Aliases for ZC3H13 Gene

Aliases for ZC3H13 Gene

  • Zinc Finger CCCH-Type Containing 13 2 3 5
  • KIAA0853 2 3 4
  • Zinc Finger CCCH Domain-Containing Protein 13 3 4
  • Xio 3

External Ids for ZC3H13 Gene

Previous HGNC Symbols for ZC3H13 Gene

  • KIAA0853

Previous GeneCards Identifiers for ZC3H13 Gene

  • GC13M045426
  • GC13M046528
  • GC13M027333

Summaries for ZC3H13 Gene

GeneCards Summary for ZC3H13 Gene

ZC3H13 (Zinc Finger CCCH-Type Containing 13) is a Protein Coding gene. Diseases associated with ZC3H13 include Wilms Tumor 1.

UniProtKB/Swiss-Prot Summary for ZC3H13 Gene

  • Associated component of the WMM complex, a complex that mediates N6-methyladenosine (m6A) methylation of RNAs, a modification that plays a role in the efficiency of mRNA splicing and RNA processing (PubMed:29507755). Acts as a key regulator of m6A methylation by promoting m6A methylation of mRNAs at the 3'-UTR (By similarity). Controls embryonic stem cells (ESCs) pluripotency via its role in m6A methylation (By similarity). In the WMM complex, anchors component of the MACOM subcomplex in the nucleus (By similarity). Also required for bridging WTAP to the RNA-binding component RBM15 (RBM15 or RBM15B) (By similarity).

Gene Wiki entry for ZC3H13 Gene

Additional gene information for ZC3H13 Gene

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for ZC3H13 Gene

Genomics for ZC3H13 Gene

GeneHancer (GH) Regulatory Elements for ZC3H13 Gene

Promoters and enhancers for ZC3H13 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
GH13J046051 Promoter/Enhancer 2 EPDnew Ensembl ENCODE CraniofacialAtlas 500.7 +0.8 761 4.8 ZBTB40 ZNF217 EP300 CTCF ZSCAN5C SIN3A NRF1 POLR2G GTF2E2 PHF8 CPB2-AS1 ZC3H13 lnc-CPB2-1 RF00017-1415 CPB2
GH13J046123 Enhancer 1.2 Ensembl ENCODE dbSUPER 13 -72.4 -72440 4.7 ZNF217 CTCF ZNF510 REST RAD21 TRIM22 POLR2A TEAD1 SMC3 FOXA2 ZC3H13 RF00017-1416 lnc-LCP1-1 CPB2-AS1 LCP1
GH13J046113 Enhancer 1.2 FANTOM5 Ensembl ENCODE dbSUPER 12.4 -61.0 -61040 3.2 ZIC2 ZNF592 FOSL1 ZNF395 FOS BHLHE40 ZNF384 MITF MEIS2 ZBTB33 ZC3H13 CPB2-AS1 LCP1 CPB2 RF00998-038 lnc-LCP1-1
GH13J046119 Enhancer 1 Ensembl ENCODE 13.1 -68.2 -68240 2.4 ZNF217 JUND ZIC2 MYC CTBP1 JUN ZNF341 NCOR1 ZNF195 NFIC RF00998-038 lnc-LCP1-1 SLC25A30-AS1 ZC3H13 CPB2-AS1
GH13J046100 Enhancer 1.2 FANTOM5 Ensembl ENCODE 11.5 -48.0 -48040 4.4 MEF2C FOXA2 ZNF316 NCOR1 MEF2B JUND BATF TAL1 TCF12 ATF2 CPB2-AS1 CPB2 ZC3H13
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around ZC3H13 on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for ZC3H13

Top Transcription factor binding sites by QIAGEN in the ZC3H13 gene promoter:
  • AML1a
  • c-Ets-1
  • Cdc5
  • FOXO3
  • FOXO3a
  • FOXO3b
  • Hlf
  • HNF-4alpha1
  • HNF-4alpha2
  • PPAR-alpha

Genomic Locations for ZC3H13 Gene

Genomic Locations for ZC3H13 Gene
chr13:45,954,465-46,052,761
(GRCh38/hg38)
Size:
98,297 bases
Orientation:
Minus strand
chr13:46,528,600-46,626,894
(GRCh37/hg19)
Size:
98,295 bases
Orientation:
Minus strand

Genomic View for ZC3H13 Gene

Genes around ZC3H13 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
ZC3H13 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for ZC3H13 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for ZC3H13 Gene

Proteins for ZC3H13 Gene

  • Protein details for ZC3H13 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q5T200-ZC3HD_HUMAN
    Recommended name:
    Zinc finger CCCH domain-containing protein 13
    Protein Accession:
    Q5T200
    Secondary Accessions:
    • A2A323
    • O94936
    • Q5T1Z9
    • Q7Z7J3
    • Q8NDT6
    • Q9H0L6

