Aliases for ZC3H12D Gene

Aliases for ZC3H12D Gene

  • Zinc Finger CCCH-Type Containing 12D 2 3 5
  • MCPIP4 2 3 4
  • Zinc Finger CCCH Domain-Containing Protein 12D 3 4
  • Transformed Follicular Lymphoma 3 4
  • Probable Ribonuclease ZC3H12D 3 4
  • DJ281H8.1 2 3
  • C6orf95 3 4
  • TFL 3 4
  • P34 3 4
  • Chromosome 6 Open Reading Frame 95 2
  • MCP Induced Protein 4 2
  • MCP-Induced Protein 4 4
  • Tumor Suppressor TFL 3
  • EC 3.1.-.- 4
  • ZC3H12D 5

External Ids for ZC3H12D Gene

Previous HGNC Symbols for ZC3H12D Gene

  • C6orf95

Previous GeneCards Identifiers for ZC3H12D Gene

  • GC06M149811
  • GC06M147335

Summaries for ZC3H12D Gene

GeneCards Summary for ZC3H12D Gene

ZC3H12D (Zinc Finger CCCH-Type Containing 12D) is a Protein Coding gene. Diseases associated with ZC3H12D include Follicular Lymphoma and Lymphoma. Gene Ontology (GO) annotations related to this gene include endonuclease activity. An important paralog of this gene is ZC3H12A.

UniProtKB/Swiss-Prot Summary for ZC3H12D Gene

  • May regulate cell growth likely by suppressing RB1 phosphorylation (PubMed:19531561). May function as RNase and regulate the levels of target RNA species (Potential). In association with ZC3H12A enhances the degradation of interleukin IL-6 mRNA level in activated macrophages (PubMed:26134560). Serve as a tumor suppressor in certain leukemia cells (PubMed:17210687). Overexpression inhibits the G1 to S phase progression through suppression of RB1 phosphorylation (PubMed:19531561).

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for ZC3H12D Gene

Genomics for ZC3H12D Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for ZC3H12D Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH06J149479 Promoter/Enhancer 2.2 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 631.1 +2.1 2061 7 SP1 HNRNPL GATAD2A PRDM10 SOX13 NFKBIZ RCOR2 BACH1 LARP7 STAT3 ZC3H12D GINM1 RPS18P9 ENSG00000231760 PPIL4 TAB2 LATS1 KATNA1 SUMO4 piR-41195-044
GH06J149486 Enhancer 0.2 dbSUPER 600.7 -1.9 -1898 0.6 ZC3H12D piR-41195-044 ENSG00000219553 MN298114-221 PPIL4
GH06J149508 Enhancer 0.8 FANTOM5 Ensembl dbSUPER 17.4 -23.5 -23487 2.6 PRDM1 ZBTB17 PRDM6 ZC3H12D ENSG00000231760 TAB2-AS1 RPS18P9 ENSG00000233330 ENSG00000202343 PPIL4 LATS1 TAB2 KATNA1
GH06J149147 Enhancer 1.3 FANTOM5 Ensembl ENCODE dbSUPER 8.3 +336.8 336813 3.2 RFX1 LEF1 PKNOX1 IKZF2 TRIM22 SOX6 FOXJ2 EED MGA DPF2 TAB2 ENSG00000228408 TAB2-AS1 ZC3H12D PPIL4 HSALNG0054234 piR-44858-005 UST
GH06J149137 Enhancer 1.4 FANTOM5 ENCODE dbSUPER 7 +344.8 344769 4.5 ZNF512 LEF1 IKZF1 POLR2A JUND FOXA1 STAT3 DDX20 RELA PKNOX1 LATS1 TAB2 ZC3H12D PPIL4 HSALNG0054234 piR-44858-005 UST
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around ZC3H12D on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for ZC3H12D

Top Transcription factor binding sites by QIAGEN in the ZC3H12D gene promoter:
  • AML1a
  • COUP
  • COUP-TF
  • COUP-TF1
  • CP2
  • HNF-4alpha1
  • HNF-4alpha2
  • NF-kappaB
  • NF-kappaB1
  • RelA

