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Aliases for ZFR Gene

Aliases for ZFR Gene

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

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 Cri-Du-Chat Syndrome. Among its related pathways are Diurnally Regulated Genes with Circadian Orthologs. GO annotations related to this gene include nucleic acid binding and poly(A) RNA binding. An important paralog of this gene is ZFR2.

UniProtKB/Swiss-Prot 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 , fRNAdb sequence ontologies and piRNA Summary for ZFR Gene

Genomics for ZFR Gene

Regulatory Elements for ZFR Gene

Enhancers for ZFR 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
GH05G032582 1.9 FANTOM5 Ensembl ENCODE dbSUPER 10.4 -140.2 -140213 5.3 CREB3L1 MLX AGO1 DMAP1 FEZF1 YY1 SLC30A9 ZNF143 SP3 TBX21 SUB1 LOC646616 ZFR MTMR12 GC05M032623
GH05G032230 1.5 Ensembl ENCODE dbSUPER 11.2 +211.8 211848 5.3 FOXA2 MLX ZFP64 ARID4B DMAP1 ZNF2 ZNF48 YY1 SLC30A9 ZNF121 GOLPH3 MIR579 ZFR MTMR12 RNU6-1079P GC05M032236 GC05P032221
GH05G032329 1.5 Ensembl ENCODE dbSUPER 11.1 +113.9 113858 3.2 FOXA2 ATF1 ARID4B DMAP1 ZNF143 DEK SP5 REST PPARG KAT8 MTMR12 MIR579 ZFR GOLPH3 LOC646616 SUB1 GC05P032360
GH05G032297 1.3 Ensembl ENCODE dbSUPER 10.8 +146.6 146603 0.9 PKNOX1 TBL1XR1 TCF12 EGR1 EGR2 ZNF592 CREB3 MBD2 NFIC MAFF GOLPH3 MIR579 ZFR MTMR12 GC05P032310 GC05M032181
GH05G032489 1.2 Ensembl ENCODE 11.3 -45.5 -45462 1.7 FOXA2 SIN3A ARID4B FEZF1 ZNF2 ZNF48 ZNF121 ZNF143 DEK REST LOC646616 SUB1 ZFR MIR579
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around ZFR on UCSC Golden Path with GeneCards custom track

Promoters for ZFR Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000179077 561 2001 HDGF HNRNPUL1 PKNOX1 CREB3L1 MLX ARNT ARID4B SIN3A DMAP1 YY1

Genomic Location for ZFR Gene

Chromosome:
5
Start:
32,354,350 bp from pter
End:
32,444,761 bp from pter
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=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=CAC40818.1; Type=Frameshift; Positions=1057; Evidence={ECO:0000305};

neXtProt entry for ZFR Gene

Post-translational modifications for ZFR Gene

  • Ubiquitination at posLast=730730 and isoforms=796
  • Modification sites at PhosphoSitePlus

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

Protein Domains for ZFR Gene

Suggested Antigen Peptide Sequences for ZFR Gene

Graphical View of Domain Structure for InterPro Entry

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

No data available for Gene Families 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).

Gene Ontology (GO) - Molecular Function for ZFR Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding IEA --
GO:0003723 RNA binding IDA,IEA 22658674
GO:0005515 protein binding IPI 20195357
GO:0008270 zinc ion binding IEA --
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with ZFR: view
genes like me logo Genes that share phenotypes with ZFR: view

Animal Models for ZFR Gene

MGI Knock Outs for ZFR:

Animal Model Products

CRISPR Products

Inhibitory RNA Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , 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

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

Unigene Clusters for ZFR Gene

Zinc finger RNA binding protein:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

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
ECgene alternative splicing isoforms for
ZFR

Expression for ZFR Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP 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, PaxDb, MaxQB, and MOPED for ZFR Gene



Protein tissue co-expression partners for ZFR Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of ZFR Gene:

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(4.7)
  • Intestine(4.3)
  • Lung(4.3)
  • Bone marrow(4.2)
  • Eye(4.2)
  • Adrenal gland(2.7)
genes like me logo Genes that share expression patterns with ZFR: view

Primer Products

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 34 35
  • 99.84 (n)
dog
(Canis familiaris)
Mammalia ZFR 34 35
  • 96.02 (n)
cow
(Bos Taurus)
Mammalia ZFR 34 35
  • 95.42 (n)
oppossum
(Monodelphis domestica)
Mammalia ZFR 35
  • 95 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia ZFR 35
  • 94 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Zfr 34
  • 93.48 (n)
mouse
(Mus musculus)
Mammalia Zfr 34 16 35
  • 92.83 (n)
chicken
(Gallus gallus)
Aves -- 35
  • 93 (a)
OneToMany
-- 35
  • 91 (a)
OneToMany
ZFR 34
  • 84.35 (n)
lizard
(Anolis carolinensis)
Reptilia ZFR 35
  • 90 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia zfr 34
  • 77.06 (n)
Str.6545 34
African clawed frog
(Xenopus laevis)
Amphibia Xl.5370 34
zebrafish
(Danio rerio)
Actinopterygii zfr 34 35
  • 71.86 (n)
wufb25b08 34
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP001905 34
  • 50.84 (n)
fruit fly
(Drosophila melanogaster)
Insecta Zn72D 34 35
  • 49.05 (n)
worm
(Caenorhabditis elegans)
Secernentea Y95B8A.8 34 35
  • 48.47 (n)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.9218 35
  • 23 (a)
OneToMany
Species where no ortholog for ZFR 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)
  • 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 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)

Paralogs for ZFR Gene

Paralogs for ZFR Gene

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

Pseudogenes.org Pseudogenes for ZFR Gene

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

Variants for ZFR Gene

Sequence variations from dbSNP and Humsavar for ZFR Gene

SNP ID Clin Chr 05 pos Sequence Context AA Info Type
rs587777203 Uncertain significance 32,406,850(+) GTTTC(A/G)GTTGT nc-transcript-variant, reference, missense
rs1000007444 -- 32,390,340(+) TGGAG(G/T)ACCAT nc-transcript-variant, reference, missense
rs1000039354 -- 32,431,291(+) TGAGC(C/T)ATCAT intron-variant
rs1000055073 -- 32,415,350(+) ACCAA(C/T)ATGAA intron-variant
rs1000131702 -- 32,422,330(+) ACATG(C/T)CTCAG intron-variant

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)

Relevant External Links for ZFR Gene

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

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

Disorders for ZFR Gene

MalaCards: The human disease database

(2) MalaCards diseases for ZFR Gene - From: Orphanet, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
autosomal recessive spastic paraplegia type 71
  • spg71
cri-du-chat syndrome
  • 5p deletion syndrome
- elite association - COSMIC cancer census association via MalaCards
Search ZFR in MalaCards View complete list of genes associated with diseases

Relevant External Links for ZFR

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
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 J.G. (Science 2014) 2 3 4 64
  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 64
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T. … Sugano S. (Nat. Genet. 2004) 3 4 64
  4. Knockdown of ZFR suppresses cell proliferation and invasion of human pancreatic cancer. (PMID: 27177590) Zhao X. … Tan J. (Biol. Res. 2016) 3 64
  5. Proteomic analyses reveal distinct chromatin-associated and soluble transcription factor complexes. (PMID: 25609649) Li X. … Chen J. (Mol. Syst. Biol. 2015) 3 64

Products for ZFR Gene

Sources for ZFR Gene

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