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

C11orf88 Gene

protein-coding   GIFtS: 37
GCID: GC11P111392

chromosome 11 open reading frame 88
  Search for C11orf88
in
MalaCards
our new
 Human Malady Compendium 
Biological research products
for C11orf88    

Aliases
for C11orf88 gene

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section
Aliases
Chromosome 11 Open Reading Frame 881 2
FLJ462661
Hypothetical Gene Supported By BC0395052
UPF0722 Protein C11orf882

External Ids:    HGNC: 250611   Entrez Gene: 3999492   Ensembl: ENSG000001836447   UniProtKB: Q6PI973   

Export aliases for C11orf88 gene to outside databases

Previous GC identifers: GC11P110903 GC11P110904 GC11P110907 GC11P111386 GC11P107309 GC11P111387


Summaries
for C11orf88 gene

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

Genomic Views
for C11orf88 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_000011.9  NC_018922.1  NT_033899.8  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the C11orf88 gene promoter:
         POU2F2 (Oct-2.1)   Oct-B1   oct-B2   oct-B3   POU2F2   C/EBPalpha   Nkx6-1   POU2F1   POU2F1a   POU2F2B   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search SABiosciences Chromatin IP Primers for C11orf88

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat C11orf88


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

Entrez Gene cytogenetic band: 11q23.1   Ensembl cytogenetic band:  11q23.1   HGNC cytogenetic band: 11q23.1

C11orf88 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
C11orf88 gene location

GeneLoc information about chromosome 11         GeneLoc Exon Structure

GeneLoc location for GC11P111392:  view genomic region     (about GC identifiers)

Start:
 111,385,510 bp from pter      End:
 111,407,756 bp from pter
Size:
 22,247 bases      Orientation:
 plus strand

Proteins
for C11orf88 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: CK088_HUMAN, Q6PI97 (See protein sequence)
Recommended Name: UPF0722 protein C11orf88  
Size: 169 amino acids; 19340 Da
Sequence caution: Sequence=AAH39505.1; Type=Erroneous initiation;
Secondary accessions: Q6ZRL3
Alternative splicing: 2 isoforms:  Q6PI97-1   Q6PI97-2   

Explore the universe of human proteins at neXtProt for C11orf88: NX_Q6PI97

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q6PI97

    • C11orf88 Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins (2 alternative transcripts): 
    NP_001093858.1  NP_997313.2  

    ENSEMBL proteins: 
     ENSP00000364768   ENSP00000432911   ENSP00000333845   ENSP00000435029  

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    Protein Domains /
    Families
    for C11orf88 gene

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

    ProtoNet protein and cluster: Q6PI97

    UniProtKB/Swiss-Prot: CK088_HUMAN, Q6PI97
    Similarity: Belongs to the UPF0722 family


    Function
    for C11orf88 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
    miRNA
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    Pathways & Interactions
    for C11orf88 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 C11orf88

    Drugs & Compounds
    for C11orf88 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
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    Browse Tocris compounds for C11orf88
    Search CenterWatch for drugs/clinical trials and news about C11orf88 / CK088 

    Transcripts
    for C11orf88 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,
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    About This Section
    REFSEQ mRNAs for C11orf88 gene (2 alternative transcripts): 
    NM_001100388.1  NM_207430.2  

    Unigene Cluster for C11orf88:

    Chromosome 11 open reading frame 88
    Hs.411600  [show with all ESTs]
    Unigene Representative Sequence: BM473494
    4 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000375618 ENST00000529167(uc001plo.1) ENST00000332814(uc009yyd.3 uc001pln.4)
    ENST00000529661

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    Additional cDNA sequence: BC039505.2 

    4 DOTS entries:

    DT.100014985  DT.101975691  DT.75101281  DT.100668118 

    21 AceView cDNA sequences:

    AK128145 BC039505 NM_207430 BQ030099 AI351754 AI564524 AL119993 BI768737 
    AI808828 BM473494 BU568804 AW004000 AI628891 AI829856 AI699629 CD704138 
    BG194830 CD687808 CD694134 CD688334 BG202098 

    GeneLoc Exon Structure

    2 Alternative Splicing Database (ASD) splice patterns (SP) for C11orf88    About this scheme

    ExUns: 1a · 1b ^ 2 ^ 3 ^ 4 ^ 5a · 5b ^ 6 ^ 7
    SP1:                          -                           
    SP2:                                                      


    ECgene alternative splicing isoforms for C11orf88

    Expression
    for C11orf88 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

    C11orf88 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: GCAGAGGATG

    Microarray
    RNAseq (Illumina Body Map)
    (100×FPKM)½
    SAGE (Serial Analysis of Gene Expression)
    About this image

    C11orf88 expression in embryonic tissues and stem cells
    Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine    About this table
    Stem Cell Differentiation: 1 LifeMap Cell 
    NameCategory
    Dorsal forebrain-like neurons (Generation of midbra...)Brain
    Expression: Positive    Negative     Selective marker
    Experimental details: Curated     Microarrays     In-situ hybridization

    See C11orf88 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for C11orf88

    SOURCE GeneReport for Unigene cluster: Hs.411600
        SABiosciences Custom PCR Arrays for C11orf88
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    In Situ
    Assay Products:     
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    Orthologs
    for C11orf88 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 chordates.

