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    PDS5A PDS5 cohesin associated factor A [ Homo sapiens (human) ]

    Gene ID: 23244, updated on 5-May-2024

    Summary

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    Official Symbol
    PDS5Aprovided by HGNC
    Official Full Name
    PDS5 cohesin associated factor Aprovided by HGNC
    Primary source
    HGNC:HGNC:29088
    See related
    Ensembl:ENSG00000121892 MIM:613200; AllianceGenome:HGNC:29088
    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
    PIG54; SCC112; SCC-112
    Summary
    The protein encoded by this gene binds to the cohesin complex and associates with chromatin through most of the cell cycle. The encoded protein may play a role in regulating sister chromatid cohesion during mitosis. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2010]
    Expression
    Ubiquitous expression in thyroid (RPKM 18.1), lymph node (RPKM 17.1) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    4p14
    Exon count:
    36
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (39822863..39977911, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (39792793..39947875, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (39824483..39979531, complement)

    Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene ubiquitin conjugating enzyme E2 K Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15372 Neighboring gene RNA, 7SL, cytoplasmic 558, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:39787697-39788198 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:39788199-39788698 Neighboring gene zinc finger and BTB domain containing 12B, pseudogene Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr4:39821819-39822356 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21469 Neighboring gene RNA, 5S ribosomal pseudogene 159 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21470 Neighboring gene Sharpr-MPRA regulatory region 4409 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr4:39977870-39978778 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15374 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:39991585-39992282 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr4:40000455-40000959 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:40001597-40002110 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:40002111-40002626 Neighboring gene poly(A) binding protein cytoplasmic 1 pseudogene 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:40002627-40003140 Neighboring gene keratin 18 pseudogene 25 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15375 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15376 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15377 Neighboring gene acyl-CoA thioesterase 7 pseudogene Neighboring gene NEDD4 binding protein 2

    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
    • 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. The cohesin acetylation cycle controls chromatin loop length through a PDS5A brake mechanism. van Ruiten MS, et al. Nat Struct Mol Biol, 2022 Jun. PMID 35710836, Free PMC Article
    2. Higher Order Chromatin Modulator Cohesin SA1 Is an Early Biomarker for Colon Carcinogenesis: Race-Specific Implications. Wali RK, et al. Cancer Prev Res (Phila), 2016 Nov. PMID 27549371, Free PMC Article
    3. HIV-1 infection suppresses expression of host cell cycle-associated gene PDS5A. Capalbo G, et al. Intervirology, 2012. PMID 21865657
    4. SCC-112 gene is involved in tumor progression and promotes the cell proliferation in G2/M phase. Zheng MZ, et al. J Cancer Res Clin Oncol, 2008 Apr. PMID 17846787
    5. SCC-112, a novel cell cycle-regulated molecule, exhibits reduced expression in human renal carcinomas. Kumar D, et al. Gene, 2004 Mar 17. PMID 15019998

    See all (124) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. The cohesin acetylation cycle controls chromatin loop length through a PDS5A brake mechanism.
      Title: The cohesin acetylation cycle controls chromatin loop length through a PDS5A brake mechanism.
    2. Knockdown of CDCA5 suppresses malignant progression of breast cancer cells by regulating PDS5A.
      Title: Knockdown of CDCA5 suppresses malignant progression of breast cancer cells by regulating PDS5A.
    3. PDS5A and PDS5B in Cohesin Function and Human Disease.
      Title: PDS5A and PDS5B in Cohesin Function and Human Disease.
    4. PDS5 proteins are required for proper cohesin dynamics and participate in replication fork protection.
      Title: PDS5 proteins are required for proper cohesin dynamics and participate in replication fork protection.
    5. depletion of Rad21 in a Pds5-deficient background rescues the phenotype observed upon Pds5 depletion alone. These findings support a model where loss of either component of the cohesin releasin complex perturbs cohesin dynamics on replication forks, hindering fork progression and promoting MRE11-dependent fork slowing
      Title: Perturbing cohesin dynamics drives MRE11 nuclease-dependent replication fork slowing.
    6. The results show that cohesin has an essential genome-wide function in mediating long-range chromatin interactions and support the hypothesis that cohesin creates these by loop extrusion, until it is delayed by CTCF in a manner dependent on PDS5 proteins, or until it is released from DNA by WAPL.
      Title: Topologically associating domains and chromatin loops depend on cohesin and are regulated by CTCF, WAPL, and PDS5 proteins.
    7. These results provide the first evidence indicating a tumor suppressor role of SA1 in early colon carcinogenesis
      Title: Higher Order Chromatin Modulator Cohesin SA1 Is an Early Biomarker for Colon Carcinogenesis: Race-Specific Implications.
    8. By interacting with a unique domain of Esco1, Pds5 recruits Esco1 to chromatin-bound cohesin complexes to form cohesion.
      Title: Esco1 Acetylates Cohesin via a Mechanism Different from That of Esco2.
    9. The data show a downregulation of proliferation-associated host gene PDS5A and suggest a role of PDS5A in HIV-1-induced cellular pathogenesis but not viral replication.
      Title: HIV-1 infection suppresses expression of host cell cycle-associated gene PDS5A.
    10. Data show that the siRNA-mediated knockdown of Pds5A affects sister chromatid cohesion but does not influence mitotic checkpoint function or the proliferation and survival of glioblastoma multiforme cells.
      Title: The cohesin-interacting protein, precocious dissociation of sisters 5A/sister chromatid cohesion protein 112, is up-regulated in human astrocytic tumors.
    Submit: New GeneRIF Correction See all GeneRIFs (13)

