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

Gene ID: 5887, updated on 3-Mar-2019

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
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 Apr 4 07:08:55 2018

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 
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_002874.5NP_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)
    AL137852, D21090, DC404422
    Consensus CDS
    CCDS6769.1
    UniProtKB/Swiss-Prot
    P54727
    Related
    ENSP00000350708.3, ENST00000358015.7
    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

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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