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

C6orf1 Gene

protein-coding   GIFtS: 45
GCID: GC06M034214

Chromosome 6 Open Reading Frame 1

  See related disease
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
About This Section

Aliases
Chromosome 6 Open Reading Frame 11 2
LBH2 3 5
Uncharacterized Protein C6orf12
Protein LBH3

External Ids:    HGNC: 13401   Entrez Gene: 2214912   Ensembl: ENSG000001865777   OMIM: 6114195   UniProtKB: Q86T203   

Export aliases for C6orf1 gene to outside databases

Previous GC identifers: GC06U990175 GC06M034323 GC06M033936


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

GeneCards Summary for C6orf1 Gene: 
C6orf1 (chromosome 6 open reading frame 1) is a protein-coding gene. Diseases associated with C6orf1 include prostatitis.


(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 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000006.11  NT_007592.15  NC_018917.2  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the C6orf1 gene promoter:
         C/EBPbeta   p300   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidC6orf1 promoter sequence
   Search SABiosciences Chromatin IP Primers for C6orf1

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat C6orf1


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

Entrez Gene cytogenetic band: 6p21.31   Ensembl cytogenetic band:  6p21.31   HGNC cytogenetic band: 6p21.3

C6orf1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
C6orf1 gene location

GeneLoc information about chromosome 6         GeneLoc Exon Structure

GeneLoc location for GC06M034214:  view genomic region     (about GC identifiers)

Start:
34,214,157 bp from pter      End:
34,217,247 bp from pter
Size:
3,091 bases      Orientation:
minus strand

(According to UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB 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., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
About This Section

UniProtKB/Swiss-Prot: CF001_HUMAN, Q86T20 (See protein sequence)
Recommended Name: Uncharacterized protein C6orf1 precursor  
Size: 159 amino acids; 17113 Da
Subcellular location: Secreted (Potential)
Secondary accessions: A8K299

Explore the universe of human proteins at neXtProt for C6orf1: NX_Q86T20

Explore proteomics data for C6orf1 at MOPED 

C6orf1 Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

C6orf1 Protein Expression

REFSEQ proteins (3 alternative transcripts): 
NP_001008703.1  NP_001008704.1  NP_848603.2  

ENSEMBL proteins: 
 ENSP00000417604   ENSP00000418062   ENSP00000387460   ENSP00000378441   ENSP00000334260  
 ENSP00000418884  

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

GO IDQualified GO termEvidencePubMed IDs
GO:0005576extracellular region IEA--

C6orf1 for ontologies           About GeneDecksing



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(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
About This Section

ProtoNet protein and cluster: Q86T20


(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,
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, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
About This Section

Molecular Function:
     Genatlas biochemistry entry for C6orf1:
chromosome 6 open reading frame 1,located 3'of HMGIY,in opposite orientation

Phenotypes:
     2 GenomeRNAi human phenotypes for C6orf1:
 Decreased Tat-dependent transc  Decreased p24 protein expressi 

Animal Models:
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(Pathways according to EMD Millipore, 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 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 Oct 2013 via Entrez Gene).
About This Section



Interactions:

    Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for C6orf1

(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, 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 C6orf1 (CF001)

Search CenterWatch for drugs/clinical trials and news about C6orf1 / CF001

(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,
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, Sirion Biotech, Primers from OriGene, SABiosciences, and/or QIAGEN )
About This Section

REFSEQ mRNAs for C6orf1 gene (3 alternative transcripts): 
NM_001008703.1  NM_001008704.1  NM_178508.3  

Unigene Cluster for C6orf1:

Chromosome 6 open reading frame 1
Hs.381300  [show with all ESTs]
Unigene Representative Sequence: NM_178508
8 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000476320(uc003ojg.3 uc003ojh.3) ENST00000481533 ENST00000413013
ENST00000394990 ENST00000335352(uc003ojf.3 uc003oji.3) ENST00000463083
ENST00000468145 ENST00000495581
miRNA
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Inhib. RNA
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  QIAGEN QuantiFast Probe-based Assays in human, mouse, rat C6orf1

Additional mRNA sequence: 

AK290164.1 BC009526.1 BC023627.2 BC047919.1 

11 DOTS entries:

DT.100036494  DT.92422661  DT.92422662  DT.211470  DT.121373596  DT.100776593  DT.95153763  DT.121373564 
DT.100036493  DT.97795136  DT.121373517 

24/134 AceView cDNA sequences (see all 134):

BM704613 BQ059575 BU194178 BC009526 NM_178508 BM423397 BC047919 BM761380 
BQ066439 BM840355 CB125631 BX354053 AA767552 AW631387 BM700276 BQ671349 
BQ058686 BU184027 CR592917 AW631270 BM808233 BI524010 CR619587 CF994102 

GeneLoc Exon Structure

5/7 Alternative Splicing Database (ASD) splice patterns (SP) for C6orf1 (see all 7)    About this scheme

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


ECgene alternative splicing isoforms for C6orf1

(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

C6orf1 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: GTGATGGGGC
C6orf1 Expression
About this image


See C6orf1 Protein Expression from SPIRE MOPED and PaxDB
Genevestigator expression for C6orf1

SOURCE GeneReport for Unigene cluster: Hs.381300

UniProtKB/Swiss-Prot: CF001_HUMAN, Q86T20
Tissue specificity: Expressed in spleen, thymus, prostate, testis, uterus, small intestine, colon and peripheral
blood leukocytes

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In Situ
Assay Products:
 

 
Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for C6orf1

(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 chordates.