    Protein attributes for ZC3H13 Gene

    Size:
    1668 amino acids
    Molecular mass:
    196635 Da
    Quaternary structure:
    • Component of the WMM complex, a N6-methyltransferase complex composed of a catalytic subcomplex, named MAC, and of an associated subcomplex, named MACOM (PubMed:29507755). The MAC subcomplex is composed of METTL3 and METTL14. The MACOM subcomplex is composed of WTAP, ZC3H13, CBLL1/HAKAI, VIRMA, and, in some cases of RBM15 (RBM15 or RBM15B) (PubMed:29507755). Also component of a MACOM-like complex, named WTAP complex, composed of WTAP, ZC3H13, CBLL1/HAKAI, VIRMA, RBM15, BCLAF1 and THRAP3 (PubMed:24100041).

    Alternative splice isoforms for ZC3H13 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for ZC3H13 Gene

Post-translational modifications for ZC3H13 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for ZC3H13 Gene

Domains & Families for ZC3H13 Gene

Gene Families for ZC3H13 Gene

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

Protein Domains for ZC3H13 Gene

Blocks:
  • Zn-finger, C-x8-C-x5-C-x3-H type
InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for ZC3H13 Gene

GenScript: Design optimal peptide antigens:
  • ZC3H13 protein (A0PJJ2_HUMAN)
  • ZC3H13 protein (Q32Q34_HUMAN)
  • Zinc finger CCCH-type containing 13 (Q5T9K0_HUMAN)
  • ZC3H13 protein (Q6PJ96_HUMAN)
  • Zinc finger CCCH domain-containing protein 13 (ZC3HD_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q5T200

UniProtKB/Swiss-Prot:

ZC3HD_HUMAN :
  • Belongs to the ZC3H13 family.
Family:
  • Belongs to the ZC3H13 family.
genes like me logo Genes that share domains with ZC3H13: view

Function for ZC3H13 Gene

Molecular function for ZC3H13 Gene

UniProtKB/Swiss-Prot Function:
Associated component of the WMM complex, a complex that mediates N6-methyladenosine (m6A) methylation of RNAs, a modification that plays a role in the efficiency of mRNA splicing and RNA processing (PubMed:29507755). Acts as a key regulator of m6A methylation by promoting m6A methylation of mRNAs at the 3'-UTR (By similarity). Controls embryonic stem cells (ESCs) pluripotency via its role in m6A methylation (By similarity). In the WMM complex, anchors component of the MACOM subcomplex in the nucleus (By similarity). Also required for bridging WTAP to the RNA-binding component RBM15 (RBM15 or RBM15B) (By similarity).

Phenotypes From GWAS Catalog for ZC3H13 Gene

Gene Ontology (GO) - Molecular Function for ZC3H13 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003723 RNA binding HDA 22681889
GO:0005515 protein binding IPI 20195357
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with ZC3H13: view
genes like me logo Genes that share phenotypes with ZC3H13: view

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for ZC3H13 Gene

Localization for ZC3H13 Gene

Subcellular locations from UniProtKB/Swiss-Prot for ZC3H13 Gene

Nucleus speckle. Nucleus, nucleoplasm.

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 ZC3H13 gene
Compartment Confidence
nucleus 5
cytosol 2
plasma membrane 1
cytoskeleton 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Actin filaments (2)
  • Nuclear membrane (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for ZC3H13 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
GO:0005654 nucleoplasm IDA,IEA 24100041
GO:0016607 nuclear speck IDA,IBA 24100041
GO:0036396 RNA N6-methyladenosine methyltransferase complex IDA 29507755
genes like me logo Genes that share ontologies with ZC3H13: view

Pathways & Interactions for ZC3H13 Gene

PathCards logo

SuperPathways for ZC3H13 Gene

No Data Available

Gene Ontology (GO) - Biological Process for ZC3H13 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006397 mRNA processing IEA --
GO:0007275 multicellular organism development IEA --
GO:0008380 RNA splicing IEA --
GO:0080009 mRNA methylation IMP 29507755
GO:2000036 regulation of stem cell population maintenance ISS --
genes like me logo Genes that share ontologies with ZC3H13: view

No data available for Pathways by source and SIGNOR curated interactions for ZC3H13 Gene

Drugs & Compounds for ZC3H13 Gene

No Compound Related Data Available

Transcripts for ZC3H13 Gene

mRNA/cDNA for ZC3H13 Gene

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

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for ZC3H13 Gene

ExUns: 1a · 1b · 1c · 1d ^ 2 ^ 3 ^ 4 ^ 5a · 5b · 5c ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15 ^ 16 ^ 17 ^ 18 ^ 19 ^ 20a · 20b ^
SP1: -
SP2:
SP3:
SP4:
SP5:
SP6: -
SP7:
SP8:
SP9:

