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    KDM5C lysine demethylase 5C [ Homo sapiens (human) ]

    Gene ID: 8242, updated on 10-Dec-2024

    Summary

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    Official Symbol
    KDM5Cprovided by HGNC
    Official Full Name
    lysine demethylase 5Cprovided by HGNC
    Primary source
    HGNC:HGNC:11114
    See related
    Ensembl:ENSG00000126012 MIM:314690; AllianceGenome:HGNC:11114
    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
    MRXJ; SMCX; MRX13; MRXSJ; XE169; MRXSCJ; JARID1C; DXS1272E
    Summary
    This gene is a member of the SMCY homolog family and encodes a protein with one ARID domain, one JmjC domain, one JmjN domain and two PHD-type zinc fingers. The DNA-binding motifs suggest this protein is involved in the regulation of transcription and chromatin remodeling. Mutations in this gene have been associated with X-linked cognitive disability. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2009]
    Expression
    Ubiquitous expression in endometrium (RPKM 14.4), lymph node (RPKM 13.5) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See KDM5C in Genome Data Viewer
    Location:
    Xp11.22
    Exon count:
    29
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (53176277..53225207, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (52462547..52511471, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (53205459..53254389, complement)

    Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene KANTR integral membrane protein Neighboring gene RNA, U7 small nuclear 37 pseudogene Neighboring gene actin gamma 1 pseudogene 10 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chrX:53192545-53193079 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20856 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29654 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29655 Neighboring gene microRNA 6895 Neighboring gene microRNA 6894 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29656 Neighboring gene Sharpr-MPRA regulatory region 5919 Neighboring gene IQ motif and Sec7 domain ArfGEF 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:53285843-53286438 Neighboring gene ReSE screen-validated silencer GRCh37_chrX:53309250-53309449 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:53310370-53311197 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:53317293-53318184 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20857 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20858 Neighboring gene ribosomal protein SA pseudogene 62

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    1. DNA methylation fingerprint of monozygotic twins and their singleton sibling with intellectual disability carrying a novel KDM5C mutation. Guerra JVS, et al. Eur J Med Genet, 2020 Mar. PMID 31419599
    2. Functional correlation of genome-wide DNA methylation profiles in genetic neurodevelopmental disorders. Levy MA, et al. Hum Mutat, 2022 Nov. PMID 35904121
    3. Molecular and cellular events linking variants in the histone demethylase KDM5C to the intellectual disability disorder Claes-Jensen syndrome. Hatch HAM, et al. FEBS J, 2022 Dec. PMID 34536985, Free PMC Article
    4. Deficiency of the X-inactivation escaping gene KDM5C in clear cell renal cell carcinoma promotes tumorigenicity by reprogramming glycogen metabolism and inhibiting ferroptosis. Zheng Q, et al. Theranostics, 2021. PMID 34522206, Free PMC Article
    5. Caregiver-reported characteristics of children diagnosed with pathogenic variants in KDM5C. Hatch HAM, et al. Am J Med Genet A, 2021 Oct. PMID 34089235, Free PMC Article

