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    RAD23B RAD23 homolog B, nucleotide excision repair protein [ Homo sapiens (human) ]

    Gene ID: 5887, updated on 7-Oct-2018

    Summary

    Official Symbol
    RAD23Bprovided by HGNC
    Official Full Name
    RAD23 homolog B, nucleotide excision repair proteinprovided by HGNC
    Primary source
    HGNC:HGNC:9813
    See related
    Ensembl:ENSG00000119318 MIM:600062; Vega:OTTHUMG00000020446
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    P58; HR23B; HHR23B
    Summary
    The protein encoded by this gene is one of two human homologs of Saccharomyces cerevisiae Rad23, a protein involved in the nucleotide excision repair (NER). This protein was found to be a component of the protein complex that specifically complements the NER defect of xeroderma pigmentosum group C (XP-c) cell extracts in vitro. This protein was also shown to interact with, and elevate the nucleotide excision activity of 3-methyladenine-DNA glycosylase (MPG), which suggested a role in DNA damage recognition in base excision repair. This protein contains an N-terminal ubiquitin-like domain, which was reported to interact with 26S proteasome, and thus this protein may be involved in the ubiquitin mediated proteolytic pathway in cells. Alternative splicing results in multiple transcript variants encoding distinct isoforms. [provided by RefSeq, Sep 2011]
    Expression
    Ubiquitous expression in liver (RPKM 44.7), fat (RPKM 43.3) and 25 other tissues See more
    Orthologs

    Genomic context

    See RAD23B in Genome Data Viewer
    Location:
    9q31.2
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    109 current GRCh38.p12 (GCF_000001405.38) 9 NC_000009.12 (107283236..107332194)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (110045517..110094475)

    Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene importin subunit alpha-1 pseudogene Neighboring gene uncharacterized LOC107987110 Neighboring gene translation initiation factor IF-2-like Neighboring gene uncharacterized LOC107987111 Neighboring gene long intergenic non-protein coding RNA 1509 Neighboring gene high mobility group nucleosomal binding domain 2 pseudogene 32

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Jun 15 11:32:44 2016

    Bibliography

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    Phenotypes

    NHGRI GWAS Catalog

    Description
    Genome-wide association study in Chinese men identifies two new prostate cancer risk loci at 9q31.2 and 19q13.4.
    NHGRI GWA Catalog
    Genome-wide association study of anthropometric traits and evidence of interactions with age and study year in Filipino women.
    NHGRI GWA Catalog
    Novel breast cancer susceptibility locus at 9q31.2: results of a genome-wide association study.
    NHGRI GWA Catalog

    HIV-1 interactions

    Replication interactions

    Interaction Pubs
    Screening in Jurkat T-cells with a short-hairpin-RNA (shRNA) library identifies RAD23 homolog B (RAD23B) is important for HIV-1 replication PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from BioSystems

