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    SMARCAD1 SNF2 related chromatin remodeling ATPase with DExD box 1 [ Homo sapiens (human) ]

    Gene ID: 56916, updated on 2-Nov-2024

    Summary

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    Official Symbol
    SMARCAD1provided by HGNC
    Official Full Name
    SNF2 related chromatin remodeling ATPase with DExD box 1provided by HGNC
    Primary source
    HGNC:HGNC:18398
    See related
    Ensembl:ENSG00000163104 MIM:612761; AllianceGenome:HGNC:18398
    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
    HRZ; TYS; ETL1; HEL1; ADERM; BASNS
    Summary
    This gene encodes a member of the SNF subfamily of helicase proteins. The encoded protein plays a critical role in the restoration of heterochromatin organization and propagation of epigenetic patterns following DNA replication by mediating histone H3/H4 deacetylation. Mutations in this gene are associated with adermatoglyphia. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Dec 2011]
    Expression
    Ubiquitous expression in thyroid (RPKM 8.6), testis (RPKM 7.8) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SMARCAD1 in Genome Data Viewer
    Location:
    4q22.3
    Exon count:
    32
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (94207608..94291292)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (97523080..97606799)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (95128759..95212443)

    Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene SMARCAD1 divergent transcript Neighboring gene Sharpr-MPRA regulatory region 519 Neighboring gene uncharacterized LOC124900734 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:95086553-95087260 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:95087971-95088678 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21729 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:95129093-95129596 Neighboring gene high mobility group box 3 pseudogene 15 Neighboring gene hematopoietic prostaglandin D synthase Neighboring gene ribosomal protein L35a pseudogene 11

    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. Mutations in SMARCAD1 cause autosomal dominant adermatoglyphia and perturb the expression of epidermal differentiation-associated genes. Nousbeck J, et al. Br J Dermatol, 2014 Dec. PMID 24909267
    2. Huriez syndrome caused by a large deletion that abrogates the skin-specific isoform of SMARCAD1. Loh AYT, et al. Br J Dermatol, 2021 Jun. PMID 33400266
    3. SMARCAD1 in Breast Cancer Progression. Arafat K, et al. Cell Physiol Biochem, 2018. PMID 30308496
    4. SMARCAD1 Haploinsufficiency Underlies Huriez Syndrome and Associated Skin Cancer Susceptibility. Günther C, et al. J Invest Dermatol, 2018 Jun. PMID 29409814
    5. SMARCAD1 knockdown uncovers its role in breast cancer cell migration, invasion, and metastasis. Al Kubaisy E, et al. Expert Opin Ther Targets, 2016 Sep. PMID 27232533

    See all (85) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Basan syndrome in a family from South India: a novel SMARCAD1 variant.
      Title: Basan syndrome in a family from South India: a novel SMARCAD1 variant.
    2. The Conserved Chromatin Remodeler SMARCAD1 Interacts with TFIIIC and Architectural Proteins in Human and Mouse.
      Title: The Conserved Chromatin Remodeler SMARCAD1 Interacts with TFIIIC and Architectural Proteins in Human and Mouse.
    3. MSH2-MSH3 promotes DNA end resection during homologous recombination and blocks polymerase theta-mediated end-joining through interaction with SMARCAD1 and EXO1.
      Title: MSH2-MSH3 promotes DNA end resection during homologous recombination and blocks polymerase theta-mediated end-joining through interaction with SMARCAD1 and EXO1.
    4. Huriez syndrome caused by a large deletion that abrogates the skin-specific isoform of SMARCAD1.
      Title: Huriez syndrome caused by a large deletion that abrogates the skin-specific isoform of SMARCAD1.
    5. SMARCAD1-mediated recruitment of the DNA mismatch repair protein MutLalpha to MutSalpha on damaged chromatin induces apoptosis in human cells.
      Title: SMARCAD1-mediated recruitment of the DNA mismatch repair protein MutLα to MutSα on damaged chromatin induces apoptosis in human cells.
    6. A structural model of the KAP1 RBCC domain-SMARCAD1 CUE1 domain complex is presented. SMARCAD1 CUE1 has higher affinity for KAP1 RBCC than monoubiquitin. CUE1 binds an exposed coiled-coil surface on KAP1, not a domain resembling ubiquitin.
      Title: A Ubiquitin-Binding Domain that Binds a Structural Fold Distinct from that of Ubiquitin.
    7. Whole-genome sequencing on DNA from affected individuals with Huriez syndrome from three families revealed three not previously reported SNPs in SMARCAD1 gene. Western blot experiments confirmed the reduced expression of Smarcad1 protein in keratinocytes and fibroblasts from patients compared with healthy controls. Study concluded that haploinsufficiency for the skin-specific SMARCAD1 isoform accounts for Huriez syndrome.
      Title: SMARCAD1 Haploinsufficiency Underlies Huriez Syndrome and Associated Skin Cancer Susceptibility.
    8. Data suggest that retention of SMARCAD1 in nucleus is dependent on interaction of CUE1 domain of SMARCAD1 with RBCC domain of KAP1; these studies were conducted with recombinant proteins expressed in mouse embryonic stem cell line and human somatic cell line. (SMARCAD1 = ATP-dependent helicase-1; KAP1 = KRAB-interacting protein-1)
      Title: The CUE1 domain of the SNF2-like chromatin remodeler SMARCAD1 mediates its association with KRAB-associated protein 1 (KAP1) and KAP1 target genes.
    9. SMARCAD1 knockdown resulted in a significant decrease in breast cancer cell proliferation and colony formation, leading to the significant inhibition of tumour growth in both the chick embryo and nude mouse xenograft models. This inhibition was due, at least in part, to a decrease in IKKbeta expression.
      Title: SMARCAD1 in Breast Cancer Progression.
    10. identifies Smarcad1/Fun30 as an accessory factor for the mismatch repair reaction
      Title: Nucleosomes around a mismatched base pair are excluded via an Msh2-dependent reaction with the aid of SNF2 family ATPase Smarcad1.
    Submit: New GeneRIF Correction See all GeneRIFs (18)

