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FAM78A Gene

protein-coding   GIFtS: 40
GCID: GC09M134133

Family With Sequence Similarity 78, Member A

(Previous name: chromosome 9 open reading frame 59)
(Previous symbol: C9orf59)
  Search for FAM78A
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 A1 2
C9orf591 2 3
Chromosome 9 Open Reading Frame 591
Protein FAM78A2

External Ids:    HGNC: 254651   Entrez Gene: 2863362   Ensembl: ENSG000001268827   UniProtKB: Q5JUQ03   

Export aliases for FAM78A gene to outside databases

Previous GC identifers: GC09M131165 GC09M133123 GC09M103624


(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 FAM78A Gene:
FAM78A (family with sequence similarity 78, member A) is a protein-coding gene. An important paralog of this gene is FAM78B.


(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_000009.11  NC_018920.2  NT_008470.20  
Regulatory elements:
   Regulatory transcription factor binding sites in the FAM78A gene promoter:
         STAT5B   RelA   Nkx2-5   Meis-1b   GATA-1   POU2F1   Zic1   POU2F1a   Meis-1a   Meis-1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidFAM78A promoter sequence
   Search Chromatin IP Primers for FAM78A

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat FAM78A


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

Entrez Gene cytogenetic band: 9q34   Ensembl cytogenetic band:  9q34.13   HGNC cytogenetic band: 9q34

FAM78A Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
FAM78A gene location

GeneLoc information about chromosome 9         GeneLoc Exon Structure

GeneLoc location for GC09M134133:  view genomic region     (about GC identifiers)

Start:
134,133,463 bp from pter      End:
134,151,934 bp from pter
Size:
18,472 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: FA78A_HUMAN, Q5JUQ0 (See protein sequence)
Recommended Name: Protein FAM78A  
Size: 283 amino acids; 31968 Da
Sequence caution: Sequence=AAH49388.1; Type=Erroneous initiation;
Secondary accessions: Q86VQ9 Q9H7P4

Explore the universe of human proteins at neXtProt for FAM78A: NX_Q5JUQ0

Explore proteomics data for FAM78A at MOPED

Post-translational modifications: 

  • Ubiquitination2 at Lys241
  • Glycosylation2 at Ser26
  • Modification sites at PhosphoSitePlus

  • See FAM78A Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_203745.2  
    ENSEMBL proteins: 
     ENSP00000361343   ENSP00000361345   ENSP00000419959  

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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: Q5JUQ0

    UniProtKB/Swiss-Prot: FA78A_HUMAN, Q5JUQ0
    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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    Animal Models:
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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
    cytoskeleton2
    cytosol1
    extracellular1
    golgi apparatus1
    mitochondrion1
    nucleus1
    plasma membrane1

    (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 FAM78A
    Interactions:

        Search GeneGlobe Interaction Network for FAM78A

    (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 FAM78A (FA78A)



    (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 FAM78A gene: 
    NM_033387.3  

    Unigene Cluster for FAM78A:

    Family with sequence similarity 78, member A
    Hs.143878  [show with all ESTs]
    Unigene Representative Sequence: AK024434
    4 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000247295 ENST00000372269(uc004caj.3) ENST00000372271(uc004cak.3)
    ENST00000464831
    miRNA
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    Additional mRNA sequence: 

    AK024434.1 AK095423.1 BC029924.2 BC049388.2 

    5 DOTS entries:

    DT.205230  DT.100779860  DT.428775  DT.100021970  DT.95202709 

    Selected AceView cDNA sequences (see all 88):

    BX483006 AI298227 BX280962 T12580 BC029924 AW403583 BM455452 BM854739 
    BX281711 AA913953 AA810499 AI190772 BM150304 BC037559 AI025500 BM972587 
    BM725866 AK095423 AI826238 BM917900 F19409 AW082984 BM972149 AA972900 

    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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    FAM78A expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: CGGCCTTATG
    FAM78A Expression
    About this image

    FAM78A Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    FAM78A Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.143878
        Custom PCR Arrays for FAM78A
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for FAM78A

