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

ZC3H12D Gene

protein-coding   GIFtS: 43
GCID: GC06M149811

zinc finger CCCH-type containing 12D

(Previous name: chromosome 6 open reading frame 95 )
(Previous symbol: C6orf95)
 Explore 12 diseases affiliated with
ZC3H12D via
MalaCards
our new
 Human Malady Compendium 
Biological research products
for ZC3H12D    

Aliases
for ZC3H12D gene

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section
Aliases
Zinc Finger CCCH-Type Containing 12D1 2     MCP-Induced Protein 42 3
C6orf951 2 3 5     Zinc Finger CCCH Domain-Containing Protein 12D2 3
MCPIP41 2 3     Chromosome 6 Open Reading Frame 951
P341     Probable Ribonuclease ZC3H12D2
DJ281H8.11     Tumor Suppressor TFL2
Transformed Follicular Lymphoma2 3     EC 3.1.-.-3
TFL2 3     

External Ids:    HGNC: 211751   Entrez Gene: 3401522   Ensembl: ENSG000001781997   OMIM: 6111065   UniProtKB: A2A2883   

Export aliases for ZC3H12D gene to outside databases

Previous GC identifer: GC06M147335


Summaries
for ZC3H12D gene

(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section
UniProtKB/Swiss-Prot: ZC12D_HUMAN, A2A288
Function: May regulate cell growth likely by suppressing RB1 phosphorylation. May function as RNase and regulate the
levels of target RNA species (Potential). Serve as a tumor suppressor in certain leukemia cells. Overexpression
inhibits the G1 to S phase progression through suppression of RB1 phosphorylation




Genomic Views
for ZC3H12D 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_000006.11  NC_018917.1  NT_025741.15  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the ZC3H12D gene promoter:
         COUP-TF1   AML1a   COUP   RelA   HNF-4alpha2   NF-kappaB   HNF-4alpha1   CP2   COUP-TF   NF-kappaB1   
         Other transcription factors

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Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat ZC3H12D


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

Entrez Gene cytogenetic band: 6q25.1   Ensembl cytogenetic band:  6q25.1   HGNC cytogenetic band: 6q25.1

ZC3H12D Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
ZC3H12D gene location

GeneLoc information about chromosome 6         GeneLoc Exon Structure

GeneLoc location for GC06M149811:  view genomic region     (about GC identifiers)

Start:
 149,768,766 bp from pter      End:
 149,806,197 bp from pter
Size:
 37,432 bases      Orientation:
 minus strand

Proteins
for ZC3H12D 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: ZC12D_HUMAN, A2A288 (See protein sequence)
Recommended Name: Probable ribonuclease ZC3H12D  
Size: 527 amino acids; 58078 Da
Cofactor: Magnesium (Potential)
Subcellular location: Isoform 1: Cytoplasm. Note=Localized as discrete granules. Colocalized with mRNA-processing body
markers, EIF2C2 and DCP1A, but not with a stress granule maker, TIA1, in the cytoplasm
Subcellular location: Isoform 3: Cytoplasm. Nucleus
Secondary accessions: A1L178 B2RXF4 B7WNU7 B9ZZP9 B9ZZQ0 Q6ZRW2
Alternative splicing: 3 isoforms:  A2A288-1   A2A288-3   A2A288-4   (Ref.1 (BAH28269) sequence is in conflict in positions: 300:V->G, 301:L->V, 302:P->R. Ref.2 (BAC87196) sequence is in conflict in positions: 300:V->G, 301:L->V, 302:P->R)

Explore the universe of human proteins at neXtProt for ZC3H12D: NX_A2A288

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_A2A288

    • ZC3H12D Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins: NP_997243.2  
    ENSEMBL proteins: 
     ENSP00000386616   ENSP00000395209   ENSP00000387062   ENSP00000374592   ENSP00000408686  
     ENSP00000440813  

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    Uscn Proteins for ZC3H12D

    Gene Ontology (GO): 4 cellular component terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus IDA--
    GO:0005730NOT nucleolus IDA--
    GO:0005737cytoplasm IEA--
    GO:0043231intracellular membrane-bounded organelle IDA--


    ZC3H12D for ontologies           About GeneDecksing



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    Uscn ELISAs and CLIAs for ZC3H12D

    Protein Domains /
    Families
    for ZC3H12D gene

    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    ZC3H12D for domains           About GeneDecksing

    2 InterPro domains/families:
     IPR000571 Znf_CCCH
     IPR021869 RNase_Zc3h12

    Graphical View of Domain Structure for InterPro Entry A2A288

    ProtoNet protein and cluster: A2A288

    UniProtKB/Swiss-Prot: ZC12D_HUMAN, A2A288
    Similarity: Belongs to the ZC3H12 family
    Similarity: Contains 1 C3H1-type zinc finger


