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C5orf54 Gene

protein-coding   GIFtS: 42
GCID: GC05M159752

Chromosome 5 Open Reading Frame 54

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(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
Chromosome 5 Open Reading Frame 541 2     ZBED82 5
Transposon-Derived Buster3 Transposase-Like Protein2 3     Protein ZBED82
Zinc Finger BED Domain-Containing Protein 82 3     BUSTER35
Buster32 3     

External Ids:    HGNC: 308041   Entrez Gene: 639202   Ensembl: ENSG000002218867   OMIM: 6152535   UniProtKB: Q8IZ133   

Export aliases for C5orf54 gene to outside databases

Previous GC identifer: GC05M154913


(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 C5orf54 Gene:
C5orf54 (chromosome 5 open reading frame 54) is a protein-coding gene. GO annotations related to this gene include nucleic acid binding. An important paralog of this gene is ZBED5.


(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_000005.9  NT_023133.14  NC_018916.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the C5orf54 gene promoter:
         Oct-B1   Elk-1   Lmo2   IRF-1   LCR-F1   POU2F2C   PPAR-gamma1   POU2F1   POU2F1a   PPAR-gamma2   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search Chromatin IP Primers for C5orf54

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat C5orf54


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

Entrez Gene cytogenetic band: 5q33.3   Ensembl cytogenetic band:  5q33.3   HGNC cytogenetic band: 5q33.3

C5orf54 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
C5orf54 gene location

GeneLoc information about chromosome 5         GeneLoc Exon Structure

GeneLoc location for GC05M159752:  view genomic region     (about GC identifiers)

Start:
159,820,155 bp from pter      End:
159,827,104 bp from pter
Size:
6,950 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., 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: ZBED8_HUMAN, Q8IZ13 (See protein sequence)
Recommended Name: Protein ZBED8  
Size: 594 amino acids; 68327 Da
Miscellaneous: May be derived from an ancient transposon that has lost its ability to translocate. Exhibits a
close evolutionary relationship with ZBED5, but does not contain any zinc finger
Secondary accessions: D3DQJ9 Q9H5S8 Q9UH87

Explore the universe of human proteins at neXtProt for C5orf54: NX_Q8IZ13

Explore proteomics data for C5orf54 at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See C5orf54 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_071373.2  
    ENSEMBL proteins: 
     ENSP00000386184   ENSP00000428831  

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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:
     IPR012337 RNaseH-like_dom

    Graphical View of Domain Structure for InterPro Entry Q8IZ13

    ProtoNet protein and cluster: Q8IZ13


    Find genes that share domains with C5orf54           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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         Gene Ontology (GO): 1 molecular function term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003676nucleic acid binding IEA--
         
    Find genes that share ontologies with C5orf54           About GenesLikeMe


    Animal Models:
       genOway: Develop your customized and physiologically relevant rodent model for C5orf54

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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
    cytosol3
    mitochondrion2
    plasma membrane2
    nucleus1

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005739mitochondrion ----

    Find genes that share ontologies with C5orf54           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 C5orf54
    Interactions:

        Search GeneGlobe Interaction Network for C5orf54

    STRING Interaction Network Preview (showing 2 interactants - click image to see more details)

    Selected Interacting proteins for C5orf54 (Q8IZ132, 3 ENSP000003861844) via UniProtKB, MINT, STRING, and/or I2D (see all 7)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    HSF4Q9ULV52, 3, ENSP000002640094MINT-8259318 I2D: score=2 STRING: ENSP00000264009
    EEDO755302, 3MINT-8259296 I2D: score=2 
    EEF1GP266412, 3MINT-8259307 I2D: score=2 
    KIAA1377Q9P2H02, 3MINT-8259329 I2D: score=2 
    MBTPS1Q147032, 3MINT-8259340 I2D: score=2 
    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 C5orf54 (ZBED8)



    (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 C5orf54 gene: 
    NM_022090.3  

    Unigene Cluster for C5orf54:

    Chromosome 5 open reading frame 54
    Hs.529464  [show with all ESTs]
    Unigene Representative Sequence: NM_022090
    2 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000408953(uc003lye.1 uc003lyf.1) ENST00000523213
    miRNA
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    hsa-miR-616* hsa-miR-590-3p hsa-miR-373*
    Browse SwitchGear 3'UTR luciferase reporter plasmids
    Inhib. RNA
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      QuantiFast Probe-based Assays in human, mouse, rat C5orf54

    4 DOTS entries:

    DT.311239  DT.120860028  DT.87010368  DT.120860025 

    Selected AceView cDNA sequences (see all 61):

    AI193935 D62521 CR612548 CK903902 AA450377 AA403133 BM052948 CB052583 
    AA577540 AW236662 AA954962 W94245 CB052584 BG104921 AW182259 BM464355 
    W94204 BX391577 BX333441 BX333279 BX114784 BM314495 BX327680 AA728782 

