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Aliases for ZNRD1 Gene

Aliases for ZNRD1 Gene

  • Zinc Ribbon Domain Containing 1 2 3 5
  • Rpa12 3 4
  • RNA Polymerase I Small Specific Subunit Rpa12 3
  • Transcription-Associated Zinc Ribbon Protein 3
  • DNA-Directed RNA Polymerase I Subunit RPA12 3
  • Zinc Ribbon Domain-Containing Protein 1 4
  • Zinc Ribbon Domain Containing, 1 2
  • Tctex-6 3
  • HTEX-6 3
  • TCTEX6 3
  • HTEX6 3
  • HZR14 3
  • TEX6 3
  • ZR14 3

External Ids for ZNRD1 Gene

Previous GeneCards Identifiers for ZNRD1 Gene

  • GC06P030085
  • GC06P029799
  • GC06P030135
  • GC06P030137
  • GC06P030026
  • GC06P030233
  • GC06P030265
  • GC06P030360
  • GC06P030508
  • GC06P030715
  • GC06P030873

Summaries for ZNRD1 Gene

Entrez Gene Summary for ZNRD1 Gene

  • This gene encodes a DNA-directed RNA polymerase I subunit. The encoded protein contains two potential zinc-binding motifs and may play a role in regulation of cell proliferation. The encoded protein may be involved in cancer and human immunodeficiency virus progression. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2013]

GeneCards Summary for ZNRD1 Gene

ZNRD1 (Zinc Ribbon Domain Containing 1) is a Protein Coding gene. Diseases associated with ZNRD1 include Gastric Cancer, Somatic. Among its related pathways are Metabolism and RNA Polymerase I Promoter Escape. GO annotations related to this gene include nucleic acid binding and RNA polymerase I activity.

UniProtKB/Swiss-Prot for ZNRD1 Gene

  • DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase I which synthesizes ribosomal RNA precursors.

Gene Wiki entry for ZNRD1 Gene

Additional gene information for ZNRD1 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for ZNRD1 Gene

Genomics for ZNRD1 Gene

Regulatory Elements for ZNRD1 Gene

Enhancers for ZNRD1 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
GH06H030611 1.7 Ensembl ENCODE dbSUPER 45.3 +556.7 556654 8 MLX ZFP64 DMAP1 YY1 SLC30A9 ZNF143 SP3 NFYC MEF2D SSRP1 MDC1 DDX39B TRIM39 PPP1R10 ABCF1 NRM DHX16 ZNRD1 GTF2H4 TRIM26
GH06H030715 1.5 ENCODE dbSUPER 45.5 +660.6 660628 7 MLX ZFP64 FEZF1 DMAP1 YY1 SLC30A9 ZNF143 ZNF548 SP3 NFYC MDC1 LY6G5B TRIM39 DDX39B DHX16 ABCF1 PPP1R10 ZNRD1 NRM HCG18
GH06H029963 2 FANTOM5 Ensembl ENCODE dbSUPER 33 -92.7 -92650 4 MLX ZFP64 FEZF1 DMAP1 YY1 SLC30A9 ZNF143 SP3 PPARGC1A MEF2D HLA-A HLA-K ENSG00000237669 ZNRD1 HLA-W TRIM39 HLA-H PPP1R10 MDC1 HLA-J
GH06H030907 1.2 ENCODE 45.1 +849.6 849559 2 DMAP1 YBX1 YY1 ZNF416 ZNF143 ZNF548 SP3 NFYC ZC3H11A MEF2D MDC1 GTF2H4 TRIM39 LY6G5B LSM2 DDX39B HCG18 PPP1R10 ENSG00000233892 DHX16
GH06H030810 1.6 Ensembl ENCODE dbSUPER 31.2 +754.3 754338 5 HDGF PKNOX1 ARNT ZNF766 CBX5 ZNF143 ZNF207 FOS SP3 NFYC MDC1 DDX39B LY6G5B LSM2 TRIM39 NFKBIL1 DDR1 ZNRD1 DHX16 PPP1R10
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around ZNRD1 on UCSC Golden Path with GeneCards custom track

Genomic Location for ZNRD1 Gene

Chromosome:
6
Start:
30,058,899 bp from pter
End:
30,064,909 bp from pter
Size:
6,011 bases
Orientation:
Plus strand

Genomic View for ZNRD1 Gene

Genes around ZNRD1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
ZNRD1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for ZNRD1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

Proteins for ZNRD1 Gene

  • Protein details for ZNRD1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9P1U0-RPA12_HUMAN
    Recommended name:
    DNA-directed RNA polymerase I subunit RPA12
    Protein Accession:
    Q9P1U0

    Protein attributes for ZNRD1 Gene

    Size:
    126 amino acids
    Molecular mass:
    13904 Da
    Quaternary structure:
    • Component of the RNA polymerase I (Pol I) complex consisting of at least 13 subunits.

