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C22orf42 Gene

protein-coding   GIFtS: 34
GCID: GC22M032544

Chromosome 22 Open Reading Frame 42

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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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Aliases
Chromosome 22 Open Reading Frame 421 2
dJ90G24.62
Uncharacterized Protein C22orf422

External Ids:    HGNC: 271601   Entrez Gene: 1502972   Ensembl: ENSG000002058567   UniProtKB: Q6IC833   

Export aliases for C22orf42 gene to outside databases

Previous GC identifers: GC22M030875 GC22M015501


(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 C22orf42 Gene:
C22orf42 (chromosome 22 open reading frame 42) 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  NT_011520.13  NC_018933.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the C22orf42 gene promoter:
         Sox5   Nkx2-2   XBP-1   Nkx2-5   E47   PPAR-gamma1   Pax-3   HSF2   PPAR-gamma2   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
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Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat C22orf42


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

Entrez Gene cytogenetic band: 22q12.3   Ensembl cytogenetic band:  22q12.3   HGNC cytogenetic band: 22q12.3

C22orf42 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
C22orf42 gene location

GeneLoc information about chromosome 22         GeneLoc Exon Structure

GeneLoc location for GC22M032544:  view genomic region     (about GC identifiers)

Start:
32,544,993 bp from pter      End:
32,555,309 bp from pter
Size:
10,317 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, 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, Abcam, Cloud-Clone Corp, antibodies-online, and/or others.)
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UniProtKB/Swiss-Prot: CV042_HUMAN, Q6IC83 (See protein sequence)
Recommended Name: Uncharacterized protein C22orf42  
Size: 251 amino acids; 27691 Da
Secondary accessions: A4QPH5

Explore the universe of human proteins at neXtProt for C22orf42: NX_Q6IC83

Explore proteomics data for C22orf42 at MOPED


See C22orf42 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

REFSEQ proteins: NP_001010859.1  
ENSEMBL proteins: 
 ENSP00000371529  

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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: Q6IC83


(According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, 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:
   genOway: Develop your customized and physiologically relevant rodent model for C22orf42

miRNA
Products:
    
miRTarBase miRNAs that target C22orf42:
hsa-mir-423-3p (MIRT042594)

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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
extracellular2
nucleus2
cytosol1
plasma membrane1

(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 C22orf42
Interactions:

    Search GeneGlobe Interaction Network for C22orf42

(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 C22orf42 (CV042)



(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 C22orf42 gene: 
NM_001010859.1  

Unigene Cluster for C22orf42:

Chromosome 22 open reading frame 42
Hs.426551  [show with all ESTs]
Unigene Representative Sequence: BC040263
3 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000382097(uc003amd.3) ENST00000467813 ENST00000490640
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Additional mRNA sequence: 

BC040263.1 BC139845.1 CR456485.1 

2 DOTS entries:

DT.95235835  DT.102820721 

17 AceView cDNA sequences:

AI624017 AA953775 BC040263 CR456485 BU072847 BI830282 BX110215 CA849111 
BV173548 BQ776649 BI438926 BI438599 AA860241 BE466410 CA775679 CA848928 
AW117314 

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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See probesets specificity/sensitivity at GeneAnnot
CGAP TAG: --


C22orf42 expression in embryonic tissues and stem cells    About this table
Data from LifeMap, the Embryonic Development and Stem Cells Database
 selected tissues (see all 4) fully expand
 
 Neurons
         Ventral/hypothalamic-like neurons
 
 Brain (Nervous System)
         Ventral/hypothalamic-like neurons
 
 Pancreas (Endocrine System)
 
 Testis (Reproductive System)
C22orf42 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

C22orf42 Protein Expression

SOURCE GeneReport for Unigene cluster: Hs.426551
    Custom PCR Arrays for C22orf42
Primer
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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 chimp.

Orthologs for C22orf42 gene from 1 species (see representative species )    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
chimpanzee
(Pan troglodytes)
Mammalia C22H22orf421 chromosome 22 open reading frame, human C22orf42 98.07(n)
95.65(a)
  738338  XM_003953875.1  XP_003953924.1 


ENSEMBL Gene Tree for C22orf42 (if available)
TreeFam Gene Tree for C22orf42 (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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Paralogs for C22orf42 gene

Find genes that share paralogs with C22orf42           About GenesLikeMe


1 Pseudogenes.org Pseudogene for C22orf42
PGOHUM00000246556


(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 C22orf42 (see all 322)    About this table                                 

Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 22 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs792571451,2
C,F--32545097(+) TGAGAT/CAAAAT 1 -- ds50011Minor allele frequency- C:0.05NA 120
rs59982531,2
C,F,A,H--32545152(+) ATTAGT/CTCTTC 1 -- ds5001 trp39Minor allele frequency- C:0.34NS EA WA CSA NA 662
rs121688951,2
C,H--32545378(+) TGCAGC/TCACAA 1 -- ds5001 ese34Minor allele frequency- T:0.00NS EA 418
rs1931288431,2
--32545459(+) GGAAAC/TATGCA 1 -- ds50010--------
rs1438391381,2
C--32545501(+) CAGGCA/GTCTGT 1 -- ds50010--------
rs1152755351,2
C,F--32545526(+) GGAACA/GCTAAA 1 -- ut311Minor allele frequency- G:0.22WA 118
rs3731169521,2
C--32545535(+) AAGCCA/GGAGAA 2 R W mis10--------
rs1848807381,2
C--32545581(+) CGAGAC/TCGTGC 2 R syn10--------
rs96069131,2
C--32545637(+) AAAAAA/TATATA 1 -- int1 trp30--------
rs585896891,2
--32545639(+) AAAAAA/TATATA 1 -- int10--------

HapMap Linkage Disequilibrium report for C22orf42 (32544993 - 32555309 bp)

Structural Variations
     Database of Genomic Variants (DGV) 3 variations for C22orf42:    About this table    
Variant IDTypeSubtypePubMed ID
esv2422247CNV Duplication17116639
nsv834178CNV Loss17160897
nsv834177CNV Gain17160897

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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 C22orf42 gene integrated from 10 sources:
(articles sorted by number of sources associating them with C22orf42)
    Utopia: connect your pdf to the dynamic
world of online information

  1. A genome annotation-driven approach to cloning the human ORFeome. (PubMed id 15461802)1, 2 Collins J.E.... Dunham I. (Genome Biol. 2004)
  2. 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)
  3. 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: 150297 HGNC: 27160 AceView: LOC150297 Ensembl:ENSG00000205856 euGenes: HUgn150297
ECgene: C22orf42 H-InvDB: C22orf42

(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 C22orf42 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 C22orf42 gene:
Search GeneIP for patents involving C22orf42

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



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