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C20orf196 Gene

protein-coding   GIFtS: 38
GCID: GC20P005731          (predicted)

Chromosome 20 Open Reading Frame 196

  Search for C20orf196
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 20 Open Reading Frame 1961 2
Uncharacterized Protein C20orf1962

External Ids:    HGNC: 263181   Entrez Gene: 1498402   Ensembl: ENSG000001719847   UniProtKB: Q8IYI03   

Export aliases for C20orf196 gene to outside databases

Previous GC identifer: GC20P005680


(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 C20orf196 Gene:
C20orf196 (chromosome 20 open reading frame 196) 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_000020.10  NT_011387.9  NC_018931.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the C20orf196 gene promoter:
         MZF-1   AREB6   PPAR-gamma1   ARP-1   PPAR-gamma2   HNF-4alpha2   Nkx2-5   HNF-4alpha1   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search Chromatin IP Primers for C20orf196

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat C20orf196


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

Entrez Gene cytogenetic band: 20p12.3   Ensembl cytogenetic band:  20p12.3   HGNC cytogenetic band: 20p12.3

C20orf196 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
C20orf196 gene location

GeneLoc information about chromosome 20         GeneLoc Exon Structure

GeneLoc location for GC20P005731:  view genomic region     (about GC identifiers)

Start:
5,731,039 bp from pter      End:
5,844,558 bp from pter
Size:
113,520 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., 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: CT196_HUMAN, Q8IYI0 (See protein sequence)
Recommended Name: Uncharacterized protein C20orf196  
Size: 205 amino acids; 22938 Da
Secondary accessions: A8K9J3 Q5TGA9 Q96LU1
Alternative splicing: 2 isoforms:  Q8IYI0-1   Q8IYI0-2   

Explore the universe of human proteins at neXtProt for C20orf196: NX_Q8IYI0

Explore proteomics data for C20orf196 at MOPED


See C20orf196 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

REFSEQ proteins: NP_689717.2  
ENSEMBL proteins: 
 ENSP00000368263   ENSP00000305875   ENSP00000399331   ENSP00000410534  

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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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1 InterPro protein domain:
 IPR027821 DUF4521

Graphical View of Domain Structure for InterPro Entry Q8IYI0

ProtoNet protein and cluster: Q8IYI0


Find genes that share domains with C20orf196           About GenesLikeMe


(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 C20orf196
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SwitchGear 3'UTR luciferase reporter plasmidC20orf196 3' UTR sequence
Inhib. RNA
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Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat C20orf196

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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
cytosol2
nucleus2
endoplasmic reticulum1
extracellular1
golgi apparatus1

(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 C20orf196
Interactions:

    Search GeneGlobe Interaction Network for C20orf196

(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 C20orf196 (CT196)



(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 C20orf196 gene: 
NM_152504.2  

Unigene Cluster for C20orf196:

Chromosome 20 open reading frame 196
Hs.529340  [show with all ESTs]
Unigene Representative Sequence: AK292708
4 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000378979 ENST00000303142(uc002wmf.3) ENST00000445603 ENST00000442185

miRNA
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hsa-miR-3194-5p hsa-miR-548s
SwitchGear 3'UTR luciferase reporter plasmidC20orf196 3' UTR sequence
Inhib. RNA
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  QuantiFast Probe-based Assays in human, mouse, rat C20orf196

Additional mRNA sequence: 

AK057796.1 AK292708.1 BC035800.1 

5 DOTS entries:

DT.112012  DT.205610  DT.99974196  DT.95368078  DT.91677572 

Selected AceView cDNA sequences (see all 71):

AI140556 AA341344 NM_152504 CA427539 AI357165 H55860 BU626204 AA978290 
BC035800 AA577516 AV715251 BU656896 AI654149 BM809033 BU660655 BM793918 
BG216148 BU664303 AA856720 AA953536 AK057796 AI241414 CD692558 AA856721 

GeneLoc Exon Structure

Selected Alternative Splicing Database (ASD) splice patterns (SP) for C20orf196 (see all 6)    About this scheme

ExUns: 1a · 1b ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9a · 9b · 9c
SP1:              -                 -     -     -     -                     
SP2:              -     -           -     -     -     -                     
SP3:              -     -                                                   
SP4:                    -           -     -     -     -                     
SP5:                                -                                       


ECgene alternative splicing isoforms for C20orf196

(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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C20orf196 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: AAATCACACC
C20orf196 Expression
About this image

C20orf196 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

C20orf196 Protein Expression

SOURCE GeneReport for Unigene cluster: Hs.529340
    Custom PCR Arrays for C20orf196
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In Situ
Assay Products:
 

