This gene encodes an RNA-binding protein characterized by its DZF (domain associated with zinc fingers) domain. The encoded protein may play a role in the nucleocytoplasmic shuttling of another RNA-binding protein, Staufen homolog 2, in neurons. Expression of this gene is regulated through alternative polyadenylation that mediates differential microRNA targeting. Elevated expre... See more...

Aliases for ZFR Gene

Aliases for ZFR Gene

  • Zinc Finger RNA Binding Protein 2 3 5
  • Zinc Finger RNA-Binding Protein 3 4
  • M-Phase Phosphoprotein Homolog 3 4
  • SPG71 2 3
  • ZFR1 2 3
  • HZFR 4
  • ZFR 5

External Ids for ZFR Gene

Previous GeneCards Identifiers for ZFR Gene

  • GC05M032141
  • GC05M032800
  • GC05M032354
  • GC05M032399

Summaries for ZFR Gene

Entrez Gene Summary for ZFR Gene

  • This gene encodes an RNA-binding protein characterized by its DZF (domain associated with zinc fingers) domain. The encoded protein may play a role in the nucleocytoplasmic shuttling of another RNA-binding protein, Staufen homolog 2, in neurons. Expression of this gene is regulated through alternative polyadenylation that mediates differential microRNA targeting. Elevated expression of this gene has been observed in human patients with pancreatic cancer and knockdown of this gene may result in reduced viability and invasion of pancreatic cancer cells. [provided by RefSeq, Sep 2016]

GeneCards Summary for ZFR Gene

ZFR (Zinc Finger RNA Binding Protein) is a Protein Coding gene. Diseases associated with ZFR include Autosomal Recessive Spastic Paraplegia Type 71 and Pure Or Complex Autosomal Recessive Spastic Paraplegia. Among its related pathways are Diurnally Regulated Genes with Circadian Orthologs. Gene Ontology (GO) annotations related to this gene include nucleic acid binding. An important paralog of this gene is ZFR2.

UniProtKB/Swiss-Prot Summary for ZFR Gene

  • Involved in postimplantation and gastrulation stages of development. Involved in the nucleocytoplasmic shuttling of STAU2. Binds to DNA and RNA (By similarity).

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

Genomics for ZFR Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for ZFR Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

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

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

Top Transcription factor binding sites by QIAGEN in the ZFR gene promoter:
  • AhR
  • aMEF-2
  • AP-4
  • FOXI1
  • HFH-3
  • MEF-2A
  • Pax-2
  • Pax-2a
  • Pax-6
  • Sox5

Genomic Locations for ZFR Gene

Latest Assembly
chr5:32,354,350-32,444,740
(GRCh38/hg38)
Size:
90,391 bases
Orientation:
Minus strand

Previous Assembly
chr5:32,354,456-32,444,846
(GRCh37/hg19 by Entrez Gene)
Size:
90,391 bases
Orientation:
Minus strand

chr5:32,354,456-32,444,867
(GRCh37/hg19 by Ensembl)
Size:
90,412 bases
Orientation:
Minus strand

Genomic View for ZFR Gene

Genes around ZFR on UCSC Golden Path with GeneCards custom track

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

RefSeq DNA sequence for ZFR Gene

Proteins for ZFR Gene

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

    Protein Symbol:
    Q96KR1-ZFR_HUMAN
    Recommended name:
    Zinc finger RNA-binding protein
    Protein Accession:
    Q96KR1
    Secondary Accessions:
    • B2RNR5
    • Q05C08
    • Q3B7X5
    • Q6P5A3
    • Q86UA0
    • Q9H6V4
    • Q9NTI1
    • Q9Y687

    Protein attributes for ZFR Gene

    Size:
    1074 amino acids
    Molecular mass:
    117012 Da
    Quaternary structure:
    • Found in a cytoplasmic RNP complex with STAU2. Interacts with STAU2. Does not interact with STAU1 (By similarity).
    SequenceCaution:
    • Sequence=AAD40385.1; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=AAH30540.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential poly-A sequence.; Evidence={ECO:0000305}; Sequence=AAI07418.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential poly-A sequence.; Evidence={ECO:0000305}; Sequence=BAB15147.1; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=CAC40818.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305}; Sequence=CAC40818.1; Type=Frameshift; Evidence={ECO:0000305};

neXtProt entry for ZFR Gene

Post-translational modifications for ZFR Gene

  • Glycosylation at Ser148, Thr149, Ser195, and Thr202
  • Ubiquitination at Lys730 and Lys796
  • Modification sites at PhosphoSitePlus
  • Glycosylation from GlyConnect

Other Protein References for ZFR Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for ZFR Gene

Domains & Families for ZFR Gene

Gene Families for ZFR Gene

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

Protein Domains for ZFR Gene

InterPro:
Blocks:
  • Zn-finger, U1-like

Suggested Antigen Peptide Sequences for ZFR Gene

GenScript: Design optimal peptide antigens:
  • Zinc finger RNA binding protein (B2RNR6_HUMAN)
  • ZFR protein (Q05D65_HUMAN)
  • M-phase phosphoprotein homolog (ZFR_HUMAN)
genes like me logo Genes that share domains with ZFR: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for ZFR Gene

Function for ZFR Gene

Molecular function for ZFR Gene

UniProtKB/Swiss-Prot Function:
Involved in postimplantation and gastrulation stages of development. Involved in the nucleocytoplasmic shuttling of STAU2. Binds to DNA and RNA (By similarity).