neXtProt entry for ZNRD1 Gene

Post-translational modifications for ZNRD1 Gene

No Post-translational modifications

Other Protein References for ZNRD1 Gene

No data available for DME Specific Peptides for ZNRD1 Gene

Domains & Families for ZNRD1 Gene

Gene Families for ZNRD1 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Suggested Antigen Peptide Sequences for ZNRD1 Gene

Graphical View of Domain Structure for InterPro Entry

Q9P1U0

UniProtKB/Swiss-Prot:

RPA12_HUMAN :
  • Belongs to the archaeal RpoM/eukaryotic RPA12/RPB9/RPC11 RNA polymerase family.
Family:
  • Belongs to the archaeal RpoM/eukaryotic RPA12/RPB9/RPC11 RNA polymerase family.
genes like me logo Genes that share domains with ZNRD1: view

Function for ZNRD1 Gene

Molecular function for ZNRD1 Gene

UniProtKB/Swiss-Prot Function:
DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase I which synthesizes ribosomal RNA precursors.

Phenotypes From GWAS Catalog for ZNRD1 Gene

Gene Ontology (GO) - Molecular Function for ZNRD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001054 contributes_to RNA polymerase I activity IBA --
GO:0003676 nucleic acid binding IEA --
GO:0003899 DNA-directed 5-3 RNA polymerase activity IEA --
GO:0008270 zinc ion binding IEA --
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with ZNRD1: view
genes like me logo Genes that share phenotypes with ZNRD1: view

Animal Model Products

CRISPR Products

miRNA for ZNRD1 Gene

miRTarBase miRNAs that target ZNRD1

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for ZNRD1
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for ZNRD1 Gene

Localization for ZNRD1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for ZNRD1 Gene

Nucleus, nucleolus.

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 ZNRD1 gene
Compartment Confidence
nucleus 5
extracellular 3
cytosol 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoli fibrillar center (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for ZNRD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
GO:0005654 nucleoplasm TAS --
GO:0005730 nucleolus IEA --
GO:0005736 DNA-directed RNA polymerase I complex IBA --
genes like me logo Genes that share ontologies with ZNRD1: view

Pathways & Interactions for ZNRD1 Gene

genes like me logo Genes that share pathways with ZNRD1: view

Gene Ontology (GO) - Biological Process for ZNRD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006139 nucleobase-containing compound metabolic process TAS 10662553
GO:0006351 transcription, DNA-templated IEA --
GO:0006361 transcription initiation from RNA polymerase I promoter TAS --
GO:0006362 transcription elongation from RNA polymerase I promoter TAS --
GO:0006363 termination of RNA polymerase I transcription IBA,TAS --
genes like me logo Genes that share ontologies with ZNRD1: view

No data available for SIGNOR curated interactions for ZNRD1 Gene

Drugs & Compounds for ZNRD1 Gene

(7) Drugs for ZNRD1 Gene - From: HMDB and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Phosphoric acid Approved Pharma 0
Cytidine triphosphate Experimental Pharma 0
Guanosine triphosphate Experimental Pharma 0
Uridine triphosphate Experimental Pharma 0
ATP Nutra Agonist 0

(2) Additional Compounds for ZNRD1 Gene - From: Novoseek and HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
pyrophosphate
  • (4-)Diphosphoric acid ion
  • (P2O74-)Diphosphate
  • Diphosphate
  • Diphosphoric acid
  • PPi
14000-31-8
genes like me logo Genes that share compounds with ZNRD1: view

Transcripts for ZNRD1 Gene

mRNA/cDNA for ZNRD1 Gene

Unigene Clusters for ZNRD1 Gene

Zinc ribbon domain containing 1:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for ZNRD1
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

Alternative Splicing Database (ASD) splice patterns (SP) for ZNRD1 Gene

ExUns: 1a · 1b · 1c · 1d · 1e · 1f ^ 2 ^ 3 ^ 4 ^ 5a · 5b · 5c
SP1: -
SP2:
SP3: - -
SP4:
SP5: - -
SP6:

Relevant External Links for ZNRD1 Gene

GeneLoc Exon Structure for
ZNRD1
ECgene alternative splicing isoforms for
ZNRD1

Expression for ZNRD1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for ZNRD1 Gene

Protein differential expression in normal tissues from HIPED for ZNRD1 Gene

This gene is overexpressed in Peripheral blood mononuclear cells (37.4) and Fetal ovary (31.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for ZNRD1 Gene



Protein tissue co-expression partners for ZNRD1 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of ZNRD1 Gene:

ZNRD1

SOURCE GeneReport for Unigene cluster for ZNRD1 Gene:

Hs.57813

Evidence on tissue expression from TISSUES for ZNRD1 Gene

  • Muscle(4.2)
  • Skin(4.1)
  • Nervous system(2.9)
genes like me logo Genes that share expression patterns with ZNRD1: view

