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C22orf39 Gene

protein-coding   GIFtS: 38
GCID: GC22M019428

Chromosome 22 Open Reading Frame 39

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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 391 2
UPF0545 Protein C22orf392

External Ids:    HGNC: 270121   Entrez Gene: 1289772   Ensembl: ENSG000002422597   UniProtKB: Q6P5X53   

Export aliases for C22orf39 gene to outside databases

Previous GC identifers: GC22M017808 GC22M003049


(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 C22orf39 Gene:
C22orf39 (chromosome 22 open reading frame 39) 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:
   Regulatory transcription factor binding sites in the C22orf39 gene promoter:
         Elk-1   AML1a   AP-1   ATF-2   GATA-1   PPAR-gamma1   c-Jun   PPAR-gamma2   Ik-1   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search Chromatin IP Primers for C22orf39

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat C22orf39


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

Entrez Gene cytogenetic band: 22q11.21   Ensembl cytogenetic band:  22q11.21   HGNC cytogenetic band: 22q11.21

C22orf39 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
C22orf39 gene location

GeneLoc information about chromosome 22         GeneLoc Exon Structure

GeneLoc location for GC22M019428:  view genomic region     (about GC identifiers)

Start:
19,338,891 bp from pter      End:
19,435,755 bp from pter
Size:
96,865 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., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, 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: CV039_HUMAN, Q6P5X5 (See protein sequence)
Recommended Name: UPF0545 protein C22orf39  
Size: 142 amino acids; 16805 Da
Caution: It is uncertain whether Met-1 or Met-38 is the initiator. Orthologous sequences can not be extended
Sequence caution: Sequence=AAH62599.1; Type=Erroneous initiation; Note=Translation N-terminally extended;
Sequence=BAF82762.1; Type=Erroneous initiation; Note=Translation N-terminally extended; Sequence=CAG30225.1;
Type=Erroneous initiation; Note=Translation N-terminally extended; Sequence=EAX03040.1; Type=Erroneous gene model
prediction;
Secondary accessions: A8MTW6 D3DX18 F5H3A8 J3KNP9
Alternative splicing: 2 isoforms:  Q6P5X5-1   Q6P5X5-2   

Explore the universe of human proteins at neXtProt for C22orf39: NX_Q6P5X5

Explore proteomics data for C22orf39 at MOPED


See C22orf39 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

REFSEQ proteins (2 alternative transcripts): 
NP_001159714.1  NP_776154.3  

ENSEMBL proteins: 
 ENSP00000424903   ENSP00000382478   ENSP00000382474   ENSP00000333064   ENSP00000439212  

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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: Q6P5X5

UniProtKB/Swiss-Prot: CV039_HUMAN, Q6P5X5
Similarity: Belongs to the UPF0545 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, 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:
   inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for C22orf39
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5 qRT-PCR Assays for microRNAs that regulate C22orf39:
hsa-miR-200c hsa-miR-429 hsa-miR-3127-5p hsa-miR-200b hsa-miR-3126-5p
SwitchGear 3'UTR luciferase reporter plasmidC22orf39 3' UTR sequence
Inhib. RNA
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GenScript: all cDNA clones in your preferred vector (see all 2): C22orf39 (NM_173793)
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Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat C22orf39

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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
extracellular3
nucleus3
cytosol1

(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 C22orf39
Interactions:

    Search GeneGlobe Interaction Network for C22orf39

STRING Interaction Network Preview (showing 1 interactants - click image to see more details)

1 Interacting protein for C22orf39 (Q6P5X52, 3 ENSP000003824744) via UniProtKB, MINT, STRING, and/or I2D
InteractantInteraction Details
GeneCardExternal ID(s)
PPP2CBP627142, 3, ENSP000002211384MINT-8267140 I2D: score=2 STRING: ENSP00000221138
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 C22orf39 (CV039)



(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 C22orf39 gene (2 alternative transcripts): 
NM_001166242.1  NM_173793.4  

Unigene Cluster for C22orf39:

Chromosome 22 open reading frame 39
Hs.659565  [show with all ESTs]
Unigene Representative Sequence: AK095271
5 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000509549(uc010grp.3) ENST00000399568 ENST00000399562(uc002zpk.2)
ENST00000333059 ENST00000542103(uc002zpi.3)
miRNA
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5 qRT-PCR Assays for microRNAs that regulate C22orf39:
hsa-miR-200c hsa-miR-429 hsa-miR-3127-5p hsa-miR-200b hsa-miR-3126-5p
SwitchGear 3'UTR luciferase reporter plasmidC22orf39 3' UTR sequence
Inhib. RNA
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Predesigned siRNA for gene silencing in human, mouse, rat C22orf39
Clone
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GenScript: all cDNA clones in your preferred vector (see all 2): C22orf39 (NM_173793)
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Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat C22orf39
Primer
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Pre-validated RT2 qPCR Primer Assay in human, mouse, rat C22orf39
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  QuantiFast Probe-based Assays in human, mouse, rat C22orf39

Additional mRNA sequence: 

AK095271.1 AK290073.1 BC030758.1 BC046204.1 BC062599.1 BX648073.1 CR456339.1 

11 DOTS entries:

DT.440867  DT.95200588  DT.100703514  DT.100024516  DT.120652603  DT.75173115  DT.92434651  DT.100716790 
DT.120652505  DT.120652622  DT.75169720 

