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    UVSSA UV stimulated scaffold protein A [ Homo sapiens (human) ]

    Gene ID: 57654, updated on 2-Nov-2024

    Summary

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    Official Symbol
    UVSSAprovided by HGNC
    Official Full Name
    UV stimulated scaffold protein Aprovided by HGNC
    Primary source
    HGNC:HGNC:29304
    See related
    Ensembl:ENSG00000163945 MIM:614632; AllianceGenome:HGNC:29304
    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
    UVSS3; KIAA1530
    Summary
    The protein encoded by this gene appears to be involved in ubiquitination and dephosphorylation of RNA polymerase II subunits that stall after UV irradiation. The encoded protein interacts with several members of the nucleotide excision repair complex, and is thought to be involved in the transcription-coupled nucleotide excision repair (TC-NER) pathway to help remove lesions in the DNA that block transcription. Defects in this gene can cause UV-sensitive syndrome 3. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2015]
    Expression
    Ubiquitous expression in testis (RPKM 2.2), spleen (RPKM 1.5) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See UVSSA in Genome Data Viewer
    Location:
    4p16.3
    Exon count:
    26
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (1342011..1395989)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (1340627..1394173)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (1340996..1381837)

    Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105374347 Neighboring gene uncharacterized LOC105374346 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15126 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15127 Neighboring gene ReSE screen-validated silencer GRCh37_chr4:1285078-1285260 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:1288606-1289569 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:1291085-1291798 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:1301806-1302703 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:1303601-1304498 Neighboring gene macrophage erythroblast attacher, E3 ubiquitin ligase Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:1311232-1311732 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr4:1317288-1318487 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr4:1319662-1320861 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:1332970-1333488 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:1338713-1339236 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:1339237-1339759 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15128 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15129 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15130 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21153 Neighboring gene ReSE screen-validated silencer GRCh37_chr4:1344739-1344907 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:1353821-1354342 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:1354343-1354864 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr4:1388225-1389424 Neighboring gene Sharpr-MPRA regulatory region 8056 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:1399591-1400181 Neighboring gene Sharpr-MPRA regulatory region 3424 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:1408939-1409612 Neighboring gene NK1 homeobox 1 Neighboring gene uncharacterized LOC105374348

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues 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

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    Related articles in PubMed

    1. Transcription coupled DNA repair protein UVSSA binds to DNA and RNA: Mapping of nucleic acid interaction sites on human UVSSA. Mistry H, et al. Arch Biochem Biophys, 2023 Feb. PMID 36623745
    2. [Molecular cloning and characterisation of UVSSA, the responsible gene for UV-sensitive syndrome]. Ogi T, et al. Seikagaku, 2013 Mar. PMID 23631307
    3. UV-sensitive syndrome: Whole exome sequencing identified a nonsense mutation in the gene UVSSA in two consanguineous pedigrees from Pakistan. Ijaz A, et al. J Dermatol Sci, 2019 Sep. PMID 31421932
    4. Structural characterization of transcription-coupled repair protein UVSSA and its interaction with TFIIH protein. Mistry H, et al. Int J Biol Macromol, 2023 Aug 30. PMID 37442507
    5. Mutations in UVSSA cause UV-sensitive syndrome and impair RNA polymerase IIo processing in transcription-coupled nucleotide-excision repair. Nakazawa Y, et al. Nat Genet, 2012 May. PMID 22466610

