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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

C6orf170 Gene

protein-coding   GIFtS: 43
GCID: GC06M121400

chromosome 6 open reading frame 170

(Previous name: chromosome 6 open reading frame 171 )
(Previous symbol: C6orf171)
  Search for C6orf170
in
MalaCards
our new
 Human Malady Compendium 
Biological research products
for C6orf170    

Aliases
for C6orf170 gene

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section
Aliases
Chromosome 6 Open Reading Frame 1701 2     Chromosome 6 Open Reading Frame 1711
C6orf1711 2 3     BA301B7.21
BROMI1 2     BA301B7.2 (Novel Protein)2
BA57L9.11     Broad-Minded Homolog2
DJ310J6.11     DJ310J6.1 (Novel Protein)2
FLJ308991     Protein Broad-Minded2
FLJ342351     

External Ids:    HGNC: 214851   Entrez Gene: 2213222   Ensembl: ENSG000001463507   UniProtKB: Q96NH33   

Export aliases for C6orf170 gene to outside databases

Previous GC identifers: GC06M121336 GC06M121381 GC06M121443 GC06M118984


Summaries
for C6orf170 gene

(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section
UniProtKB/Swiss-Prot: BROMI_HUMAN, Q96NH3
Function: Required for high-level Shh responses in the developing neural tube. Together with CDK20, controls the
structure of the primary cilium by coordinating assembly of the ciliary membrane and axoneme, allowing GLI2 to be
properly activated in response to Shh signaling (By similarity)




Genomic Views
for C6orf170 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 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000006.11  NC_018917.1  NT_025741.15  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the C6orf170 gene promoter:
         RFX1   ATF-2   Nkx5-1   Gfi-1   CREB   CRE-BP1   deltaCREB   c-Jun   ATF   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search SABiosciences Chromatin IP Primers for C6orf170

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat C6orf170


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

Entrez Gene cytogenetic band: 6q22.31   Ensembl cytogenetic band:  6q22.31   HGNC cytogenetic band: 6q22.31

C6orf170 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
C6orf170 gene location

GeneLoc information about chromosome 6         GeneLoc Exon Structure

GeneLoc location for GC06M121400:  view genomic region     (about GC identifiers)

Start:
 121,400,627 bp from pter      End:
 121,655,891 bp from pter
Size:
 255,265 bases      Orientation:
 minus strand

Proteins
for C6orf170 gene

(According to 1UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to 2PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, 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 Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section
UniProtKB/Swiss-Prot: BROMI_HUMAN, Q96NH3 (See protein sequence)
Recommended Name: Protein broad-minded  
Size: 1257 amino acids; 144756 Da
Subunit: Interacts with CDK20, which promotes CDK20 stability and function (By similarity)
Subcellular location: Cytoplasm (By similarity). Cell projection, cilium (By similarity)
Caution: The Rab-GAP TBC domain appears to be inactive, probably due to a lack of the essential Arg and Gln in the
catalytic finger motifs
Sequence caution: Sequence=BAB70925.1; Type=Frameshift; Positions=717; Sequence=BAC03694.1; Type=Frameshift;
Positions=143; Sequence=BAC03694.1; Type=Miscellaneous discrepancy; Note=Aberrant splicing; Sequence=BAC86152.1;
Type=Erroneous initiation; Note=Translation N-terminally extended; Sequence=BAD18591.1; Type=Erroneous translation;
Note=Wrong choice of CDS; Sequence=CAI16051.2; Type=Erroneous gene model prediction; Sequence=CAI20000.2;
Type=Erroneous gene model prediction; Sequence=CAM16339.1; Type=Erroneous gene model prediction; Sequence=CAM17813.1;
Type=Erroneous gene model prediction; Sequence=CAM28224.1; Type=Erroneous gene model prediction;
Secondary accessions: Q5SZD6 Q5SZM6 Q6ZMY4 Q6ZUR7 Q8NB47
Alternative splicing: 3 isoforms:  Q96NH3-1   Q96NH3-4   Q96NH3-5   (No experimental confirmation available. May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay)

Explore the universe of human proteins at neXtProt for C6orf170: NX_Q96NH3

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q96NH3

    • C6orf170 Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins: NP_689943.4  
    ENSEMBL proteins: 
     ENSP00000275159   ENSP00000428839   ENSP00000381270   ENSP00000429928   ENSP00000397993  

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    Uscn Proteins for C6orf170

    Gene Ontology (GO): 2 cellular component terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005737cytoplasm IEA--
    GO:0005929cilium IEA--


    C6orf170 for ontologies           About GeneDecksing



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    Uscn ELISAs and CLIAs for C6orf170

    Protein Domains /
    Families
    for C6orf170 gene

    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    C6orf170 for domains           About GeneDecksing

    2 InterPro domains/families:
     IPR000195 Rab-GTPase-TBC_dom
     IPR005373 UPF0183

    Graphical View of Domain Structure for InterPro Entry Q96NH3

    ProtoNet protein and cluster: Q96NH3

    1 Blocks protein family: IPB000195 RabGAP/TBC domain

    UniProtKB/Swiss-Prot: BROMI_HUMAN, Q96NH3
    Similarity: Contains 1 Rab-GAP TBC domain


