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Aliases for ZC3H11A Gene

Aliases for ZC3H11A Gene

  • Zinc Finger CCCH-Type Containing 11A 2 3 5
  • Zinc Finger CCCH-Type Domain Containing 11A 2 3
  • ZC3HDC11A 3 4
  • Zinc Finger CCCH Domain-Containing Protein 11A 3
  • EC 58
  • EC 58
  • KIAA0663 4

External Ids for ZC3H11A Gene

Previous HGNC Symbols for ZC3H11A Gene

  • ZC3HDC11A

Previous GeneCards Identifiers for ZC3H11A Gene

  • GC01P200497
  • GC01P202031
  • GC01P203765
  • GC01P174930

Summaries for ZC3H11A Gene

GeneCards Summary for ZC3H11A Gene

ZC3H11A (Zinc Finger CCCH-Type Containing 11A) is a Protein Coding gene. Among its related pathways are Formation of HIV elongation complex in the absence of HIV Tat and RNA Polymerase II Transcription Termination. GO annotations related to this gene include poly(A) RNA binding. An important paralog of this gene is ZC3H11B.

UniProtKB/Swiss-Prot for ZC3H11A Gene

  • Involved in nuclear mRNA export; probably mediated by assoociation with the TREX complex.

Gene Wiki entry for ZC3H11A Gene

Additional gene information for ZC3H11A Gene

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for ZC3H11A Gene

Genomics for ZC3H11A Gene

Regulatory Elements for ZC3H11A Gene

Enhancers for ZC3H11A Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH01H204511 2 FANTOM5 Ensembl ENCODE dbSUPER 94.6 +721.5 721544 11.9 ZFP64 FEZF1 DMAP1 YBX1 YY1 SLC30A9 ZNF416 ZNF143 ZNF548 SP3 MDM4 ZC3H11A SNRPE ZBED6 PPP1R15B PIK3C2B LOC101929459 ENSG00000236108 NFASC SNRPGP10
GH01H203526 1.4 Ensembl ENCODE dbSUPER 96.4 -268.7 -268720 1.3 HDGF PKNOX1 ZNF133 GLI4 ZNF2 ZBTB7B ZNF207 MCM3 YY2 ZNF488 ZC3H11A SNRPE MDM4 ZBED6 KLHL12 PPP1R15B KDM5B HNRNPA1P59 PRELP FMOD
GH01H204193 1.2 Ensembl ENCODE 97.1 +401.2 401249 6.6 YBX3 PKNOX1 ZNF473 ZSCAN4 SIN3A YBX1 NFXL1 RAD21 ZNF155 TCF12 ZC3H11A MDM4 ZBED6 PPP1R15B SNRPE ETNK2 ERLNC1 RPL13AP11 ENSG00000231691 PLEKHA6
GH01H204505 1.7 Ensembl ENCODE dbSUPER 67 +711.6 711561 3.3 MLX YBX1 DMAP1 YY1 ZNF143 ZNF548 SP3 NFYC ZFP41 SSRP1 ZC3H11A MDM4 SNRPE ZBED6 PPP1R15B RBBP5 LRRN2 PIK3C2B TRK-TTT3-1 TRK-TTT3-2
GH01H202802 1.7 Ensembl ENCODE dbSUPER 63.8 -989.5 -989549 6.1 HDGF PKNOX1 MLX ZFP64 ARID4B SIN3A YBX1 FEZF1 DMAP1 ZNF2 ZC3H11A ZBED6 KDM5B IPO9 RNPEP PCAT6 LOC100506672 ENSG00000273478 HNRNPA1P59 ELF3-AS1
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around ZC3H11A on UCSC Golden Path with GeneCards custom track

Promoters for ZC3H11A Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

Genomic Locations for ZC3H11A Gene

Genomic Locations for ZC3H11A Gene
59,463 bases
Plus strand

Genomic View for ZC3H11A Gene

Genes around ZC3H11A on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
ZC3H11A Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for ZC3H11A Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for ZC3H11A Gene

