RAD54B Gene (Protein Coding)

RAD54 Homolog B

GC08M094371
GIFtS:
43
The protein encoded by this gene belongs to the DEAD-like helicase superfamily. It shares similarity with Saccharomyces cerevisiae RAD54 and RDH54, both of which are involved in homologous recombination and repair of DNA. This protein binds to double-stranded DNA, and displays ATPase activity in the presence of DNA. This gene is highly expressed in testis and spleen, which sugg... See more...

Aliases for RAD54B Gene

Aliases for RAD54B Gene

  • RAD54 Homolog B 2 3 4 5
  • DNA Repair And Recombination Protein RAD54B 3 4
  • RDH54 2 3
  • RAD54 Homolog B (S. Cerevisiae) 2
  • EC 3.6.4.- 4
  • EC 3.6.1 51
  • RAD54B 5

External Ids for RAD54B Gene

Previous GeneCards Identifiers for RAD54B Gene

  • GC08M094130
  • GC08M095230
  • GC08M095052
  • GC08M095340
  • GC08M095453
  • GC08M095384
  • GC08M090593

Summaries for RAD54B Gene

Entrez Gene Summary for RAD54B Gene

  • The protein encoded by this gene belongs to the DEAD-like helicase superfamily. It shares similarity with Saccharomyces cerevisiae RAD54 and RDH54, both of which are involved in homologous recombination and repair of DNA. This protein binds to double-stranded DNA, and displays ATPase activity in the presence of DNA. This gene is highly expressed in testis and spleen, which suggests active roles in meiotic and mitotic recombination. Homozygous mutations of this gene were observed in primary lymphoma and colon cancer. [provided by RefSeq, Jul 2008]

GeneCards Summary for RAD54B Gene

RAD54B (RAD54 Homolog B) is a Protein Coding gene. Diseases associated with RAD54B include Lymphoma, Non-Hodgkin, Familial and Colorectal Cancer. Among its related pathways are Resolution of D-loop Structures through Holliday Junction Intermediates. Gene Ontology (GO) annotations related to this gene include hydrolase activity and RNA helicase activity. An important paralog of this gene is RAD54L.

UniProtKB/Swiss-Prot Summary for RAD54B Gene

  • Involved in DNA repair and mitotic recombination. May play an active role in recombination processes in concert with other members of the RAD52 epistasis group.

Gene Wiki entry for RAD54B Gene

Additional gene information for RAD54B Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for RAD54B Gene

Genomics for RAD54B Gene

GeneHancer (GH) Regulatory Elements Pubs

Download GeneHancer 2017 data
Promoters and enhancers for RAD54B 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
GH08J094434 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 261.2 +38.6 38585 6.7 TBP CEBPA MNT IKZF1 SMAD5 IRF2 HES1 SIN3A GTF2E2 CUX1 RAD54B FSBP VIRMA LOC101926977 HSALNG0067028 GEM
GH08J094473 Promoter/Enhancer 2 EPDnew Ensembl ENCODE CraniofacialAtlas 250.7 +0.6 615 3 TBP ZBTB10 SP1 MXD4 MNT IKZF1 SMAD5 ETS1 ZNF217 POLR2A RAD54B VIRMA FSBP INTS8 piR-57461-260 RF00017-7178
GH08J094380 Promoter 0.4 EPDnew 250.2 +94.8 94832 0.1 PKNOX1 RAD54B MK280607-124 HSALNG0067023 FSBP GEM
GH08J094552 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE CraniofacialAtlas 10.7 -78.3 -78286 3.6 CHD2 TBP MXD4 ZBTB10 SP1 FEZF1 SIX5 NR2C1 MNT IKZF1 VIRMA LOC101926977 lnc-VIRMA-2 RAD54B ENSG00000254315
GH08J093990 Promoter/Enhancer 1.7 FANTOM5 ENCODE CraniofacialAtlas 9.3 +483.7 483701 1.8 BCL11A MNT DEK ZNF217 POLR2A BRCA1 CTCF BHLHE40 ZBTB7B ELF1 RAD54B HSALNG0067007 HSALNG0067008 PDP1 CDH17
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around RAD54B on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for RAD54B

Top Transcription factor binding sites by QIAGEN in the RAD54B gene promoter:
  • aMEF-2
  • AML1a
  • Evi-1
  • FOXJ2
  • FOXJ2 (long isoform)
  • GATA-1
  • MEF-2
  • MEF-2A
  • Pbx1a
  • POU2F1a

