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Aliases for ZRANB3 Gene

Aliases for ZRANB3 Gene

  • Zinc Finger RANBP2-Type Containing 3 2 3 5
  • Zinc Finger Ran-Binding Domain-Containing Protein 3 3 4
  • Zinc Finger, RAN-Binding Domain Containing 3 2 3
  • Annealing Helicase 2 3 4
  • AH2 3 4
  • DNA Annealing Helicase And Endonuclease ZRANB3 3
  • 4933425L19Rik 3
  • EC 3.6.1 56

External Ids for ZRANB3 Gene

Previous GeneCards Identifiers for ZRANB3 Gene

  • GC02M135728
  • GC02M135894
  • GC02M127950

Summaries for ZRANB3 Gene

GeneCards Summary for ZRANB3 Gene

ZRANB3 (Zinc Finger RANBP2-Type Containing 3) is a Protein Coding gene. Gene Ontology (GO) annotations related to this gene include nucleic acid binding and endonuclease activity. An important paralog of this gene is SMARCAL1.

UniProtKB/Swiss-Prot for ZRANB3 Gene

  • DNA annealing helicase and endonuclease required to maintain genome stability at stalled or collapsed replication forks by facilitating fork restart and limiting inappropriate recombination that could occur during template switching events (PubMed:21078962, PubMed:22704558, PubMed:22705370, PubMed:22759634, PubMed:26884333). Recruited to the sites of stalled DNA replication by polyubiquitinated PCNA and acts as a structure-specific endonuclease that cleaves the replication fork D-loop intermediate, generating an accessible 3-OH group in the template of the leading strand, which is amenable to extension by DNA polymerase (PubMed:22759634). In addition to endonuclease activity, also catalyzes the fork regression via annealing helicase activity in order to prevent disintegration of the replication fork and the formation of double-strand breaks (PubMed:22705370, PubMed:22704558).

Additional gene information for ZRANB3 Gene

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for ZRANB3 Gene

Genomics for ZRANB3 Gene

GeneHancer (GH) Regulatory Elements for ZRANB3 Gene

Promoters and enhancers for ZRANB3 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
GH02I135529 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 550.8 +0.1 109 4.4 HDGF PKNOX1 SMAD1 ARID4B SIN3A FEZF1 DMAP1 YY1 POLR2B ZNF766 R3HDM1 ZRANB3 MCM6 MAP3K19 UBXN4 CCNT2 LOC100422338
GH02I136247 Enhancer 1.6 FANTOM5 Ensembl ENCODE dbSUPER 10 -716.8 -716830 1.7 FEZF1 GLI4 ZNF2 GLIS2 ZNF213 FOS SP3 YY2 REST TSHZ1 UBXN4 ZRANB3 R3HDM1 CXCR4 ENSG00000279024 UBBP1
GH02I135051 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 4.5 +477.7 477726 3.8 HDGF PKNOX1 SMAD1 ARNT ARID4B SIN3A DMAP1 ZNF2 IRF4 YY1 RAB3GAP1 MAP3K19 CCNT2 UBXN4 DARS ZRANB3 GC02P135138
GH02I135586 Promoter 0.7 EPDnew 10.6 -55.0 -55011 0.1 MXI1 POLR2A CEBPB R3HDM1 ZRANB3 MAP3K19 RAB3GAP1 GC02M135657
GH02I136381 Enhancer 1.4 FANTOM5 Ensembl ENCODE 3.9 -851.1 -851102 2 HDGF PKNOX1 SMAD1 YBX1 BATF KLF5 IRF4 ZNF143 ATF7 ETV6 CXCR4 ZRANB3 RN7SKP141 UBBP1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around ZRANB3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the ZRANB3 gene promoter:

Genomic Locations for ZRANB3 Gene

Genomic Locations for ZRANB3 Gene
chr2:135,136,916-135,531,322
(GRCh38/hg38)
Size:
394,407 bases
Orientation:
Minus strand
chr2:135,894,486-136,288,806
(GRCh37/hg19)

Genomic View for ZRANB3 Gene

Genes around ZRANB3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
ZRANB3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for ZRANB3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for ZRANB3 Gene

