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    PDS5B PDS5 cohesin associated factor B [ Homo sapiens (human) ]

    Gene ID: 23047, updated on 27-Nov-2024

    Summary

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    Official Symbol
    PDS5Bprovided by HGNC
    Official Full Name
    PDS5 cohesin associated factor Bprovided by HGNC
    Primary source
    HGNC:HGNC:20418
    See related
    Ensembl:ENSG00000083642 MIM:605333; AllianceGenome:HGNC:20418
    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
    AS3; APRIN; CG008
    Summary
    This gene encodes a protein that interacts with the conserved protein complex termed cohesin. The cohesin complex holds together sister chromatids and facilitates accurate chromosome segregation during mitosis and meiosis. This protein is also a negative regulator of cell proliferation and may be a tumor-suppressor gene. [provided by RefSeq, Jul 2015]
    Expression
    Ubiquitous expression in brain (RPKM 8.3), endometrium (RPKM 8.1) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See PDS5B in Genome Data Viewer
    Location:
    13q13.1
    Exon count:
    38
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 13 NC_000013.11 (32586452..32778019)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 13 NC_060937.1 (31803785..31995311)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 13 NC_000013.10 (33160589..33352157)

    Chromosome 13 - NC_000013.11Genomic Context describing neighboring genes Neighboring gene NEDD4 binding protein 2 like 2 Neighboring gene N4BPL2 intronic transcript 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:33112107-33112666 Neighboring gene H3K27ac hESC enhancer GRCh37_chr13:33112667-33113227 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5249 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5250 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5251 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7563 Neighboring gene PDS5B divergent transcript Neighboring gene NANOG hESC enhancer GRCh37_chr13:33200082-33200597 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7564 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5252 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr13:33288052-33289036 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr13:33294729-33295322 Neighboring gene MPRA-validated peak2067 silencer Neighboring gene Sharpr-MPRA regulatory region 5009 Neighboring gene RNY1 pseudogene 4 Neighboring gene ReSE screen-validated silencer GRCh37_chr13:33395368-33395536 Neighboring gene long intergenic non-protein coding RNA 423 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7565 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7566 Neighboring gene TOMM22 pseudogene 3

    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. Loss of a cohesin-linked suppressor APRIN (Pds5b) disrupts stem cell programs in embryonal carcinoma: an emerging cohesin role in tumor suppression. Denes V, et al. Oncogene, 2010 Jun 10. PMID 20383194
    2. Structural Basis and IP6 Requirement for Pds5-Dependent Cohesin Dynamics. Ouyang Z, et al. Mol Cell, 2016 Apr 21. PMID 26971492, Free PMC Article
    3. Topology and structure of an engineered human cohesin complex bound to Pds5B. Hons MT, et al. Nat Commun, 2016 Aug 23. PMID 27549742, Free PMC Article
    4. Early gene expression during androgen-induced inhibition of proliferation of prostate cancer cells: a new suppressor candidate on chromosome 13, in the BRCA2-Rb1 locus. Geck P, et al. J Steroid Biochem Mol Biol, 1999 Jan. PMID 10215036
    5. Correlation of genomic and expression alterations of AS3 with esophageal squamous cell carcinoma. Zhang Y, et al. J Genet Genomics, 2008 May. PMID 18499069

    See all (120) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. [PDS5B inhibits the proliferation of A549 human lung cancer cells via downregulation of Wnt5a].
      Title: [PDS5B inhibits the proliferation of A549 human lung cancer cells via downregulation of Wnt5a].
    2. PDS5A and PDS5B in Cohesin Function and Human Disease.
      Title: PDS5A and PDS5B in Cohesin Function and Human Disease.
    3. 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.
    4. Pds5b/Ptch2 axis regulates cell proliferation and invasion in pancreatic tumor cells.
      Title: PDS5B regulates cell proliferation and motility via upregulation of Ptch2 in pancreatic cancer cells.
    5. our study uncovers a protein complex, which consists of SWS1, SWSAP1, SPIDR and PDS5B, involved in DNA repair and provides insight into Shu complex function and composition.
      Title: The human Shu complex functions with PDS5B and SPIDR to promote homologous recombination.
    6. Pds5B forms an integral part of the cohesin ring by contacting all other cohesin subunits, a property that may reflect the complex role of Pds5 proteins in controlling cohesin-DNA interactions.
      Title: Topology and structure of an engineered human cohesin complex bound to Pds5B.
    7. MAGI2-AS3 plays an important role as a tumour suppressor by targeting Fas and FasL signalling.
      Title: Long non-coding RNA (lncRNA) MAGI2-AS3 inhibits breast cancer cell growth by targeting the Fas/FasL signalling pathway.
    8. The authors' data identify the HIM of Pds5 as a binding motif for Haspin/Hrk1 in fission yeast. The authors' analyses also show that human PDS5B binds Haspin through the same HIM-PIM interaction module, indicating that the Haspin localization mechanism is highly conserved.
      Title: Pds5 Regulates Sister-Chromatid Cohesion and Chromosome Bi-orientation through a Conserved Protein Interaction Module.
    9. The mitotic histone kinase Haspin binds to the cohesin regulatory subunit Pds5B through a conserved YGA/R motif in its non-catalytic N terminus, which is similar to the recently reported YSR-motif-dependent binding of Wapl to Pds5B.
      Title: The N-Terminal Non-Kinase-Domain-Mediated Binding of Haspin to Pds5B Protects Centromeric Cohesion in Mitosis.
    10. 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.
    Submit: New GeneRIF Correction See all GeneRIFs (19)

