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C22orf46 Gene

protein-coding   GIFtS: 37
GCID: GC22P042085

Chromosome 22 Open Reading Frame 46

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(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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This gene clusters with an RNA gene
Subcategory (RNA class): lncRNA

Quality score for the ORGUL clustered with this gene is 3

Aliases
Chromosome 22 Open Reading Frame 461 2
CTA-216E10.62
Putative Uncharacterized Protein C22orf462
Uncharacterized Protein C22orf462

External Ids:    HGNC: 262941   Entrez Gene: 796402   Ensembl: ENSG000001842087   UniProtKB: C9J4423   
ORGUL members:         

Export aliases for C22orf46 gene to outside databases

Previous GC identifers: GC22P040418 GC22P025051


(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 C22orf46 Gene:
C22orf46 (chromosome 22 open reading frame 46) 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 at NCBI GenBank:
NC_000022.10  NC_018933.2  NT_011520.13  
Regulatory elements:
   Search for regulatory transcription factor binding sites for C22orf46
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search Chromatin IP Primers for C22orf46

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat C22orf46


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

Entrez Gene cytogenetic band: 22q13.2   Ensembl cytogenetic band:  22q13.2   HGNC cytogenetic band: 22q13.2

C22orf46 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
C22orf46 gene location

GeneLoc information about chromosome 22         GeneLoc Exon Structure

GeneLoc location for GC22P042085:  view genomic region     (about GC identifiers)

Start:
42,084,943 bp from pter      End:
42,094,140 bp from pter
Size:
9,198 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, Cloud-Clone Corp., eBioscience, and/or antibodies-online,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., eBioscience, and/or antibodies-online, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, antibodies-online, and/or others.)
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UniProtKB/Swiss-Prot: CV046_HUMAN, C9J442 (See protein sequence)
Recommended Name: Uncharacterized protein C22orf46 precursor  
Size: 243 amino acids; 27532 Da
Sequence caution: Sequence=EAW60455.1; Type=Erroneous gene model prediction;

Explore the universe of human proteins at neXtProt for C22orf46: NX_C9J442

Explore proteomics data for C22orf46 at MOPED

Post-translational modifications: 

  • Glycosylation2 at Asn30, Asn165

  • See C22orf46 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_001136436.1  
    ENSEMBL proteins: 
     ENSP00000385467  

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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: C9J442


    (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, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, 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 UniProtKB/Swiss-Prot
    CV046_HUMAN, C9J442: Secreted (Potential)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    extracellular3
    nucleus1

    Gene Ontology (GO): 1 cellular component term:    About this table

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

    Find genes that share ontologies with C22orf46           About GenesLikeMe


    (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 C22orf46
    Interactions:

        Search GeneGlobe Interaction Network for C22orf46

    1 Interacting protein for C22orf46 (C9J4423) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    SMAD2Q157963I2D: score=1 
    About this table

    (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 C22orf46 (CV046)



    (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, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    REFSEQ mRNAs for C22orf46 gene (2 alternative transcripts): 
    NM_024588.3  NM_001142964.1  

    Unigene Cluster for C22orf46:

    Chromosome 22 open reading frame 46
    Hs.517653  [show with all ESTs]
    Unigene Representative Sequence: BC035403
    2 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000472110 ENST00000402966(uc003bax.1)
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    hsa-miR-29b-1* hsa-miR-4267 hsa-miR-877* hsa-miR-629* hsa-miR-508-5p hsa-miR-3116 hsa-miR-4273 hsa-miR-3144-5p
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    Additional mRNA sequence: 

    AK027237.1 AK095008.1 BC007210.1 BC035403.1 

    7 DOTS entries:

    DT.442537  DT.97822702  DT.100707128  DT.100856292  DT.97814139  DT.91704443  DT.450040 

    Selected AceView cDNA sequences (see all 82):

    N66693 AA384853 NM_024588 BC035403 BU156065 BI062000 AK131457 BQ226586 
    BX486924 BF941186 BX281640 BI060079 AW136743 N98960 BC007210 BQ182168 
    BQ005198 AK095008 BE389349 BQ218780 CD558924 AK027237 BU584859 BU584797 

    GeneLoc Exon Structure

    3 Alternative Splicing Database (ASD) splice patterns (SP) for C22orf46    About this scheme

    ExUns: 1 ^ 2a · 2b · 2c ^ 3a · 3b ^ 4a · 4b
    SP1:        -     -                                 
    SP2:                                                
    SP3:                                                


    ECgene alternative splicing isoforms for C22orf46

    (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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    C22orf46 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: TCAGAGCCCA
    C22orf46 Expression
    About this image

    C22orf46 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    C22orf46 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.517653
        Custom PCR Arrays for C22orf46
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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 human and mouse.

    Orthologs for C22orf46 gene from Selected species (see all 2)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia 4930407I10Rik5 RIKEN cDNA 4930407I10 gene   --   15 (38.40 cM) 82059151 


    ENSEMBL Gene Tree for C22orf46 (if available)
    TreeFam Gene Tree for C22orf46 (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 C22orf46 (see all 137)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 22 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs121575331,2
    H--42086944(+) TACCAG/TAAATG 1 -- int14Minor allele frequency- T:0.00NS EA 418
    rs762677151,2
    F--42087012(+) AGTCAC/TCCTGA 1 -- int11Minor allele frequency- T:0.03WA 118
    rs781950011,2
    --42087059(+) TCTGCA/GGGTCC 1 -- int10--------
    rs1412467081,2
    --42087118(+) ACACCA/GCACCC 1 -- int10--------
    rs1384842441,2
    C--42087249(+) CTCTC-/TCTCTCT 1 -- int10--------
    rs356484321,2
    C--42087274(+) TCTCT-/C/CT  
            
    TCTTT
    1 -- int11NA 2
    rs664833741,2
    C--42087274(+) TCTCTT/CTCTTT 1 -- int11Minor allele frequency- C:0.00NA 2
    rs57584181,2
    C--42087276(+) tctctC/Tttttt 1 -- int1 trp30--------
    rs589803441,2
    C--42087276(+) TCTCT-/CTTTTT 1 -- int10--------
    rs1479380361,2
    C--42087366(+) CCTGGA/TTCAAG 1 -- int10--------

    HapMap Linkage Disequilibrium report for C22orf46 (42084943 - 42094140 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 3 variations for C22orf46:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv915155CNV Loss21882294
    nsv834209CNV Loss17160897
    nsv524585CNV Loss19592680

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    (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 C22orf46 gene integrated from 10 sources:
    (articles sorted by number of sources associating them with C22orf46)
        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. Interactions of pathological hallmark proteins: tubulin polymerization promoting protein/p25, beta-amyloid, and alpha-synuclein. (PubMed id 21832049)1 OlA!h J....OvA!di J. (J. Biol. Chem. 2011)
    3. Functional proteomics mapping of a human signaling pathway. (PubMed id 15231748)1 Colland F....Gauthier J.M. (Genome Res. 2004)
    4. 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)
    5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1 Ota T.... Sugano S. (Nat. Genet. 2004)
    6. The DNA sequence of human chromosome 22. (PubMed id 10591208)2 Dunham I.... Wright H. (Nature 1999)

    (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: 79640 HGNC: 26294 AceView: FLJ23584 Ensembl:ENSG00000184208 euGenes: HUgn79640
    ECgene: C22orf46 H-InvDB: C22orf46

    (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 C22orf46 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 C22orf46 gene:
    Search GeneIP for patents involving C22orf46

    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, eBioscience, antibodies-online, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, 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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