Proteins for ZRANB3 Gene

  • Protein details for ZRANB3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q5FWF4-ZRAB3_HUMAN
    Recommended name:
    DNA annealing helicase and endonuclease ZRANB3
    Protein Accession:
    Q5FWF4
    Secondary Accessions:
    • B3KYA1
    • B4E375
    • B5MDI3
    • D3DP76
    • E9PBP0
    • Q53SM1
    • Q6P2C4
    • Q8N1P4
    • Q9H0E8

    Protein attributes for ZRANB3 Gene

    Size:
    1079 amino acids
    Molecular mass:
    123248 Da
    Quaternary structure:
    • Interacts (via PIP-box and RanBP2-type zinc finger) with PCNA (when PCNA is polyubiquitinated via Lys-63-linked polyubiquitin).
    Miscellaneous:
    • In contrast to classical helicases that unwing DNA, annealing helicases rewind it.
    SequenceCaution:
    • Sequence=AAX93066.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305}; Sequence=BAG54763.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=BAG65387.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=EAX11631.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305}; Sequence=EAX11633.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for ZRANB3 Gene

    Alternative splice isoforms for ZRANB3 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for ZRANB3 Gene

Selected DME Specific Peptides for ZRANB3 Gene

Q5FWF4:
  • DEMGLGKT
  • KFLVFAHH
  • MGLGKTIQ
  • RAHRIGQ

Post-translational modifications for ZRANB3 Gene

  • Ubiquitination at isoforms=3, 5179 and posLast=322322

Domains & Families for ZRANB3 Gene

Gene Families for ZRANB3 Gene

HGNC:
Human Protein Atlas (HPA):
  • Cancer-related genes
  • Predicted intracellular proteins

Graphical View of Domain Structure for InterPro Entry

Q5FWF4

UniProtKB/Swiss-Prot:

ZRAB3_HUMAN :
  • The PIP-box mediates the interaction with PCNA, while the RanBP2-type zinc finger mediates binding to Lys-63-linked polyubiquitin (PubMed:22704558, PubMed:22705370 and PubMed:22759634).
  • Belongs to the SNF2/RAD54 helicase family.
Domain:
  • The PIP-box mediates the interaction with PCNA, while the RanBP2-type zinc finger mediates binding to Lys-63-linked polyubiquitin (PubMed:22704558, PubMed:22705370 and PubMed:22759634).
Family:
  • Belongs to the SNF2/RAD54 helicase family.
genes like me logo Genes that share domains with ZRANB3: view

Function for ZRANB3 Gene

Molecular function for ZRANB3 Gene

UniProtKB/Swiss-Prot Function:
DNA annealing helicase and endonuclease required to maintain genome stability at stalled or collapsed replication forks by facilitating fork restart and limiting inappropriate recombination that could occur during template switching events (PubMed:21078962, PubMed:22704558, PubMed:22705370, PubMed:22759634, PubMed:26884333). Recruited to the sites of stalled DNA replication by polyubiquitinated PCNA and acts as a structure-specific endonuclease that cleaves the replication fork D-loop intermediate, generating an accessible 3-OH group in the template of the leading strand, which is amenable to extension by DNA polymerase (PubMed:22759634). In addition to endonuclease activity, also catalyzes the fork regression via annealing helicase activity in order to prevent disintegration of the replication fork and the formation of double-strand breaks (PubMed:22705370, PubMed:22704558).

Enzyme Numbers (IUBMB) for ZRANB3 Gene

Phenotypes From GWAS Catalog for ZRANB3 Gene

Gene Ontology (GO) - Molecular Function for ZRANB3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003676 nucleic acid binding IEA --
GO:0003678 NOT DNA helicase activity IDA 21078962
GO:0003824 catalytic activity IEA --
GO:0004386 helicase activity IEA --
GO:0004518 nuclease activity IEA --
genes like me logo Genes that share ontologies with ZRANB3: view

Phenotypes for ZRANB3 Gene

genes like me logo Genes that share phenotypes with ZRANB3: view

Animal Model Products

Clone Products

No data available for Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for ZRANB3 Gene

Localization for ZRANB3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for ZRANB3 Gene

Nucleus. Chromosome. Note=Following DNA damage, recruited to sites of DNA damage and stalled replication forks by polyubiquitinated PCNA (PubMed:22704558, PubMed:22705370, PubMed:22759634). {ECO:0000269 PubMed:22704558, ECO:0000269 PubMed:22705370, ECO:0000269 PubMed:22759634}.

