Human Gene PDS5A (ENST00000303538.13_7) from GENCODE V47lift37
  Description: PDS5 cohesin associated factor A, transcript variant 1 (from RefSeq NM_001100399.2)
Gencode Transcript: ENST00000303538.13_7
Gencode Gene: ENSG00000121892.15_15
Transcript (Including UTRs)
   Position: hg19 chr4:39,824,483-39,979,531 Size: 155,049 Total Exon Count: 33 Strand: -
Coding Region
   Position: hg19 chr4:39,827,105-39,978,197 Size: 151,093 Coding Exon Count: 32 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr4:39,824,483-39,979,531)mRNA (may differ from genome)Protein (1337 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
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-  Comments and Description Text from UniProtKB
  ID: PDS5A_HUMAN
DESCRIPTION: RecName: Full=Sister chromatid cohesion protein PDS5 homolog A; AltName: Full=Cell proliferation-inducing gene 54 protein; AltName: Full=Sister chromatid cohesion protein 112; Short=SCC-112;
FUNCTION: Probable regulator of sister chromatid cohesion in mitosis which may stabilize cohesin complex association with chromatin. May couple sister chromatid cohesion during mitosis to DNA replication. Cohesion ensures that chromosome partitioning is accurate in both meiotic and mitotic cells and plays an important role in DNA repair.
SUBUNIT: Interacts with the cohesin complex. Interacts with WAPAL (via FGF motifs) or CDCA5 (via the FGF motif); the interaction is direct, cohesin-dependent and competitive. Interacts with SMC3. Interacts with TP63.
INTERACTION: Q96FF9:CDCA5; NbExp=2; IntAct=EBI-1175454, EBI-718805; O60216:RAD21; NbExp=3; IntAct=EBI-1175454, EBI-80739; Q9UQE7:SMC3; NbExp=4; IntAct=EBI-1175454, EBI-80718; Q8WVM7:STAG1; NbExp=3; IntAct=EBI-1175454, EBI-1175097; Q8N3U4:STAG2; NbExp=3; IntAct=EBI-1175454, EBI-1057252;
SUBCELLULAR LOCATION: Nucleus. Note=Associated with chromatin through most of the cell cycle. Dissociates from chromatin in late prophase, reassociates during late telophase.
TISSUE SPECIFICITY: Highest level in colon. Low levels in lung, ovary, breast and kidney. Reduced level in renal tumor tissue. Isoform 2 is expressed in kidney.
DEVELOPMENTAL STAGE: Cell cycle-regulated with highest level in G2 phase.
MISCELLANEOUS: HeLa cells with a reduced level of PDS5A show a mild defect in sister chromatid cohesion. HeLa cells with a reduced level of RAD21 show reduced association of PDS5A with chromatin.
SIMILARITY: Belongs to the PDS5 family.
SIMILARITY: Contains 1 HEAT repeat.
SEQUENCE CAUTION: Sequence=AAI26226.1; Type=Erroneous initiation; Sequence=AAM82347.1; Type=Miscellaneous discrepancy; Note=Probable cloning artifact; Sequence=CAH18263.1; Type=Erroneous initiation;

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 22.88 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 549.89 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -272.60495-0.551 Picture PostScript Text
3' UTR -631.802622-0.241 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR011989 - ARM-like
IPR016024 - ARM-type_fold

SCOP Domains:
48371 - ARM repeat
48431 - Lipovitellin-phosvitin complex, superhelical domain

ModBase Predicted Comparative 3D Structure on Q29RF7
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding

Biological Process:
GO:0006281 DNA repair
GO:0007049 cell cycle
GO:0007064 mitotic sister chromatid cohesion
GO:0008156 negative regulation of DNA replication
GO:0051301 cell division

Cellular Component:
GO:0000775 chromosome, centromeric region
GO:0000785 chromatin
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005694 chromosome
GO:0005829 cytosol
GO:0005886 plasma membrane


