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C11orf40 Gene

protein-coding   GIFtS: 36
GCID: GC11M004550          (predicted)

Chromosome 11 Open Reading Frame 40

  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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Aliases
Chromosome 11 Open Reading Frame 401 2
Ro/SSA1-Related Protein2 3
NOV12 3
Putative Uncharacterized Protein C11orf402

External Ids:    HGNC: 239861   Entrez Gene: 1435012   Ensembl: ENSG000001719877   UniProtKB: Q8WZ693   

Export aliases for C11orf40 gene to outside databases

Previous GC identifer: GC11M004251


(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 C11orf40 Gene:
C11orf40 (chromosome 11 open reading frame 40) is a protein-coding gene. Diseases associated with C11orf40 include multidrug-resistant tuberculosis, and tuberculosis.


(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_000011.10  NC_018922.2  NT_009237.19  
Regulatory elements:
   Search for regulatory transcription factor binding sites for C11orf40
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search Chromatin IP Primers for C11orf40

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat C11orf40


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

Entrez Gene cytogenetic band: 11p15.5   Ensembl cytogenetic band:  11p15.4   HGNC cytogenetic band: 11p15.5

C11orf40 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
C11orf40 gene location

GeneLoc information about chromosome 11         GeneLoc Exon Structure

GeneLoc location for GC11M004550:  view genomic region     (about GC identifiers)

Start:
4,592,653 bp from pter      End:
4,599,050 bp from pter
Size:
6,398 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, 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: CK040_HUMAN, Q8WZ69 (See protein sequence)
Recommended Name: Putative uncharacterized protein C11orf40  
Size: 217 amino acids; 24620 Da

Explore the universe of human proteins at neXtProt for C11orf40: NX_Q8WZ69

Explore proteomics data for C11orf40 at MOPED


See C11orf40 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

REFSEQ proteins: NP_653264.1  
ENSEMBL proteins: 
 ENSP00000302918  

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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: Q8WZ69


(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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Animal Models:
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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
cytosol2
nucleus2
extracellular1
peroxisome1

(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 C11orf40
Interactions:

    Search GeneGlobe Interaction Network for C11orf40

(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 C11orf40 (CK040)



(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 C11orf40 gene: 
NM_144663.1  

Unigene Cluster for C11orf40:

Chromosome 11 open reading frame 40
Hs.350556
Unigene Representative Sequence: AF439154
1 Ensembl transcript including schematic representation, and UCSC links where relevant:
ENST00000307616(uc010qyg.2)
miRNA
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  QuantiFast Probe-based Assays in human, mouse, rat C11orf40

Additional mRNA sequence: AF439154.1 

1 DOTS entry:

DT.95113658 

2 AceView cDNA sequences:

NM_144663 AF439154 

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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C11orf40 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: TGGATGTGAA
C11orf40 Expression
About this image

C11orf40 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

C11orf40 Protein Expression

SOURCE GeneReport for Unigene cluster: Hs.350556
    Custom PCR Arrays for C11orf40
Primer
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In Situ
Assay Products:
 

 
Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for C11orf40

(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 human and chimp.

Orthologs for C11orf40 gene from 1 species (see representative species )    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
chimpanzee
(Pan troglodytes)
Mammalia C11H11orf401 chromosome 11 open reading frame, human C11orf40 98.76(n)
96.73(a)
  748279  XM_001160493.2  XP_001160493.2 


ENSEMBL Gene Tree for C11orf40 (if available)
TreeFam Gene Tree for C11orf40 (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 C11orf40 (see all 522)    About this table    
Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 11 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs1824101851,2
--4592164(+) GGAGGA/CCAGGT 1 -- ds50010--------
rs122700241,2
C,F,A,H--4592224(+) GATCCT/CGATTC 1 -- ds500114Minor allele frequency- C:0.31NS EA WA CSA NA 1203
rs15052091,2
C,F,A,H--4592277(-) ACATAT/CCTATT 1 -- ds500122Minor allele frequency- C:0.13MN NS EA NA 2718
rs1877973671,2
--4592314(+) AAGTGC/GTATCA 1 -- ds50010--------
rs15052081,2
C,F,A,H--4592340(-) AAAGGC/TTTCTA 1 -- ds500125Minor allele frequency- T:0.32MN NS EA NA WA 2950
rs1932990601,2
--4592364(+) CTCTGC/GACAAG 1 -- ds50010--------
rs1833874691,2
--4592424(+) AATGGC/TTTCAA 1 -- ds50010--------
rs616782091,2
C,F--4592427(+) GGTTTC/TAAGGT 1 -- ds50012Minor allele frequency- T:0.11WA 120
rs752574481,2
C--4592449(+) CTCTCAT/-ATATC 1 -- ds50011Minor allele frequency- -:0.50CSA 2
rs769898331,2
C,F--4592473(+) CCAGTA/GTAGCA 1 -- ds50011Minor allele frequency- G:0.07NA 120

HapMap Linkage Disequilibrium report for C11orf40 (4592653 - 4599050 bp)

Structural Variations
     Database of Genomic Variants (DGV) 3 variations for C11orf40:    About this table    
Variant IDTypeSubtypePubMed ID
nsv832055CNV Loss17160897
nsv896914CNV Gain21882294
nsv896911CNV Gain21882294

Human Gene Mutation Database (HGMD): C11orf40
Site Specific Mutation Identification with PCR Assays
SeqTarget long-range PCR primers for resequencing C11orf40
DNA2.0 Custom Variant and Variant Library Synthesis for C11orf40

(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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4 diseases for C11orf40:    About MalaCards
multidrug-resistant tuberculosis    tuberculosis    hepatitis b    hepatitis


C11orf40 for disorders           About GeneDecksing

Genetic Association Database (GAD): C11orf40
Human Genome Epidemiology (HuGE) Navigator: C11orf40 (1 document)

Export disorders for C11orf40 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 article for C11orf40 gene integrated from 10 sources:
(articles sorted by number of sources associating them with C11orf40)
    Utopia: connect your pdf to the dynamic
world of online information

  1. New genetic associations detected in a host response study to hepatitis B vaccine. (PubMed id 20237496)1 Davila S....Seielstad M. (Genes Immun. 2010)

(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: 143501 HGNC: 23986 AceView: NOV1 Ensembl:ENSG00000171987 euGenes: HUgn143501
ECgene: C11orf40 H-InvDB: C11orf40

(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 C11orf40 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 C11orf40 gene:
Search GeneIP for patents involving C11orf40

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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