    (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 FAM78A gene from Selected species (see all 12)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Fam78a1 , 5 family with sequence similarity 78, member A1, 5 92.34(n)1
    97.17(a)1
      2 (22.00 cM)5
    2413031  NM_175511.41  NP_780720.11 
     320500555 
    chicken
    (Gallus gallus)
    Aves FAM78A1 family with sequence similarity 78, member A 83.9(n)
    86.31(a)
      771980  XM_001233856.3  XP_001233857.1 
    lizard
    (Anolis carolinensis)
    Reptilia FAM78A6
    family with sequence similarity 78, member A
    81(a)
    1 ↔ 1
    GL344605.1(2727-3272)
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia fam78a1 family with sequence similarity 78, member A 73.76(n)
    74.9(a)
      100145734  NM_001127108.1  NP_001120580.1 
    zebrafish
    (Danio rerio)
    Actinopterygii Dr.168882 Transcribed sequences 77.46(n)    BI476430.1 


    ENSEMBL Gene Tree for FAM78A (if available)
    TreeFam Gene Tree for FAM78A (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for FAM78A gene
    FAM78B2  
    8 SIMAP similar genes for FAM78A using alignment to 4 protein entries:     FA78A_HUMAN (see all proteins):
    AURA2    NF2    FAM78B    EIF3L    LINC00596    GLT8D2
    NRAMP1    FAM175A

    Find genes that share paralogs with FAM78A           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 FAM78A (see all 453)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 9 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1883955641,2
    --103644488(+) ATGAGG/TCTGTA 1 -- us2k10--------
    rs1150729601,2
    C,F--103644584(+) GGCAGC/TTACAT 1 -- us2k11Minor allele frequency- T:0.02WA 118
    rs1813452831,2
    --103644624(+) CCCCAC/TGACTC 1 -- us2k10--------
    rs1918057751,2
    --134133136(+) CTGTTC/TGCCAA 1 -- int10--------
    rs3529581,2
    C,F,H--134133142(-) GACTTT/ATTGGC 1 -- int17Minor allele frequency- A:0.01NS EA NA 512
    rs3529571,2
    C,F,H--134133338(-) CCCGTG/ACTCAG 1 -- int118Minor allele frequency- A:0.06NS EA NA WA CSA 1067
    rs745079191,2
    F--134133382(+) GATACG/ATTCAC 1 -- int11Minor allele frequency- A:0.05NA 120
    rs1852357771,2
    --134133385(+) ACGTTC/TACCCC 1 -- int10--------
    rs1477393601,2
    --134133445(+) GAAACA/TTCCAG 1 -- int10--------
    rs1885504611,2
    --134133451(+) TCCAGA/GACCTA 1 -- int10--------

    HapMap Linkage Disequilibrium report for FAM78A (134133463 - 134151934 bp)

    Structural Variations
         Database of Genomic Variants (DGV) Selected variations for FAM78A (see all 13):    About this table    
    Variant IDTypeSubtypePubMed ID
    esv2660985CNV Deletion23128226
    nsv509327CNV Insertion20534489
    dgv8312n71CNV Loss21882294
    nsv466602CNV Loss19166990
    nsv893987CNV Loss21882294
    nsv831739CNV Loss17160897
    dgv8311n71CNV Loss21882294
    dgv8310n71CNV Loss21882294
    nsv893979CNV Loss21882294
    nsv893983CNV Loss21882294

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    (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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      --

    (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 FAM78A gene integrated from 10 sources:
    (articles sorted by number of sources associating them with FAM78A)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. DNA sequence and analysis of human chromosome 9. (PubMed id 15164053)1, 2 Humphray S.J.... Dunham I. (Nature 2004)
    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. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (Nat. Genet. 2004)
    4. Characterization of long cDNA clones from human adult spleen. (PubMed id 11214971)1, 3 Hattori A.... Ohara O. (DNA Res. 2000)
    5. A proteome-wide, quantitative survey of in vivo ubiquitylation sites reveals widespread regulatory roles. (PubMed id 21890473)1 Wagner S.A....Choudhary C. (amp 2011)
    6. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (Proc. Natl. Acad. Sci. U.S.A. 2002)

    (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: 286336 HGNC: 25465 AceView: C9orf59 Ensembl:ENSG00000126882 euGenes: HUgn286336
    ECgene: FAM78A H-InvDB: FAM78A

    (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 FAM78A 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 FAM78A gene:
    Search GeneIP for patents involving FAM78A

    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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     Search Addgene for plasmids for FAM78A
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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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