    See all (121) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Histone demethylase JARID1C/KDM5C regulates Th17 cells by increasing IL-6 expression in diabetic plasmacytoid dendritic cells.
      Title: Histone demethylase JARID1C/KDM5C regulates Th17 cells by increasing IL-6 expression in diabetic plasmacytoid dendritic cells.
    2. Histone demethylase KDM5 regulates cardiomyocyte maturation by promoting fatty acid oxidation, oxidative phosphorylation, and myofibrillar organization.
      Title: Histone demethylase KDM5 regulates cardiomyocyte maturation by promoting fatty acid oxidation, oxidative phosphorylation, and myofibrillar organization.
    3. KDM5C-Mediated Recruitment of BRD4 to Chromatin Regulates Enhancer Activation and BET Inhibitor Sensitivity.
      Title: KDM5C-Mediated Recruitment of BRD4 to Chromatin Regulates Enhancer Activation and BET Inhibitor Sensitivity.
    4. WNT signalling control by KDM5C during development affects cognition.
      Title: WNT signalling control by KDM5C during development affects cognition.
    5. Lysine demethylase 5C inhibits transcription of prefoldin subunit 5 to activate c-Myc signal transduction and colorectal cancer progression.
      Title: Lysine demethylase 5C inhibits transcription of prefoldin subunit 5 to activate c-Myc signal transduction and colorectal cancer progression.
    6. KDM5 family of demethylases promotes CD44-mediated chemoresistance in pancreatic adenocarcinomas.
      Title: KDM5 family of demethylases promotes CD44-mediated chemoresistance in pancreatic adenocarcinomas.
    7. The X-linked histone demethylases KDM5C and KDM6A as regulators of T cell-driven autoimmunity in the central nervous system.
      Title: The X-linked histone demethylases KDM5C and KDM6A as regulators of T cell-driven autoimmunity in the central nervous system.
    8. Elevated PSPC1 and KDM5C expression indicates poor prognosis in prostate cancer.
      Title: Elevated PSPC1 and KDM5C expression indicates poor prognosis in prostate cancer.
    9. The histone demethylase KDM5C controls female bone mass by promoting energy metabolism in osteoclasts.
      Title: The histone demethylase KDM5C controls female bone mass by promoting energy metabolism in osteoclasts.
    10. The histone demethylase KDM5C functions as a tumor suppressor in AML by repression of bivalently marked immature genes.
      Title: The histone demethylase KDM5C functions as a tumor suppressor in AML by repression of bivalently marked immature genes.
    Submit: New GeneRIF Correction See all GeneRIFs (67)

    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
    Syndromic X-linked intellectual disability Claes-Jensen type
    MedGen: C1845243 OMIM: 300534 GeneReviews: Not available
    		not available

    Copy number response

    Description
    Copy number response
    Haploinsufficency

    Sufficient evidence for dosage pathogenicity (Last evaluated 2023-07-27)

    ClinGen Genome Curation PagePubMed
    Triplosensitivity

    No evidence available (Last evaluated 2023-07-27)

    ClinGen Genome Curation Page

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    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

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables histone H3K4 demethylase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables histone H3K4 demethylase activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables histone H3K4me/H3K4me2/H3K4me3 demethylase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables histone demethylase activity TAS
    Traceable Author Statement
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables zinc ion binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in chromatin remodeling IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in negative regulation of DNA-templated transcription ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in regulation of DNA-templated transcription IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in response to toxic substance IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in rhythmic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in chromatin IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    lysine-specific demethylase 5C
    Names
    JmjC domain-containing protein SMCX
    Jumonji, AT rich interactive domain 1C (RBP2-like)
    Jumonji/ARID domain-containing protein 1C
    Smcx homolog, X chromosome
    Smcy homolog, X-linked
    [histone H3]-trimethyl-L-lysine(4) demethylase 5C
    histone demethylase JARID1C
    lysine (K)-specific demethylase 5C
    NP_001140174.1
    NP_001269551.1
    NP_001340907.1
    NP_001340908.1
    NP_001340910.1
    NP_001340911.1
    NP_001340913.1
    NP_004178.2

    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_008085.2 RefSeqGene

      Range
      5216..38265
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001146702.2 → NP_001140174.1  lysine-specific demethylase 5C isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR, 3' UTR, and coding region compared to variant 1, resulting in a protein (isoform 2) that maintains the reading frame but is shorter at both the N- and C-termini, compared to isoform 1.
      Source sequence(s)
      AL139396
      Consensus CDS
      CCDS55417.1
      UniProtKB/TrEMBL
      A0A6M4C8G8, A0A8I5KQR8
      Related
      ENSP00000445176.1, ENST00000452825.7
      Conserved Domains (7) summary
      smart00545
      Location:13 → 50
      JmjN; Small domain found in the jumonji family of transcription factors
      cd15604
      Location:259 → 304
      PHD1_KDM5C_5D; PHD finger 1 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
      cl28902
      Location:51 → 103
      ARID; ARID/BRIGHT DNA binding domain family
      pfam02373
      Location:434 → 550
      JmjC; JmjC domain, hydroxylase
      pfam02928
      Location:640 → 692
      zf-C5HC2; C5HC2 zinc finger
      pfam08429
      Location:705 → 1033
      PLU-1; PLU-1-like protein
      cl22851
      Location:1120 → 1180
      PHD_SF; PHD finger superfamily