Selected AceView cDNA sequences (see all 146):

BC046204 BG055265 AI936449 BI826040 AI636916 BE645397 BM762291 AA378258 
AA640003 CB242419 BF434837 AW275326 AI655672 AA706462 AA282884 AI669748 
BI829441 AI391657 AI480382 CR599972 BX646538 BE672091 BI914758 BM676417 

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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C22orf39 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: AAGTTAAAAT
C22orf39 Expression
About this image


C22orf39 expression in embryonic tissues and stem cells    About this table
Data from LifeMap, the Embryonic Development and Stem Cells Database
 selected tissues (see all 2) fully expand
 
 Testis (Reproductive System)
         Secondary Spermatocyte Seminiferous Tubules
 
 Gonad
         Secondary Spermatocyte Seminiferous Tubules
C22orf39 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

C22orf39 Protein Expression

SOURCE GeneReport for Unigene cluster: Hs.659565
    Custom PCR Arrays for C22orf39
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In Situ
Assay Products:
 

 
Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for C22orf39

(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 C22orf39 gene from Selected species (see all 8)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
mouse
(Mus musculus)
Mammalia 2510002D24Rik5 RIKEN cDNA 2510002D24 gene   --   16 (11.67 cM) 18836578 
chicken
(Gallus gallus)
Aves C22orf396
chromosome 22 open reading frame 39
49(a)
1 ↔ 1
15(656749-657344)
lizard
(Anolis carolinensis)
Reptilia C22orf396
chromosome 22 open reading frame 39
47(a)
1 ↔ 1
GL343282.1(1470214-1470832)
zebrafish
(Danio rerio)
Actinopterygii C8H22orf396
chromosome 22 open reading frame 39
44(a)
1 ↔ 1
8(2711348-2718395) ENSDARG00000092360


ENSEMBL Gene Tree for C22orf39 (if available)
TreeFam Gene Tree for C22orf39 (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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Paralogs for C22orf39 gene
1 SIMAP similar gene for C22orf39 using alignment to 2 protein entries:     CV039_HUMAN (see all proteins):
HIRA

Find genes that share paralogs with C22orf39           About GenesLikeMe



(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 C22orf39 (see all 184)    About this table                                 

Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 22 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs1448771131,2
C--19427935(+) TCTAAA/GTCCTT 1 -- int10--------
rs1422888191,2
--19428005(+) CTGAGA/GTCCAC 1 -- int10--------
rs96049651,2
C,F,A,H--19428077(+) TCTCCG/ACACAG 1 -- int113Minor allele frequency- A:0.16NA WA CSA EA 376
rs1835548171,2
--19428126(+) TGGCTA/GCCTGC 1 -- int10--------
rs57467371,2
C,F,A,H--19428145(+) GAATCT/GCATAC 1 -- int118Minor allele frequency- G:0.19NS EA NA WA CSA 965
rs1177072801,2
C,F--19428178(+) CAGCAC/TCCGCT 1 -- int11Minor allele frequency- T:0.05EA 120
rs1864353591,2
--19428343(+) AGTGTG/TTTTTT 1 -- int10--------
rs1462289701,2
--19428392(+) TTTGGC/TAGGTC 1 -- int10--------
rs1389047281,2
C--19428441(+) AATTAC/TAGATT 1 -- ut310--------
rs117441,2
C,F,H--19428511(-) TAACAT/CTGGGG 1 -- ut3122Minor allele frequency- C:0.32MN NA NS EA CSA WA 3003

HapMap Linkage Disequilibrium report for C22orf39 (19338891 - 19435755 bp)

Structural Variations
     Database of Genomic Variants (DGV) 7 variations for C22orf39:    About this table    
Variant IDTypeSubtypePubMed ID
nsv435744CNV Deletion17901297
nsv834124CNV Loss17160897
dgv4839n71CNV Loss21882294
nsv834127CNV Loss17160897
dgv4840n71CNV Loss21882294
nsv914263CNV Gain21882294
esv2751940CNV Gain17911159

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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 C22orf39 gene integrated from 10 sources:
(articles sorted by number of sources associating them with C22orf39)
    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. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (Nat. Genet. 2004)
  3. Effects of chronic ascariasis and trichuriasis on cytokine production and gene expression in human blood: a cross-sectional study. (PubMed id 21666788)1 Reina Ortiz M....Cooper P.J. (PLoS Negl Trop Dis 2011)
  4. A directed protein interaction network for investigating intracellular signal transduction. (PubMed id 21900206)1 Vinayagam A....Wanker E.E. (Sci Signal 2011)
  5. 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)
  6. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (Proc. Natl. Acad. Sci. U.S.A. 2002)
  7. 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: 128977 HGNC: 27012 AceView: LOC128977 Ensembl:ENSG00000242259 euGenes: HUgn128977
ECgene: C22orf39 H-InvDB: C22orf39

(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 C22orf39 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 C22orf39 gene:
Search GeneIP for patents involving C22orf39

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, 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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GeneCards Homepage - Last full update: 7 May 2014 - Incrementals: 9 May 2014 , 2 Jun 2014 , 26 Jun 2014 , 30 Jun 2014 , 21 Aug 2014 , 8 Sep 2014

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