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 ZRANB3 gene
Compartment Confidence
nucleus 5
cytosol 3
plasma membrane 2
cytoskeleton 2
golgi apparatus 2
mitochondrion 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for ZRANB3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA --
GO:0005694 chromosome IEA --
GO:0043596 nuclear replication fork IDA 22704558
genes like me logo Genes that share ontologies with ZRANB3: view

Pathways & Interactions for ZRANB3 Gene

SuperPathways for ZRANB3 Gene

No Data Available

Gene Ontology (GO) - Biological Process for ZRANB3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000733 DNA strand renaturation IEA --
GO:0006281 DNA repair IDA,IEA 22759634
GO:0006974 cellular response to DNA damage stimulus IEA,IDA 22704558
GO:0008152 metabolic process IEA --
GO:0009411 response to UV IDA 22704558
genes like me logo Genes that share ontologies with ZRANB3: view

No data available for Pathways by source and SIGNOR curated interactions for ZRANB3 Gene

Drugs & Compounds for ZRANB3 Gene

No Compound Related Data Available

Transcripts for ZRANB3 Gene

Unigene Clusters for ZRANB3 Gene

Zinc finger, RAN-binding domain containing 3:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for ZRANB3 Gene

No ASD Table

Relevant External Links for ZRANB3 Gene

GeneLoc Exon Structure for
ZRANB3
ECgene alternative splicing isoforms for
ZRANB3

Expression for ZRANB3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for ZRANB3 Gene

Protein differential expression in normal tissues from HIPED for ZRANB3 Gene

This gene is overexpressed in Plasma (42.0), Heart (17.9), and Adipocyte (8.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for ZRANB3 Gene



Protein tissue co-expression partners for ZRANB3 Gene

NURSA nuclear receptor signaling pathways regulating expression of ZRANB3 Gene:

ZRANB3

SOURCE GeneReport for Unigene cluster for ZRANB3 Gene:

Hs.658422

Evidence on tissue expression from TISSUES for ZRANB3 Gene

  • Kidney(2.3)
  • Skin(2.2)
  • Lung(2)
genes like me logo Genes that share expression patterns with ZRANB3: 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 ZRANB3 Gene

Orthologs for ZRANB3 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for ZRANB3 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia ZRANB3 33 34
  • 99.44 (n)
cow
(Bos Taurus)
Mammalia ZRANB3 33 34
  • 88.45 (n)
dog
(Canis familiaris)
Mammalia ZRANB3 33 34
  • 88.43 (n)
mouse
(Mus musculus)
Mammalia Zranb3 33 16 34
  • 81.26 (n)
rat
(Rattus norvegicus)
Mammalia Zranb3 33
  • 79.38 (n)
oppossum
(Monodelphis domestica)
Mammalia ZRANB3 34
  • 70 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia ZRANB3 34
  • 63 (a)
OneToOne
chicken
(Gallus gallus)
Aves ZRANB3 33 34
  • 69.02 (n)
lizard
(Anolis carolinensis)
Reptilia ZRANB3 34
  • 62 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia zranb3 33
  • 63.87 (n)
Str.7449 33
zebrafish
(Danio rerio)
Actinopterygii zranb3 34
  • 71 (a)
OneToMany
LOC100331496 33
  • 57.73 (n)
CABZ01044943.1 34
  • 47 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea btf-1 34
  • 7 (a)
ManyToMany
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes MOT1 34
  • 7 (a)
OneToMany
thale cress
(Arabidopsis thaliana)
eudicotyledons AT5G07810 33
  • 45.92 (n)
rice
(Oryza sativa)
Liliopsida Os07g0598300 33
  • 47.74 (n)
Species where no ortholog for ZRANB3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • 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)
  • 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 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)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for ZRANB3 Gene

ENSEMBL:
Gene Tree for ZRANB3 (if available)
TreeFam:
Gene Tree for ZRANB3 (if available)

