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CXorf56 Gene

protein-coding   GIFtS: 44
GCID: GC0XM118672

Chromosome X Open Reading Frame 56

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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 X Open Reading Frame 561 2
UPF0428 Protein CXorf562

External Ids:    HGNC: 262391   Entrez Gene: 639322   Ensembl: ENSG000000186107   UniProtKB: Q9H5V93   

Export aliases for CXorf56 gene to outside databases

Previous GC identifers: GC0XM118556 GC0XM108165


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for CXorf56 Gene:
While this gene is well-supported by transcript data, no functional information on its protein products is
currently available. Three transcript variants encoding different isoforms have been found for this gene.
(provided by RefSeq, Dec 2009)

GeneCards Summary for CXorf56 Gene:
CXorf56 (chromosome X open reading frame 56) is a protein-coding gene.




(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_000023.10  NC_018934.2  NT_011786.17  
Regulatory elements:
   Regulatory transcription factor binding sites in the CXorf56 gene promoter:
         MEF-2   AP-2gamma   MEF-2A   FOXJ2 (long isoform)   AP-2beta   FOXJ2   aMEF-2   AP-2alpha   AP-2alphaA   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidCXorf56 promoter sequence
   Search Chromatin IP Primers for CXorf56

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat CXorf56


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

Entrez Gene cytogenetic band: Xq23   Ensembl cytogenetic band:  Xq24   HGNC cytogenetic band: Xq24

CXorf56 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
CXorf56 gene location

GeneLoc information about chromosome X         GeneLoc Exon Structure

GeneLoc location for GC0XM118672:  view genomic region     (about GC identifiers)

Start:
118,672,112 bp from pter      End:
118,699,397 bp from pter
Size:
27,286 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: CX056_HUMAN, Q9H5V9 (See protein sequence)
Recommended Name: UPF0428 protein CXorf56  
Size: 222 amino acids; 25625 Da
Caution: May be duplicated on chromosome 8, within an intron of the ERLIN2 gene
Sequence caution: Sequence=AAB96348.1; Type=Erroneous gene model prediction;
Secondary accessions: A8MPX7 B4DQN2 D3DWH9 F5GWL7 O43351
Alternative splicing: 3 isoforms:  Q9H5V9-1   Q9H5V9-2   Q9H5V9-3   

Explore the universe of human proteins at neXtProt for CXorf56: NX_Q9H5V9

Explore proteomics data for CXorf56 at MOPED

Post-translational modifications: 

  • Ubiquitination2 at Lys67, Lys121, Lys128
  • Modification sites at PhosphoSitePlus

  • See CXorf56 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins (3 alternative transcripts): 
    NP_001164040.1  NP_001164041.1  NP_071384.1  

    ENSEMBL proteins: 
     ENSP00000320345   ENSP00000360652   ENSP00000441786  

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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: Q9H5V9

    1 Blocks protein domain: IPB003746 Protein of unknown function DUF167

    UniProtKB/Swiss-Prot: CX056_HUMAN, Q9H5V9
    Similarity: Belongs to the UPF0428 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:
         3 MGI mutant phenotypes (inferred from 2 alleles(MGI details for C330007P06Rik):
     embryogenesis  growth/size/body  nervous system 

    Find genes that share phenotypes with CXorf56           About GenesLikeMe

    Animal Models:
       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for CXorf56
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    miRTarBase miRNAs that target CXorf56:
    hsa-mir-92a-3p (MIRT049078)

    Block miRNA regulation of human, mouse, rat CXorf56 using miScript Target Protectors
    5 qRT-PCR Assays for microRNAs that regulate CXorf56:
    hsa-miR-425 hsa-miR-3185 hsa-miR-3614-3p hsa-miR-3119 hsa-miR-548c-3p
    SwitchGear 3'UTR luciferase reporter plasmidCXorf56 3' UTR sequence
    Inhib. RNA
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    Predesigned siRNA for gene silencing in human, mouse, rat CXorf56

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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for CXorf56


    (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
    nucleus2

    (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 CXorf56
    Interactions:

        Search GeneGlobe Interaction Network for CXorf56

    STRING Interaction Network Preview (showing 5 interactants - click image to see 6)

    Selected Interacting proteins for CXorf56 (Q9H5V91, 2, 3 ENSP000003606524) via UniProtKB, MINT, STRING, and/or I2D (see all 12)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    NFKBIL1Q9UBC11, 3, ENSP000003653184EBI-1053419,EBI-1043728 I2D: score=2 STRING: ENSP00000365318
    ENSG00000227565Q9UBC11, 3EBI-1053419,EBI-1043728 I2D: score=2 
    ENSG00000234530Q9UBC11, 3EBI-1053419,EBI-1043728 I2D: score=2 
    ENSG00000235125Q9UBC11, 3EBI-1053419,EBI-1043728 I2D: score=2 
    ENSG00000236196Q9UBC11, 3EBI-1053419,EBI-1043728 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 CXorf56 (CX056)



    (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 CXorf56 gene (3 alternative transcripts): 
    NM_001170569.1  NM_001170570.1  NM_022101.3  

    Unigene Cluster for CXorf56:

    Chromosome X open reading frame 56
    Hs.248572  [show with all ESTs]
    Unigene Representative Sequence: NM_001170569
    4 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000320339(uc004erj.2) ENST00000469448 ENST00000371594(uc004erk.2)
    ENST00000536133(uc011mtu.2)
    miRNA
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    5 qRT-PCR Assays for microRNAs that regulate CXorf56:
    hsa-miR-425 hsa-miR-3185 hsa-miR-3614-3p hsa-miR-3119 hsa-miR-548c-3p
    SwitchGear 3'UTR luciferase reporter plasmidCXorf56 3' UTR sequence
    Inhib. RNA
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    Predesigned siRNA for gene silencing in human, mouse, rat CXorf56
    Clone
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    GenScript: all cDNA clones in your preferred vector (see all 3): CXorf56 (NM_022101)
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for CXorf56
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat CXorf56
    Primer
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    OriGene qPCR primer pairs and template standards for CXorf56
    OriGene qSTAR qPCR primer pairs in human, mouse for CXorf56
    Pre-validated RT2 qPCR Primer Assay in human, mouse, rat CXorf56
      QuantiTect SYBR Green Assays in human, mouse, rat CXorf56
      QuantiFast Probe-based Assays in human, mouse, rat CXorf56

    Additional mRNA sequence: 

    AK096297.1 AK298877.1 

    9 DOTS entries:

    DT.435130  DT.100025376  DT.91755382  DT.100697914  DT.121289973  DT.100685266  DT.102823753  DT.92432771 
    DT.95268685 

    Selected AceView cDNA sequences (see all 117):

    BE155819 AW817149 BQ935396 BX092669 BE902841 BG169730 BG769258 BP343539 
    BM012461 BX283804 BE731943 BQ671448 CB122543 BG421690 BE902266 BI918714 
    BG281988 CB959711 BM553330 BM474690 BE903297 BQ070480 BG482180 AI917132 

    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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    CXorf56 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: AGCAAGAGGC
    CXorf56 Expression
    About this image

    CXorf56 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    CXorf56 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.248572
        Custom PCR Arrays for CXorf56
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    QuantiFast Probe-based Assays in human, mouse, rat CXorf56
    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for CXorf56

    (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 CXorf56 gene from Selected species (see all 16)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia C330007P06Rik1 , 5 RIKEN cDNA C330007P06 gene1, 5 92.04(n)1
    99.55(a)1
      X (21.23 cM)5
    776441  NM_029951.11  NP_084227.11 
     368237375 
    chicken
    (Gallus gallus)
    Aves CXORF561 chromosome 4 open reading frame, human CXorf56 82.85(n)
    95.67(a)
      428719  XM_003641123.2  XP_003641171.1 
    African clawed frog
    (Xenopus laevis)
    Amphibia c330007p06-A-prov2 hypothetical protein RIKEN cDNA C330007P06 gene 80.95(n)    BC046270.1 
    zebrafish
    (Danio rerio)
    Actinopterygii Dr.178872 Transcribed sequence with moderate similarity to protein more 78(n)    CK237411.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG168651 CG16865 58.46(n)
    57.07(a)
      34788  NM_001273522.1  NP_001260451.1 
    worm
    (Caenorhabditis elegans)
    Secernentea Y66D12A.81 Y66D12A.8 52.33(n)
    43.02(a)
      176589  NM_001268201.1  NP_001255130.1 