Genomic Locations for ZC3H12D Gene

Genomic Locations for ZC3H12D Gene
chr6:149,446,795-149,485,014
(GRCh38/hg38)
Size:
38,220 bases
Orientation:
Minus strand
chr6:149,768,766-149,806,197
(GRCh37/hg19)
Size:
37,432 bases
Orientation:
Minus strand

Genomic View for ZC3H12D Gene

Genes around ZC3H12D on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
ZC3H12D Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for ZC3H12D Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for ZC3H12D Gene

Proteins for ZC3H12D Gene

  • Protein details for ZC3H12D Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    A2A288-ZC12D_HUMAN
    Recommended name:
    Probable ribonuclease ZC3H12D
    Protein Accession:
    A2A288
    Secondary Accessions:
    • A1L178
    • B2RXF4
    • B7WNU7
    • B9ZZP9
    • B9ZZQ0
    • Q6ZRW2

    Protein attributes for ZC3H12D Gene

    Size:
    527 amino acids
    Molecular mass:
    58078 Da
    Cofactor:
    Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
    Quaternary structure:
    • Interacts with ZC3H12A (PubMed:26134560).

    Alternative splice isoforms for ZC3H12D Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for ZC3H12D Gene

Post-translational modifications for ZC3H12D Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for ZC3H12D Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for ZC3H12D Gene

Domains & Families for ZC3H12D Gene

Gene Families for ZC3H12D Gene

HGNC:
Human Protein Atlas (HPA):
  • Disease related genes
  • Predicted intracellular proteins

Protein Domains for ZC3H12D Gene

Suggested Antigen Peptide Sequences for ZC3H12D Gene

GenScript: Design optimal peptide antigens:
  • Zinc finger CCCH-type containing 12D (B7ZBA4_HUMAN)
  • Zinc finger CCCH-type containing 12D (B7ZBA5_HUMAN)
  • p34 (ZC12D_HUMAN)

Graphical View of Domain Structure for InterPro Entry

A2A288

UniProtKB/Swiss-Prot:

ZC12D_HUMAN :
  • Belongs to the ZC3H12 family.
Family:
  • Belongs to the ZC3H12 family.
genes like me logo Genes that share domains with ZC3H12D: view

Function for ZC3H12D Gene

Molecular function for ZC3H12D Gene

UniProtKB/Swiss-Prot Function:
May regulate cell growth likely by suppressing RB1 phosphorylation (PubMed:19531561). May function as RNase and regulate the levels of target RNA species (Potential). In association with ZC3H12A enhances the degradation of interleukin IL-6 mRNA level in activated macrophages (PubMed:26134560). Serve as a tumor suppressor in certain leukemia cells (PubMed:17210687). Overexpression inhibits the G1 to S phase progression through suppression of RB1 phosphorylation (PubMed:19531561).
UniProtKB/Swiss-Prot Induction:
By prolonged exposure to bacterial lipopolysaccharides (LPS) in acute monocytic leukemia cell line THP-1 cells.

Enzyme Numbers (IUBMB) for ZC3H12D Gene

Phenotypes From GWAS Catalog for ZC3H12D Gene

Gene Ontology (GO) - Molecular Function for ZC3H12D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003729 mRNA binding IBA 21873635
GO:0004518 nuclease activity IEA --
GO:0004519 endonuclease activity IEA --
GO:0004521 endoribonuclease activity IBA 21873635
GO:0005515 protein binding IPI 26134560
genes like me logo Genes that share ontologies with ZC3H12D: view
genes like me logo Genes that share phenotypes with ZC3H12D: view

Animal Models for ZC3H12D Gene

MGI Knock Outs for ZC3H12D:

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for ZC3H12D

No data available for Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for ZC3H12D Gene