Primer Products

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 ZNRD1 Gene

Orthologs for ZNRD1 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for ZNRD1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia ZNRD1 33 34
  • 100 (n)
cow
(Bos Taurus)
Mammalia ZNRD1 33 34
  • 89.43 (n)
rat
(Rattus norvegicus)
Mammalia Znrd1 33
  • 82.66 (n)
dog
(Canis familiaris)
Mammalia ZNRD1 33 34
  • 80.95 (n)
mouse
(Mus musculus)
Mammalia Znrd1 33 16 34
  • 80.76 (n)
oppossum
(Monodelphis domestica)
Mammalia ZNRD1 34
  • 73 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia ZNRD1 34
  • 26 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia ZNRD1 34
  • 59 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia znrd1 33
  • 65.29 (n)
Str.20223 33
African clawed frog
(Xenopus laevis)
Amphibia Xl.33613 33
zebrafish
(Danio rerio)
Actinopterygii znrd1 33 34
  • 62.36 (n)
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.1899 33
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP002375 33
  • 53.15 (n)
fruit fly
(Drosophila melanogaster)
Insecta RpI12 33 34
  • 47.86 (n)
worm
(Caenorhabditis elegans)
Secernentea rpoa-12 34
  • 39 (a)
OneToOne
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes RPA12 34 36
  • 34 (a)
OneToOne
Species where no ortholog for ZNRD1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • 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)
  • 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)
  • 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)

Evolution for ZNRD1 Gene

ENSEMBL:
Gene Tree for ZNRD1 (if available)
TreeFam:
Gene Tree for ZNRD1 (if available)

Paralogs for ZNRD1 Gene

No data available for Paralogs for ZNRD1 Gene

Variants for ZNRD1 Gene

Sequence variations from dbSNP and Humsavar for ZNRD1 Gene

SNP ID Clin Chr 06 pos Sequence Context AA Info Type
rs1002141658 -- 30,059,986(+) AAGGA(A/G)ACACA intron-variant, upstream-variant-2KB
rs1003323055 -- 30,063,259(+) TAGAA(A/G)GAGGT intron-variant
rs1003414227 -- 30,063,764(+) TAGGT(A/G)CCTTG intron-variant
rs1003930310 -- 30,061,134(+) TCCCT(C/T)GGAAG nc-transcript-variant, upstream-variant-2KB
rs1005603451 -- 30,063,724(+) TTGGG(C/T)GAGTG intron-variant

Structural Variations from Database of Genomic Variants (DGV) for ZNRD1 Gene

Variant ID Type Subtype PubMed ID
esv2731777 CNV deletion 23290073
esv3411275 CNV duplication 20981092
nsv1074389 CNV deletion 25765185
nsv1122126 CNV deletion 24896259
nsv1144137 CNV deletion 24896259
nsv477598 CNV novel sequence insertion 20440878
nsv601264 CNV loss 21841781

Variation tolerance for ZNRD1 Gene

Residual Variation Intolerance Score: 64% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.65; 45.62% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for ZNRD1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
ZNRD1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for ZNRD1 Gene

Disorders for ZNRD1 Gene

MalaCards: The human disease database

(1) MalaCards diseases for ZNRD1 Gene - From: Novoseek

Disorder Aliases PubMed IDs
gastric cancer, somatic
  • gastric cancer
- elite association - COSMIC cancer census association via MalaCards
Search ZNRD1 in MalaCards View complete list of genes associated with diseases

Relevant External Links for ZNRD1

Genetic Association Database (GAD)
ZNRD1
Human Genome Epidemiology (HuGE) Navigator
ZNRD1
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
ZNRD1
genes like me logo Genes that share disorders with ZNRD1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for ZNRD1 Gene

Publications for ZNRD1 Gene

  1. A new zinc ribbon gene (ZNRD1) is cloned from the human MHC class I region. (PMID: 10662553) Fan W … Lennon G (Genomics 2000) 2 3 4 22 60
  2. Examination of genetic polymorphisms in newborns for signatures of sex-specific prenatal selection. (PMID: 20587610) Ucisik-Akkaya E … Dorak MT (Molecular human reproduction 2010) 3 45 60
  3. ZNRD1 (zinc ribbon domain-containing 1) is a host cellular factor that influences HIV-1 replication and disease progression. (PMID: 20192730) Ballana E … Esté JA (Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2010) 3 45 60
  4. High-density SNP screening of the major histocompatibility complex in systemic lupus erythematosus demonstrates strong evidence for independent susceptibility regions. (PMID: 19851445) Barcellos LF … Criswell LA (PLoS genetics 2009) 3 45 60
  5. Common genetic variation and the control of HIV-1 in humans. (PMID: 20041166) Fellay J … NIAID Center for HIV/AIDS Vaccine Immunology (CHAVI) (PLoS genetics 2009) 3 45 60

Products for ZNRD1 Gene

Sources for ZNRD1 Gene

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