Genomic Locations for RAD54B Gene

Latest Assembly
chr8:94,371,960-94,475,115
(GRCh38/hg38)
Size:
103,156 bases
Orientation:
Minus strand

Previous Assembly
chr8:95,384,188-95,487,343
(GRCh37/hg19 by Entrez Gene)
Size:
103,156 bases
Orientation:
Minus strand

chr8:95,384,188-95,487,337
(GRCh37/hg19 by Ensembl)
Size:
103,150 bases
Orientation:
Minus strand

Genomic View for RAD54B Gene

Genes around RAD54B on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
RAD54B Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for RAD54B Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for RAD54B Gene

Proteins for RAD54B Gene

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  • Protein details for RAD54B Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9Y620-RA54B_HUMAN
    Recommended name:
    DNA repair and recombination protein RAD54B
    Protein Accession:
    Q9Y620
    Secondary Accessions:
    • F6WBS8

    Protein attributes for RAD54B Gene

    Size:
    910 amino acids
    Molecular mass:
    102967 Da
    Quaternary structure:
    • Interacts with RAD51 through the NH2-terminal domain. Immunoprecipitation experiments show that the interaction is constitutive and not induced by ionizing radiation. The interaction may be indirect.

    Alternative splice isoforms for RAD54B Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for RAD54B Gene

Protein Expression for RAD54B Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Selected DME Specific Peptides for RAD54B Gene

Q9Y620:
  • GTIEEKI
  • IYRLLTT
  • DEMGLGKT
  • KEFQKWL
  • GGVGLNL
  • MGLGKTL
  • RVWRDGQK

Post-translational modifications for RAD54B Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for RAD54B Gene

ENSEMBL proteins:
REFSEQ proteins:

Domains & Families for RAD54B Gene

Gene Families for RAD54B Gene

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

Protein Domains for RAD54B Gene

InterPro:
Blocks:
  • SNF2 related domain
ProtoNet:

Suggested Antigen Peptide Sequences for RAD54B Gene

GenScript: Design optimal peptide antigens:
  • RAD54 homolog B (RA54B_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q9Y620

UniProtKB/Swiss-Prot:

RA54B_HUMAN :
  • Belongs to the SNF2/RAD54 helicase family.
Family:
  • Belongs to the SNF2/RAD54 helicase family.
genes like me logo Genes that share domains with RAD54B: view

Function for RAD54B Gene

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  6. Cell Lines for research

Molecular function for RAD54B Gene

UniProtKB/Swiss-Prot Function:
Involved in DNA repair and mitotic recombination. May play an active role in recombination processes in concert with other members of the RAD52 epistasis group.
GENATLAS Biochemistry:
yeast (S cerevisiae) RAD54 homolog,recombination gene,highly expressed in testis and spleen,homozygously mutated in primary lymphoma and colon cancer

Enzyme Numbers (IUBMB) for RAD54B Gene

Phenotypes From GWAS Catalog for RAD54B Gene

Gene Ontology (GO) - Molecular Function for RAD54B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000166 nucleotide binding IEA --
GO:0003677 DNA binding IEA --
GO:0003678 DNA helicase activity TAS 10362364
GO:0003724 RNA helicase activity TAS 10362364
GO:0004386 helicase activity IEA --
genes like me logo Genes that share ontologies with RAD54B: view
genes like me logo Genes that share phenotypes with RAD54B: view

Human Phenotype Ontology for RAD54B Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for RAD54B Gene

MGI Knock Outs for RAD54B:

Animal Models for research

miRNA for RAD54B Gene

miRTarBase miRNAs that target RAD54B

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for RAD54B

No data available for Transcription Factor Targets and HOMER Transcription for RAD54B Gene

Localization for RAD54B Gene

Subcellular locations from UniProtKB/Swiss-Prot for RAD54B Gene

Nucleus.

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 RAD54B gene
Compartment Confidence
nucleus 4
cytosol 2
plasma membrane 1
extracellular 1
cytoskeleton 1
mitochondrion 1

Gene Ontology (GO) - Cellular Components for RAD54B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IBA 21873635
genes like me logo Genes that share ontologies with RAD54B: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for RAD54B Gene

Pathways & Interactions for RAD54B Gene

genes like me logo Genes that share pathways with RAD54B: view

Pathways by source for RAD54B Gene

1 BioSystems pathway for RAD54B Gene
1 KEGG pathway for RAD54B Gene

Gene Ontology (GO) - Biological Process for RAD54B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000724 double-strand break repair via homologous recombination IDA 16428451
GO:0006281 DNA repair IEA --
GO:0006312 mitotic recombination TAS 10362364
GO:0006974 cellular response to DNA damage stimulus IEA --
GO:0007131 reciprocal meiotic recombination TAS,IBA 21873635
genes like me logo Genes that share ontologies with RAD54B: view