    • Asparagine N-linked glycosylation, organism-specific biosystem (from REACTOME)
      Asparagine N-linked glycosylation, organism-specific biosystemN-linked glycosylation is the most important form of post-translational modification for proteins synthesized and folded in the Endoplasmic Reticulum (Stanley et al. 2009). An early study in 1999 rev...
    • DNA Damage Recognition in GG-NER, organism-specific biosystem (from REACTOME)
      DNA Damage Recognition in GG-NER, organism-specific biosystemIn global genome nucleotide excision repair (GG-NER), the DNA damage is recognized by two protein complexes. The first complex consists of XPC, RAD23A or RAD23B, and CETN2. This complex probes the DN...
    • DNA Repair, organism-specific biosystem (from REACTOME)
      DNA Repair, organism-specific biosystemDNA repair is a phenomenal multi-enzyme, multi-pathway system required to ensure the integrity of the cellular genome. Living organisms are constantly exposed to harmful metabolic by-products, enviro...
    • Deubiquitination, organism-specific biosystem (from REACTOME)
      Deubiquitination, organism-specific biosystemUbiquitination, the modification of proteins by the covalent attachment of ubiquitin (Ub), is a key regulatory mechanism for many many cellular processes, including protein degradation by the 26S pro...
    • Formation of Incision Complex in GG-NER, organism-specific biosystem (from REACTOME)
      Formation of Incision Complex in GG-NER, organism-specific biosystemAfter the XPC complex and the UV-DDB complex bind damaged DNA, a basal transcription factor TFIIH is recruited to the nucleotide excision repair (NER) site (Volker et al. 2001, Riedl et al. 2003). DN...
    • Global Genome Nucleotide Excision Repair (GG-NER), organism-specific biosystem (from REACTOME)
      Global Genome Nucleotide Excision Repair (GG-NER), organism-specific biosystemThe DNA damage in GG-NER is recognized by the joint action of two protein complexes. The first complex is composed of XPC, RAD23A or RAD23B and CETN2. The second complex, known as the UV-DDB complex,...
    • Josephin domain DUBs, organism-specific biosystem (from REACTOME)
      Josephin domain DUBs, organism-specific biosystemThe Josephin domain is present in four human DUBs: Ataxin-3 (ATXN3), ATXN3L, Josephin-1 (JOSD1) and JOSD2. All have been shown to possess DUB activity (Tzveltkov & Breuer 2007, Weeks et al. 2011). Jo...
    • Metabolism of proteins, organism-specific biosystem (from REACTOME)
      Metabolism of proteins, organism-specific biosystemProtein metabolism comprises the pathways of translation, post-translational modification and protein folding.
    • N-glycan trimming in the ER and Calnexin/Calreticulin cycle, organism-specific biosystem (from REACTOME)
      N-glycan trimming in the ER and Calnexin/Calreticulin cycle, organism-specific biosystemAfter being synthesized in the ER membrane the 14-sugars lipid-linked oligosaccharide is co-translationally transferred to an unfolded protein, as described in the previous steps. After this point th...
    • Nucleotide Excision Repair, organism-specific biosystem (from REACTOME)
      Nucleotide Excision Repair, organism-specific biosystemNucleotide excision repair (NER) was first described in the model organism E. coli in the early 1960s as a process whereby bulky base damage is enzymatically removed from DNA, facilitating the recove...
    • Nucleotide excision repair, organism-specific biosystem (from KEGG)
      Nucleotide excision repair, organism-specific biosystemNucleotide excision repair (NER) is a mechanism to recognize and repair bulky DNA damage caused by compounds, environmental carcinogens, and exposure to UV-light. In humans hereditary defects in the ...
    • Nucleotide excision repair, conserved biosystem (from KEGG)
      Nucleotide excision repair, conserved biosystemNucleotide excision repair (NER) is a mechanism to recognize and repair bulky DNA damage caused by compounds, environmental carcinogens, and exposure to UV-light. In humans hereditary defects in the ...
    • Post-translational protein modification, organism-specific biosystem (from REACTOME)
      Post-translational protein modification, organism-specific biosystemAfter translation, many newly formed proteins undergo further covalent modifications that alter their functional properties and that are essentially irreversible under physiological conditions in the...
    • Protein processing in endoplasmic reticulum, organism-specific biosystem (from KEGG)
      Protein processing in endoplasmic reticulum, organism-specific biosystemThe endoplasmic reticulum (ER) is a subcellular organelle where proteins are folded with the help of lumenal chaperones. Newly synthesized peptides enter the ER via the sec61 pore and are glycosylate...
    • Protein processing in endoplasmic reticulum, conserved biosystem (from KEGG)
      Protein processing in endoplasmic reticulum, conserved biosystemThe endoplasmic reticulum (ER) is a subcellular organelle where proteins are folded with the help of lumenal chaperones. Newly synthesized peptides enter the ER via the sec61 pore and are glycosylate...

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    damaged DNA binding IEA
    Inferred from Electronic Annotation
    more info
     
    polyubiquitin modification-dependent protein binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    polyubiquitin modification-dependent protein binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    proteasome binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    single-stranded DNA binding TAS
    Traceable Author Statement
    more info
    PubMed 
    ubiquitin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    Process Evidence Code Pubs
    embryonic organ development IEA
    Inferred from Electronic Annotation
    more info
     
    global genome nucleotide-excision repair TAS
    Traceable Author Statement
    more info
     
    nucleotide-excision repair IDA
    Inferred from Direct Assay
    more info
    PubMed 
    nucleotide-excision repair, DNA damage recognition IDA
    Inferred from Direct Assay
    more info
    PubMed 
    nucleotide-excision repair, DNA damage recognition TAS
    Traceable Author Statement
    more info
     
    nucleotide-excision repair, preincision complex assembly TAS
    Traceable Author Statement
    more info
     
    proteasome-mediated ubiquitin-dependent protein catabolic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    protein deubiquitination TAS
    Traceable Author Statement
    more info
     
