,F--166038922(+) TCCATT/CGAGTG 1 -- ds50011Minor allele frequency- C:0.06WA 118
rs46397331,2
C,F,A,H--166038967(+) TATTAA/GTGTGT 1 -- ds500131Minor allele frequency- G:0.25NS EA NA WA CSA 3196

HapMap Linkage Disequilibrium report for FAM78B (166026674 - 166136206 bp)

Structural Variations
     Database of Genomic Variants (DGV) 1 variation for FAM78B:    About this table    
Variant IDTypeSubtypePubMed ID
esv2719162CNV Deletion23290073

Site Specific Mutation Identification with PCR Assays
SeqTarget long-range PCR primers for resequencing FAM78B
DNA2.0 Custom Variant and Variant Library Synthesis for FAM78B

(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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Find genes that share disorders with FAM78B           About GenesLikeMe

Genetic Association Database (GAD): FAM78B
Human Genome Epidemiology (HuGE) Navigator: FAM78B (2 documents)

Export disorders for FAM78B gene to outside databases

(in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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PubMed articles for FAM78B gene, integrated from 10 sources (see all 13):
(articles sorted by number of sources associating them with FAM78B)
    Utopia: connect your pdf to the dynamic
world of online information

  1. Follow-up of a major linkage peak on chromosome 1 reveals suggestive QTLs associated with essential hypertension: GenNet study. (PubMed id 19536175)1, 4 Ehret G.B....Chakravarti A. (Eur. J. Hum. Genet. 2009)
  2. Pre-B-cell leukemia homeobox 1 (PBX1) shows functional and possible genetic association with bone mineral density variation. (PubMed id 19064610)1, 4 Cheung C.L....Kung A.W. (Hum. Mol. Genet. 2009)
  3. The DNA sequence and biological annotation of human chromosome 1. (PubMed id 16710414)1, 2 Gregory S.G.... Bentley D.R. (Nature 2006)
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S.... Malek J. (Genome Res. 2004)
  5. Full-length transcriptome analysis of human retina-derived cell lines ARPE-19 and Y79 using the vector-capping method. (PubMed id 21697133)1 Oshikawa M.... Kato S. (Invest. Ophthalmol. Vis. Sci. 2011)
  6. Chromosome 6p22 locus associated with clinically aggressive neuroblastoma. (PubMed id 18463370)4 Maris J.M....Hakonarson H. (N. Engl. J. Med. 2008)
  7. A genome-wide association study for blood lipid phenotypes in the Framingham Heart Study. (PubMed id 17903299)4 Kathiresan S....Cupples L.A. (BMC Med. Genet. 2007)
  8. A genome-wide association for kidney function and endocrine-related traits in the NHLBI's Framingham Heart Study. (PubMed id 17903292)4 Hwang S.J....Fox C.S. (BMC Med. Genet. 2007)
  9. Genome-wide association with select biomarker traits in the Framingham Heart Study. (PubMed id 17903293)4 Benjamin E.J....Vasan R.S. (BMC Med. Genet. 2007)
  10. Genome-wide association and linkage analyses of hemostatic factors and hematological phenotypes in the Framingham Heart Study. (PubMed id 17903294)4 Yang Q....O'Donnell C.J. (BMC Med. Genet. 2007)

(in PubMed, OMIM, and NCBI Bookshelf)
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 ANDOR
Aliases
Free Text  

  Query String
PubMed
OMIM
NCBI Bookshelf
  (Note: In FireFox, select the above section and copy using Ctrl-C)

(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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Entrez Gene: 149297 HGNC: 13495 AceView: LOC149297 Ensembl:ENSG00000188859 euGenes: HUgn149297
ECgene: FAM78B H-InvDB: FAM78B

(According to HUGE)
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  --

(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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NameDescription
PharmGKB entry for FAM78B Pharmacogenomics, SNPs, Pathways

(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from LifeMap Sciences, Inc.)
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Patent Information for FAM78B gene:
Search GeneIP for patents involving FAM78B

GeneCards and IP:
Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



(Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, eBioscience, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
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GeneCards Homepage - Last full update: 7 May 2014 - Incrementals: 9 May 2014 , 2 Jun 2014 , 26 Jun 2014 , 30 Jun 2014 , 21 Aug 2014 , 8 Sep 2014

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