    2. NM_001282622.3 → NP_001269551.1  lysine-specific demethylase 5C isoform 3

      See identical proteins and their annotated locations for NP_001269551.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) uses an alternate in-frame splice site compared to variant 1. The encoded isoform (3) is shorter than isoform 1.
      Source sequence(s)
      AL139396, BC054499, L25270
      Consensus CDS
      CCDS65269.1
      UniProtKB/TrEMBL
      A6N6J7
      Related
      ENSP00000385394.3, ENST00000404049.7
      Conserved Domains (7) summary
      smart00501
      Location:80 → 170
      BRIGHT; BRIGHT, ARID (A/T-rich interaction domain) domain
      smart00545
      Location:13 → 54
      JmjN; Small domain found in the jumonji family of transcription factors
      pfam02373
      Location:500 → 616
      JmjC; JmjC domain, hydroxylase
      cd15604
      Location:325 → 370
      PHD1_KDM5C_5D; PHD finger 1 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
      cd15608
      Location:1186 → 1246
      PHD2_KDM5C_5D; PHD finger 2 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
      pfam02928
      Location:706 → 758
      zf-C5HC2; C5HC2 zinc finger
      pfam08429
      Location:771 → 1097
      PLU-1; PLU-1-like protein

    3. NM_001353978.3 → NP_001340907.1  lysine-specific demethylase 5C isoform 4

      Status: REVIEWED

      Source sequence(s)
      AL139396
      Consensus CDS
      CCDS87747.1
      UniProtKB/TrEMBL
      A0A8I5KQR8
      Related
      ENSP00000364528.3, ENST00000375379.7
      Conserved Domains (7) summary
      smart00501
      Location:80 → 170
      BRIGHT; BRIGHT, ARID (A/T-rich interaction domain) domain
      smart00545
      Location:13 → 54
      JmjN; Small domain found in the jumonji family of transcription factors
      pfam02373
      Location:501 → 617
      JmjC; JmjC domain, hydroxylase
      cd15604
      Location:326 → 371
      PHD1_KDM5C_5D; PHD finger 1 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
      cd15608
      Location:1187 → 1247
      PHD2_KDM5C_5D; PHD finger 2 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
      pfam02928
      Location:707 → 759
      zf-C5HC2; C5HC2 zinc finger
      pfam08429
      Location:772 → 1098
      PLU-1; PLU-1-like protein

    4. NM_001353979.2 → NP_001340908.1  lysine-specific demethylase 5C isoform 5

      Status: REVIEWED

      Source sequence(s)
      AL139396
      UniProtKB/TrEMBL
      A6N6J7
      Related
      ENSP00000508806.1, ENST00000685423.1
      Conserved Domains (7) summary
      smart00501
      Location:80 → 170
      BRIGHT; BRIGHT, ARID (A/T-rich interaction domain) domain
      smart00545
      Location:13 → 54
      JmjN; Small domain found in the jumonji family of transcription factors
      pfam02373
      Location:500 → 616
      JmjC; JmjC domain, hydroxylase
      cd15604
      Location:325 → 370
      PHD1_KDM5C_5D; PHD finger 1 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
      cd15608
      Location:1186 → 1246
      PHD2_KDM5C_5D; PHD finger 2 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
      pfam02928
      Location:706 → 758
      zf-C5HC2; C5HC2 zinc finger
      pfam08429
      Location:771 → 1097
      PLU-1; PLU-1-like protein

    5. NM_001353981.2 → NP_001340910.1  lysine-specific demethylase 5C isoform 6

      Status: REVIEWED

      Source sequence(s)
      AL139396
      Consensus CDS
      CCDS94610.1
      UniProtKB/TrEMBL
      A0A8I5KQR8, A0A8I5KTT1
      Related
      ENSP00000509818.1, ENST00000685641.2
      Conserved Domains (7) summary
      smart00501
      Location:80 → 170
      BRIGHT; BRIGHT, ARID (A/T-rich interaction domain) domain
      smart00545
      Location:13 → 54
      JmjN; Small domain found in the jumonji family of transcription factors
      pfam02373
      Location:501 → 617
      JmjC; JmjC domain, hydroxylase
      cd15604
      Location:326 → 371
      PHD1_KDM5C_5D; PHD finger 1 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
      cd15608
      Location:1187 → 1247
      PHD2_KDM5C_5D; PHD finger 2 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
      pfam02928
      Location:707 → 759
      zf-C5HC2; C5HC2 zinc finger
      pfam08429
      Location:772 → 1098
      PLU-1; PLU-1-like protein

