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

Gene ID: 23244, updated on 5-Mar-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
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Genomic context

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See PDS5A in Genome Data Viewer
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

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