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C1orf85 Gene

protein-coding   GIFtS: 45
GCID: GC01M156259

Chromosome 1 Open Reading Frame 85

  Search for C1orf85
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): antisense

Quality score for the ORGUL clustered with this gene is 3

Aliases
Chromosome 1 Open Reading Frame 851 2
Kidney Lysosomal Membrane Protein1 2
NCU-G12
Kidney Predominant Protein NCU-G12
Lysosomal Protein NCU-G12

External Ids:    HGNC: 294361   Entrez Gene: 1127702   Ensembl: ENSG000001987157   UniProtKB: Q8WWB73   
ORGUL members:         

Export aliases for C1orf85 gene to outside databases

Previous GC identifers: GC01M153076 GC01M154531 GC01M156250 GC01M127623


(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 C1orf85 Gene:
C1orf85 (chromosome 1 open reading frame 85) is a protein-coding gene. GO annotations related to this gene include ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity and sequence-specific DNA binding transcription factor activity.


(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:
NC_000001.11  NT_004487.20  NC_018912.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the C1orf85 gene promoter:
         SRF   Max   SRF (504 AA)   HOXA5   Nkx2-5   c-Myc   YY1   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search Chromatin IP Primers for C1orf85

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat C1orf85


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

Entrez Gene cytogenetic band: 1q22   Ensembl cytogenetic band:  1q22   HGNC cytogenetic band: 1q22

C1orf85 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
C1orf85 gene location

GeneLoc information about chromosome 1         GeneLoc Exon Structure

GeneLoc location for GC01M156259:  view genomic region     (about GC identifiers)

Start:
156,259,880 bp from pter      End:
156,265,463 bp from pter
Size:
5,584 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: NCUG1_HUMAN, Q8WWB7 (See protein sequence)
Recommended Name: Lysosomal protein NCU-G1 precursor  
Size: 406 amino acids; 43864 Da
Caution: According to PubMed:18021396, it binds DNA and acts as a transcription factor. However, the localization
in lysosomes which was confirmed by different groups and the presence of transmembrane region strongly suggests
that it does not have coactivator activity
Sequence caution: Sequence=AAH11575.1; Type=Erroneous initiation; Sequence=CAI14165.1; Type=Erroneous gene model
prediction;
Secondary accessions: A6NH16 B4DJN4 Q5SZX4 Q6UX96 Q8IV07 Q96F65
Alternative splicing: 2 isoforms:  Q8WWB7-1   Q8WWB7-2   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for C1orf85: NX_Q8WWB7

Explore proteomics data for C1orf85 at MOPED

Post-translational modifications: 

  • Highly N-glycosylated (By similarity)1
  • Glycosylation2 at Asn65, Asn134, Asn159, Asn187, Asn230

  • See C1orf85 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins (5 alternative transcripts): 
    NP_001243533.1  NP_001243534.1  NP_001243537.1  NP_001243538.1  NP_653181.1  

    ENSEMBL proteins: 
     ENSP00000476260   ENSP00000477180   ENSP00000354553   ENSP00000477187   ENSP00000477253  
     ENSP00000357247  

    C1orf85 Human Recombinant Protein Products:

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    Cloud-Clone Corp. Proteins for C1orf85

     
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    Search eBioscience for ELISAs for C1orf85 


    (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: Q8WWB7


    (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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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: NCUG1_HUMAN, Q8WWB7
    Induction: Transcription is activated by TFEB

         Gene Ontology (GO): 4 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003700sequence-specific DNA binding transcription factor activity IMP18021396
    GO:0004879ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity IMP18021396
    GO:0030374ligand-dependent nuclear receptor transcription coactivator activity IDA18021396
    GO:0044212transcription regulatory region DNA binding IDA18021396
         
    Find genes that share ontologies with C1orf85           About GenesLikeMe


    Phenotypes:
         1 GenomeRNAi human phenotype for C1orf85:
     Increased circadian rhythm amp 

         1 MGI phenotypic allele for 0610031J06Rik (no phenotypes)

    Find genes that share phenotypes with C1orf85           About GenesLikeMe

    Animal Models:
         MGI mouse knock-out 0610031J06Riktm1Lex for C1orf85

       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for C1orf85
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       genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for C1orf85

    miRNA
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    miRTarBase miRNAs that target C1orf85:
    hsa-mir-124-3p (MIRT022683), hsa-mir-652-3p (MIRT039517)

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    2 qRT-PCR Assays for microRNAs that regulate C1orf85:
    hsa-miR-138-2* hsa-miR-3144-5p
    SwitchGear 3'UTR luciferase reporter plasmidC1orf85 3' UTR sequence
    Inhib. RNA
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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 UniProtKB/Swiss-Prot
    NCUG1_HUMAN, Q8WWB7: Lysosome membrane; Single-pass type I membrane protein
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    lysosome5
    vacuole5
    cytosol4
    nucleus4
    plasma membrane3
    extracellular2
    mitochondrion1
    peroxisome1