    Function
    for ZC3H12D 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: ZC12D_HUMAN, A2A288
    Function: May regulate cell growth likely by suppressing RB1 phosphorylation. May function as RNase and regulate the
    levels of target RNA species (Potential). Serve as a tumor suppressor in certain leukemia cells. Overexpression
    inhibits the G1 to S phase progression through suppression of RB1 phosphorylation
    Induction: By prolonged exposure to bacterial lipopolysaccharides (LPS) in acute monocytic leukemia cell line THP-1
    cells

    Enzyme Number (IUBMB): EC 3.1.-.-1

    miRNA
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    Gene Editing
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    In Situ Assay
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    Gene Ontology (GO): 3 molecular function terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003676nucleic acid binding IEA--
    GO:0004519endonuclease activity IEA--
    GO:0008270zinc ion binding IEA--


    ZC3H12D for ontologies           About GeneDecksing


    1 GenomeRNAi human phenotype for ZC3H12D:
     Increased S DNA content 


    Pathways & Interactions
    for ZC3H12D 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 ZC3H12D

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0030308negative regulation of cell growth IDA19531561
    GO:2000134negative regulation of G1/S transition of mitotic cell cycle IDA19531561


    ZC3H12D for ontologies           About GeneDecksing



    Drugs & Compounds
    for ZC3H12D 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 ZC3H12D
    Search CenterWatch for drugs/clinical trials and news about ZC3H12D / ZC12D 

    Transcripts
    for ZC3H12D 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,
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    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 ZC3H12D gene: 
    NM_207360.2  

    Unigene Cluster for ZC3H12D:

    Zinc finger CCCH-type containing 12D
    Hs.632618  [show with all ESTs]
    Unigene Representative Sequence: AK090441
    8 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000498662 ENST00000409806 ENST00000458251 ENST00000409948 ENST00000462655
    ENST00000389942(uc010kid.3) ENST00000416573 ENST00000542614(uc003qmn.1)


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    hsa-miR-3942-5p hsa-miR-128 hsa-miR-371-5p hsa-miR-29b-1* hsa-miR-548a-3p hsa-miR-641 hsa-miR-7-1* hsa-miR-3148
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    Inhib. RNA
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    Primer
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    Additional cDNA sequence: 

    AK090441.1 BC127762.1 BC157832.1 

    5 DOTS entries:

    DT.40223841  DT.95086605  DT.430132  DT.100666862  DT.100763576 

    24/154 AceView cDNA sequences (see all 154):

    CN478570 AX747342 AA425562 BC016984 AA132257 BE887609 AA132362 CB160330 
    BX504568 CA418740 CA441139 BQ019209 BC064134 BM562747 AF357880 AA346646 
    AK092069 BQ719311 AI880208 BU076634 AI720056 BQ019220 AI915665 AA053882 

    GeneLoc Exon Structure


    Expression
    for ZC3H12D 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

    ZC3H12D expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: CTTCAAAAAT

    Microarray
    RNAseq (Illumina Body Map)
    (100×FPKM)½
    SAGE (Serial Analysis of Gene Expression)
    About this image
    See ZC3H12D Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for ZC3H12D

    SOURCE GeneReport for Unigene cluster: Hs.632618

    UniProtKB/Swiss-Prot: ZC12D_HUMAN, A2A288
    Tissue specificity: Expressed in normal human lymphocytes but defective in some leukemia/lymphoma cell lines

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    In Situ
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    Orthologs
    for ZC3H12D 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 animals.

    Orthologs for ZC3H12D gene from 4/16 species (see all 16)    About this table
    Organism Taxonomic
    classification    		 Gene Description Human
    Similarity    		 Orthology
    Type    		 Details
    chicken
    (Gallus gallus)    		 Aves ZC3H12D1 zinc finger CCCH-type containing 12D 67.09(n)
    68.67(a)    		   421623  XM_419661.3  XP_419661.3 
    lizard
    (Anolis carolinensis)    		 Reptilia ZC3H12D6
    		 --
    		 62(a)
    		 1 ↔ 1
    		 GL343259.1(170270-182259)
    fruit fly
    (Drosophila melanogaster)    		 Insecta CG108896
    		 --
    		 29(a)
    		 1 → many
    		 3R(15859603-15861777)
    worm
    (Caenorhabditis elegans)    		 Secernentea C30F12.16
    		 Protein C30F12.1
    		 25(a)
    		 1 → many
    		 I(6954410-6961138)


    ENSEMBL Gene Tree for ZC3H12D (if available)
    TreeFam Gene Tree for ZC3H12D (if available) 

    Paralogs
    for ZC3H12D gene

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for ZC3H12D gene
    NYNRIN2  ZC3H12C2  N4BP12  ZC3H12B2  KHNYN2  ZC3H12A2  
    5 SIMAP similar genes for ZC3H12D using alignment to 4 protein entries:     ZC12D_HUMAN (see all proteins):
    ZC3H12B    ZC3H12C    FLJ00361    KHNYN    ZC3H12A

    ZC3H12D for paralogs           About GeneDecksing



    Genomic Variants
    for ZC3H12D 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