ExUns: 21a · 21b ^ 22 ^ 23 ^ 24
SP1:
SP2:
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:

Relevant External Links for ZC3H13 Gene

GeneLoc Exon Structure for
ZC3H13

Expression for ZC3H13 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for ZC3H13 Gene

Protein differential expression in normal tissues from HIPED for ZC3H13 Gene

This gene is overexpressed in Liver (20.8) and Brain (16.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for ZC3H13 Gene



Protein tissue co-expression partners for ZC3H13 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for ZC3H13

SOURCE GeneReport for Unigene cluster for ZC3H13 Gene:

Hs.136102

Evidence on tissue expression from TISSUES for ZC3H13 Gene

  • Nervous system(4.7)
  • Liver(4.5)
  • Skin(2.4)
  • Spleen(2.3)
  • Heart(2.1)
  • Muscle(2.1)
  • Kidney(2)
  • Lung(2)
genes like me logo Genes that share expression patterns with ZC3H13: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for ZC3H13 Gene

Orthologs for ZC3H13 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for ZC3H13 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia ZC3H13 31
  • 100 (a)
OneToOne
dog
(Canis familiaris)
Mammalia ZC3H13 31
  • 88 (a)
OneToOne
cow
(Bos Taurus)
Mammalia ZC3H13 31
  • 85 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia ZC3H13 31
  • 77 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Zc3h13 31
  • 77 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia ZC3H13 31
  • 75 (a)
OneToOne
chicken
(Gallus gallus)
Aves ZC3H13 31
  • 73 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia ZC3H13 31
  • 68 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia Str.6022 30
African clawed frog
(Xenopus laevis)
Amphibia Xl.4590 30
zebrafish
(Danio rerio)
Actinopterygii zc3h13 31
  • 44 (a)
OneToOne
zgc66359 30
rice
(Oryza sativa)
Liliopsida Os.5417 30
Species where no ortholog for ZC3H13 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • 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)
  • 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)
  • rat (Rattus norvegicus)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (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)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for ZC3H13 Gene

ENSEMBL:
Gene Tree for ZC3H13 (if available)
TreeFam:
Gene Tree for ZC3H13 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for ZC3H13: view image

Paralogs for ZC3H13 Gene

No data available for Paralogs for ZC3H13 Gene

Variants for ZC3H13 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for ZC3H13 Gene

SNP ID Clinical significance and condition Chr 13 pos Variation AA Info Type
rs11537603 Uncertain Significance: Severe Myopia 45,988,993(-) C/A MISSENSE_VARIANT
rs9534264 - p.Glu1429Asp

Additional dbSNP identifiers (rs#s) for ZC3H13 Gene

Structural Variations from Database of Genomic Variants (DGV) for ZC3H13 Gene

Variant ID Type Subtype PubMed ID
dgv223e201 CNV deletion 23290073
esv2507198 CNV deletion 19546169
esv2666736 CNV deletion 23128226
esv2673081 CNV deletion 23128226
esv2747355 CNV deletion 23290073
esv3631971 CNV loss 21293372
esv3631972 CNV loss 21293372
nsv455876 CNV gain 19166990
nsv561581 CNV gain 21841781
nsv832597 CNV loss 17160897
nsv832598 CNV gain 17160897

Variation tolerance for ZC3H13 Gene

Residual Variation Intolerance Score: 3.27% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.16; 51.69% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for ZC3H13 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
ZC3H13

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for ZC3H13 Gene

Disorders for ZC3H13 Gene

MalaCards: The human disease database

(1) MalaCards diseases for ZC3H13 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
wilms tumor 1
  • wt1
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for ZC3H13

genes like me logo Genes that share disorders with ZC3H13: view

No data available for UniProtKB/Swiss-Prot and Genatlas for ZC3H13 Gene

Publications for ZC3H13 Gene

  1. Prediction of the coding sequences of unidentified human genes. XII. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro. (PMID: 10048485) Nagase T … Ohara O (DNA research : an international journal for rapid publication of reports on genes and genomes 1998) 2 3 4 54
  2. VIRMA mediates preferential m6A mRNA methylation in 3'UTR and near stop codon and associates with alternative polyadenylation. (PMID: 29507755) Yue Y … Liu J (Cell discovery 2018) 3 4 54
  3. Identification of Wilms' tumor 1-associating protein complex and its role in alternative splicing and the cell cycle. (PMID: 24100041) Horiuchi K … Hamakubo T (The Journal of biological chemistry 2013) 3 4 54
  4. A probability-based approach for high-throughput protein phosphorylation analysis and site localization. (PMID: 16964243) Beausoleil SA … Gygi SP (Nature biotechnology 2006) 3 4 54
  5. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. (PMID: 17081983) Olsen JV … Mann M (Cell 2006) 3 4 54

Products for ZC3H13 Gene

Sources for ZC3H13 Gene