    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
    Adermatoglyphia
    MedGen: C1852150 OMIM: 136000 GeneReviews: Not available
    		Compare labs
    Basan syndrome
    MedGen: C0406707 OMIM: 129200 GeneReviews: Not available
    		Compare labs
    Keratoderma with scleroatrophy of the extremities
    MedGen: C0406767 OMIM: 181600 GeneReviews: Not available
    		Compare labs

    EBI GWAS Catalog

    Description
    A genome-wide meta-analysis identifies novel loci associated with schizophrenia and bipolar disorder.
    EBI GWAS Catalog
    Genetic association study of QT interval highlights role for calcium signaling pathways in myocardial repolarization.
    EBI GWAS Catalog
    Identification of novel germline polymorphisms governing capecitabine sensitivity.
    EBI GWAS Catalog
    Meta-analysis identifies four new loci associated with testicular germ cell tumor.
    EBI GWAS Catalog
    Parent-of-origin-specific allelic associations among 106 genomic loci for age at menarche.
    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

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • KIAA1122, DKFZp762K2015

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables ATP binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables ATP hydrolysis activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables ATP-dependent chromatin remodeler activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables DNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables chromatin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables helicase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables nucleosome array spacer activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables ubiquitin binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in DNA double-strand break processing IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in DNA double-strand break processing IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in chromatin remodeling IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in chromatin remodeling NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in chromosome separation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in heterochromatin formation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in positive regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of DNA recombination IEP
    Inferred from Expression Pattern
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in chromatin IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in heterochromatin ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in nuclear replication fork IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in site of double-strand break IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1
    Names
    ATP-dependent helicase 1
    SWI/SNF-related, matrix-associated actin-dependent regulator of chromatin, subfamily a, containing DEAD/H box 1
    sclerotylosis
    NP_001121901.1
    NP_001121902.1
    NP_001241878.1
    NP_001362784.1
    NP_001362785.1
    NP_001362786.1
    NP_001362787.1
    NP_001362788.1
    NP_064544.2
    XP_024309922.1
    XP_047271943.1
    XP_054206523.1
    XP_054206524.1

    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_031945.1 RefSeqGene

      Range
      5258..88685
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001128429.3 → NP_001121901.1  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1 isoform a

      See identical proteins and their annotated locations for NP_001121901.1

      Status: REVIEWED

      Source sequence(s)
      AB032948, AL704040, AY008271, BC045534
      Consensus CDS
      CCDS47101.1
      UniProtKB/Swiss-Prot
      Q9H4L7
      Related
      ENSP00000415576.2, ENST00000457823.6
      Conserved Domains (2) summary
      pfam03288
      Location:318 → 362
      Pox_D5; Poxvirus D5 protein-like
      cl26465
      Location:476 → 1000
      SNF2_N; SNF2 family N-terminal domain

    2. NM_001128430.2 → NP_001121902.1  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1 isoform a

      See identical proteins and their annotated locations for NP_001121902.1

      Status: REVIEWED

      Source sequence(s)
      AB032948, AY008271, DA798320
      Consensus CDS
      CCDS47101.1
      UniProtKB/Swiss-Prot
      Q9H4L7
      Related
      ENSP00000351947.4, ENST00000359052.8
      Conserved Domains (2) summary
      pfam03288
      Location:318 → 362
      Pox_D5; Poxvirus D5 protein-like
      cl26465
      Location:476 → 1000
      SNF2_N; SNF2 family N-terminal domain

    3. NM_001254949.2 → NP_001241878.1  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1 isoform c

      See identical proteins and their annotated locations for NP_001241878.1

      Status: REVIEWED

      Source sequence(s)
      AB032948, AK301668, AL359929, AY008271
      Consensus CDS
      CCDS58914.1
      UniProtKB/Swiss-Prot
      Q9H4L7
      Related
      ENSP00000423286.1, ENST00000509418.1
      Conserved Domains (2) summary
      PLN03142
      Location:46 → 568
      PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional
      cd17998
      Location:67 → 249
      DEXHc_SMARCAD1; DEXH-box helicase domain of SMARCAD1

