Human Gene RAD23A (ENST00000586534.6_8) from GENCODE V47lift37
  Description: RAD23 homolog A, nucleotide excision repair protein, transcript variant 1 (from RefSeq NM_005053.4)
Gencode Transcript: ENST00000586534.6_8
Gencode Gene: ENSG00000179262.10_12
Transcript (Including UTRs)
   Position: hg19 chr19:13,056,676-13,064,456 Size: 7,781 Total Exon Count: 9 Strand: +
Coding Region
   Position: hg19 chr19:13,056,763-13,063,863 Size: 7,101 Coding Exon Count: 9 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr19:13,056,676-13,064,456)mRNA (may differ from genome)Protein (363 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: RD23A_HUMAN
DESCRIPTION: RecName: Full=UV excision repair protein RAD23 homolog A; Short=HR23A; Short=hHR23A;
FUNCTION: Multiubiquitin chain receptor involved in modulation of proteasomal degradation. Binds to 'Lys-48'-linked polyubiquitin chains in a length-dependent manner and with a lower affinity to 'Lys-63'-linked polyubiquitin chains. Proposed to be capable to bind simultaneously to the 26S proteasome and to polyubiquitinated substrates and to deliver ubiquitinated proteins to the proteasome.
FUNCTION: Involved in nucleotide excision repair and is thought to be functional equivalent for RAD23B in global genome nucleotide excision repair (GG-NER) by association with XPC. In vitro, the XPC:RAD23A dimer has NER activity. Can stabilize XPC.
FUNCTION: Involved in vpr-dependent replication of HIV-1 in non- proliferating cells and primary macrophages. Required for the association of HIV-1 vpr with the host proteasome.
SUBUNIT: Interacts with XPC; the interaction is suggesting the existence of a functional equivalent variant XPC complex. Interacts with PSMD4 and PSMC5. Interacts with ATXN3. Interacts with HIV-1 vpr. Interacts with UBQLN2.
INTERACTION: P55036:PSMD4; NbExp=2; IntAct=EBI-746453, EBI-359318; Q13501:SQSTM1; NbExp=2; IntAct=EBI-746453, EBI-307104; Q9UHD9:UBQLN2; NbExp=3; IntAct=EBI-746453, EBI-947187;
SUBCELLULAR LOCATION: Nucleus.
DOMAIN: The ubiquitin-like domain mediates interaction with ATXN3.
DOMAIN: The ubiquitin-like (UBL) and the UBA (ubiquitin- associated) domains interact intramolecularly in a highly dynamic manner, as each UBA domain competes for an overlapping UBL domain surface. Binding of ubiquitin or proteasome subunit PSMD4 disrupt the UBL-UBA domain interactions and drive RAD23A in to an open conformation.
PTM: Phosphorylated upon DNA damage, probably by ATM or ATR.
SIMILARITY: Belongs to the RAD23 family.
SIMILARITY: Contains 2 UBA domains.
SIMILARITY: Contains 1 ubiquitin-like domain.
WEB RESOURCE: Name=NIEHS-SNPs; URL="http://egp.gs.washington.edu/data/rad23a/";

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: RAD23A
Diseases sorted by gene-association score: xeroderma pigmentosum, variant type (3), hiv-1 (3)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 284.38 RPKM in Muscle - Skeletal
Total median expression: 3251.30 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -43.1087-0.495 Picture PostScript Text
3' UTR -184.30593-0.311 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR004806 - Rad23
IPR006636 - STI1_HS-bd
IPR009060 - UBA-like
IPR000449 - UBA/transl_elong_EF1B_N
IPR015940 - UBA/transl_elong_EF1B_N_euk
IPR000626 - Ubiquitin
IPR019955 - Ubiquitin_supergroup
IPR015360 - XPC-bd

Pfam Domains:
PF00240 - Ubiquitin family
PF00627 - UBA/TS-N domain
PF09280 - XPC-binding domain
PF13881 - Ubiquitin-2 like Rad60 SUMO-like
PF14560 - Ubiquitin-like domain

SCOP Domains:
101238 - XPC-binding domain
46934 - UBA-like
54236 - Ubiquitin-like

Protein Data Bank (PDB) 3-D Structure
MuPIT help
1DV0 - NMR MuPIT 1F4I - NMR 1IFY - NMR MuPIT 1OQY - NMR MuPIT 1P98 - NMR MuPIT 1P9D - NMR MuPIT 1QZE - NMR MuPIT 1TP4 - NMR MuPIT 1ZO6 - Model 2WYQ - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on P54725
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003684 damaged DNA binding
GO:0003697 single-stranded DNA binding
GO:0005515 protein binding
GO:0019900 kinase binding
GO:0031593 polyubiquitin binding
GO:1990381 ubiquitin-specific protease binding

Biological Process:
GO:0006281 DNA repair
GO:0006289 nucleotide-excision repair
GO:0006974 cellular response to DNA damage stimulus
GO:0016032 viral process
GO:0016579 protein deubiquitination
GO:0031648 protein destabilization
GO:0032434 regulation of proteasomal ubiquitin-dependent protein catabolic process
GO:0032436 positive regulation of proteasomal ubiquitin-dependent protein catabolic process
GO:0043161 proteasome-mediated ubiquitin-dependent protein catabolic process
GO:0045070 positive regulation of viral genome replication
GO:0045787 positive regulation of cell cycle