    ENSEMBL Gene Tree for CXorf56 (if available)
    TreeFam Gene Tree for CXorf56 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    (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 CXorf56 (see all 511)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr X posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1882934631,2
    --118667931(+) ATGACA/GGTTAA 3 -- ds50010--------
    rs59106061,2
    C,F,A,H--118667971(+) GGTAGG/AGAGGA 3 -- ds500114Minor allele frequency- A:0.43NS EA NA CSA 1854
    rs59106071,2
    C,F,A,H--118667989(+) GTTGCA/GAAGAC 3 -- ds500128Minor allele frequency- G:0.36NS EA NA WA CSA 2779
    rs1384567661,2
    --118668005(+) TGGATA/GCAGGA 3 -- ds50010--------
    rs2009045521,2
    --118668184(+) CAAAC-/AAAAAA 3 -- ds50010--------
    rs1809133111,2
    --118668251(+) GGGCAC/TCTACT 3 -- ds50010--------
    rs1872594821,2
    --118668294(+) TTAACA/TCAACT 3 -- ds50010--------
    rs59106081,2
    C,F,A,H--118668313(+) AACACT/CTTTTA 3 -- ut31 ese314Minor allele frequency- C:0.40NS EA NA CSA 1978
    rs1460592971,2
    --118668371(+) TATCAC/TTGAAG 3 -- ut310--------
    rs455377401,2
    C--118668432(+) CAAATA/GTAAAG 3 -- ut310--------

    HapMap Linkage Disequilibrium report for CXorf56 (118672112 - 118699397 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 1 variation for CXorf56:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv525652CNV Gain19592680

    Locus Specific Mutation Databases (LSDB): CXorf56

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing CXorf56
    DNA2.0 Custom Variant and Variant Library Synthesis for CXorf56

    (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 CXorf56 gene, integrated from 10 sources (see all 16):
    (articles sorted by number of sources associating them with CXorf56)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (Nat. Genet. 2004)
    2. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1, 3 Strausberg R.L....Marra M.A. (Proc. Natl. Acad. Sci. U.S.A. 2002)
    3. Dynamic protein-protein interaction wiring of the human spliceosome. (PubMed id 22365833)1 Hegele A....Stelzl U. (Mol. Cell 2012)
    4. A census of human soluble protein complexes. (PubMed id 22939629)1 Havugimana P.C....Emili A. (Cell 2012)
    5. Systems-wide analysis of ubiquitylation dynamics reveals a key role for PAF15 ubiquitylation in DNA-damage bypass. (PubMed id 23000965)1 Povlsen L.K....Choudhary C. (Nat. Cell Biol. 2012)
    6. A promiscuous biotin ligase fusion protein identifies proximal and interacting proteins in mammalian cells. (PubMed id 22412018)1 Roux K.J.... Burke B. (J. Cell Biol. 2012)
    7. Initial characterization of the human central proteome. (PubMed id 21269460)2 Burkard T.R.... Colinge J. (BMC Syst. Biol. 2011)
    8. 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)
    9. Interactions of pathological hallmark proteins: tubulin polymerization promoting protein/p25, beta-amyloid, and alpha-synuclein. (PubMed id 21832049)1 OlA!h J....OvA!di J. (J. Biol. Chem. 2011)
    10. Mass spectrometric analysis of lysine ubiquitylation reveals promiscuity at site level. (PubMed id 21139048)1 Danielsen J.M....Nielsen M.L. (amp 2011)

    (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: 63932 HGNC: 26239 AceView: FLJ22965 Ensembl:ENSG00000018610 euGenes: HUgn63932
    ECgene: CXorf56 H-InvDB: CXorf56

    (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 CXorf56 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 CXorf56 gene:
    Search GeneIP for patents involving CXorf56

    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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