    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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    C5orf54 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: --
    C5orf54 Expression
    About this image


    C5orf54 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
     
     Blood (Hematopoietic System)
             Hematopoietic Stem Cells Hematopoietic Bone Marrow
     
     Ovary (Reproductive System)
    C5orf54 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    C5orf54 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.529464
        Custom PCR Arrays for C5orf54
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    In Situ
    Assay Products:
     

     
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    (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 C5orf54 gene from Selected species (see all 6)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    dog
    (Canis familiaris)
    Mammalia C4H5orf541 chromosome 4 open reading frame, human C5orf54 92.93(n)
    94.78(a)
      100856326  XM_005619238.1  XP_005619295.1 
    lizard
    (Anolis carolinensis)
    Reptilia --
    Uncharacterized protein
    29(a)
    many ↔ many
    3(128791951-128792994)
    zebrafish
    (Danio rerio)
    Actinopterygii BX664605.16
    Uncharacterized protein
    31(a)
    many ↔ many
    4(39828194-39829633) ENSDARG00000006874


    ENSEMBL Gene Tree for C5orf54 (if available)
    TreeFam Gene Tree for C5orf54 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for C5orf54 gene
    ZBED52  KRBA22  SCAND32  GTF2IRD22  FAM200A2  FAM200B2  EPM2AIP12  GTF2IRD2B2  

    Find genes that share paralogs with C5orf54           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 C5orf54 (see all 205)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 5 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1931996191,2
    --159819946(+) GTAAAA/GGAAAA 1 -- ds50010--------
    rs1436108911,2
    --159819956(+) AATAAA/GTATAG 1 -- ds50010--------
    rs1150786631,2
    C,F--159820335(+) AAAGAC/TGGGCG 1 -- ut311Minor allele frequency- T:0.03WA 118
    rs11338351,2
    C--159820486(-) CTAAGT/CATCTG 1 -- ut312Minor allele frequency- C:0.00MN NA 186
    rs1849822631,2
    --159820645(+) AAAGAG/TACAGA 1 -- ut310--------
    rs793628711,2
    C,F--159820661(+) AGCTTA/CATTTT 1 -- ut311Minor allele frequency- C:0.09WA 118
    rs1885814431,2
    --159820739(+) CTGTAA/GCTTTT 2 L syn10--------
    rs1397373781,2
    C,F--159820751(+) TTCAAT/CGATGT 2 /I /V mis11Minor allele frequency- C:0.00NA 2384
    rs728143741,2
    C--159820792(+) CCACAC/TGGATA 2 H R mis10--------
    rs1437166221,2
    C--159820847(+) TAAAAG/ATGATG 2 /L /F mis11Minor allele frequency- A:0.00NA 4468

    HapMap Linkage Disequilibrium report for C5orf54 (159820155 - 159827104 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 2 variations for C5orf54:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv883072CNV Loss21882294
    nsv5097CNV Loss18451855

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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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    OMIM gene information: 615253    OMIM disorders: --


    Find genes that share disorders with C5orf54           About GenesLikeMe


    Export disorders for C5orf54 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 C5orf54 gene integrated from 10 sources:
    (articles sorted by number of sources associating them with C5orf54)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. ZBED evolution: repeated utilization of DNA transposons as regulators of diverse host functions. (PubMed id 23533661)1, 2, 3 Hayward A.... Jern P. (PLoS ONE 2013)
    2. Interspersed repeats and other mementos of transposable elements in mammalian genomes. (PubMed id 10607616)1, 2, 3 Smit A.F.A. (Curr. Opin. Genet. Dev. 1999)
    3. Weight loss after gastric bypass is associated with a variant at 15q26.1. (PubMed id 23643386)1 Hatoum I.J....Kaplan L.M. (Am. J. Hum. Genet. 2013)
    4. Pathway Analysis of ChIP-Seq-Based NRF1 Target Genes Suggests a Logical Hypothesis of their Involvement in the Pathogenesis of Neurodegenerative Diseases. (PubMed id 24250222)1 Satoh J....Yamamoto Y. (Gene Regul Syst Bio 2013)
    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. A directed protein interaction network for investigating intracellular signal transduction. (PubMed id 21900206)1 Vinayagam A....Wanker E.E. (Sci Signal 2011)
    7. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)2 Gerhard D.S.... Malek J. (Genome Res. 2004)
    8. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)2 Ota T.... Sugano S. (Nat. Genet. 2004)
    9. 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: 63920 HGNC: 30804 AceView: LOC63920 Ensembl:ENSG00000221886 euGenes: HUgn63920
    ECgene: C5orf54 H-InvDB: C5orf54

    (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 C5orf54 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 C5orf54 gene:
    Search GeneIP for patents involving C5orf54

    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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