Cellular Component:
GO:0000502 proteasome complex
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005815 microtubule organizing center
GO:0005829 cytosol
GO:0032991 macromolecular complex
GO:0043231 intracellular membrane-bounded organelle


-  Descriptions from all associated GenBank mRNAs
  LP895375 - Sequence 239 from Patent EP3253886.
LF208183 - JP 2014500723-A/15686: Polycomb-Associated Non-Coding RNAs.
AK293219 - Homo sapiens cDNA FLJ51789 complete cds, highly similar to UV excision repair protein RAD23 homolog A.
AK289908 - Homo sapiens cDNA FLJ78534 complete cds, highly similar to Homo sapiens RAD23 homolog A (S. cerevisiae), mRNA.
BC088364 - Homo sapiens RAD23 homolog A (S. cerevisiae), mRNA (cDNA clone MGC:111083 IMAGE:30389208), complete cds.
BC014026 - Homo sapiens RAD23 homolog A (S. cerevisiae), mRNA (cDNA clone MGC:20578 IMAGE:4300551), complete cds.
JD462704 - Sequence 443728 from Patent EP1572962.
AB209713 - Homo sapiens mRNA for UV excision repair protein RAD23 homolog A variant protein.
D21235 - Homo sapiens mRNA for HHR23A protein, complete cds.
AB463210 - Synthetic construct DNA, clone: pF1KB5018, Homo sapiens RAD23A gene for RAD23 homolog A, without stop codon, in Flexi system.
JF432697 - Synthetic construct Homo sapiens clone IMAGE:100073936 RAD23 homolog A (S. cerevisiae) (RAD23A) gene, encodes complete protein.
KJ891974 - Synthetic construct Homo sapiens clone ccsbBroadEn_01368 RAD23A gene, encodes complete protein.
L37720 - Homo sapiens (clone 15) macronuclear mRNA.
LF373315 - JP 2014500723-A/180818: Polycomb-Associated Non-Coding RNAs.
LF373314 - JP 2014500723-A/180817: Polycomb-Associated Non-Coding RNAs.
M77024 - H.sapiens sequence isolated by cross-reactivity of ARF sera with heart cDNA library.
JD181250 - Sequence 162274 from Patent EP1572962.
LF213945 - JP 2014500723-A/21448: Polycomb-Associated Non-Coding RNAs.
JD312319 - Sequence 293343 from Patent EP1572962.
JD072611 - Sequence 53635 from Patent EP1572962.
JD390776 - Sequence 371800 from Patent EP1572962.
JD133500 - Sequence 114524 from Patent EP1572962.
JD431694 - Sequence 412718 from Patent EP1572962.
JD385107 - Sequence 366131 from Patent EP1572962.
JD494057 - Sequence 475081 from Patent EP1572962.
JD491684 - Sequence 472708 from Patent EP1572962.
LF373312 - JP 2014500723-A/180815: Polycomb-Associated Non-Coding RNAs.
MA608892 - JP 2018138019-A/180818: Polycomb-Associated Non-Coding RNAs.
MA608891 - JP 2018138019-A/180817: Polycomb-Associated Non-Coding RNAs.
MA449522 - JP 2018138019-A/21448: Polycomb-Associated Non-Coding RNAs.
MA608889 - JP 2018138019-A/180815: Polycomb-Associated Non-Coding RNAs.
MA443760 - JP 2018138019-A/15686: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein P54725 (Reactome details) participates in the following event(s):

R-HSA-5688786 ATXN3 binds RAD23
R-HSA-5691004 XPC binds RAD23 and CETN2
R-HSA-5691006 XPC:RAD23:CETN2 and UV-DDB bind distorted dsDNA site
R-HSA-6790487 RNF111 ubiquitinates SUMOylated XPC
R-HSA-6782943 UV-DDB ubiquitinates XPC
R-HSA-5696664 PARP1 or PARP2 binds DDB2 at GG-NER site
R-HSA-6790454 SUMOylation of XPC
R-HSA-5690996 ERCC2 and ERCC3 DNA helicases form an open bubble structure in damaged DNA
R-HSA-5691000 TFIIH binds GG-NER site to form a verification complex
R-HSA-5696655 PARP1 or PARP2 PARylates DDB2 and autoPARylates
R-HSA-5696670 CHD1L is recruited to GG-NER site
R-HSA-5689861 Recruitment of XPA and release of CAK
R-HSA-5689877 Josephin domain DUBs
R-HSA-5696394 DNA Damage Recognition in GG-NER
R-HSA-5688426 Deubiquitination
R-HSA-5696395 Formation of Incision Complex in GG-NER
R-HSA-5696399 Global Genome Nucleotide Excision Repair (GG-NER)
R-HSA-597592 Post-translational protein modification
R-HSA-5696398 Nucleotide Excision Repair
R-HSA-392499 Metabolism of proteins
R-HSA-73894 DNA Repair

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000586534.1, ENST00000586534.2, ENST00000586534.3, ENST00000586534.4, ENST00000586534.5, K7ESE3, NM_005053, P54725, Q59EU8, Q5M7Z1, RD23A_HUMAN, uc326qdy.1, uc326qdy.2
UCSC ID: ENST00000586534.6_8
RefSeq Accession: NM_005053.4
Protein: P54725 (aka RD23A_HUMAN or R23A_HUMAN)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.