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C11orf88 Gene

protein-coding   GIFtS: 34
GCID: GC11P111404

Chromosome 11 Open Reading Frame 88

  Search for C11orf88
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 881 2
Hypothetical Gene Supported By BC0395051 2
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 GC11P111392 GC11P111398


(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 C11orf88 Gene:
C11orf88 (chromosome 11 open reading frame 88) is a protein-coding 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 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_033899.9  
Regulatory elements:
   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 Chromatin IP Primers for C11orf88

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing 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 GC11P111404:  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

(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, Cloud-Clone Corp, and/or others.)
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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; Note=Translation N-terminally shortened;
Secondary accessions: E9PAN0 Q6ZRL3
Alternative splicing: 3 isoforms:  Q6PI97-1   Q6PI97-2   Q6PI97-3   (No experimental confirmation available. Gene prediction based on EST data)

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

Explore proteomics data for C11orf88 at MOPED


See C11orf88 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

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

ENSEMBL proteins: 
 ENSP00000364768   ENSP00000432911   ENSP00000333845   ENSP00000435029  

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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: Q6PI97

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


(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
nucleus3
cytosol2

(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 C11orf88
Interactions:

    Search GeneGlobe Interaction Network for C11orf88

(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 C11orf88 (CK088)



(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, Primers from OriGene, and/or QIAGEN )
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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 mRNA sequence: BC039505.2 

4 DOTS entries:

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

21 AceView cDNA sequences:

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

(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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C11orf88 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: GCAGAGGATG
C11orf88 Expression
About this image

C11orf88 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

C11orf88 Protein Expression

SOURCE GeneReport for Unigene cluster: Hs.411600
    Custom PCR Arrays for C11orf88
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In Situ
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(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 chordates.

Orthologs for C11orf88 gene from Selected species (see all 8)    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
chromosome 11 open reading frame 88
43(a)
1 ↔ 1
24(5562886-5564970) ENSGALG00000024430
zebrafish
(Danio rerio)
Actinopterygii C5H11orf886
chromosome 11 open reading frame 88
38(a)
1 ↔ 1
5(59250279-59269711) ENSDARG00000075714


ENSEMBL Gene Tree for C11orf88 (if available)
TreeFam Gene Tree for C11orf88 (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 C11orf88 (see all 396)    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-/GGTTGC 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
C,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
     Database of Genomic Variants (DGV) 1 variation for C11orf88:    About this table    
Variant IDTypeSubtypePubMed ID
nsv832268CNV Loss17160897

Site Specific Mutation Identification with PCR Assays
SeqTarget long-range PCR primers for resequencing C11orf88
DNA2.0 Custom Variant and Variant Library Synthesis for C11orf88

(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 C11orf88 gene integrated from 10 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. (Proc. Natl. Acad. Sci. U.S.A. 2002)
  2. Human chromosome 11 DNA sequence and analysis including novel gene identification. (PubMed id 16554811)2 Taylor T.D....Sakaki Y. (Nature 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. (Genome Res. 2004)
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)2 Ota T.... Sugano S. (Nat. Genet. 2004)

(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: 399949 HGNC: 25061 AceView: FLJ46266 Ensembl:ENSG00000183644 euGenes: HUgn399949
ECgene: C11orf88 H-InvDB: C11orf88

(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 C11orf88 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 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



(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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The GeneCards human gene database gene index: 1 3 5 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z 


Developed at the Crown Human Genome Center, Department of Molecular Genetics, the Weizmann Institute of Science

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