No data available for SIGNOR curated interactions for RAD54B Gene

Drugs & Compounds for RAD54B Gene

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No Compound Related Data Available

Transcripts for RAD54B Gene

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mRNA/cDNA for RAD54B Gene

5 REFSEQ mRNAs :
12 NCBI additional mRNA sequence :
8 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 RAD54B

Alternative Splicing Database (ASD) splice patterns (SP) for RAD54B Gene

ExUns: 1a · 1b ^ 2 ^ 3 ^ 4a · 4b ^ 5 ^ 6 ^ 7 ^ 8a · 8b ^ 9a · 9b ^ 10 ^ 11a · 11b ^ 12a · 12b ^ 13a · 13b
SP1: - -
SP2: - -
SP3:
SP4:
SP5: -
SP6:

Relevant External Links for RAD54B Gene

GeneLoc Exon Structure for
RAD54B

Expression for RAD54B Gene

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mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for RAD54B Gene

mRNA expression in normal human tissues for RAD54B Gene
mRNA expression by GTEx for RAD54B GenemRNA expression by BioGPS for RAD54B Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for RAD54B Gene



Transcriptomic regulation report from SPP (The Signaling Pathways Project) for RAD54B

SOURCE GeneReport for Unigene cluster for RAD54B Gene:

Hs.744229

mRNA Expression by UniProt/SwissProt for RAD54B Gene:

Q9Y620-RA54B_HUMAN
Tissue specificity: Abundantly expressed in testis and spleen. Relatively low levels observed in thymus, prostate, ovary and colon.

Phenotype-based relationships between genes and organs from Gene ORGANizer for RAD54B Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • digestive
  • immune
  • reproductive
  • urinary
Regions:
Abdomen:
  • intestine
  • kidney
  • large intestine
  • stomach
Pelvis:
  • anus
  • rectum
  • ureter
  • urethra
  • urinary bladder
  • uterus
General:
  • blood
  • white blood cell
genes like me logo Genes that share expression patterns with RAD54B: view

Primer products for research

No data available for mRNA differential expression in normal tissues , Protein differential expression in normal tissues , Protein tissue co-expression partners and Evidence on tissue expression from TISSUES for RAD54B Gene

Orthologs for RAD54B Gene

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

Orthologs for RAD54B Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
 Mammalia RAD54B 30 31
  • 99.63 (n)
 OneToOne
Dog
(Canis familiaris)
 Mammalia RAD54B 30 31
  • 89.66 (n)
 OneToOne
Cow
(Bos Taurus)
 Mammalia RAD54B 30 31
  • 89.46 (n)
 OneToOne
Mouse
(Mus musculus)
 Mammalia Rad54b 30 17 31
  • 83.07 (n)
 OneToOne
Rat
(Rattus norvegicus)
 Mammalia Rad54b 30
  • 81.35 (n)
Oppossum
(Monodelphis domestica)
 Mammalia RAD54B 31
  • 77 (a)
 OneToOne
Platypus
(Ornithorhynchus anatinus)
 Mammalia RAD54B 31
  • 77 (a)
 OneToOne
Chicken
(Gallus gallus)
 Aves RAD54B 30 31
  • 72.2 (n)
 OneToOne
Lizard
(Anolis carolinensis)
 Reptilia RAD54B 31
  • 71 (a)
 OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
 Amphibia rad54b 30
  • 65.83 (n)
Str.5565 30
African clawed frog
(Xenopus laevis)
 Amphibia Xl.32066 30
Zebrafish
(Danio rerio)
 Actinopterygii rad54b 30 31
  • 57.95 (n)
 OneToOne
African malaria mosquito
(Anopheles gambiae)
 Insecta AgaP_AGAP006945 30
  • 48.5 (n)
Worm
(Caenorhabditis elegans)
 Secernentea Y116A8C.13 32
  • 41 (a)
K. Lactis Yeast
(Kluyveromyces lactis)
 Saccharomycetes KLLA0F11814g 30
  • 55.53 (n)
Baker's yeast
(Saccharomyces cerevisiae)
 Saccharomycetes RDH54 30 33
  • 49.37 (n)
RAD54 31
  • 33 (a)
 OneToMany
A. gosspyii yeast
(Eremothecium gossypii)
 Saccharomycetes AGOS_AGL212W 30
  • 48.74 (n)
Fission Yeast
(Schizosaccharomyces pombe)
 Schizosaccharomycetes rdh54 30
  • 49.9 (n)
Species where no ortholog for RAD54B was found in the sources mined by GeneCards:
  • 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)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fruit Fly (Drosophila melanogaster)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • 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 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 RAD54B Gene