    Orthologs for C11orf88 gene from 3/7 species (see all 7)    About this table
    Organism Taxonomic
    classification    		 Gene Description Human
    Similarity    		 Orthology
    Type    		 Details
    mouse
    (Mus musculus)    		 Mammalia 4833427G06Rik1 , 5 RIKEN cDNA 4833427G06 gene1, 5 76.79(n)1
    71.43(a)1    		   9 (27.81 cM)5
    2353451  NM_177702.31  NP_808370.11 
     510813135 
    chicken
    (Gallus gallus)    		 Aves C11orf886
    		 Uncharacterized protein
    		 42(a)
    		 1 ↔ 1
    		 24(5686008-5687803)
    zebrafish
    (Danio rerio)    		 Actinopterygii si:dkey-27p23.36
    		 si:dkey-27p23.3
    		 38(a)
    		 1 ↔ 1
    		 5(59250279-59269711)


    ENSEMBL Gene Tree for C11orf88 (if available)
    TreeFam Gene Tree for C11orf88 (if available) 

    Paralogs
    for C11orf88 gene

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

    Genomic Variants
    for C11orf88 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

    10/335 NCBI SNPs in C11orf88 are shown (see all 335)     About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance    		Chr 11 posSequence#AA
    Chg    		TypeMore#Allele
    freq    		PopTotal
    sample    		More
    ----------
    rs1482421821,2
    		--111385296(+) TGACTC/TTCCCA 2 -- us2k10--------
    rs1413825261,2
    		--111385339(+) TCACCG/TCAGGG 2 -- us2k10--------
    rs1504816471,2
    		C,--111385504(+) CCTCA-/GTTGCC 2 -- us2k10--------
    rs1112478211,2
    		C--111385534(+) AAGAAG/CCTAGC 4 /P /A mis11Minor allele frequency- C:0.50NA 2
    rs1154464081,2
    		C,--111385636(+) GGATCT/ACGGCG 4 /T /S mis12Minor allele frequency- A:0.01WA EU 1435
    rs44188471,2
    		H--111385654(+) ATCCCC/GCTAGC 4 P A mis1 ese32Minor allele frequency- G:0.00NS 206
    rs128018631,2
    		C--111385685(+) CAGAGA/GCAGCA 4 D G mis1 ese31Minor allele frequency- G:0.00NA 2
    rs1121383971,2
    		C,--111385687(+) GAGACG/AGCAGT 4 /S /G mis11Minor allele frequency- A:0.50CSA 2
    rs1824572391,2
    		--111385701(+) CGTCTC/GCCGGT 4 L syn10--------
    rs779687581,2
    		C,F,--111385712(+) GGCGCG/CGCCCA 4 /P /R mis11Minor allele frequency- C:0.06WA 118

    HapMap Linkage Disequilibrium report for C11orf88 (111385510 - 111407756 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
    Database of Genomic Variants (DGV): 1 variation for C11orf88
         1 CNV: 86042

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    Disorders / Diseases
    for C11orf88 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
    		   --

    Publications
    for C11orf88 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 C11orf88 gene integrated from 9 sources:
    (articles sorted by number of sources associating them with C11orf88)    		    Utopia: connect your pdf to the dynamic
    world of online information

    1. 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. (2002)
    2. Human chromosome 11 DNA sequence and analysis including novel gene identification. (PubMed id 16554811)2 Taylor T.D....Sakaki Y. (2006)
    3. 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. (2004)
    4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)2 Ota T.... Sugano S. (2004)

    External Searches for C11orf88 gene

    (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)

    Genome Databases showing C11orf88 gene

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 399949 HGNC: 25061 AceView: FLJ46266 Ensembl:ENSG00000183644 euGenes: HUgn399949
    ECgene: C11orf88 H-InvDB: C11orf88

    Other Databases showing C11orf88 gene

    (According to HUGE)
    About This Section
    		   --

    Specialized Databases showing C11orf88 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 C11orf88 Pharmacogenomics, SNPs, Pathways

    Intellectual Property
    for C11orf88 gene

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    		Patent Information for C11orf88 gene:
    Search GeneIP for patents involving C11orf88

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



    Products
    for C11orf88 gene

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    About This Section

     
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