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

Gene ID: 23047, updated on 7-Apr-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
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Genomic context

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Location:
13q13.1
Exon count:
38
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 13 NC_000013.11 (32586452..32778019)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 13 NC_060937.1 (31803785..31995311)
105.20220307 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. 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
  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. 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
  4. Correlation of genomic and expression alterations of AS3 with esophageal squamous cell carcinoma. Zhang Y, et al. J Genet Genomics, 2008 May. PMID 18499069
  5. 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

See all (107) 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)

Genotypes

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
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 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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NEW Try the new Transcript table

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_2023_10

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

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