    4. NM_001375855.1 → NP_001362784.1  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1 isoform b

      Status: REVIEWED

      Source sequence(s)
      AC096746
      Consensus CDS
      CCDS3639.1
      UniProtKB/Swiss-Prot
      B7Z799, Q05D56, Q96SX1, Q9H017, Q9H4L7, Q9H860, Q9NPU9, Q9ULU7
      Conserved Domains (2) summary
      PLN03142
      Location:476 → 998
      PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional
      cd17998
      Location:497 → 679
      DEXHc_SMARCAD1; DEXH-box helicase domain of SMARCAD1

    5. NM_001375856.1 → NP_001362785.1  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1 isoform b

      Status: REVIEWED

      Source sequence(s)
      AC096746
      Consensus CDS
      CCDS3639.1
      UniProtKB/Swiss-Prot
      B7Z799, Q05D56, Q96SX1, Q9H017, Q9H4L7, Q9H860, Q9NPU9, Q9ULU7
      Conserved Domains (2) summary
      PLN03142
      Location:476 → 998
      PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional
      cd17998
      Location:497 → 679
      DEXHc_SMARCAD1; DEXH-box helicase domain of SMARCAD1

    6. NM_001375857.1 → NP_001362786.1  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1 isoform d

      Status: REVIEWED

      Source sequence(s)
      AC096746
      Conserved Domains (2) summary
      PLN03142
      Location:475 → 997
      PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional
      cd17998
      Location:496 → 678
      DEXHc_SMARCAD1; DEXH-box helicase domain of SMARCAD1

    7. NM_001375858.1 → NP_001362787.1  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1 isoform e

      Status: REVIEWED

      Source sequence(s)
      AC096746
      Conserved Domains (2) summary
      PLN03142
      Location:476 → 991
      PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional
      cd17998
      Location:497 → 672
      DEXHc_SMARCAD1; DEXH-box helicase domain of SMARCAD1

    8. NM_001375859.1 → NP_001362788.1  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1 isoform f

      Status: REVIEWED

      Source sequence(s)
      AC096746
      Conserved Domains (2) summary
      PLN03142
      Location:46 → 570
      PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional
      cd17998
      Location:67 → 249
      DEXHc_SMARCAD1; DEXH-box helicase domain of SMARCAD1

    9. NM_020159.5 → NP_064544.2  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1 isoform b

      See identical proteins and their annotated locations for NP_064544.2

      Status: REVIEWED

      Source sequence(s)
      AB032948, AL704040, AY008271
      Consensus CDS
      CCDS3639.1
      UniProtKB/Swiss-Prot
      B7Z799, Q05D56, Q96SX1, Q9H017, Q9H4L7, Q9H860, Q9NPU9, Q9ULU7
      Related
      ENSP00000346217.4, ENST00000354268.9
      Conserved Domains (2) summary
      PLN03142
      Location:476 → 998
      PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional
      cd17998
      Location:497 → 679
      DEXHc_SMARCAD1; DEXH-box helicase domain of SMARCAD1

    RNA

    1. NR_045644.2 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC096746

    2. NR_164722.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC096746

    3. NR_164723.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC096746

    4. NR_164724.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC096746

    5. NR_164725.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC096746

    6. NR_164726.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC096746

    7. NR_164727.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC096746

    8. NR_164728.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC096746

    9. NR_164729.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC096746

    10. NR_164730.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC096746

    11. NR_164731.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC096746

    12. NR_164732.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC096746

    13. NR_164733.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC096746

    14. NR_164734.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC096746

    15. NR_164735.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC096746

    16. NR_164736.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC096746

    17. NR_164737.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC096746

    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
      94207608..94291292
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_024454154.2 → XP_024309922.1  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1 isoform X1

      Conserved Domains (2) summary
      pfam03288
      Location:318 → 362
      Pox_D5; Poxvirus D5 protein-like
      cl26465
      Location:476 → 1000
      SNF2_N; SNF2 family N-terminal domain

    2. XM_047415987.1 → XP_047271943.1  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1 isoform X2

    RNA

    1. XR_007057943.1 RNA Sequence

    2. XR_007057944.1 RNA Sequence

    3. XR_007057945.1 RNA Sequence

    4. XR_007057946.1 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060928.1 Alternate T2T-CHM13v2.0

      Range
      97523080..97606799
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054350548.1 → XP_054206523.1  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1 isoform X1

    2. XM_054350549.1 → XP_054206524.1  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1 isoform X2

    RNA

    1. XR_008487016.1 RNA Sequence

    2. XR_008487017.1 RNA Sequence

    3. XR_008487018.1 RNA Sequence

    4. XR_008487019.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9H4L7.2 GenPept UniProtKB/Swiss-Prot:Q9H4L7

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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