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FAM50B Gene

protein-coding   GIFtS: 46
GCID: GC06P003849

Family With Sequence Similarity 50, Member B

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disease database 

(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 50, Member B1 2
X5L2 3 5
D6S2654E2
Protein FAM50B2
Protein XAP-5-Like3
FAM60B5

External Ids:    HGNC: 187891   Entrez Gene: 262402   Ensembl: ENSG000001459457   OMIM: 6146865   UniProtKB: Q9Y2473   

Export aliases for FAM50B gene to outside databases

Previous GC identifers: GC06P003795 GC06P003726


(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 FAM50B Gene:
FAM50B (family with sequence similarity 50, member B) is a protein-coding gene. An important paralog of this gene is FAM50A.


(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_000006.11  NC_018917.2  NT_007592.16  
Regulatory elements:
   Regulatory transcription factor binding sites in the FAM50B gene promoter:
         STAT5A   c-Ets-1   HNF-1A   GATA-1   N-Myc   PPAR-gamma1   E2F-1   E2F   HNF-1   PPAR-gamma2   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidFAM50B promoter sequence
   Search Chromatin IP Primers for FAM50B

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat FAM50B


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

Entrez Gene cytogenetic band: 6p25.2   Ensembl cytogenetic band:  6p25.2   HGNC cytogenetic band: 6p25.2

FAM50B Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
FAM50B gene location

GeneLoc information about chromosome 6         GeneLoc Exon Structure

GeneLoc location for GC06P003849:  view genomic region     (about GC identifiers)

Start:
3,849,620 bp from pter      End:
3,851,551 bp from pter
Size:
1,932 bases      Orientation:
plus 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., eBioscience, and/or antibodies-online,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., eBioscience, and/or antibodies-online, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, Cloud-Clone Corp, antibodies-online, and/or others.)
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UniProtKB/Swiss-Prot: FA50B_HUMAN, Q9Y247 (See protein sequence)
Recommended Name: Protein FAM50B  
Size: 325 amino acids; 38709 Da
Secondary accessions: Q5T2L6

Explore the universe of human proteins at neXtProt for FAM50B: NX_Q9Y247

Explore proteomics data for FAM50B at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See FAM50B Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_036267.1  
    ENSEMBL proteins: 
     ENSP00000369627   ENSP00000369625  

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    antibodies-online proteins for FAM50B (3 products) 

     
    antibodies-online peptides for FAM50B

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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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    1 InterPro protein domain:
     IPR007005 XAP5

    Graphical View of Domain Structure for InterPro Entry Q9Y247

    ProtoNet protein and cluster: Q9Y247

    UniProtKB/Swiss-Prot: FA50B_HUMAN, Q9Y247
    Similarity: Belongs to the FAM50 family


    Find genes that share domains with FAM50B           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, 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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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: FA50B_HUMAN, Q9Y247
    Induction: Imprinted. Promoter methylation of the maternal allele may restrict expression to the paternal allele
    in placenta

    Animal Models:

       genOway: Develop your customized and physiologically relevant rodent model for FAM50B

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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
    nucleus3
    cytosol2

    Gene Ontology (GO): 1 cellular component term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus IEA--

    Find genes that share ontologies with FAM50B           About GenesLikeMe


    (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 FAM50B
    Interactions:

        Search GeneGlobe Interaction Network for FAM50B

    STRING Interaction Network Preview (showing 4 interactants - click image to see more details)

    Selected Interacting proteins for FAM50B (Q9Y2472, 3 ENSP000003696254) via UniProtKB, MINT, STRING, and/or I2D (see all 7)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    CCDC85BQ158342, 3, ENSP000003116954MINT-66972 I2D: score=5 STRING: ENSP00000311695
    KPNA3O005053, ENSP000002616674I2D: score=3 STRING: ENSP00000261667
    LDOC1O957513, ENSP000003595574I2D: score=1 STRING: ENSP00000359557
    IKZF1Q134223I2D: score=1 
    SUMO2ENSP000004059654STRING: ENSP00000405965
    About this table

    (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 FAM50B (FA50B)



    (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 FAM50B gene: 
    NM_012135.1  

    Unigene Cluster for FAM50B:

    Family with sequence similarity 50, member B
    Hs.140944  [show with all ESTs]
    Unigene Representative Sequence: BC001261
    2 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000380274(uc021ykt.1) ENST00000380272(uc003mvu.3)
    miRNA
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    Primer
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      QuantiFast Probe-based Assays in human, mouse, rat FAM50B

    Additional mRNA sequence: 

    BC001261.1 Y18503.1 

    2 DOTS entries:

    DT.454081  DT.92004053 

    Selected AceView cDNA sequences (see all 84):

    BQ068002 BC001261 CR590152 BU957044 BU732878 CR623120 CR600946 BI768136 
    NM_012135 CR597441 BM553857 BM920833 CR602326 BQ278643 BM768583 BI258091 
    BU623307 CA423816 CD244667 CR605415 Y18503 BM663313 BQ777321 BI833616 

    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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    FAM50B expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: CCTCAGTTTG
    FAM50B Expression
    About this image


    FAM50B expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 3) fully expand
     
     Paraxial Mesoderm (Gastrulation Derivatives)
             PureStem E15, Meso-prx/latp Progenitor
     
     Lateral Plate Mesoderm (Gastrulation Derivatives)
             PureStem E15, Meso-prx/latp Progenitor
     
     Testis (Reproductive System)
    FAM50B Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    FAM50B Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.140944

    UniProtKB/Swiss-Prot: FA50B_HUMAN, Q9Y247
    Tissue specificity: Widely expressed. Mostly abundant in testis and adult and fetal brain

        Custom PCR Arrays for FAM50B
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for FAM50B

    (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 animals.

