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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

C3orf52 Gene

protein-coding   GIFtS: 43
GCID: GC03P111805

chromosome 3 open reading frame 52
 Explore 2 diseases affiliated with
C3orf52 via
MalaCards
our new
 Human Malady Compendium 
Biological research products
for C3orf52    

Aliases
for C3orf52 gene

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section
Aliases
Chromosome 3 Open Reading Frame 521 2
TTMP1 2 5
FLJ231861
Novel Endoplasmic Reticulum Transmembrane Protein2
TPA Induced Trans-Membrane Protein2
TPA-Induced Transmembrane Protein2

External Ids:    HGNC: 262551   Entrez Gene: 796692   Ensembl: ENSG000001145297   OMIM: 6119565   UniProtKB: Q5BVD13   

Export aliases for C3orf52 gene to outside databases

Previous GC identifers: GC03P113289 GC03P109180


Summaries
for C3orf52 gene

(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section
  --

Genomic Views
for C3orf52 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 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000003.11  NC_018914.1  NT_005612.16  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the C3orf52 gene promoter:
         CUTL1   NF-E2 p45   AREB6   POU2F1   FOXJ2 (long isoform)   POU2F1a   POU2F1b   POU2F1c   FOXJ2   NF-E2   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmid: C3orf52 promoter sequence
   Search SABiosciences Chromatin IP Primers for C3orf52

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat C3orf52


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

Entrez Gene cytogenetic band: 3q13.2   Ensembl cytogenetic band:  3q13.2   HGNC cytogenetic band: 3q13.2

C3orf52 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
C3orf52 gene location

GeneLoc information about chromosome 3         GeneLoc Exon Structure

GeneLoc location for GC03P111805:  view genomic region     (about GC identifiers)

Start:
 111,805,182 bp from pter      End:
 111,849,851 bp from pter
Size:
 44,670 bases      Orientation:
 plus strand

Proteins
for C3orf52 gene

(According to 1UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to 2PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, 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 Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section
UniProtKB/Swiss-Prot: TTMP_HUMAN, Q5BVD1 (See protein sequence)
Recommended Name: TPA-induced transmembrane protein  
Size: 217 amino acids; 24295 Da
Subcellular location: Endoplasmic reticulum membrane; Single-pass type I membrane protein (Potential)
Sequence caution: Sequence=AAH17064.1; Type=Erroneous initiation; Note=Translation N-terminally extended;
Sequence=BAB15569.1; Type=Frameshift; Positions=1; Sequence=BAG60364.1; Type=Erroneous initiation; Note=Translation
N-terminally extended;
Secondary accessions: B4DNV2 B4E0Z2 Q96AJ4 Q9H5Q1
Alternative splicing: 3 isoforms:  Q5BVD1-1   Q5BVD1-2   Q5BVD1-3   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for C3orf52: NX_Q5BVD1

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q5BVD1

    • C3orf52 Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins (2 alternative transcripts): 
    NP_001165218.1  NP_078892.2  

    ENSEMBL proteins: 
     ENSP00000420539   ENSP00000264848   ENSP00000420077   ENSP00000390333   ENSP00000399392  

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    Uscn Proteins for C3orf52

    Gene Ontology (GO): 2 cellular component terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005789endoplasmic reticulum membrane IEA--
    GO:0016021integral to membrane IEA--


    C3orf52 for ontologies           About GeneDecksing



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    Uscn ELISAs and CLIAs for C3orf52

    Protein Domains /
    Families
    for C3orf52 gene

    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section

    ProtoNet protein and cluster: Q5BVD1


    Function
    for C3orf52 gene

    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
    About This Section
    Function Summary:

         UniProtKB/Swiss-Prot: TTMP_HUMAN, Q5BVD1
    Induction: Up-regulated following treatment with 12-O-tetradecanoylphorbol-13-acetate (TPA) in the pancreatic cancer
    cell line HPAF-II. The up-regulation by TPA is triggered at the promoter level

    miRNA
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    hsa-let-7d hsa-let-7c hsa-miR-583 hsa-miR-3916 hsa-miR-3125 hsa-let-7g hsa-miR-1323 hsa-let-7a
    SwitchGear 3'UTR luciferase reporter plasmid: C3orf52 3' UTR sequence
    Inhib. RNA
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    Gene Editing
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    Clone
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    In Situ Assay
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    Pathways & Interactions
    for C3orf52 gene

    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, 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 Mar 2013 via Entrez Gene).
    About This Section