    See all (33) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Structural characterization of transcription-coupled repair protein UVSSA and its interaction with TFIIH protein.
      Title: Structural characterization of transcription-coupled repair protein UVSSA and its interaction with TFIIH protein.
    2. Transcription coupled DNA repair protein UVSSA binds to DNA and RNA: Mapping of nucleic acid interaction sites on human UVSSA.
      Title: Transcription coupled DNA repair protein UVSSA binds to DNA and RNA: Mapping of nucleic acid interaction sites on human UVSSA.
    3. The UVSSA protein is part of a genome integrity homeostasis network with links to transcription-coupled DNA repair and ATM signaling.
      Title: The UVSSA protein is part of a genome integrity homeostasis network with links to transcription-coupled DNA repair and ATM signaling.
    4. The UVSSA complex alleviates MYC-driven transcription stress.
      Title: The UVSSA complex alleviates MYC-driven transcription stress.
    5. USP7-mediated deubiquitination differentially regulates CSB but not UVSSA upon UV radiation-induced DNA damage.
      Title: USP7-mediated deubiquitination differentially regulates CSB but not UVSSA upon UV radiation-induced DNA damage.
    6. TCR is initiated by RNAPIIo-bound CSB, which recruits CSA through a newly identified CSA-interaction motif (CIM); once recruited, CSA facilitates the association of UVSSA with stalled RNAPIIo; in addition, UVSSA is the key factor that recruits the TFIIH complex in a manner that is stimulated by CSB and CSA
      Title: The cooperative action of CSB, CSA, and UVSSA target TFIIH to DNA damage-stalled RNA polymerase II.
    7. Study reports nine UV-sensitive syndrome cases from two Pakistani families with a novel homozygous nonsense mutation, (c.1040 G > A [p.(Trp347*)]) in exon 6 of the UVSSA gene.
      Title: UV-sensitive syndrome: Whole exome sequencing identified a nonsense mutation in the gene UVSSA in two consanguineous pedigrees from Pakistan.
    8. FACT subunit Spt16 controls UVSSA recruitment to lesion-stalled RNA Pol II and stimulates transcription-coupled nucleotide excision repair.
      Title: FACT subunit Spt16 controls UVSSA recruitment to lesion-stalled RNA Pol II and stimulates TC-NER.
    9. UVSSA is mono-ubiquitinated in vitro. Lys(414) is the target of ubiquitination. Lys(414) was also modified by poly-ubiquitin chains in vivo. The substitution of Lys(414) by Arg of UVSSA inhibited its degradation and thereby suppressed the deficiency in transcription-coupled nucleotide excision repair.
      Title: Inhibition of UVSSA ubiquitination suppresses transcription-coupled nucleotide excision repair deficiency caused by dissociation from USP7.
    10. Data suggest that a common TFIIH subunit p62 recruitment mechanism is shared by UV-stimulated scaffold protein A (UVSSA) in transcription-coupled repair (TCR) and xeroderma pigmentosum, complementation group C protein (XPC) in global genome repair (GGR).
      Title: Common TFIIH recruitment mechanism in global genome and transcription-coupled repair subpathways.
    Submit: New GeneRIF Correction See all GeneRIFs (17)

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Associated conditions

    Description Tests
    UV-sensitive syndrome 3
    MedGen: C3553328 OMIM: 614640 GeneReviews: Not available
    		Compare labs

    EBI GWAS Catalog

    Description
    Joint influence of small-effect genetic variants on human longevity.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • KIAA1530, MGC117169, AC078852.1

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables RNA polymerase II complex binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables RNA polymerase II complex binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables RNA polymerase II complex binding IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in protein ubiquitination IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in response to UV IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in response to UV IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in transcription-coupled nucleotide-excision repair IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in transcription-coupled nucleotide-excision repair IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in chromosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in chromosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
    		  

    General protein information

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    Preferred Names
    UV-stimulated scaffold protein A

    NCBI Reference Sequences (RefSeq)

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    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.

    Genomic

    1. NG_032753.2 RefSeqGene

      Range
      10199..51040
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001317934.2 → NP_001304863.1  UV-stimulated scaffold protein A

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1, 2 and 3 encode the same protein.
      Source sequence(s)
      AC078852, AL390128, BC021930, BC110331
      Consensus CDS
      CCDS33938.1
      UniProtKB/Swiss-Prot
      A8K9E6, B2RU11, Q2YD98, Q8WTX4, Q9P1Z8
      UniProtKB/TrEMBL
      A0A7I2V554
      Related
      ENSP00000425130.1, ENST00000511216.6
      Conserved Domains (1) summary
      pfam09740
      Location:498 → 601
      DUF2043; Uncharacterized conserved protein (DUF2043)