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    Genome-wide association with MRI atrophy measures as a quantitative trait locus for Alzheimer's disease.
    EBI GWAS Catalog
    Genome-wide meta-analysis identifies 11 new loci for anthropometric traits and provides insights into genetic architecture.
    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)

    HIV-1 interactions

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    Replication interactions

    Interaction Pubs
    Knockdown of PDS5, regulator of cohesion maintenance, homolog B (S. cerevisiae, PDS5B) by shRNA library screening inhibits HIV-1 replication in cultured Jurkat T-cells PubMed

    Protein interactions

    Protein Gene Interaction Pubs
    Tat tat Interaction of HIV-1 Tat with PDS5B 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

    • FLJ23236, KIAA0979

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    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 cell population proliferation TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in mitotic sister chromatid cohesion IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in mitotic sister chromatid cohesion IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in negative regulation of cell population proliferation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    acts_upstream_of_or_within regulation of cell population proliferation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in chromatin IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in 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 nucleus ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  

    General protein information

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    Preferred Names
    sister chromatid cohesion protein PDS5 homolog B
    Names
    androgen induced inhibitor of proliferation
    androgen-induced proliferation inhibitor
    androgen-induced prostate proliferative shutoff-associated protein AS3
    androgen-induced shutoff 3

    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_021308.2 RefSeqGene

      Range
      5026..196593
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_015032.4 → NP_055847.1  sister chromatid cohesion protein PDS5 homolog B

      See identical proteins and their annotated locations for NP_055847.1

      Status: REVIEWED

      Source sequence(s)
      AB023196, AL137201, DA856411
      Consensus CDS
      CCDS41878.1
      UniProtKB/Swiss-Prot
      Q5R3S3, Q5W0K8, Q6NSC3, Q8IXT6, Q9H5N8, Q9NTI5, Q9Y2I5, Q9Y451
      UniProtKB/TrEMBL
      B7Z5S1, E9PHV0
      Related
      ENSP00000313851.10, ENST00000315596.15
      Conserved Domains (3) summary
      PTZ00449
      Location:1215 → 1410
      PTZ00449; 104 kDa microneme/rhoptry antigen; Provisional
      sd00044
      Location:240 → 261
      HEAT; HEAT repeat [structural motif]
      cd19953
      Location:31 → 661
      PDS5; Sister chromatid cohesion protein PDS5

    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_000013.11 Reference GRCh38.p14 Primary Assembly

      Range
      32586452..32778019
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005266298.5 → XP_005266355.1  sister chromatid cohesion protein PDS5 homolog B isoform X1

      See identical proteins and their annotated locations for XP_005266355.1

      UniProtKB/TrEMBL
      B7Z5S1, E9PHV0
      Conserved Domains (3) summary
      PTZ00449
      Location:1042 → 1295
      PTZ00449; 104 kDa microneme/rhoptry antigen; Provisional
      sd00044
      Location:240 → 261
      HEAT; HEAT repeat [structural motif]
      cd19953
      Location:31 → 661
      PDS5; Sister chromatid cohesion protein PDS5

    2. XM_017020452.3 → XP_016875941.1  sister chromatid cohesion protein PDS5 homolog B isoform X4

      UniProtKB/TrEMBL
      B7Z5S1, E9PHV0
      Conserved Domains (3) summary
      PTZ00449
      Location:1042 → 1295
      PTZ00449; 104 kDa microneme/rhoptry antigen; Provisional
      sd00044
      Location:240 → 261
      HEAT; HEAT repeat [structural motif]
      cd19953
      Location:31 → 661
      PDS5; Sister chromatid cohesion protein PDS5