    Gene Ontology (GO): 5 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus IDA18021396
    GO:0005764lysosome IDA19556463
    GO:0005765lysosomal membrane IEA--
    GO:0005829cytosol IDA18021396
    GO:0016021integral component of membrane ISS--

    Find genes that share ontologies with C1orf85           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 C1orf85
    Interactions:

        Search GeneGlobe Interaction Network for C1orf85

    1 Interacting protein for C1orf85 (Q8WWB73) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    SLC2A4P146723I2D: score=1 
    About this table

    Gene Ontology (GO): 2 biological process terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0030522intracellular receptor signaling pathway IMP18021396
    GO:0045944positive regulation of transcription from RNA polymerase II promoter IMP18021396

    Find genes that share ontologies with C1orf85           About GenesLikeMe



    (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 C1orf85 (NCUG1)



    (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 C1orf85 gene (5 alternative transcripts): 
    NM_001256604.1  NM_001256605.1  NM_001256608.1  NM_001256609.1  NM_144580.2  

    Unigene Cluster for C1orf85:

    Chromosome 1 open reading frame 85
    Hs.202522  [show with all ESTs]
    Unigene Representative Sequence: NM_001256609
    12 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000461597(uc001fof.4) ENST00000497831 ENST00000472870 ENST00000480968
    ENST00000482579 ENST00000362007(uc001foh.3) ENST00000481050 ENST00000476177
    ENST00000497955 ENST00000368264 ENST00000479084 ENST00000484214
    miRNA
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    Block miRNA regulation of human, mouse, rat C1orf85 using miScript Target Protectors
    2 qRT-PCR Assays for microRNAs that regulate C1orf85:
    hsa-miR-138-2* hsa-miR-3144-5p
    SwitchGear 3'UTR luciferase reporter plasmidC1orf85 3' UTR sequence
    Inhib. RNA
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    GenScript: all cDNA clones in your preferred vector: C1orf85 (NM_144580)
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    Primer
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      QuantiTect SYBR Green Assays in human, mouse, rat C1orf85
      QuantiFast Probe-based Assays in human, mouse, rat C1orf85

    Additional mRNA sequence: 

    AK075349.1 AK296157.1 AY358450.1 BC011575.1 BC018757.1 BC036340.1 

    14 DOTS entries:

    DT.411705  DT.121329939  DT.70100287  DT.100845588  DT.95342523  DT.100845576  DT.121329908  DT.100674311 
    DT.100845584  DT.100706748  DT.100845579  DT.121329955  DT.411707  DT.121329944 

    Selected AceView cDNA sequences (see all 255):

    CR591234 BX380314 CR618333 CR597923 CR625850 BM833126 BX380248 CR625843 
    BX336388 BX339563 AV753139 CR597258 BM991589 AI681458 AL519237 CR615363 
    BX342376 CD369021 BX099160 CR600990 CR625752 BE293585 CA418600 BM758427 

    GeneLoc Exon Structure

    Selected Alternative Splicing Database (ASD) splice patterns (SP) for C1orf85 (see all 6)    About this scheme

    ExUns: 1a · 1b · 1c ^ 2 ^ 3a · 3b · 3c · 3d ^ 4a · 4b ^ 5a · 5b · 5c · 5d ^ 6a · 6b · 6c
    SP1:                                                        -     -                                       
    SP2:                    -                                   -     -                                       
    SP3:                    -                                   -                                             
    SP4:                                                        -     -     -     -     -                     
    SP5:                                                        -     -     -                                 


    ECgene alternative splicing isoforms for C1orf85

    (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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    C1orf85 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: CTGCTAGGGG
    C1orf85 Expression
    About this image

    C1orf85 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    C1orf85 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.202522
        Custom PCR Arrays for C1orf85
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for C1orf85

    (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 C1orf85 gene from Selected species (see all 12)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia 0610031J06Rik1 , 5 RIKEN cDNA 0610031J06 gene1, 5 81.57(n)1
    80.3(a)1
      3 (38.80 cM)5
    567001  NM_020003.11  NP_064387.11 
     883250235 
    chicken
    (Gallus gallus)
    Aves LOC7771361 lysosomal protein NCU-G1-A-like 56.58(n)
    43.7(a)
      777136  XM_003643914.2  XP_003643962.1 
    lizard
    (Anolis carolinensis)
    Reptilia C1orf856
    chromosome 1 open reading frame 85
    41(a)
    1 ↔ 1
    GL344271.1(16101-30002)
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia c1orf851 chromosome 1 open reading frame 85 53.8(n)
    45.56(a)
      100379979  XM_002945070.2  XP_002945116.2 
    zebrafish
    (Danio rerio)
    Actinopterygii zgc:923081 zgc:92308 47.67(n)
    37.5(a)
      447841  NM_001004580.1  NP_001004580.1 
    mosquito
    (Anopheles gambiae)
    Insecta AgaP_AGAP0044311 AgaP_AGAP004431 42.11(n)
    24.67(a)
      1274574  XM_313717.5  XP_313717.5 