    2. NM_001317935.2 → NP_001304864.1  UV-stimulated scaffold protein A

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. Variants 1, 2 and 3 encode the same protein.
      Source sequence(s)
      AC078852, AL390128, BC021930, BC110331, HY104489
      Consensus CDS
      CCDS33938.1
      UniProtKB/Swiss-Prot
      A8K9E6, B2RU11, Q2YD98, Q8WTX4, Q9P1Z8
      UniProtKB/TrEMBL
      A0A7I2V554
      Related
      ENSP00000421741.1, ENST00000507531.5
      Conserved Domains (1) summary
      pfam09740
      Location:498 → 601
      DUF2043; Uncharacterized conserved protein (DUF2043)

    3. NM_020894.4 → NP_065945.2  UV-stimulated scaffold protein A

      See identical proteins and their annotated locations for NP_065945.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript. Variants 1, 2 and 3 encode the same protein.
      Source sequence(s)
      AB040963, AC078852, AL390128, BC021930, BC110331, EL735271
      Consensus CDS
      CCDS33938.1
      UniProtKB/Swiss-Prot
      A8K9E6, B2RU11, Q2YD98, Q8WTX4, Q9P1Z8
      UniProtKB/TrEMBL
      A0A7I2V554
      Related
      ENSP00000374501.4, ENST00000389851.10
      Conserved Domains (1) summary
      pfam09740
      Location:498 → 601
      DUF2043; Uncharacterized conserved protein (DUF2043)

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000004.12 Reference GRCh38.p14 Primary Assembly

      Range
      1342011..1395989
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017008493.3 → XP_016863982.1  UV-stimulated scaffold protein A isoform X2

      UniProtKB/Swiss-Prot
      A8K9E6, B2RU11, Q2YD98, Q8WTX4, Q9P1Z8
      UniProtKB/TrEMBL
      A0A7I2V554
      Related
      ENSP00000503948.1, ENST00000677286.1
      Conserved Domains (1) summary
      pfam09740
      Location:498 → 601
      DUF2043; Uncharacterized conserved protein (DUF2043)

    2. XM_047416025.1 → XP_047271981.1  UV-stimulated scaffold protein A isoform X1

    3. XM_047416026.1 → XP_047271982.1  UV-stimulated scaffold protein A isoform X1

      Related
      ENSP00000503485.1, ENST00000679242.1

    4. XM_017008498.3 → XP_016863987.1  UV-stimulated scaffold protein A isoform X7

    5. XM_047416028.1 → XP_047271984.1  UV-stimulated scaffold protein A isoform X9

      UniProtKB/TrEMBL
      A0A7I2V4K1
      Related
      ENSP00000504075.1, ENST00000678994.1

    6. XM_017008496.2 → XP_016863985.2  UV-stimulated scaffold protein A isoform X4

    7. XM_017008497.3 → XP_016863986.2  UV-stimulated scaffold protein A isoform X6

    8. XM_017008499.2 → XP_016863988.1  UV-stimulated scaffold protein A isoform X8

    9. XM_017008494.3 → XP_016863983.1  UV-stimulated scaffold protein A isoform X2

      UniProtKB/Swiss-Prot
      A8K9E6, B2RU11, Q2YD98, Q8WTX4, Q9P1Z8
      UniProtKB/TrEMBL
      A0A7I2V554
      Related
      ENSP00000504268.1, ENST00000677428.1
      Conserved Domains (1) summary
      pfam09740
      Location:498 → 601
      DUF2043; Uncharacterized conserved protein (DUF2043)

    10. XM_017008490.1 → XP_016863979.1  UV-stimulated scaffold protein A isoform X2

      UniProtKB/Swiss-Prot
      A8K9E6, B2RU11, Q2YD98, Q8WTX4, Q9P1Z8
      UniProtKB/TrEMBL
      A0A7I2V554
      Related
      ENSP00000504544.1, ENST00000679192.1
      Conserved Domains (1) summary
      pfam09740
      Location:498 → 601
      DUF2043; Uncharacterized conserved protein (DUF2043)