Localization for ZC3H12D Gene

Subcellular locations from UniProtKB/Swiss-Prot for ZC3H12D Gene

Cytoplasm, P-body. Note=Colocalizes with ZC3H12A in GW bodies (GWBs) (PubMed:26134560). {ECO:0000269 PubMed:26134560}.
[Isoform 1]: Cytoplasm. Note=Localized as discrete granules. Colocalized with mRNA-processing body markers, AGO2 and DCP1A, but not with a stress granule maker, TIA1, in the cytoplasm.
[Isoform 3]: Cytoplasm. Nucleus.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for ZC3H12D gene
Compartment Confidence
nucleus 5
cytosol 2
plasma membrane 1
extracellular 1
cytoskeleton 1
mitochondrion 1
endoplasmic reticulum 1
endosome 1
lysosome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytoplasmic bodies (3)
  • Nucleoplasm (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for ZC3H12D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000932 P-body IEA,IDA 24415781
GO:0005634 nucleus IEA,IBA 21873635
GO:0005654 nucleoplasm IDA --
GO:0005737 cytoplasm IEA --
GO:0036464 cytoplasmic ribonucleoprotein granule IDA --
genes like me logo Genes that share ontologies with ZC3H12D: view

Pathways & Interactions for ZC3H12D Gene

PathCards logo

SuperPathways for ZC3H12D Gene

No Data Available

Interacting Proteins for ZC3H12D Gene

Gene Ontology (GO) - Biological Process for ZC3H12D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006402 mRNA catabolic process IBA 21873635
GO:0061158 3'-UTR-mediated mRNA destabilization ISS --
GO:0090305 nucleic acid phosphodiester bond hydrolysis IEA --
GO:0090502 RNA phosphodiester bond hydrolysis, endonucleolytic IBA 21873635
genes like me logo Genes that share ontologies with ZC3H12D: view

No data available for Pathways by source and SIGNOR curated interactions for ZC3H12D Gene

Drugs & Compounds for ZC3H12D Gene

No Compound Related Data Available

Transcripts for ZC3H12D Gene

mRNA/cDNA for ZC3H12D Gene

1 REFSEQ mRNAs :
6 NCBI additional mRNA sequence :
5 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for ZC3H12D

Alternative Splicing Database (ASD) splice patterns (SP) for ZC3H12D Gene

No ASD Table

Relevant External Links for ZC3H12D Gene

GeneLoc Exon Structure for
ZC3H12D

Expression for ZC3H12D Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for ZC3H12D Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for ZC3H12D Gene

This gene is overexpressed in Spleen (x6.5), Small Intestine - Terminal Ileum (x4.7), and Whole Blood (x4.6).

Protein differential expression in normal tissues from HIPED for ZC3H12D Gene

This gene is overexpressed in Peripheral blood mononuclear cells (42.2), Blymphocyte (8.0), and CD8 Tcells (7.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for ZC3H12D Gene



Protein tissue co-expression partners for ZC3H12D Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for ZC3H12D

SOURCE GeneReport for Unigene cluster for ZC3H12D Gene:

Hs.632618

mRNA Expression by UniProt/SwissProt for ZC3H12D Gene:

A2A288-ZC12D_HUMAN
Tissue specificity: Expressed in normal human lymphocytes but defective in some leukemia/lymphoma cell lines.

Evidence on tissue expression from TISSUES for ZC3H12D Gene

  • Blood(2.6)
  • Muscle(2.5)
  • Lymph node(2.5)
  • Heart(2.1)
  • Spleen(2.1)
  • Nervous system(2.1)
  • Intestine(2)
  • Skin(2)
genes like me logo Genes that share expression patterns with ZC3H12D: view

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for ZC3H12D Gene

Orthologs for ZC3H12D Gene

This gene was present in the common ancestor of chordates.

