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C7orf55 Gene

protein-coding   GIFtS: 39
GCID: GC07P139024

Chromosome 7 Open Reading Frame 55

  See related diseases
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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This gene clusters with an RNA gene
Subcategory (RNA class): lncRNA

Quality score for the ORGUL clustered with this gene is 3

Aliases
Chromosome 7 Open Reading Frame 551 2
Formation Of Mitochondrial Complexes 1 Homolog (S. Cerevisiae)1
FMC12
Formation Of Mitochondrial Complexes 1 Homolog2
UPF0562 Protein C7orf552

External Ids:    HGNC: 269461   Entrez Gene: 1547912   Ensembl: ENSG000001648987   UniProtKB: Q96HJ93   
ORGUL members:         

Export aliases for C7orf55 gene to outside databases

Previous GC identifers: GC07P138679 GC07P133335


(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 C7orf55 Gene:
C7orf55 (chromosome 7 open reading frame 55) is a protein-coding gene. Diseases associated with C7orf55 include intrahepatic cholangiocarcinoma, and cholangiocarcinoma.


(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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Regulatory elements:
   Regulatory transcription factor binding sites in the C7orf55 gene promoter:
         E2F-4   E2F-3a   E2F-5   STAT1   Elk-1   HTF   E2F-2   FOXL1   YY1   Nkx6-1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidC7orf55 promoter sequence
   Search Chromatin IP Primers for C7orf55

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat C7orf55


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

Entrez Gene cytogenetic band: 7q34   Ensembl cytogenetic band:  7q34   HGNC cytogenetic band: 7q34

C7orf55 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
C7orf55 gene location

GeneLoc information about chromosome 7         GeneLoc Exon Structure

GeneLoc location for GC07P139024:  view genomic region     (about GC identifiers)

Start:
139,024,203 bp from pter      End:
139,031,065 bp from pter
Size:
6,863 bases      Orientation:
plus strand

1 alternative location:
Chr7+,CRA_TCAG 138,370,469-138,375,111     

(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, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
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UniProtKB/Swiss-Prot: CG055_HUMAN, Q96HJ9 (See protein sequence)
Recommended Name: UPF0562 protein C7orf55  
Size: 113 amino acids; 12749 Da
Sequence caution: Sequence=AAF28946.1; Type=Erroneous initiation; Note=Translation N-terminally shortened;
Sequence=AAF28946.1; Type=Frameshift; Positions=64;
Secondary accessions: B7Z4Q3 Q75M90 Q9P0B3
Alternative splicing: 2 isoforms:  Q96HJ9-1   Q96HJ9-2   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for C7orf55: NX_Q96HJ9

Explore proteomics data for C7orf55 at MOPED

Post-translational modifications: 

  • Ubiquitination2 at Lys252
  • Modification sites at PhosphoSitePlus

  • See C7orf55 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_932068.2  
    ENSEMBL proteins: 
     ENSP00000297534  

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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: Q96HJ9

    UniProtKB/Swiss-Prot: CG055_HUMAN, Q96HJ9
    Similarity: Belongs to the UPF0562 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, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Phenotypes:
         2 GenomeRNAi human phenotypes for C7orf55:
     G2 arrest  Increased G2M DNA content 

         1 MGI phenotypic allele for 1110001J03Rik (no phenotypes)

    C7orf55 for phenotypes           About GeneDecksing

    Animal Models:
       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for C7orf55
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    hsa-mir-103a-3p (MIRT027056)

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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

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

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

    C7orf55 for ontologies           About GeneDecksing


    (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 C7orf55
    Interactions:

        Search GeneGlobe Interaction Network for C7orf55

    (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 C7orf55 (CG055)



    (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,
    Conferences by KenesGroup, 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, Primers from OriGene, and/or QIAGEN )
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    REFSEQ mRNAs for C7orf55 gene: 
    NM_197964.4  

    5 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000468383 ENST00000481123 ENST00000482181 ENST00000488886 ENST00000297534(uc003vuw.4)

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      QuantiTect SYBR Green Assays in human, mouse, rat C7orf55
      QuantiFast Probe-based Assays in human, mouse, rat C7orf55

    Selected AceView cDNA sequences (see all 129):

    AI292139 BE857372 N73669 AI138857 AW612658 BX116138 AI479418 CB125801 
    BM693181 AI300972 BQ680999 AI306499 BQ889014 AI094689 BF446095 AI208569 
    AI138856 AI951379 AI306498 BM672187 AK093018 BM668413 AI680820 AI469870 

    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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    C7orf55 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: GAGAATATCC
    C7orf55 Expression
    About this image

    C7orf55 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    C7orf55 Protein Expression
        Custom PCR Arrays for C7orf55
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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 animals.