Paralogs for ZRANB3 Gene

Paralogs for ZRANB3 Gene

(1) SIMAP similar genes for ZRANB3 Gene using alignment to 3 proteins:

genes like me logo Genes that share paralogs with ZRANB3: view

Variants for ZRANB3 Gene

Sequence variations from dbSNP and Humsavar for ZRANB3 Gene

SNP ID Clin Chr 02 pos Variation AA Info Type
rs10170125 likely-benign, Warburg micro syndrome 135,168,916(-) C/G genic_downstream_transcript_variant, intron_variant
rs1050515610 uncertain-significance, Warburg micro syndrome 135,169,105(-) T/G genic_downstream_transcript_variant, intron_variant
rs11558413 likely-benign, Warburg micro syndrome 135,168,952(-) G/A genic_downstream_transcript_variant, intron_variant
rs116237324 likely-benign, Warburg micro syndrome 135,169,776(-) T/C genic_downstream_transcript_variant, intron_variant
rs143703110 benign, Warburg micro syndrome 135,169,037(-) GGGGGG/GGGGGGG genic_downstream_transcript_variant, intron_variant

Structural Variations from Database of Genomic Variants (DGV) for ZRANB3 Gene

Variant ID Type Subtype PubMed ID
esv3893415 CNV loss 25118596
esv3592578 CNV gain 21293372
esv3592575 CNV loss 21293372
esv3592573 CNV loss 21293372
esv3592568 CNV loss 21293372
esv3431049 CNV insertion 20981092
esv34026 CNV loss 18971310
esv3304011 CNV mobile element insertion 20981092
esv29203 CNV loss 19812545
esv2762862 CNV loss 21179565
esv2720863 CNV deletion 23290073
esv2720861 CNV deletion 23290073
esv2668909 CNV deletion 23128226
esv2664308 CNV deletion 23128226
esv2661092 CNV deletion 23128226
esv2467285 CNV deletion 19546169
esv2421388 CNV deletion 20811451
esv2410901 CNV deletion 18987734
esv2058333 CNV deletion 18987734
nsv834386 CNV gain 17160897
nsv583172 CNV gain 21841781
nsv514095 CNV loss 21397061
nsv498936 CNV loss 21111241
nsv476642 CNV novel sequence insertion 20440878
nsv472777 CNV novel sequence insertion 20440878
nsv441786 CNV gain 18776908
nsv2941 CNV insertion 18451855
nsv2940 CNV deletion 18451855
nsv1127766 CNV deletion 24896259
nsv1123396 CNV deletion 24896259
nsv1116796 CNV deletion 24896259
nsv1003723 CNV loss 25217958
nsv1000750 CNV gain 25217958

Variation tolerance for ZRANB3 Gene

Residual Variation Intolerance Score: 92.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 12.81; 94.77% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for ZRANB3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
ZRANB3

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for ZRANB3 Gene

Disorders for ZRANB3 Gene

Additional Disease Information for ZRANB3

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

No disorders were found for ZRANB3 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for ZRANB3 Gene

Publications for ZRANB3 Gene

  1. Toward a catalog of human genes and proteins: sequencing and analysis of 500 novel complete protein coding human cDNAs. (PMID: 11230166) Wiemann S … Poustka A (Genome research 2001) 2 3 4 58
  2. Identification of a Substrate Recognition Domain in the Replication Stress Response Protein Zinc Finger Ran-binding Domain-containing Protein 3 (ZRANB3). (PMID: 26884333) Badu-Nkansah A … Cortez D (The Journal of biological chemistry 2016) 3 4 58
  3. ZRANB3 is a structure-specific ATP-dependent endonuclease involved in replication stress response. (PMID: 22759634) Weston R … Ahel D (Genes & development 2012) 3 4 58
  4. The HARP-like domain-containing protein AH2/ZRANB3 binds to PCNA and participates in cellular response to replication stress. (PMID: 22705370) Yuan J … Chen J (Molecular cell 2012) 3 4 58
  5. Polyubiquitinated PCNA recruits the ZRANB3 translocase to maintain genomic integrity after replication stress. (PMID: 22704558) Ciccia A … Elledge SJ (Molecular cell 2012) 3 4 58

Products for ZRANB3 Gene

Sources for ZRANB3 Gene

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