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TMEM239 Gene

protein-coding   GIFtS: 32
GCID: GC20P002806

Transmembrane Protein 239

  Search for TMEM239
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
Transmembrane Protein 2391 2

External Ids:    HGNC: 400441   Entrez Gene: 1002887972   Ensembl: ENSG000001983267   UniProtKB: Q8WW343   

Export aliases for TMEM239 gene to outside databases


(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 TMEM239 Gene:
TMEM239 (transmembrane protein 239) 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_000020.11  NT_011387.9  NC_018931.2  
Regulatory elements:
   Search for regulatory transcription factor binding sites for TMEM239
         Other transcription factors

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Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat TMEM239


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

Entrez Gene cytogenetic band: 20p13   Ensembl cytogenetic band:  20p13   HGNC cytogenetic band: 20p13

TMEM239 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
TMEM239 gene location

GeneLoc information about chromosome 20         GeneLoc Exon Structure

GeneLoc location for GC20P002806:  view genomic region     (about GC identifiers)

Start:
2,795,614 bp from pter      End:
2,800,930 bp from pter
Size:
5,317 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.,
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UniProtKB/Swiss-Prot: TM239_HUMAN, Q8WW34 (See protein sequence)
Recommended Name: Transmembrane protein 239  
Size: 195 amino acids; 21842 Da
Sequence caution: Sequence=AAH21178.1; Type=Erroneous initiation; Note=Translation N-terminally extended;
Secondary accessions: Q5JY54 Q6ZU23
Alternative splicing: 2 isoforms:  Q8WW34-1   Q8WW34-2   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for TMEM239: NX_Q8WW34

REFSEQ proteins: NP_001161142.1  
ENSEMBL proteins: 
 ENSP00000354312   ENSP00000369959   ENSP00000452175  

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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: Q8WW34


(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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Phenotypes:
     1 GenomeRNAi human phenotype for TMEM239:
 Increased G1 DNA content 

Animal Models:
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hsa-mir-335-5p (MIRT018265)

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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
TM239_HUMAN, Q8WW34: Membrane; Multi-pass membrane protein (Potential)

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

GO IDQualified GO termEvidencePubMed IDs
GO:0016021integral component of membrane IEA--

TMEM239 for ontologies           About GeneDecksing


(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 TMEM239
Interactions:

    Search GeneGlobe Interaction Network for TMEM239

(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 TMEM239 (TM239)



(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,
Conferences by KenesGroup, 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 TMEM239 gene: 
NM_001167670.1  

Unigene Cluster for TMEM239:

Transmembrane protein 239
Hs.664180  [show with all ESTs]
Unigene Representative Sequence: AK126033
3 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000361033(uc002wgx.2) ENST00000380585 ENST00000554164
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Additional mRNA sequence: 

AK126033.1 BC021178.2 

5 DOTS entries:

DT.40302056  DT.75195984  DT.120800116  DT.100009732  DT.308541 

GeneLoc Exon Structure

2 Alternative Splicing Database (ASD) splice patterns (SP) for TMEM239    About this scheme

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


ECgene alternative splicing isoforms for TMEM239

(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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TMEM239 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: ACTCACCCAG
TMEM239 Expression
About this image

TMEM239 Protein expression data from MOPED1, PaxDb2 and MaxQB3 --

SOURCE GeneReport for Unigene cluster: Hs.664180
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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 TMEM239 gene from Selected species (see all 6)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
mouse
(Mus musculus)
Mammalia Tmem2391 , 5 RIKEN cDNA 4933425O20 gene5
transmembrane 2391
86.09(n)1
84.11(a)1
  2 (63.22 cM)5
667661  NM_025753.31  NP_080029.11 
 1304064785 


ENSEMBL Gene Tree for TMEM239 (if available)
TreeFam Gene Tree for TMEM239 (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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Paralogs for TMEM239 gene
1 SIMAP similar gene for TMEM239 using alignment to 2 protein entries:     TM239_HUMAN (see all proteins):
C20orf141

TMEM239 for paralogs           About GeneDecksing



(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 TMEM239 (see all 42)    About this table    
Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 20 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs2155611,2
C,F,A,H--2797015(+) AGGCCG/ATCCTG 1 -- ut51 ese320Minor allele frequency- A:0.30NS EA NA WA 2346
rs73525931,2
H--2797065(+) AGGTAA/GGTCCC 1 -- int14Minor allele frequency- G:0.00NS EA 420
rs114698691,2
C--2797148(+) CCCCC-/C/CC  
        
AAGGT
1 -- int11NA 2
rs1819787061,2
--2797324(+) ACATGC/GCCCCG 2 P A mis10--------
rs1155704861,2
C,F--2797325(+) CATGCC/TCCCGA 2 P L mis11Minor allele frequency- T:0.02WA 118
rs1168169931,2
C,F--2797461(+) TCCCAC/GCTGCT 2 H Q mis11Minor allele frequency- G:0.02WA 118
rs1870191191,2
C--2797465(+) ACCTGC/TTGAGC 2 L syn10--------
rs1390867041,2
--2797486(+) CTGTCA/GTGGCC 2 M V mis10--------
rs2018468671,2
C--2797563(+) TTCACG/AGCCTC 2 /T syn11Minor allele frequency- A:0.00EU 567
rs1424040831,2
C--2797635(+) CCAGGC/TGACAC 2 G syn10--------

HapMap Linkage Disequilibrium report for TMEM239 (2795614 - 2800930 bp)

Structural Variations
     Database of Genomic Variants (DGV) 4 variations for TMEM239:    About this table    
Variant IDTypeSubtypePubMed ID
nsv833895CNV Loss17160897
nsv518364CNV Loss19592680
nsv510780CNV Loss20534489
nsv522009CNV Gain19592680

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(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, 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 TMEM239 gene integrated from 10 sources:
(articles sorted by number of sources associating them with TMEM239)
    Utopia: connect your pdf to the dynamic
world of online information

  1. White matter integrity as an intermediate phenotype: exploratory genome-wide association analysis in individuals at high risk of bipolar disorder. (PubMed id 23218918)1 Sprooten E....McIntosh A.M. (Psychiatry Res 2013)
  2. 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)
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)2 Ota T.... Sugano S. (Nat. Genet. 2004)
  4. 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)
  5. 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: 100288797 HGNC: 40044 Ensembl:ENSG00000198326 euGenes: HUgn100288797 ECgene: TMEM239
H-InvDB: TMEM239

(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 TMEM239 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 TMEM239 gene:
Search GeneIP for patents involving TMEM239

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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