ENSEMBL:
Gene Tree for RAD54B (if available)
TreeFam:
Gene Tree for RAD54B (if available)
Aminode:
Evolutionary constrained regions (ECRs) for RAD54B: view image

Paralogs for RAD54B Gene

Paralogs for RAD54B Gene

(2) SIMAP similar genes for RAD54B Gene using alignment to 4 proteins:

  • RA54B_HUMAN
  • E5RHN9_HUMAN
  • E5RI14_HUMAN
  • E5RJF7_HUMAN
genes like me logo Genes that share paralogs with RAD54B: view

Variants for RAD54B Gene

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Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for RAD54B Gene

SNP ID Clinical significance and condition Chr 08 pos Variation AA Info Type
870770 Likely Pathogenic: not provided 94,393,847(-) CA/C
NM_012415.3(RAD54B):c.1413del (p.Phe471fs) 		FRAMESHIFT
rs113276250 Benign: not provided 94,407,566(-) C/T
NM_012415.3(RAD54B):c.654G>A (p.Ser218=) 		SYNONYMOUS
rs114216685 Benign: Non-Hodgkin lymphoma; not provided. A non-Hodgkin lymphoma sample 94,391,640(-) T/Cp.Asn593Ser
NM_012415.3(RAD54B):c.1778A>G (p.Asn593Ser) 		MISSENSE
rs114429444 Likely Benign: not provided 94,378,363(-) T/C
NM_012415.3(RAD54B):c.2332A>G (p.Ile778Val) 		MISSENSE
rs116312454 Likely Benign: not provided 94,372,264(-) T/C
NM_012415.3(RAD54B):c.2639A>G (p.Asp880Gly) 		MISSENSE

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for RAD54B 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 RAD54B Gene

Variant ID Type Subtype PubMed ID
dgv2104e212 CNV loss 25503493
dgv2105e212 CNV loss 25503493
esv3572904 CNV loss 25503493
esv3572905 CNV loss 25503493
esv3572908 CNV loss 25503493
esv3618077 CNV loss 21293372
nsv1031480 CNV gain 25217958
nsv611749 CNV loss 21841781
nsv6313 CNV insertion 18451855
nsv831401 CNV loss 17160897

Variation tolerance for RAD54B Gene

Residual Variation Intolerance Score: 68.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.05; 50.50% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for RAD54B Gene

Human Gene Mutation Database (HGMD)
RAD54B
SNPedia medical, phenotypic, and genealogical associations of SNPs for
RAD54B

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for RAD54B Gene

Disorders for RAD54B Gene

MalaCards: The human disease database

(4) MalaCards diseases for RAD54B Gene - From: OMI, CVR, GTR, COP, and GCD

Disorder Aliases PubMed IDs
lymphoma, non-hodgkin, familial
  • non-hodgkin lymphoma; nhl
colorectal cancer
  • crc
lymphoma
  • lymphoid cancer
lynch syndrome
  • coca 1
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for RAD54B

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
genes like me logo Genes that share disorders with RAD54B: view

No data available for UniProtKB/Swiss-Prot and Genatlas for RAD54B Gene

Publications for RAD54B Gene

  1. Mutations of a novel human RAD54 homologue, RAD54B, in primary cancer. (PMID: 10362364) Hiramoto T … Kamiya K (Oncogene 1999) 2 3 4 23 74
  2. A novel human rad54 homologue, Rad54B, associates with Rad51. (PMID: 10851248) Tanaka K … Miyagawa K (The Journal of biological chemistry 2000) 2 3 4 23
  3. Human Rad54B is a double-stranded DNA-dependent ATPase and has biochemical properties different from its structural homolog in yeast, Tid1/Rdh54. (PMID: 11884632) Tanaka K … Miyagawa K (Nucleic acids research 2002) 3 4 23
  4. Variation within DNA repair pathway genes and risk of multiple sclerosis. (PMID: 20522537) Briggs FB … International Multiple Sclerosis Genetics Consortium (American journal of epidemiology 2010) 3 41
  5. Gamma-radiation sensitivity and polymorphisms in RAD51L1 modulate glioma risk. (PMID: 20610542) Liu Y … Bondy ML (Carcinogenesis 2010) 3 41

ExternalLinks

View latest publications for RAD54B gene in Mastermind

Products for RAD54B Gene

Sources for RAD54B Gene