    10/770 NCBI SNPs in ZC3H12D are shown (see all 770)     About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance    		Chr 6 posSequence#AA
    Chg    		TypeMore#Allele
    freq    		PopTotal
    sample    		More
    ----------
    rs2370071,2
    		C,F,A,H,--149768326(-) GTGTTG/TTTCCA 1 -- ds500114Minor allele frequency- T:0.12NS EA NA 986
    rs1490107571,2
    		--149768433(+) GGAGTA/GCAGAG 1 -- ds50010--------
    rs2370061,2
    		C,F,A,--149768451(-) TGAGAC/TTGTGC 1 -- ds50016Minor allele frequency- T:0.20NA WA EA 364
    rs1855813401,2
    		--149768666(+) CCATCA/GTGCCC 1 -- ds50010--------
    rs762455151,2
    		--149768755(+) ATAAAG/TAATCC 1 -- ds50011Minor allele frequency- T:0.01NA 120
    rs736179191,2
    		C,--149768786(+) TATTTC/TTGAAG 1 -- ut311Minor allele frequency- T:0.50WA 2
    rs1904368361,2
    		--149769106(+) AAAGCA/GTGTCT 1 -- ut310--------
    rs1424931821,2
    		--149769152(+) GCCAGA/GCGCGG 1 -- ut310--------
    rs1827655111,2
    		--149769174(+) TATAAA/TCCCAG 1 -- ut310--------
    rs121959221,2
    		C,--149769192(+) GGAGGT/CTGAGG 1 -- ut31 ese32Minor allele frequency- C:0.25NA WA 4

    HapMap Linkage Disequilibrium report for ZC3H12D (149768766 - 149806197 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
          Database of Genomic Variants (DGV) variations for ZC3H12D: --

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    Disorders / Diseases
    for ZC3H12D 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
    ZC3H12D for disorders           About GeneDecksing

    OMIM gene information: 611106    OMIM disorders: --

    UniProtKB/Swiss-Prot: ZC12D_HUMAN, A2A288
  • Note=A chromosomal aberration involving ZC3H12D may be the cause of the transformation of follicular lymphoma
    • (FL) to diffuse large B-cell lymphoma (DLBCL). Translocation t(2;6)(p12;q25) with IGK. Resulting protein may not be
    expressed

    12 diseases for ZC3H12D:    About MalaCards
    follicular lymphoma    diffuse large b-cell lymphoma    patellofemoral pain syndrome    b-cell lymphomas
    decubitus ulcer    penis carcinoma    monocytic leukemia    leukemia/lymphoma
    acute monocytic leukemia    paine syndrome    leukemia/lymphoma, t-cell    leukemia

    3 diseases from the University of Copenhagen DISEASES database for ZC3H12D:
    Pain agnosia     Patellofemoral pain syndrome     Decubitus ulcer

    Export disorders for ZC3H12D gene to outside databases

    Publications
    for ZC3H12D 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 ZC3H12D gene, integrated from 9 sources (see all 11):
    (articles sorted by number of sources associating them with ZC3H12D)    		    Utopia: connect your pdf to the dynamic
    world of online information

    1. A novel CCCH-zinc finger protein family regulates proinflammatory activation of macrophages. (PubMed id 18178554)1, 2, 3 Liang J....Fu M. (2008)
    2. Inhibition of G(1) to S phase progression by a novel zinc finger protein P58(TFL) at P-bodies. (PubMed id 19531561)1, 2 Minagawa K....Matsui T. (2009)
    3. Identification of a novel tumor suppressor gene p34 on human chromosome 6q25.1. (PubMed id 17210687)1, 2 Wang M....You M. (2007)
    4. Deregulation of a possible tumour suppressor gene, ZC3H12D, by translocation of IGK@ in transformed follicular lymphoma with t(2;6)(p12;q25). (PubMed id 17854321)1, 2 Minagawa K.... Matsui T. (2007)
    5. 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)
    6. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (2004)
    7. The DNA sequence and analysis of human chromosome 6. (PubMed id 14574404)1, 2 Mungall A.J.... Beck S. (2003)
    8. The putative tumor suppressor Zc3h12d modulates toll-l ike receptor signaling in macrophages. (PubMed id 22036805)1 Huang S....Fu M. (2012)
    9. Wnt signaling and Dupuytren's disease. (PubMed id 21732829)1 Dolmans G.H.... . (2011)
    10. Toward a confocal subcellular atlas of the human proteome. (PubMed id 18029348)1 Barbe L....Andersson-Svahn H. (2008)

    External Searches for ZC3H12D gene

    (in PubMed, OMIM, and NCBI Bookshelf)
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    Genome Databases showing ZC3H12D gene

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 340152 HGNC: 21175 AceView: FLJ46041 Ensembl:ENSG00000178199 euGenes: HUgn340152
    ECgene: ZC3H12D H-InvDB: ZC3H12D

    Other Databases showing ZC3H12D gene

    (According to HUGE)
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    Specialized Databases showing ZC3H12D 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 ZC3H12D Pharmacogenomics, SNPs, Pathways

    Intellectual Property
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    		Patent Information for ZC3H12D gene:
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