    11. XM_017008492.3 → XP_016863981.1  UV-stimulated scaffold protein A isoform X2

      UniProtKB/Swiss-Prot
      A8K9E6, B2RU11, Q2YD98, Q8WTX4, Q9P1Z8
      UniProtKB/TrEMBL
      A0A7I2V554
      Conserved Domains (1) summary
      pfam09740
      Location:498 → 601
      DUF2043; Uncharacterized conserved protein (DUF2043)

    12. XM_047416027.1 → XP_047271983.1  UV-stimulated scaffold protein A isoform X5

    13. XM_017008495.2 → XP_016863984.1  UV-stimulated scaffold protein A isoform X3

    14. XM_024454162.2 → XP_024309930.1  UV-stimulated scaffold protein A isoform X11

      Related
      ENSP00000427701.1, ENST00000512728.5
      Conserved Domains (1) summary
      pfam09740
      Location:49 → 152
      DUF2043; Uncharacterized conserved protein (DUF2043)

    15. XM_017008500.1 → XP_016863989.1  UV-stimulated scaffold protein A isoform X10

    RNA

    1. XR_007057948.1 RNA Sequence

    2. XR_007057949.1 RNA Sequence

    3. XR_001741304.2 RNA Sequence

    4. XR_001741303.2 RNA Sequence

    5. XR_001741302.2 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060928.1 Alternate T2T-CHM13v2.0

      Range
      1340627..1394173
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054350621.1 → XP_054206596.1  UV-stimulated scaffold protein A isoform X2

      UniProtKB/Swiss-Prot
      A8K9E6, B2RU11, Q2YD98, Q8WTX4, Q9P1Z8

    2. XM_054350615.1 → XP_054206590.1  UV-stimulated scaffold protein A isoform X12

    3. XM_054350616.1 → XP_054206591.1  UV-stimulated scaffold protein A isoform X1

    4. XM_054350617.1 → XP_054206592.1  UV-stimulated scaffold protein A isoform X1

    5. XM_054350626.1 → XP_054206601.1  UV-stimulated scaffold protein A isoform X7

    6. XM_054350628.1 → XP_054206603.1  UV-stimulated scaffold protein A isoform X9

      UniProtKB/TrEMBL
      A0A7I2V4K1

    7. XM_054350623.1 → XP_054206598.1  UV-stimulated scaffold protein A isoform X4

    8. XM_054350625.1 → XP_054206600.1  UV-stimulated scaffold protein A isoform X6

    9. XM_054350627.1 → XP_054206602.1  UV-stimulated scaffold protein A isoform X8

    10. XM_054350619.1 → XP_054206594.1  UV-stimulated scaffold protein A isoform X2

      UniProtKB/Swiss-Prot
      A8K9E6, B2RU11, Q2YD98, Q8WTX4, Q9P1Z8

    11. XM_054350618.1 → XP_054206593.1  UV-stimulated scaffold protein A isoform X2

      UniProtKB/Swiss-Prot
      A8K9E6, B2RU11, Q2YD98, Q8WTX4, Q9P1Z8

    12. XM_054350620.1 → XP_054206595.1  UV-stimulated scaffold protein A isoform X2

      UniProtKB/Swiss-Prot
      A8K9E6, B2RU11, Q2YD98, Q8WTX4, Q9P1Z8

    13. XM_054350624.1 → XP_054206599.1  UV-stimulated scaffold protein A isoform X5

    14. XM_054350622.1 → XP_054206597.1  UV-stimulated scaffold protein A isoform X3

    15. XM_054350630.1 → XP_054206605.1  UV-stimulated scaffold protein A isoform X11

    16. XM_054350629.1 → XP_054206604.1  UV-stimulated scaffold protein A isoform X10

    RNA

    1. XR_008487021.1 RNA Sequence

    2. XR_008487024.1 RNA Sequence

    3. XR_008487022.1 RNA Sequence

    4. XR_008487023.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q2YD98.2 GenPept UniProtKB/Swiss-Prot:Q2YD98

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