 
Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for C20orf196

(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 C20orf196 gene from Selected species (see all 7)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
mouse
(Mus musculus)
Mammalia 1110034G24Rik1 , 5 RIKEN cDNA 1110034G24 gene1, 5 75(n)1
62.75(a)1
  2 (64.74 cM)5
737471  NM_028637.11  NP_082913.11 
 1326869315 
chicken
(Gallus gallus)
Aves C3H20orf1961 chromosome 3 open reading frame, human C20orf196 50.17(n)
35.5(a)
  101751903  XM_004935280.1  XP_004935337.1 


ENSEMBL Gene Tree for C20orf196 (if available)
TreeFam Gene Tree for C20orf196 (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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Paralogs for C20orf196 gene

Find genes that share paralogs with C20orf196           About GenesLikeMe


1 Pseudogenes.org Pseudogene for C20orf196
PGOHUM00000244786


(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 C20orf196 (see all 2963)    About this table                                 

Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 20 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs757706271,2
F--5729095(+) AGTAAC/GTTTGA 1 -- us2k11Minor allele frequency- G:0.06WA 118
rs1422046511,2
--5729121(+) GGGCCC/GGGTGC 1 -- us2k10--------
rs575916941,2
C,F--5729136(+) GCTCAT/CGGCTG 1 -- us2k15Minor allele frequency- C:0.28WA NA CSA EA 128
rs1848014961,2
--5729255(+) TTAGCC/TGGGCA 1 -- us2k10--------
rs60852641,2
C,F,A--5729271(+) GTGCAC/TGCCTG 1 -- us2k18Minor allele frequency- T:0.23NA WA CSA EA 252
rs126248691,2
H--5729398(+) aaaagA/Gaaaaa 1 -- us2k1 trp30--------
rs1873551981,2
--5729472(+) CTATGA/TAGCTA 1 -- us2k10--------
rs559352611,2
C,F--5729729(+) ACATTC/TAAGTT 1 -- us2k16Minor allele frequency- T:0.36WA CSA NA EA 363
rs1461945201,2
C--5729842(+) GAGATC/TGAGAC 1 -- us2k10--------
rs574685671,2
C,F--5729918(+) GCGGGT/CGCCTG 1 -- us2k11Minor allele frequency- C:0.00NA 2

HapMap Linkage Disequilibrium report for C20orf196 (5731039 - 5844558 bp)

Structural Variations
     Database of Genomic Variants (DGV) 9 variations for C20orf196:    About this table    
Variant IDTypeSubtypePubMed ID
dgv777e199CNV Deletion23128226
nsv3270CNV Insertion18451855
nsv3271CNV Insertion18451855
esv27527CNV Loss19812545
esv34186CNV Loss18971310
nsv523886CNV Loss19592680
nsv912637CNV Gain21882294
nsv833905CNV Gain17160897
nsv470539CNV Gain18288195

Site Specific Mutation Identification with PCR Assays
SeqTarget long-range PCR primers for resequencing C20orf196
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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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Find genes that share disorders with C20orf196           About GenesLikeMe

Genetic Association Database (GAD): C20orf196

Export disorders for C20orf196 gene to outside databases

(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 C20orf196 gene integrated from 10 sources:
(articles sorted by number of sources associating them with C20orf196)
    Utopia: connect your pdf to the dynamic
world of online information

  1. Whole genome association scan for genetic polymorphisms influencing information processing speed. (PubMed id 21130836)1, 4 Luciano M....Deary I.J. (Biol Psychol 2011)
  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. A Y2H-seq approach defines the human protein methyltransferase interactome. (PubMed id 23455924)1 Weimann M.... Stelzl U. (Nat. Methods 2013)
  4. Systematic analysis of human protein complexes identifies chromosome segregation proteins. (PubMed id 20360068)1 Hutchins J.R.... Peters J.M. (Science 2010)
  5. Dynamics of cullin-RING ubiquitin ligase network revealed by systematic quantitative proteomics. (PubMed id 21145461)1 Bennett E.J....Harper J.W. (Cell 2010)
  6. Genome-wide association study for subclinical atherosclerosis in major arterial territories in the NHLBI's Framingham Heart Study. (PubMed id 17903303)4 O'Donnell C.J....Demissie S. (BMC Med. Genet. 2007)
  7. 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)
  8. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)2 Ota T.... Sugano S. (Nat. Genet. 2004)
  9. The DNA sequence and comparative analysis of human chromosome 20. (PubMed id 11780052)2 Deloukas P....Rogers J. (Nature 2001)

(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: 149840 HGNC: 26318 AceView: FLJ25067 Ensembl:ENSG00000171984 euGenes: HUgn149840
ECgene: C20orf196 H-InvDB: C20orf196

(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 C20orf196 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 C20orf196 gene:
Search GeneIP for patents involving C20orf196

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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