    Function
    for C6orf170 gene

    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
    About This Section
    Function Summary:

         UniProtKB/Swiss-Prot: BROMI_HUMAN, Q96NH3
    Function: Required for high-level Shh responses in the developing neural tube. Together with CDK20, controls the
    structure of the primary cilium by coordinating assembly of the ciliary membrane and axoneme, allowing GLI2 to be
    properly activated in response to Shh signaling (By similarity)

    miRNA
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    Inhib. RNA
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    Gene Editing
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    Clone
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    In Situ Assay
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    Gene Ontology (GO): 1 molecular function term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005097Rab GTPase activator activity IEA--


    C6orf170 for ontologies           About GeneDecksing


    Animal Models:
         5 MGI mutant phenotypes (inferred from 2 alleles) (MGI details for D630037F22Rik):
     embryogenesis  limbs/digits/tail  nervous system  pigmentation  vision/eye 

    C6orf170 for phenotypes           About GeneDecksing


    Pathways & Interactions
    for C6orf170 gene

    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, 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 Mar 2013 via Entrez Gene).
    About This Section



    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for C6orf170

    1 Interacting protein for C6orf170 (Q96NH33) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    RB1CC1Q8TDY23I2D: score=1 
    About this table

    Gene Ontology (GO): 1 biological process term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0007275multicellular organismal development IEA--


    C6orf170 for ontologies           About GeneDecksing



    Drugs & Compounds
    for C6orf170 gene

    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section
    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for C6orf170
    Search CenterWatch for drugs/clinical trials and news about C6orf170 / BROMI 

    Transcripts
    for C6orf170 gene

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 235 Homo sapiens; Mar 10 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,
    RNAi Products from EMD Millipore,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section
    REFSEQ mRNAs for C6orf170 gene: 
    NM_152730.4  

    Unigene Cluster for C6orf170:

    Chromosome 6 open reading frame 170
    Hs.121396  [show with all ESTs]
    Unigene Representative Sequence: AK131446
    9 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000398197(uc010kej.1) ENST00000275159(uc003pyp.1) ENST00000464622(uc003pyo.1 uc003pyq.1)
    ENST00000398212 ENST00000519972 ENST00000368464 ENST00000509492 ENST00000523345
    ENST00000422369

    miRNA
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    hsa-miR-498 hsa-miR-34c-3p hsa-miR-1297 hsa-miR-513b hsa-miR-3662 hsa-miR-26a hsa-miR-3121-3p hsa-miR-32*
    SwitchGear 3'UTR luciferase reporter plasmid: C6orf170 3' UTR sequence
    Inhib. RNA
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    Primer
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    Additional cDNA sequence: 

    AK055461.1 AK091554.1 AK125385.1 AK126259.1 AK131446.1 

    8 DOTS entries:

    DT.441800  DT.121382603  DT.100723402  DT.40199582  DT.86844356  DT.305699  DT.75121619  DT.100748711 

    24/35 AceView cDNA sequences (see all 35):

    BF509016 AL119140 AA490806 BX089961 CB156589 AK125385 BX112581 BX954564 
    AI341848 AA282814 CB157842 AK126259 BF356518 AA443680 AK131446 AK091554 
    AA683471 CD654015 AA447067 BG104550 NM_152730 AX747057 AA490615 AI984072 

    GeneLoc Exon Structure


    Expression
    for C6orf170 gene

    (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™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    C6orf170 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: AGTTTATTTC

    Microarray
    RNAseq (Illumina Body Map)
    (100×FPKM)½
    SAGE (Serial Analysis of Gene Expression)
    About this image
    See C6orf170 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for C6orf170

    SOURCE GeneReport for Unigene cluster: Hs.121396
        SABiosciences Custom PCR Arrays for C6orf170
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    In Situ
    Assay Products:     
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    Orthologs
    for C6orf170 gene

    (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)
    About This Section
    This gene was present in the common ancestor of animals.

    Orthologs for C6orf170 gene from 6/19 species (see all 19)    About this table
    Organism Taxonomic
    classification    		 Gene Description Human
    Similarity    		 Orthology
    Type    		 Details
    mouse
    (Mus musculus)    		 Mammalia D630037F22Rik1 , 5 RIKEN cDNA D630037F22 gene1, 5 84.37(n)1
    84.93(a)1    		   10 (28.45 cM)5
    5446961  NM_001033385.31  NP_001028557.21 
     560142985 
    chicken
    (Gallus gallus)    		 Aves C3H6orf1701 chromosome 3 open reading frame, human C6orf170 72.32(n)
    66.88(a)    		   421725  XM_003641035.1  XP_003641083.1 
    lizard
    (Anolis carolinensis)    		 Reptilia C6orf1706
    		 --
    		 69(a)
    		 1 ↔ 1
    		 1(182963122-183039569)
    tropical clawed frog
    (Xenopus tropicalis)    		 Amphibia Str.23692 Transcribed sequences 74.4(n)    BX770242.1 
    zebrafish
    (Danio rerio)    		 Actinopterygii si:dkey-233p4.11 si:dkey-233p4.1 60.49(n)
    57.54(a)    		   566474  NM_001100023.1  NP_001093493.1 
    honey bee
    (Apis mellifera)    		 Insecta --
    		 --
    		 21(a)
    		 1 ↔ 1
    		 GroupUn.1071(6066-9815)