    6. NM_001353982.2 → NP_001340911.1  lysine-specific demethylase 5C isoform 7

      Status: REVIEWED

      Source sequence(s)
      AL139396
      UniProtKB/TrEMBL
      A0A8I5KQR8
      Conserved Domains (7) summary
      smart00501
      Location:80 → 170
      BRIGHT; BRIGHT, ARID (A/T-rich interaction domain) domain
      smart00545
      Location:13 → 54
      JmjN; Small domain found in the jumonji family of transcription factors
      pfam02373
      Location:500 → 616
      JmjC; JmjC domain, hydroxylase
      cd15604
      Location:325 → 370
      PHD1_KDM5C_5D; PHD finger 1 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
      cd15608
      Location:1186 → 1246
      PHD2_KDM5C_5D; PHD finger 2 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
      pfam02928
      Location:706 → 758
      zf-C5HC2; C5HC2 zinc finger
      pfam08429
      Location:771 → 1097
      PLU-1; PLU-1-like protein

    7. NM_001353984.2 → NP_001340913.1  lysine-specific demethylase 5C isoform 8

      Status: REVIEWED

      Source sequence(s)
      AL139396
      Consensus CDS
      CCDS94611.1
      UniProtKB/TrEMBL
      A0A8I5KQR8, A0A8I5KYW1
      Related
      ENSP00000510430.1, ENST00000688699.1
      Conserved Domains (7) summary
      smart00501
      Location:80 → 170
      BRIGHT; BRIGHT, ARID (A/T-rich interaction domain) domain
      smart00545
      Location:13 → 54
      JmjN; Small domain found in the jumonji family of transcription factors
      pfam02373
      Location:501 → 617
      JmjC; JmjC domain, hydroxylase
      cd15604
      Location:326 → 371
      PHD1_KDM5C_5D; PHD finger 1 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
      cd15608
      Location:1187 → 1247
      PHD2_KDM5C_5D; PHD finger 2 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
      pfam02928
      Location:707 → 759
      zf-C5HC2; C5HC2 zinc finger
      pfam08429
      Location:772 → 1098
      PLU-1; PLU-1-like protein

    8. NM_004187.5 → NP_004178.2  lysine-specific demethylase 5C isoform 1

      See identical proteins and their annotated locations for NP_004178.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AL139396, BC047751, BC054499, L25270
      Consensus CDS
      CCDS14351.1
      UniProtKB/Swiss-Prot
      B0QZ44, B4E3I2, F5H3T1, P41229, Q5JUX3, Q5JUX4, Q5JUX5, Q7Z5S5
      UniProtKB/TrEMBL
      A6N6J7
      Related
      ENSP00000364550.4, ENST00000375401.8
      Conserved Domains (7) summary
      smart00501
      Location:80 → 170
      BRIGHT; BRIGHT, ARID (A/T-rich interaction domain) domain
      smart00545
      Location:13 → 54
      JmjN; Small domain found in the jumonji family of transcription factors
      pfam02373
      Location:501 → 617
      JmjC; JmjC domain, hydroxylase
      cd15604
      Location:326 → 371
      PHD1_KDM5C_5D; PHD finger 1 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
      cd15608
      Location:1187 → 1247
      PHD2_KDM5C_5D; PHD finger 2 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
      pfam02928
      Location:707 → 759
      zf-C5HC2; C5HC2 zinc finger
      pfam08429
      Location:772 → 1098
      PLU-1; PLU-1-like protein

    RNA

    1. NR_148672.2 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AL139396

    2. NR_148673.2 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AL139396
      Related
      ENST00000687695.1

    3. NR_148674.2 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AL139396

    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_000023.11 Reference GRCh38.p14 Primary Assembly

      Range
      53176277..53225207 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060947.1 Alternate T2T-CHM13v2.0

      Range
      52462547..52511471 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P41229.2 GenPept UniProtKB/Swiss-Prot:P41229

    Gene LinkOut

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

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