    protein folding TAS
    Traceable Author Statement
    more info
     
    regulation of proteasomal ubiquitin-dependent protein catabolic process IDA
    Inferred from Direct Assay
    more info
    PubMed 
    spermatogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    XPC complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    cytosol IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    cytosol IDA
    Inferred from Direct Assay
    more info
     
    cytosol TAS
    Traceable Author Statement
    more info
     
    nucleoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    nucleoplasm IDA
    Inferred from Direct Assay
    more info
     
    nucleoplasm TAS
    Traceable Author Statement
    more info
     
    nucleus TAS
    Traceable Author Statement
    more info
    PubMed 
    proteasome complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 

    General protein information

    Preferred Names
    UV excision repair protein RAD23 homolog B
    Names
    RAD23, yeast homolog of, B
    XP-C repair complementing complex 58 kDa
    XP-C repair complementing protein
    XP-C repair-complementing complex 58 kDa protein

    NCBI Reference Sequences (RefSeq)

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001244713.1NP_001231642.1  UV excision repair protein RAD23 homolog B isoform 2

      See identical proteins and their annotated locations for NP_001231642.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) has a distinct 5' UTR and 5' CDS, compared to isoform (1), which results in an isoform (2) with a shorter and distinct N-terminus, compared to isoform 1.
      Source sequence(s)
      AI375313, AK297986, AL137852, BI460482
      UniProtKB/TrEMBL
      B7Z4W4
      Conserved Domains (6) summary
      cd14377
      Location:168207
      UBA1_Rad23; UBA1 domain of Rad23 proteins found in metazoa
      cd14428
      Location:344388
      UBA2_HR23B; UBA2 domain of UV excision repair protein RAD23 homolog B (HR23B) found in vertebrates
      TIGR00601
      Location:2386
      rad23; UV excision repair protein Rad23
      pfam09280
      Location:255310
      XPC-binding; XPC-binding domain
      pfam12238
      Location:106149
      MSA-2c; Merozoite surface antigen 2c
      cl00155
      Location:257
      UBQ; Ubiquitin-like proteins
    2. NM_001244724.1NP_001231653.1  UV excision repair protein RAD23 homolog B isoform 3

      See identical proteins and their annotated locations for NP_001231653.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR and coding sequence compared to isoform (1). The resulting isoform (3) is shorter at the N-terminus compared to isoform 1.
      Source sequence(s)
      AI375313, AK297986, AL137852, AY313777
      Consensus CDS
      CCDS59138.1
      UniProtKB/Swiss-Prot
      P54727
      UniProtKB/TrEMBL
      B7Z4W4
      Related
      ENSP00000405623.2, ENST00000416373.6
      Conserved Domains (4) summary
      cd14377
      Location:117156
      UBA1_Rad23; UBA1 domain of Rad23 proteins found in metazoa
      cd14428
      Location:293337
      UBA2_HR23B; UBA2 domain of UV excision repair protein RAD23 homolog B (HR23B) found in vertebrates
      pfam09280
      Location:204259
      XPC-binding; XPC-binding domain
      pfam12238
      Location:5598
      MSA-2c; Merozoite surface antigen 2c
    3. NM_002874.4NP_002865.1  UV excision repair protein RAD23 homolog B isoform 1

      See identical proteins and their annotated locations for NP_002865.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AI375313, AL137852, D21090, DC404422
      Consensus CDS
      CCDS6769.1
      UniProtKB/Swiss-Prot
      P54727
      Related
      ENSP00000350708.3, OTTHUMP00000021857, ENST00000358015.7, OTTHUMT00000053548
      Conserved Domains (6) summary
      cd01805
      Location:178
      RAD23_N; Ubiquitin-like domain of RAD23
      cd14377
      Location:189228
      UBA1_Rad23; UBA1 domain of Rad23 proteins found in metazoa
      cd14428
      Location:365409
      UBA2_HR23B; UBA2 domain of UV excision repair protein RAD23 homolog B (HR23B) found in vertebrates
      TIGR00601
      Location:1407
      rad23; UV excision repair protein Rad23
      pfam09280
      Location:276331
      XPC-binding; XPC-binding domain
      pfam12238
      Location:127170
      MSA-2c; Merozoite surface antigen 2c

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p12 Primary Assembly

    Genomic

    1. NC_000009.12 Reference GRCh38.p12 Primary Assembly

      Range
      107283236..107332194
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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