    Orthologs for FAM50B gene from Selected species (see all 7)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Fam50b1 , 5 family with sequence similarity 50, member B1, 5 85.74(n)1
    84.92(a)1
      13 (14.18 cM)5
    1081611  NM_138746.21  NP_620085.21 
     347396425 
    zebrafish
    (Danio rerio)
    Actinopterygii fam50a6
    family with sequence similarity 50, member A
    68(a)
    1 → many
    23(34298904-34316826) ENSDARG00000024895
    fruit fly
    (Drosophila melanogaster)
    Insecta CG122596
    --
    50(a)
    1 → many
    3R(23745566-23746811)
    worm
    (Caenorhabditis elegans)
    Secernentea C47E8.46
    Protein C47E8.4, isoform b
    42(a)
    1 → many
    V(14683671-14685528) WBGene00008143


    ENSEMBL Gene Tree for FAM50B (if available)
    TreeFam Gene Tree for FAM50B (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for FAM50B gene
    FAM50A2  
    1 SIMAP similar gene for FAM50B using alignment to 1 protein entry:     FA50B_HUMAN:
    FAM50A

    Find genes that share paralogs with FAM50B           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 FAM50B (see all 98)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 6 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1822232861,2
    --3847713(+) TCCTCA/TCCTCT 1 -- us2k10--------
    rs1853253221,2
    --3847952(+) AAAGAA/GGCCTA 1 -- us2k10--------
    rs1400273001,2
    --3848012(+) CATTTC/TTAGCC 1 -- us2k10--------
    rs755486131,2
    C,F--3848118(+) TGTCTC/TAGGCA 1 -- us2k12Minor allele frequency- T:0.10CSA WA 120
    rs3776727651,2
    C--3848160(+) AGGAA-/CCCC  
            
    CAGCC
    1 -- us2k10--------
    rs1897350171,2
    C--3848243(+) CACTTC/TGGAGT 1 -- us2k10--------
    rs1419301441,2
    --3848431(+) AATCTG/TCAATT 1 -- us2k10--------
    rs1463376111,2
    --3848470(+) TCCCAA/GAGCTC 1 -- us2k10--------
    rs1827328621,2
    --3848595(+) GAAAGC/TGTGAA 1 -- us2k10--------
    rs77408801,2
    C,F,A,H--3848633(+) GAGGAA/GCGTCA 1 -- us2k130Minor allele frequency- G:0.22NS EA NA WA CSA 3207

    HapMap Linkage Disequilibrium report for FAM50B (3849620 - 3851551 bp)

    Structural Variations
          Database of Genomic Variants (DGV) variations for FAM50B: --
    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing FAM50B
    DNA2.0 Custom Variant and Variant Library Synthesis for FAM50B

    (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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    OMIM gene information: 614686    OMIM disorders: --

    1 disease from the University of Copenhagen DISEASES database for FAM50B:
    Silver-Russell syndrome

    Find genes that share disorders with FAM50B           About GenesLikeMe


    Export disorders for FAM50B 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 FAM50B gene, integrated from 10 sources (see all 13):
    (articles sorted by number of sources associating them with FAM50B)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Human and mouse XAP-5 and XAP-5-like (X5L) genes: identification of an ancient functional retroposon differentially expressed in testis. (PubMed id 10534398)1, 2, 3, 9 Sedlack Z.... Poustka A. (Genomics 1999)
    2. 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)
    3. Genome-wide association study of chemotherapeutic agent-induced severe neutropenia/leucopenia for patients in Biobank Japan. (PubMed id 23648065)1 Low S.K....Nakamura Y. (Cancer Sci. 2013)
    4. A census of human soluble protein complexes. (PubMed id 22939629)1 Havugimana P.C....Emili A. (Cell 2012)
    5. N-terminal acetylome analyses and functional insights of the N- terminal acetyltransferase NatB. (PubMed id 22814378)2 Van Damme P....Aldabe R. (Proc. Natl. Acad. Sci. U.S.A. 2012)
    6. Methylation screening of reciprocal genome-wide UPDs identifies novel human-specific imprinted genes. (PubMed id 21593219)2 Nakabayashi K.... Monk D. (Hum. Mol. Genet. 2011)
    7. Comparative proteomic analysis identifies a role for SUMO in protein quality control. (PubMed id 21693764)1 Tatham M.H....Hay R.T. (Sci Signal 2011)
    8. An empirical framework for binary interactome mapping. (PubMed id 19060904)1 Venkatesan K....Vidal M. (Nat. Methods 2009)
    9. XAP5 CIRCADIAN TIMEKEEPER coordinates light signals for proper timing of photomorphogenesis and the circadian clock in Arabidopsis. (PubMed id 18515502)1 Martin-Tryon E.L. and Harmer S.L. (Plant Cell 2008)
    10. hORFeome v3.1: a resource of human open reading frames representing over 10,000 human genes. (PubMed id 17207965)1 Lamesch P.... Vidal M. (Genomics 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: 26240 HGNC: 18789 AceView: FAM50B Ensembl:ENSG00000145945 euGenes: HUgn26240
    ECgene: FAM50B H-InvDB: FAM50B

    (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 FAM50B 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 FAM50B gene:
    Search GeneIP for patents involving FAM50B

    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, eBioscience, antibodies-online, 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 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 , 7 Oct 2014

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