    ENSEMBL Gene Tree for C1orf85 (if available)
    TreeFam Gene Tree for C1orf85 (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 C1orf85 (see all 152)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 1 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1880900981,2
    --156262821(+) TCCCTA/CCAGAG 6 W C ut31 mis10--------
    rs1464445711,2
    C,F--156262905(+) GCAGCA/GTGAGC 10 T M H mis1 syn12Minor allele frequency- G:0.00NA EU 5863
    rs1916636341,2
    C--156262945(+) GCCCAC/GGACTA 10 L V P R mis10--------
    rs2001513041,2
    C--156263012(+) CAAGC-/AGAGAGA 5 -- int10--------
    rs2016574111,2
    --156263048(+) AAGGCG/TGGGAG 5 -- int10--------
    rs109084941,2
    C,F,A,H--156263097(+) CCCAAA/GCCCTG 5 -- int121Minor allele frequency- G:0.21NS EA NA WA CSA EU 3487
    rs2011262711,2
    --156263156(+) AAGCCC/TCGAAC 9 E G mis1 int10--------
    rs2008998891,2
    --156263213(+) GGACAA/GTGGGT 9 T I mis1 int10--------
    rs1837542901,2
    C--156263239(+) TATGCC/TAAGGC 8 L syn1 int10--------
    rs1409299301,2
    C,F--156263284(+) GATTCT/ACGGCC 8 /R syn1 int11Minor allele frequency- A:0.00NA 4528

    HapMap Linkage Disequilibrium report for C1orf85 (156259880 - 156265463 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 1 variation for C1orf85:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv509524CNV Insertion20534489

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing C1orf85
    DNA2.0 Custom Variant and Variant Library Synthesis for C1orf85

    (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 C1orf85 gene, integrated from 10 sources (see all 16):
    (articles sorted by number of sources associating them with C1orf85)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Human NCU-G1 can function as a transcription factor and as a nuclear receptor co-activator. (PubMed id 18021396)1, 2, 3 Steffensen K.R.... Eskild W. (BMC Mol. Biol. 2007)
    2. The secreted protein discovery initiative (SPDI), a large-scale effort to identify novel human secreted and transmembrane proteins: a bioinformatics assessment. (PubMed id 12975309)1, 2, 3 Clark H.F.... Gray A.M. (Genome Res. 2003)
    3. NCU-G1 is a highly glycosylated integral membrane protein of the lysosome. (PubMed id 19489740)1, 3, 9 Schieweck O....LA1bke T. (Biochem. J. 2009)
    4. A gene network regulating lysosomal biogenesis and function. (PubMed id 19556463)1, 2 Sardiello M.... Ballabio A. (Science 2009)
    5. Signal sequence and keyword trap in silico for selection of full- length human cDNAs encoding secretion or membrane proteins from oligo- capped cDNA libraries. (PubMed id 16303743)1, 2 Otsuki T....Isogai T. (DNA Res. 2005)
    6. Genome-wide association study of hematological and biochemical traits in a Japanese population. (PubMed id 20139978)1 Kamatani Y....Kamatani N. (Nat. Genet. 2010)
    7. Integral and associated lysosomal membrane proteins. (PubMed id 17897319)2 Schroeder B.... Hasilik A. (Traffic 2007)
    8. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. (PubMed id 16344560)1 Kimura K.... Sugano S. (Genome Res. 2006)
    9. The DNA sequence and biological annotation of human chromosome 1. (PubMed id 16710414)2 Gregory S.G.... Bentley D.R. (Nature 2006)
    10. Transcriptome analysis of human gastric cancer. (PubMed id 16341674)1 Oh J.H.... Kim N.S. (Mamm. Genome 2005)

    (in PubMed, OMIM, and NCBI Bookshelf)
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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 112770 HGNC: 29436 AceView: MGC31963 Ensembl:ENSG00000198715 euGenes: HUgn112770
    ECgene: C1orf85 H-InvDB: C1orf85

    (According to HUGE)
    About This Section

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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 C1orf85 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 C1orf85 gene:
    Search GeneIP for patents involving C1orf85

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



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