Proteins for ZC3H11A Gene

  • Protein details for ZC3H11A Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Zinc finger CCCH domain-containing protein 11A
    Protein Accession:
    Secondary Accessions:
    • Q6AHY4
    • Q6AHY9
    • Q6AW79
    • Q6AWA1
    • Q6PJK4
    • Q86XZ7

    Protein attributes for ZC3H11A Gene

    810 amino acids
    Molecular mass:
    89131 Da
    Quaternary structure:
    • Interacts with THOC2, DDX39 and POLDIP3; the interactions are ATP-dependent and indicative for an association with the TREX complex.
    • Sequence=BAA31638.2; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=CAH10553.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential poly-A sequence.; Evidence={ECO:0000305};

neXtProt entry for ZC3H11A Gene

Selected DME Specific Peptides for ZC3H11A Gene


Post-translational modifications for ZC3H11A Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Domains & Families for ZC3H11A Gene

Gene Families for ZC3H11A Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for ZC3H11A Gene

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with ZC3H11A: view

No data available for UniProtKB/Swiss-Prot for ZC3H11A Gene

Function for ZC3H11A Gene

Molecular function for ZC3H11A Gene

UniProtKB/Swiss-Prot Function:
Involved in nuclear mRNA export; probably mediated by assoociation with the TREX complex.

Enzyme Numbers (IUBMB) for ZC3H11A Gene

Phenotypes From GWAS Catalog for ZC3H11A Gene

Gene Ontology (GO) - Molecular Function for ZC3H11A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003723 RNA binding IDA 22658674
GO:0005515 protein binding IPI 16189514
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with ZC3H11A: view
genes like me logo Genes that share phenotypes with ZC3H11A: view

Clone Products

No data available for Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for ZC3H11A Gene

Localization for ZC3H11A Gene

Subcellular locations from

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 ZC3H11A gene
Compartment Confidence
nucleus 5
plasma membrane 2
cytoskeleton 2
cytosol 2

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nuclear speckles (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for ZC3H11A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000346 colocalizes_with transcription export complex IDA 22928037
GO:0005654 nucleoplasm TAS --
genes like me logo Genes that share ontologies with ZC3H11A: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot for ZC3H11A Gene

Pathways & Interactions for ZC3H11A Gene

genes like me logo Genes that share pathways with ZC3H11A: view

Gene Ontology (GO) - Biological Process for ZC3H11A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006369 termination of RNA polymerase II transcription TAS --
GO:0006405 RNA export from nucleus TAS --
GO:0006406 mRNA export from nucleus TAS --
GO:0006810 transport IEA --
GO:0016973 poly(A)+ mRNA export from nucleus IMP 22928037
genes like me logo Genes that share ontologies with ZC3H11A: view

No data available for SIGNOR curated interactions for ZC3H11A Gene

Drugs & Compounds for ZC3H11A Gene

No Compound Related Data Available

Transcripts for ZC3H11A Gene

Unigene Clusters for ZC3H11A Gene

Zinc finger CCCH-type containing 11A:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for ZC3H11A Gene

No ASD Table

Relevant External Links for ZC3H11A Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for ZC3H11A Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for ZC3H11A Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for ZC3H11A Gene

This gene is overexpressed in Peripheral blood mononuclear cells (20.5), Testis (11.0), and CD8 Tcells (9.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for ZC3H11A Gene

Protein tissue co-expression partners for ZC3H11A Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of ZC3H11A Gene:


SOURCE GeneReport for Unigene cluster for ZC3H11A Gene:


Evidence on tissue expression from TISSUES for ZC3H11A Gene

  • Nervous system(4.8)
  • Liver(4.6)
  • Eye(4.3)
  • Kidney(4.3)
  • Intestine(2.1)
genes like me logo Genes that share expression patterns with ZC3H11A: view

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for ZC3H11A Gene

Orthologs for ZC3H11A Gene

This gene was present in the common ancestor of chordates.