    ENSEMBL Gene Tree for C6orf170 (if available)
    TreeFam Gene Tree for C6orf170 (if available) 

    Paralogs
    for C6orf170 gene

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    		  --

    Genomic Variants
    for C6orf170 gene

    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, UniProtKB, 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) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    10/4685 NCBI SNPs in C6orf170 are shown (see all 4685)     About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance    		Chr 6 posSequence#AA
    Chg    		TypeMore#Allele
    freq    		PopTotal
    sample    		More
    ----------
    rs800666331,2
    		--121400182(+) ACTACC/TGTGTA 1 -- ds50011Minor allele frequency- T:0.01EA 120
    rs1423858541,2
    		--121400183(+) CTACCA/GTGTAC 1 -- ds50010--------
    rs131966581,2
    		C,F,H,--121400216(+) CTGCAC/TGATTC 1 -- ds500111Minor allele frequency- T:0.02NS EA NA 1002
    rs1447458901,2
    		--121400376(+) CACAGC/TGGCTG 1 -- ds50010--------
    rs735364301,2
    		C,F,--121400398(+) CGCAAT/CATGTC 1 -- ds50016Minor allele frequency- C:0.19WA CSA NA EA 364
    rs1476062751,2
    		--121400533(+) CTAAAC/TATTAC 1 -- ds50010--------
    rs2011322911,2
    		--121400624(+) AAACG-/AAAAAA 1 -- ds50010--------
    rs1928830781,2
    		--121400643(+) GGTTAA/GAGTTA 1 -- ut310--------
    rs560644421,2
    		--121400649(+) AGTTAG/CAATGA 1 -- ut312Minor allele frequency- C:0.05CSA WA 120
    rs125247541,2
    		C,F,H,--121400690(+) GGAAAG/TAATAA 1 -- ut315Minor allele frequency- T:0.04NS EA NA 534

    HapMap Linkage Disequilibrium report for C6orf170 (121400627 - 121650627 bp, first 250kb of C6orf170)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
    Database of Genomic Variants (DGV): 6 variations for C6orf170
         4 CNVs: 38624 93984 64648 69596
         2 Indels: 60616 51792

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    Disorders / Diseases
    for C6orf170 gene

    (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.)
    About This Section
    C6orf170 for disorders           About MalaCards

    C6orf170 for disorders           About GeneDecksing

    Human Genome Epidemiology (HuGE) Navigator: C6orf170 (4 documents)

    Export disorders for C6orf170 gene to outside databases

    Publications
    for C6orf170 gene

    (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)
    About This Section

    PubMed articles for C6orf170 gene integrated from 9 sources:
    (articles sorted by number of sources associating them with C6orf170)    		    Utopia: connect your pdf to the dynamic
    world of online information

    1. Broad-minded links cell cycle-related kinase to cilia assembly and hedgehog signal transduction. (PubMed id 20159594)1, 3 Ko H.W....Eggenschwiler J.T. (2010)
    2. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (2004)
    3. The DNA sequence and analysis of human chromosome 6. (PubMed id 14574404)1, 2 Mungall A.J.... Beck S. (2003)
    4. Systematic and quantitative assessment of the ubiquiti n-modified proteome. (PubMed id 21906983)1 Kim W....Gygi S.P. (2011)
    5. Common genetic variation and performance on standardi zed cognitive tests. (PubMed id 20125193)1 Cirulli E.T....Goldstein D.B. (2010)
    6. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PubMed id 20379614)1 Rose J.E....Uhl G.R. (2010)
    7. Variation at the NFATC2 locus increases the risk of t hiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipr il and rosiglitazone Medication (DREAM) study. (PubMed id 20628086)1 Bailey S.D....Anand S. (2010)
    8. Gene-centric association signals for lipids and apoli poproteins identified via the HumanCVD BeadChip. (PubMed id 19913121)1 Talmud P.J.... . (2009)
    9. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. (PubMed id 16344560)1 Kimura K.... Sugano S. (2006)

    External Searches for C6orf170 gene

    (in PubMed, OMIM, and NCBI Bookshelf)
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    Genome Databases showing C6orf170 gene

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 221322 HGNC: 21485 AceView: C6orf170 Ensembl:ENSG00000146350 euGenes: HUgn221322
    ECgene: C6orf170 H-InvDB: C6orf170

    Other Databases showing C6orf170 gene

    (According to HUGE)
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    Specialized Databases showing C6orf170 gene

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    NameDescription
    PharmGKB entry for C6orf170 Pharmacogenomics, SNPs, Pathways

    Intellectual Property
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    		Patent Information for C6orf170 gene:
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