Orthologs for ZC3H12D Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia ZC3H12D 30 31
  • 98.73 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia ZC3H12D 30 31
  • 79.65 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia ZC3H12D 30 31
  • 79.29 (n)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia ZC3H12D 31
  • 79 (a)
OneToOne
Mouse
(Mus musculus)
Mammalia Zc3h12d 30 17 31
  • 75.05 (n)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia ZC3H12D 31
  • 74 (a)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Zc3h12d 30
  • 73.58 (n)
Lizard
(Anolis carolinensis)
Reptilia ZC3H12D 31
  • 63 (a)
OneToOne
Species where no ortholog for ZC3H12D was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Fruit Fly (Drosophila melanogaster)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Squirt (Ciona savignyi)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Tropical Clawed Frog (Silurana tropicalis)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)
  • Zebrafish (Danio rerio)

Evolution for ZC3H12D Gene

ENSEMBL:
Gene Tree for ZC3H12D (if available)
TreeFam:
Gene Tree for ZC3H12D (if available)
Aminode:
Evolutionary constrained regions (ECRs) for ZC3H12D: view image

Paralogs for ZC3H12D Gene

Paralogs for ZC3H12D Gene

(5) SIMAP similar genes for ZC3H12D Gene using alignment to 4 proteins:

  • ZC12D_HUMAN
  • B7ZBA4_HUMAN
  • H0Y4Y6_HUMAN
  • J3QT81_HUMAN
genes like me logo Genes that share paralogs with ZC3H12D: view

Variants for ZC3H12D Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for ZC3H12D Gene

SNP ID Clinical significance and condition Chr 06 pos Variation AA Info Type
732040 Likely Benign: not provided 149,450,902(-) C/T SYNONYMOUS_VARIANT
787837 Benign: not provided 149,474,335(-) G/A MISSENSE_VARIANT
rs61997220 Some sporadic lung cancer sample p.Lys106Arg
rs7747948 - p.Pro53Leu

Additional dbSNP identifiers (rs#s) for ZC3H12D Gene

Structural Variations from Database of Genomic Variants (DGV) for ZC3H12D Gene

Variant ID Type Subtype PubMed ID
esv2670181 CNV deletion 23128226
esv2732859 CNV deletion 23290073
esv3540623 CNV deletion 23714750
esv3611207 CNV loss 21293372
nsv464076 CNV gain 19166990
nsv470866 CNV gain 18288195
nsv5533 CNV deletion 18451855
nsv604846 CNV gain 21841781

Variation tolerance for ZC3H12D Gene

Gene Damage Index Score: 10.06; 90.14% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for ZC3H12D Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
ZC3H12D

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for ZC3H12D Gene

Disorders for ZC3H12D Gene

MalaCards: The human disease database

(8) MalaCards diseases for ZC3H12D Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
follicular lymphoma
  • lymphoma, follicular
lymphoma
  • lymphoid cancer
skin carcinoma in situ
  • carcinoma in situ of skin
relapsed/refractory diffuse large b-cell lymphoma
plica syndrome
  • synovitis
- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

ZC12D_HUMAN
  • 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.
genes like me logo Genes that share disorders with ZC3H12D: view

No data available for Genatlas for ZC3H12D Gene

Publications for ZC3H12D Gene

  1. A novel CCCH-zinc finger protein family regulates proinflammatory activation of macrophages. (PMID: 18178554) Liang J … Fu M (The Journal of biological chemistry 2008) 2 3 4
  2. Monocyte Chemotactic Protein-induced Protein 1 and 4 Form a Complex but Act Independently in Regulation of Interleukin-6 mRNA Degradation. (PMID: 26134560) Huang S … Fu M (The Journal of biological chemistry 2015) 3 4
  3. Inhibition of G(1) to S phase progression by a novel zinc finger protein P58(TFL) at P-bodies. (PMID: 19531561) Minagawa K … Matsui T (Molecular cancer research : MCR 2009) 3 4
  4. Identification of a novel tumor suppressor gene p34 on human chromosome 6q25.1. (PMID: 17210687) Wang M … You M (Cancer research 2007) 3 4
  5. Deregulation of a possible tumour suppressor gene, ZC3H12D, by translocation of IGK@ in transformed follicular lymphoma with t(2;6)(p12;q25). (PMID: 17854321) Minagawa K … Matsui T (British journal of haematology 2007) 3 4

Products for ZC3H12D Gene

Sources for ZC3H12D Gene