    Orthologs for C7orf55 gene from Selected species (see all 13)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia 1110001J03Rik1 , 5 RIKEN cDNA 1110001J03 gene1, 5 88.5(n)1
    92.92(a)1
      6 (17.84 cM)5
    661171  NM_025363.31  NP_079639.11 
     385335025 
    chicken
    (Gallus gallus)
    Aves C7orf556
    chromosome 7 open reading frame 55
    79(a)
    1 ↔ 1
    1(48973389-48974713)
    African clawed frog
    (Xenopus laevis)
    Amphibia Xl.129892 Xenopus laevis transcribed sequence with weak similarity to protein refNP_079639.1 (M.musculus) RIKEN cDNA 1110001J03 [Mus musculus] less 74(n)    BJ094950.1 
    zebrafish
    (Danio rerio)
    Actinopterygii LOC1003306601 UPF0562 protein C7orf55 homolog 54.74(n)
    47.71(a)
      100330660  XM_002661013.3  XP_002661059.2 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG341176
    --
    39(a)
    1 ↔ 1
    3R(5225292-5225771)
    worm
    (Caenorhabditis elegans)
    Secernentea C29E4.126
    Protein C29E4.12 (C29E4.12) mRNA, complete cds
    31(a)
    1 ↔ 1
    III(7941060-7941613) WBGene00016209


    ENSEMBL Gene Tree for C7orf55 (if available)
    TreeFam Gene Tree for C7orf55 (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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    1 SNPs for C7orf55    About this table    
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 7 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs102651,2,4
    ----see VAR_0425202 mis40--------

    HapMap Linkage Disequilibrium report for C7orf55 (139024203 - 139031065 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 1 variation for C7orf55:    About this table    
    Variant IDTypeSubtypePubMed ID
    esv2735212CNV Deletion23290073

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing C7orf55
    DNA2.0 Custom Variant and Variant Library Synthesis for C7orf55

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    2 diseases for C7orf55:    
    About MalaCards
    intrahepatic cholangiocarcinoma    cholangiocarcinoma


    C7orf55 for disorders           About GeneDecksing

    Genetic Association Database (GAD): C7orf55
    Human Genome Epidemiology (HuGE) Navigator: C7orf55 (1 document)

    Export disorders for C7orf55 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 C7orf55 gene, integrated from 10 sources (see all 12):
    (articles sorted by number of sources associating them with C7orf55)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression. (PubMed id 20877624)1, 4 Hendrickson S.L....O'Brien S.J. (PLoS ONE 2010)
    2. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (Nat. Genet. 2004)
    3. The DNA sequence of human chromosome 7. (PubMed id 12853948)1, 2 Hillier L.W.... Wilson R.K. (Nature 2003)
    4. 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)
    5. Initial characterization of the human central proteome. (PubMed id 21269460)2 Burkard T.R.... Colinge J. (BMC Syst. Biol. 2011)
    6. 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)
    7. Identification of intrahepatic cholangiocarcinoma related genes by comparison with normal liver tissues using expressed sequence tags. (PubMed id 16712791)1 Wang A.G....Kim N.S. (Biochem. Biophys. Res. Commun. 2006)
    8. The LIFEdb database in 2006. (PubMed id 16381901)1 Mehrle A....Wiemann S. (Nucleic Acids Res. 2006)
    9. 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)
    10. From ORFeome to biology: a functional genomics pipeline. (PubMed id 15489336)1 Wiemann S....Poustka A. (Genome Res. 2004)

    (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: 154791 HGNC: 26946 AceView: HSPC268 Ensembl:ENSG00000164898 euGenes: HUgn154791
    ECgene: C7orf55 H-InvDB: C7orf55

    (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 C7orf55 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 C7orf55 gene:
    Search GeneIP for patents involving C7orf55

    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, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript, and ESI BIO, 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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