Orthologs for C6orf1 gene from 2/3 species (see all 3)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
mouse
(Mus musculus)
Mammalia AI4135825 expressed sequence AI413582   --   17 (14.53 cM) 27563575 
zebrafish
(Danio rerio)
Actinopterygii Dr.39722 Transcribed sequence with weak similarity to protein more 71.65(n)    BI844908.1 


ENSEMBL Gene Tree for C6orf1 (if available)
TreeFam Gene Tree for C6orf1 (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
About This Section
Paralogs for C6orf1 gene
1 SIMAP similar gene for C6orf1 using alignment to 3 protein entries:     CF001_HUMAN (see all proteins):
C3orf18

C6orf1 for paralogs           About GeneDecksing



(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) 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

10/97 SNPs in C6orf1 are shown (see all 97)    About this table     
Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 6 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
VAR_0567924
----see VAR_0567922 M I mis40--------
VAR_0603834
----see VAR_0603832 G A mis40--------
rs1835595881,2
C--34214514(+) GGGGAA/GGCAGA 6 P L mis10--------
rs1401851671,2
F--34214518(+) AAGCAG/AATGGC 6 /L syn11Minor allele frequency- A:0.00NA 4340
rs1438512511,2
C,F--34214524(+) ATGGCA/GGGGCC 6 R C mis12Minor allele frequency- G:0.00NA EU 5201
rs1416105971,2
C,F--34214525(+) TGGCAG/AGGCCC 6 /P syn12Minor allele frequency- A:0.01NA EU 5221
rs2021298591,2
C--34214539(+) GCAGTA/CCAGGA 6 D Y mis10--------
rs1396591411,2
C,F--34214584(+) GTCACG/ATCTTG 6 /R /C mis11Minor allele frequency- A:0.00NA 4428
rs2019382391,2
C--34214608(+) GCATCA/CGCTTG 6 G * stg10--------
rs47113891,2
C,F--34214670(+) ACCACA/GAGGCT 3 -- int12Minor allele frequency- G:0.09WA EA 238

HapMap Linkage Disequilibrium report for C6orf1 (34214157 - 34217247 bp)

Structural Variations
     Database of Genomic Variants (DGV) 2 variations for C6orf1:    About this table     
Variant IDTypeSubtypePubMed ID
nsv885784CNV Loss21882294
nsv885781CNV Loss21882294

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(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.)
About This Section
OMIM gene information: 611419    OMIM disorders: --

2 diseases for C6orf1:    About MalaCards
prostatitis    


C6orf1 for disorders           About GeneDecksing

Genetic Association Database (GAD): C6orf1
Human Genome Epidemiology (HuGE) Navigator: C6orf1 (5 documents)

Export disorders for C6orf1 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)
About This Section

PubMed articles for C6orf1 gene, integrated from 9 sources (see all 11):
(articles sorted by number of sources associating them with C6orf1)
    Utopia: connect your pdf to the dynamic
world of online information

  1. Assignment of a new gene (LBH). (PubMed id 10036196)1, 2, 3 Kazmierczak B.... Bullerdiek J. (1999)
  2. Identification, replication, and fine-mapping of Loci associated with adult height in individuals of african ancestry. (PubMed id 21998595)1, 4 N'Diaye A....Haiman C.A. (2011)
  3. Identification of 15 loci influencing height in a Kor ean population. (PubMed id 19893584)1, 4 Kim J.J....Lee J.K. (2010)
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S....Malek J. (2004)
  5. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PubMed id 20379614)1 Rose J.E....Uhl G.R. (2010)
  6. 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)
  7. Gene-centric association signals for lipids and apoli poproteins identified via the HumanCVD BeadChip. (PubMed id 19913121)1 Talmud P.J.... . (2009)
  8. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)2 Ota T.... Sugano S. (2004)
  9. The DNA sequence and analysis of human chromosome 6. (PubMed id 14574404)2 Mungall A.J.... Beck S. (2003)
  10. 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. (2002)

(in PubMed, OMIM, and NCBI Bookshelf)
About This Section
 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)
About This Section
Entrez Gene: 221491 HGNC: 1340 AceView: MGC57858 Ensembl:ENSG00000186577 euGenes: HUgn221491
ECgene: C6orf1 H-InvDB: C6orf1

(According to HUGE)
About This Section
  --

(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 C6orf1 Pharmacogenomics, SNPs, Pathways

(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from LifeMap Sciences, Inc.)
About This Section
Patent Information for C6orf1 gene:
Search GeneIP for patents involving C6orf1

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, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0 and Sirion Biotech, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Sirion Biotech, Cell lines from GenScript, and LifeMap BioReagents, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or Enzo Life Sciences, In Situ Hybridization Assays from
Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
About This Section

 
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GeneCards Homepage - Last full update: 23 Oct 2013 - Incrementals: 4 Nov 2013 , 7 Nov 2013 , 23 Jan 2014

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transforming growth factor, beta 1
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