    3. XM_011534999.3 → XP_011533301.1  sister chromatid cohesion protein PDS5 homolog B isoform X2

      See identical proteins and their annotated locations for XP_011533301.1

      UniProtKB/TrEMBL
      B7Z5S1, E9PHV0
      Conserved Domains (2) summary
      sd00044
      Location:240 → 261
      HEAT; HEAT repeat [structural motif]
      cd19953
      Location:31 → 661
      PDS5; Sister chromatid cohesion protein PDS5

    4. XM_011535000.3 → XP_011533302.1  sister chromatid cohesion protein PDS5 homolog B isoform X3

      See identical proteins and their annotated locations for XP_011533302.1

      UniProtKB/TrEMBL
      B7Z5S1, E9PHV0
      Conserved Domains (3) summary
      PTZ00449
      Location:1205 → 1408
      PTZ00449; 104 kDa microneme/rhoptry antigen; Provisional
      sd00044
      Location:240 → 261
      HEAT; HEAT repeat [structural motif]
      cd19953
      Location:31 → 661
      PDS5; Sister chromatid cohesion protein PDS5

    5. XM_017020453.2 → XP_016875942.1  sister chromatid cohesion protein PDS5 homolog B isoform X5

      UniProtKB/TrEMBL
      B7Z5S1, E9PHV0
      Conserved Domains (2) summary
      pfam05029
      Location:1173 → 1301
      TIMELESS_C; Timeless protein C terminal region
      sd00044
      Location:240 → 261
      HEAT; HEAT repeat [structural motif]

    6. XM_047430186.1 → XP_047286142.1  sister chromatid cohesion protein PDS5 homolog B isoform X1

    7. XM_017020448.2 → XP_016875937.1  sister chromatid cohesion protein PDS5 homolog B isoform X1

      UniProtKB/TrEMBL
      B7Z5S1, E9PHV0
      Conserved Domains (3) summary
      PTZ00449
      Location:1042 → 1295
      PTZ00449; 104 kDa microneme/rhoptry antigen; Provisional
      sd00044
      Location:240 → 261
      HEAT; HEAT repeat [structural motif]
      cd19953
      Location:31 → 661
      PDS5; Sister chromatid cohesion protein PDS5

    8. XM_011535002.4 → XP_011533304.1  sister chromatid cohesion protein PDS5 homolog B isoform X6

      Conserved Domains (2) summary
      pfam05029
      Location:897 → 1027
      TIMELESS_C; Timeless protein C terminal region
      pfam13254
      Location:927 → 1139
      DUF4045; Domain of unknown function (DUF4045)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060937.1 Alternate T2T-CHM13v2.0

      Range
      31803785..31995311
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054374271.1 → XP_054230246.1  sister chromatid cohesion protein PDS5 homolog B isoform X7

    2. XM_054374272.1 → XP_054230247.1  sister chromatid cohesion protein PDS5 homolog B isoform X8

    3. XM_054374280.1 → XP_054230255.1  sister chromatid cohesion protein PDS5 homolog B isoform X11

    4. XM_054374273.1 → XP_054230248.1  sister chromatid cohesion protein PDS5 homolog B isoform X9

    5. XM_054374274.1 → XP_054230249.1  sister chromatid cohesion protein PDS5 homolog B isoform X10

    6. XM_054374281.1 → XP_054230256.1  sister chromatid cohesion protein PDS5 homolog B isoform X12

    7. XM_054374275.1 → XP_054230250.1  sister chromatid cohesion protein PDS5 homolog B isoform X1

    8. XM_054374282.1 → XP_054230257.1  sister chromatid cohesion protein PDS5 homolog B isoform X4

    9. XM_054374278.1 → XP_054230253.1  sister chromatid cohesion protein PDS5 homolog B isoform X2

    10. XM_054374279.1 → XP_054230254.1  sister chromatid cohesion protein PDS5 homolog B isoform X3

    11. XM_054374283.1 → XP_054230258.1  sister chromatid cohesion protein PDS5 homolog B isoform X5

    12. XM_054374276.1 → XP_054230251.1  sister chromatid cohesion protein PDS5 homolog B isoform X1

    13. XM_054374277.1 → XP_054230252.1  sister chromatid cohesion protein PDS5 homolog B isoform X1

    14. XM_054374284.1 → XP_054230259.1  sister chromatid cohesion protein PDS5 homolog B isoform X6

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_015928.1: Suppressed sequence

      Description
      NM_015928.1: This RefSeq was permanently suppressed because it is a nonsense-mediated decay (NMD) candidate.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9NTI5.1 GenPept UniProtKB/Swiss-Prot:Q9NTI5

    Gene LinkOut

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

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