Phenotypes From GWAS Catalog for ZFR Gene

Gene Ontology (GO) - Molecular Function for ZFR Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003676 nucleic acid binding IEA --
GO:0003677 DNA binding IEA --
GO:0003723 RNA binding IEA,HDA 22658674
GO:0003725 double-stranded RNA binding IBA 21873635
GO:0003727 single-stranded RNA binding IBA 21873635
genes like me logo Genes that share ontologies with ZFR: view
genes like me logo Genes that share phenotypes with ZFR: view

Human Phenotype Ontology for ZFR Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for ZFR Gene

MGI Knock Outs for ZFR:
  • Zfr Zfr<tm1Reb>

Inhibitory RNAs for research

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

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for ZFR Gene

Localization for ZFR Gene

Subcellular locations from UniProtKB/Swiss-Prot for ZFR Gene

Nucleus. Cytoplasm. Cytoplasmic granule. Chromosome. Note=Associated with chromosome foci in meiotic cells. Localizes in somatodendritic compartment of primary hippocampal neurons. Colocalizes with STAU2 in several cytosolic RNA granules (By similarity). {ECO:0000250}.

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 ZFR gene
Compartment Confidence
nucleus 5
cytosol 2
plasma membrane 1
extracellular 1
cytoskeleton 1
mitochondrion 1
endoplasmic reticulum 1
endosome 1
lysosome 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for ZFR Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
GO:0005694 chromosome IEA --
GO:0005737 cytoplasm IEA --
genes like me logo Genes that share ontologies with ZFR: view

Pathways & Interactions for ZFR Gene

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

Pathways by source for ZFR Gene

1 BioSystems pathway for ZFR Gene

Gene Ontology (GO) - Biological Process for ZFR Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007275 multicellular organism development IEA --
genes like me logo Genes that share ontologies with ZFR: view

No data available for SIGNOR curated interactions for ZFR Gene

Drugs & Compounds for ZFR Gene

(1) Drugs for ZFR Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
genes like me logo Genes that share compounds with ZFR: view

Transcripts for ZFR Gene

mRNA/cDNA for ZFR Gene

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

Inhibitory RNAs for research

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

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

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

ExUns: 19 ^ 20
SP1:
SP2:
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:

Relevant External Links for ZFR Gene

GeneLoc Exon Structure for
ZFR

Expression for ZFR Gene

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

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for ZFR Gene

This gene is overexpressed in Adrenal (7.9), CD8 Tcells (6.7), and Ovary (6.3).

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



Protein tissue co-expression partners for ZFR Gene

- Elite partner

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

SOURCE GeneReport for Unigene cluster for ZFR Gene:

Hs.435231

mRNA Expression by UniProt/SwissProt for ZFR Gene:

Q96KR1-ZFR_HUMAN
Tissue specificity: Expressed in lung, liver, lymphocytes, heart, pancreas, placenta, brain and kidney.

Evidence on tissue expression from TISSUES for ZFR Gene

  • Nervous system(4.8)
  • Intestine(4.4)
  • Eye(4.3)
  • Lung(4.3)
  • Bone marrow(4.2)
  • Adrenal gland(2.5)
  • Kidney(2.2)
  • Heart(2.1)
  • Muscle(2.1)
  • Skin(2)
genes like me logo Genes that share expression patterns with ZFR: view

Primer products for research

No data available for mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for ZFR Gene

Orthologs for ZFR Gene

This gene was present in the common ancestor of animals.

Orthologs for ZFR Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia ZFR 29 30
  • 99.84 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia ZFR 29 30
  • 96.02 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia ZFR 29 30
  • 95.42 (n)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia ZFR 30
  • 95 (a)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia ZFR 30
  • 94 (a)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Zfr 29
  • 93.48 (n)
Mouse
(Mus musculus)
Mammalia Zfr 29 16 30
  • 92.83 (n)
OneToOne
Chicken
(Gallus gallus)
Aves -- 30
  • 93 (a)
OneToMany
-- 30
  • 91 (a)
OneToMany
ZFR 29
  • 84.35 (n)
Lizard
(Anolis carolinensis)
Reptilia ZFR 30
  • 90 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia zfr 29
  • 77.06 (n)
Str.6545 29
African clawed frog
(Xenopus laevis)
Amphibia Xl.5370 29
Zebrafish
(Danio rerio)
Actinopterygii zfr 29 30
  • 71.86 (n)
OneToOne
wufb25b08 29
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP001905 29
  • 50.84 (n)
Fruit Fly
(Drosophila melanogaster)
Insecta Zn72D 29 30
  • 49.05 (n)
OneToMany
Worm
(Caenorhabditis elegans)
Secernentea Y95B8A.8 29 30
  • 48.47 (n)
OneToMany
Sea Squirt
(Ciona savignyi)
Ascidiacea CSA.9218 30
  • 23 (a)
OneToMany
Species where no ortholog for ZFR was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • 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)
  • 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 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 ZFR Gene