    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for C3orf52

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

    1 Interacting protein for C3orf52 (ENSP000002648484) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    ELAVL1ENSP000003852694STRING: ENSP00000385269
    About this table

    Drugs & Compounds
    for C3orf52 gene

    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section
    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for C3orf52
    Search CenterWatch for drugs/clinical trials and news about C3orf52 / TTMP 

    Transcripts
    for C3orf52 gene

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 235 Homo sapiens; Mar 10 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,
    RNAi Products from EMD Millipore,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section
    REFSEQ mRNAs for C3orf52 gene (2 alternative transcripts): 
    NM_001171747.1  NM_024616.2  

    Unigene Cluster for C3orf52:

    Chromosome 3 open reading frame 52
    Hs.434247  [show with all ESTs]
    Unigene Representative Sequence: NM_024616
    8 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000480282 ENST00000264848(uc003dyq.4) ENST00000484828 ENST00000497610
    ENST00000494096 ENST00000467942(uc011bht.1 uc003dyr.1) ENST00000430855
    ENST00000431717(uc011bhs.2)

    miRNA
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    Browse OriGene MicroRNA Expression Plasmids
    QIAGEN Custom miScript Target Protector blocks miRNA-binding site of human, mouse, rat C3orf52
    8/23 QIAGEN miScript miRNA Assays for microRNAs that regulate C3orf52 (see all 23):
    hsa-let-7d hsa-let-7c hsa-miR-583 hsa-miR-3916 hsa-miR-3125 hsa-let-7g hsa-miR-1323 hsa-let-7a
    SwitchGear 3'UTR luciferase reporter plasmid: C3orf52 3' UTR sequence
    Inhib. RNA
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    OriGene 29mer shRNA kits in GFP-retroviral vector in human, mouse, rat for C3orf52 (see all 4)
    OriGene shRNA RFP: C3orf52
    OriGene siRNA: C3orf52
    QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing in human, mouse, rat C3orf52
    Clone
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    Primer
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      QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat C3orf52
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    Additional cDNA sequence: 

    AK026839.1 AK298076.1 AK303588.1 AY830714.1 BC017064.1 

    4 DOTS entries:

    DT.441662  DT.95151813  DT.99930797  DT.408543 

    24/62 AceView cDNA sequences (see all 62):

    BC041355 AK091769 BX104180 AA868604 BF222797 AI566334 AA699297 BC017064 
    AA598410 NM_024616 BM193355 AA641836 BX951270 AI911944 BX349316 AA705470 
    AI761179 AK026839 AI860123 BX352569 BG258544 BP363008 AI650743 BX498361 

    GeneLoc Exon Structure

    5 Alternative Splicing Database (ASD) splice patterns (SP) for C3orf52    About this scheme

    ExUns: 1a · 1b · 1c ^ 2 ^ 3 ^ 4a · 4b ^ 5 ^ 6 ^ 7 ^ 8a · 8b ^ 9 ^ 10
    SP1:                                      -     -     -     -                           
    SP2:                                -     -     -     -     -     -     -     -         
    SP3:                                                                                    
    SP4:                                                        -                           
    SP5:                                                  -                                 


    ECgene alternative splicing isoforms for C3orf52

    Expression
    for C3orf52 gene

    (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™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    C3orf52 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: TTAAATGTGA

    Microarray
    RNAseq (Illumina Body Map)
    (100×FPKM)½
    SAGE (Serial Analysis of Gene Expression)
    About this image

    C3orf52 expression in embryonic tissues and stem cells
    Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine    About this table
    Stem Cell Differentiation: 1 LifeMap Cell 
    NameCategory
    Pancreatic endoderm/endocrine precursor-like cells (A scalable, suspensi...)
    Expression: Positive    Negative     Selective marker
    Experimental details: Curated     Microarrays     In-situ hybridization

    See C3orf52 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for C3orf52

    SOURCE GeneReport for Unigene cluster: Hs.434247
        SABiosciences Custom PCR Arrays for C3orf52
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    In Situ
    Assay Products:     
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    Orthologs
    for C3orf52 gene

    (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)
    About This Section
    This gene was present in the common ancestor of chordates.