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    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

    HIV-1 interactions

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    Protein interactions

    Protein Gene Interaction Pubs
    Tat tat Interaction of HIV-1 Tat with PDS5A in T-cells is identified by a proteomic strategy based on affinity chromatography coupled with mass spectrometry PubMed

    Go to the HIV-1, Human Interaction Database

    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

    • FLJ41012, KIAA0648, MGC131948, MGC161503, DKFZp686B19246

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in DNA repair IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in cell division IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in mitotic sister chromatid cohesion IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in mitotic sister chromatid cohesion IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    involved_in negative regulation of DNA replication IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of chromatin IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of chromatin IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in chromosome TAS
    Traceable Author Statement
    more info
    		  
    located_in chromosome, centromeric region TAS
    Traceable Author Statement
    more info
    		  
    located_in cytosol TAS
    Traceable Author Statement
    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 plasma membrane IDA
    Inferred from Direct Assay
    more info
    		  

    General protein information

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    Preferred Names
    sister chromatid cohesion protein PDS5 homolog A
    Names
    PDS5, regulator of cohesion maintenance, homolog A
    cell proliferation-inducing gene 54 protein
    sister chromatid cohesion protein 112

    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_021172.1 RefSeqGene

      Range
      5046..160094
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001100399.2 → NP_001093869.1  sister chromatid cohesion protein PDS5 homolog A isoform 1

      See identical proteins and their annotated locations for NP_001093869.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AC098591, BC041361, BC114218
      Consensus CDS
      CCDS47045.1
      UniProtKB/Swiss-Prot
      Q29RF7, Q2TTR5, Q68DF7, Q8N7J4, Q8NG14, Q9Y4D4
      UniProtKB/TrEMBL
      G1UI16
      Related
      ENSP00000303427.8, ENST00000303538.13
      Conserved Domains (2) summary
      sd00044
      Location:283 → 313
      HEAT; HEAT repeat [structural motif]
      cd19953
      Location:41 → 671
      PDS5; Sister chromatid cohesion protein PDS5

    2. NM_001100400.2 → NP_001093870.1  sister chromatid cohesion protein PDS5 homolog A isoform 3

      See identical proteins and their annotated locations for NP_001093870.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 3' UTR and lacks several exons in the 3' coding region, compared to variant 1. The resulting protein (isoform 3) has a distinct C-terminus and is shorter than isoform 1.
      Source sequence(s)
      AC098591, BC041361
      Consensus CDS
      CCDS54759.1
      UniProtKB/Swiss-Prot
      Q29RF7
      Related
      ENSP00000426749.1, ENST00000503396.5
      Conserved Domains (1) summary
      sd00044
      Location:283 → 313
      HEAT; HEAT repeat [structural motif]

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

    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
      39822863..39977911 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011513672.3 → XP_011511974.1  sister chromatid cohesion protein PDS5 homolog A isoform X1

      See identical proteins and their annotated locations for XP_011511974.1

      UniProtKB/Swiss-Prot
      Q29RF7, Q2TTR5, Q68DF7, Q8N7J4, Q8NG14, Q9Y4D4
      UniProtKB/TrEMBL
      G1UI16
      Conserved Domains (2) summary
      sd00044
      Location:283 → 313
      HEAT; HEAT repeat [structural motif]
      cd19953
      Location:41 → 671
      PDS5; Sister chromatid cohesion protein PDS5

    2. XM_047449932.1 → XP_047305888.1  sister chromatid cohesion protein PDS5 homolog A isoform X3

    3. XM_047449931.1 → XP_047305887.1  sister chromatid cohesion protein PDS5 homolog A isoform X2

      UniProtKB/Swiss-Prot
      Q29RF7, Q2TTR5, Q68DF7, Q8N7J4, Q8NG14, Q9Y4D4
      UniProtKB/TrEMBL
      G1UI16

    RNA

    1. XR_001741185.2 RNA Sequence

    2. XR_001741188.2 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060928.1 Alternate T2T-CHM13v2.0

      Range
      39792793..39947875 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054349456.1 → XP_054205431.1  sister chromatid cohesion protein PDS5 homolog A isoform X1

      UniProtKB/Swiss-Prot
      Q29RF7, Q2TTR5, Q68DF7, Q8N7J4, Q8NG14, Q9Y4D4
      UniProtKB/TrEMBL
      G1UI16

    2. XM_054349458.1 → XP_054205433.1  sister chromatid cohesion protein PDS5 homolog A isoform X3

    3. XM_054349457.1 → XP_054205432.1  sister chromatid cohesion protein PDS5 homolog A isoform X2

      UniProtKB/Swiss-Prot
      Q29RF7, Q2TTR5, Q68DF7, Q8N7J4, Q8NG14, Q9Y4D4
      UniProtKB/TrEMBL
      G1UI16

    RNA

    1. XR_008486958.1 RNA Sequence

    2. XR_008486959.1 RNA Sequence

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_015200.2: Suppressed sequence

      Description
      NM_015200.2: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q29RF7.1 GenPept UniProtKB/Swiss-Prot:Q29RF7

    Gene LinkOut

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

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