ENSEMBL:
Gene Tree for ZFR (if available)
TreeFam:
Gene Tree for ZFR (if available)
Aminode:
Evolutionary constrained regions (ECRs) for ZFR: view image
Alliance of Genome Resources:
Additional Orthologs for ZFR

Paralogs for ZFR Gene

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

  • ZFR_HUMAN
  • B2RNR6_HUMAN
  • H0Y8W1_HUMAN
  • L0R5H8_HUMAN
  • Q05D65_HUMAN

Pseudogenes.org Pseudogenes for ZFR Gene

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

Variants for ZFR Gene

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

SNP ID Clinical significance and condition Chr 05 pos Variation AA Info Type
1022028 Uncertain Significance: Pure or complex autosomal recessive spastic paraplegia 32,390,433(-) A/G
NM_016107.5(ZFR):c.1984T>C (p.Tyr662His)
MISSENSE_VARIANT,NON_CODING_TRANSCRIPT
1043537 Uncertain Significance: Pure or complex autosomal recessive spastic paraplegia 32,379,165(-) G/A
NM_016107.5(ZFR):c.2785C>T (p.Leu929Phe)
MISSENSE_VARIANT,NON_CODING_TRANSCRIPT
842659 Uncertain Significance: Pure or complex autosomal recessive spastic paraplegia 32,397,291(-) G/A
NM_016107.5(ZFR):c.1761C>T (p.Cys587=)
NON_CODING_TRANSCRIPT_VARIANT,SYNONYMOUS
854204 Uncertain Significance: Pure or complex autosomal recessive spastic paraplegia 32,406,909(-) T/TGCA
NM_016107.5(ZFR):c.882_884TGC[6] (p.Ala299dup)
NON_CODING_TRANSCRIPT_VARIANT,INFRAME_INSERTION
936680 Uncertain Significance: Pure or complex autosomal recessive spastic paraplegia 32,388,620(-) T/C
NM_016107.5(ZFR):c.2197A>G (p.Thr733Ala)
MISSENSE_VARIANT,NON_CODING_TRANSCRIPT

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for ZFR Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

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

Variant ID Type Subtype PubMed ID
esv2730025 CNV deletion 23290073
esv2730026 CNV deletion 23290073
esv2730027 CNV deletion 23290073
esv2730030 CNV deletion 23290073
esv2730031 CNV deletion 23290073
esv2730032 CNV deletion 23290073
esv2730033 CNV deletion 23290073
esv2730034 CNV deletion 23290073
esv2730035 CNV deletion 23290073
esv2730036 CNV deletion 23290073
esv2730037 CNV deletion 23290073
esv2730038 CNV deletion 23290073
esv2730039 CNV deletion 23290073
esv2759338 CNV loss 17122850
esv3570061 CNV loss 25503493
esv3604580 CNV gain 21293372
esv3604608 CNV loss 21293372
nsv1021781 CNV gain 25217958
nsv1114677 CNV deletion 24896259
nsv1131883 CNV deletion 24896259
nsv477712 CNV novel sequence insertion 20440878
nsv964831 CNV duplication 23825009

Variation tolerance for ZFR Gene

Residual Variation Intolerance Score: 4.77% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 8.91; 87.16% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for ZFR Gene

Human Gene Mutation Database (HGMD)
ZFR
SNPedia medical, phenotypic, and genealogical associations of SNPs for
ZFR
Leiden Open Variation Database (LOVD)
ZFR

SNP Genotyping and Copy Number Assays for research

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

Disorders for ZFR Gene

MalaCards: The human disease database

(9) MalaCards diseases for ZFR Gene - From: ORP, COP, and GCD

- elite association - COSMIC cancer census association via MalaCards
Search ZFR in MalaCards View complete list of genes associated with diseases

Additional Disease Information for ZFR

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

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

Publications for ZFR Gene

  1. Exome sequencing links corticospinal motor neuron disease to common neurodegenerative disorders. (PMID: 24482476) Novarino G … Gleeson JG (Science (New York, N.Y.) 2014) 2 3 4 72
  2. Cloning and expression of the human single copy homologue of the mouse zinc finger protein zfr. (PMID: 11574164) Kleines M … Schaade L (Gene 2001) 2 3 4
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4
  4. Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms. (PMID: 33060197) Gordon DE … Krogan NJ (Science (New York, N.Y.) 2020) 3
  5. A High-Density Human Mitochondrial Proximity Interaction Network. (PMID: 32877691) Antonicka H … Shoubridge EA (Cell metabolism 2020) 3

Products for ZFR Gene

Sources for ZFR Gene