    Orthologs for C3orf52 gene from 2/7 species (see all 7)    About this table
    Organism Taxonomic
    classification    		 Gene Description Human
    Similarity    		 Orthology
    Type    		 Details
    mouse
    (Mus musculus)    		 Mammalia BC0165791 , 5 cDNA sequence, BC0165791, 5 76.01(n)1
    69.16(a)1    		   16 (29.76 cM)5
    2129981  NM_145389.21  NP_663364.21 
     456268485 
    chicken
    (Gallus gallus)    		 Aves C1H3orf521 chromosome 1 open reading frame, human C3orf52 51.65(n)
    43.96(a)    		   418422  XM_416636.3  XP_416636.2 


    ENSEMBL Gene Tree for C3orf52 (if available)
    TreeFam Gene Tree for C3orf52 (if available) 

    Paralogs
    for C3orf52 gene

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    		  --

    Genomic Variants
    for C3orf52 gene

    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, UniProtKB, 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) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    10/619 NCBI SNPs in C3orf52 are shown (see all 619)     About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance    		Chr 3 posSequence#AA
    Chg    		TypeMore#Allele
    freq    		PopTotal
    sample    		More
    ----------
    rs20115881,2
    		C,F,A,H,--111803201(-) TAAAGA/CATTTA 2 -- us2k17Minor allele frequency- C:0.03MN NS EA WA 840
    rs1449354591,2
    		--111803360(+) AACATG/TAGAAC 2 -- us2k10--------
    rs738563621,2
    		C,--111803513(+) GGGGGC/AGTGAG 2 -- us2k11Minor allele frequency- A:0.50WA 2
    rs748803151,2
    		C,F,--111803555(+) CAGGCA/CTGGAG 2 -- us2k12Minor allele frequency- C:0.04WA EA 238
    rs761644811,2
    		F,--111803669(+) GGATGG/CGGGTG 2 -- us2k11Minor allele frequency- C:0.05EA 120
    rs42806071,2
    		C,A,--111803685(+) AATCAA/GAAGTT 2 -- us2k10--------
    rs7460271,2
    		C,F,A,H,--111803689(-) CTCAAC/ACTTCT 2 -- us2k115Minor allele frequency- A:0.46NA EA NS WA CSA 787
    rs7460261,2
    		C,F,A,H,--111803696(-) GACACG/CTCTCA 2 -- us2k118Minor allele frequency- C:0.48NS EA NA WA CSA 1138
    rs7326861,2
    		C,F,H,--111803780(-) AGCCAT/CTGAAG 2 -- us2k117Minor allele frequency- C:0.09NS EA NA 2264
    rs799387561,2
    		C,--111804011(+) AGACT-/CCCCCT 2 -- us2k10--------

    HapMap Linkage Disequilibrium report for C3orf52 (111805182 - 111849851 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
          Database of Genomic Variants (DGV) variations for C3orf52: --

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    Disorders / Diseases
    for C3orf52 gene

    (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.)
    About This Section
    C3orf52 for disorders           About GeneDecksing

    OMIM gene information: 611956    OMIM disorders: --

    2 diseases for C3orf52:    About MalaCards
    pancreatic cancer    pancreatitis


    Export disorders for C3orf52 gene to outside databases

    Publications
    for C3orf52 gene

    (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)
    About This Section

    PubMed articles for C3orf52 gene integrated from 9 sources:
    (articles sorted by number of sources associating them with C3orf52)    		    Utopia: connect your pdf to the dynamic
    world of online information

    1. Identification and in silico characterization of a novel gene: TPA induced trans-membrane protein. (PubMed id 15737651)1, 2, 3 Chan C.-Y.... Adrian T.E. (2005)
    2. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S....Malek J. (2004)
    3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (2004)
    4. Ubiquitin-mediated proteolysis of HuR by heat shock. (PubMed id 19322201)1 Abdelmohsen K....Gorospe M. (2009)
    5. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. (PubMed id 16344560)1 Kimura K.... Sugano S. (2006)
    6. The DNA sequence, annotation and analysis of human chromosome 3. (PubMed id 16641997)2 Muzny D.M....Gibbs R.A. (2006)
    7. 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. (2002)

    External Searches for C3orf52 gene

    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section
     ANDOR
    Aliases
    Free Text  
      Query String
    		PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    Genome Databases showing C3orf52 gene

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 79669 HGNC: 26255 AceView: FLJ23186 Ensembl:ENSG00000114529 euGenes: HUgn79669
    ECgene: C3orf52 H-InvDB: C3orf52

    Other Databases showing C3orf52 gene

    (According to HUGE)
    About This Section
    		   --

    Specialized Databases showing C3orf52 gene

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    NameDescription
    PharmGKB entry for C3orf52 Pharmacogenomics, SNPs, Pathways

    Intellectual Property
    for C3orf52 gene

    (Patent information from GeneIP,
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