Orthologs for ZC3H11A Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia ZC3H11A 33 34
  • 99.84 (n)
(Canis familiaris)
Mammalia ZC3H11A 33 34
  • 90.4 (n)
(Bos Taurus)
Mammalia ZC3H11A 33 34
  • 89.51 (n)
(Mus musculus)
Mammalia Zc3h11a 33 16 34
  • 83.06 (n)
(Rattus norvegicus)
Mammalia Zc3h11a 33
  • 82.04 (n)
(Monodelphis domestica)
Mammalia ZC3H11A 34
  • 77 (a)
(Ornithorhynchus anatinus)
Mammalia ZC3H11A 34
  • 67 (a)
(Gallus gallus)
Aves ZC3H11A 33 34
  • 64.94 (n)
(Anolis carolinensis)
Reptilia -- 34
  • 51 (a)
-- 34
  • 50 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia zc3h11a 33
  • 57.38 (n)
Str.17290 33
African clawed frog
(Xenopus laevis)
Amphibia Xl.6811 33
(Danio rerio)
Actinopterygii zc3h11a 33 34
  • 52.36 (n)
wufc32e10 33
Species where no ortholog for ZC3H11A 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)
  • rice (Oryza sativa)
  • 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 ZC3H11A Gene

Gene Tree for ZC3H11A (if available)
Gene Tree for ZC3H11A (if available)

Paralogs for ZC3H11A Gene

Paralogs for ZC3H11A Gene

(1) SIMAP similar genes for ZC3H11A Gene using alignment to 5 proteins: Pseudogenes for ZC3H11A Gene

genes like me logo Genes that share paralogs with ZC3H11A: view

Variants for ZC3H11A Gene

Sequence variations from dbSNP and Humsavar for ZC3H11A Gene

SNP ID Clin Chr 01 pos Sequence Context AA Info Type
rs1000050843 -- 203,840,605(+) AGGAA(A/T)TTATT intron-variant
rs1000067608 -- 203,834,155(+) AGAGG(C/T)GAGAA intron-variant
rs1000116443 -- 203,852,625(+) CTTTT(A/G)AGAAA utr-variant-3-prime
rs1000116729 -- 203,818,780(+) AAAAA(A/T)ATATT intron-variant
rs1000181035 -- 203,811,834(+) TTTTT(C/T)TTTAG intron-variant

Structural Variations from Database of Genomic Variants (DGV) for ZC3H11A Gene

Variant ID Type Subtype PubMed ID
nsv946599 CNV duplication 23825009
nsv946598 CNV duplication 23825009
nsv946597 CNV duplication 23825009
nsv946596 CNV duplication 23825009
nsv946595 CNV duplication 23825009
nsv522989 CNV loss 19592680
nsv520482 CNV loss 19592680
nsv1113213 CNV deletion 24896259
esv3588604 CNV loss 21293372
esv3588603 CNV loss 21293372
esv3588602 CNV loss 21293372
esv3545400 CNV deletion 23714750
esv2678729 CNV deletion 23128226
esv2658459 CNV deletion 23128226
esv1633923 CNV insertion 17803354

Variation tolerance for ZC3H11A Gene

Residual Variation Intolerance Score: 11.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.34; 41.70% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for ZC3H11A Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for ZC3H11A Gene

Disorders for ZC3H11A Gene

Relevant External Links for ZC3H11A

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
Atlas of Genetics and Cytogenetics in Oncology and Haematology:

No disorders were found for ZC3H11A Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for ZC3H11A Gene

Publications for ZC3H11A Gene

  1. Prediction of the coding sequences of unidentified human genes. X. The complete sequences of 100 new cDNA clones from brain which can code for large proteins in vitro. (PMID: 9734811) Ishikawa K … Ohara O (DNA research : an international journal for rapid publication of reports on genes and genomes 1998) 2 3 4 60
  2. The proteins PDIP3 and ZC11A associate with the human TREX complex in an ATP-dependent manner and function in mRNA export. (PMID: 22928037) Folco EG … Reed R (PloS one 2012) 3 4 60
  3. Follow-up of a major linkage peak on chromosome 1 reveals suggestive QTLs associated with essential hypertension: GenNet study. (PMID: 19536175) Ehret GB … Chakravarti A (European journal of human genetics : EJHG 2009) 3 45 60
  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 60
  5. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. (PMID: 17081983) Olsen JV … Mann M (Cell 2006) 3 4 60

Products for ZC3H11A Gene

Sources for ZC3H11A Gene

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