-  Descriptions from all associated GenBank mRNAs
  EU832541 - Synthetic construct Homo sapiens clone HAIB:100067570; DKFZo004B0730 PDS5, regulator of cohesion maintenance, homolog A (S. cerevisiae) protein (PDS5A) gene, encodes complete protein.
BC009650 - Homo sapiens PDS5, regulator of cohesion maintenance, homolog A (S. cerevisiae), mRNA (cDNA clone IMAGE:3461329), partial cds.
BC114218 - Homo sapiens PDS5, regulator of cohesion maintenance, homolog A (S. cerevisiae), mRNA (cDNA clone MGC:131948 IMAGE:5579832), complete cds.
LF383972 - JP 2014500723-A/191475: Polycomb-Associated Non-Coding RNAs.
AB014548 - Homo sapiens mRNA for KIAA0648 protein, partial cds.
AF294791 - Homo sapiens SCC-112 (SCC-112) mRNA, complete cds.
AB621803 - Homo sapiens PDS5A mRNA for sister chromatid cohesion protein PDS5 homolog A, complete cds, clone: HP05183-RBb02C04.
AK021757 - Homo sapiens cDNA FLJ11695 fis, clone HEMBA1005019, highly similar to Homo sapiens SCC-112 protein (SCC-112), mRNA.
CR749425 - Homo sapiens mRNA; cDNA DKFZp686B19246 (from clone DKFZp686B19246).
AK023592 - Homo sapiens cDNA FLJ13530 fis, clone PLACE1006248, highly similar to Homo sapiens mRNA for KIAA0648 protein.
BC126225 - Homo sapiens PDS5, regulator of cohesion maintenance, homolog A (S. cerevisiae), mRNA (cDNA clone MGC:161503 IMAGE:8991941), complete cds.
BC144088 - Homo sapiens cDNA clone IMAGE:9052608, containing frame-shift errors.
AK124569 - Homo sapiens cDNA FLJ42578 fis, clone BRACE3008337.
KJ902308 - Synthetic construct Homo sapiens clone ccsbBroadEn_11702 PDS5A gene, encodes complete protein.
EU832459 - Synthetic construct Homo sapiens clone HAIB:100067488; DKFZo008B0729 PDS5, regulator of cohesion maintenance, homolog A (S. cerevisiae) protein (PDS5A) gene, encodes complete protein.
CU679429 - Synthetic construct Homo sapiens gateway clone IMAGE:100018123 5' read PDS5A mRNA.
MA619549 - JP 2018138019-A/191475: Polycomb-Associated Non-Coding RNAs.
BC041361 - Homo sapiens PDS5, regulator of cohesion maintenance, homolog A (S. cerevisiae), mRNA (cDNA clone IMAGE:5273075), complete cds.
AK098331 - Homo sapiens cDNA FLJ41012 fis, clone UTERU2018523, highly similar to Human androgen-induced prostate proliferative shutoff associated protein (AS3) mRNA.
AY550968 - Homo sapiens cell proliferation-inducing protein 54 mRNA, complete cds.
KJ893347 - Synthetic construct Homo sapiens clone ccsbBroadEn_02741 PDS5A gene, encodes complete protein.
EU832553 - Synthetic construct Homo sapiens clone HAIB:100067582; DKFZo004C1230 PDS5, regulator of cohesion maintenance, homolog A (S. cerevisiae) protein (PDS5A) gene, encodes complete protein.
HQ257985 - Synthetic construct Homo sapiens clone IMAGE:100072294 PDS5, regulator of cohesion maintenance, homolog A (S. cerevisiae) (PDS5A), transcript variant 3 (PDS5A) gene, encodes complete protein.
EU832474 - Synthetic construct Homo sapiens clone HAIB:100067503; DKFZo008C1229 PDS5, regulator of cohesion maintenance, homolog A (S. cerevisiae) protein (PDS5A) gene, encodes complete protein.
AK001828 - Homo sapiens cDNA FLJ10966 fis, clone PLACE1000785, highly similar to Homo sapiens mRNA for KIAA0648 protein.
JD302525 - Sequence 283549 from Patent EP1572962.
JD296727 - Sequence 277751 from Patent EP1572962.
JD053660 - Sequence 34684 from Patent EP1572962.
JD067246 - Sequence 48270 from Patent EP1572962.
JD342786 - Sequence 323810 from Patent EP1572962.
JD237354 - Sequence 218378 from Patent EP1572962.
JD268221 - Sequence 249245 from Patent EP1572962.
JD323712 - Sequence 304736 from Patent EP1572962.
JD520935 - Sequence 501959 from Patent EP1572962.
JD506841 - Sequence 487865 from Patent EP1572962.
JD137423 - Sequence 118447 from Patent EP1572962.
JD088561 - Sequence 69585 from Patent EP1572962.
JD429261 - Sequence 410285 from Patent EP1572962.
JD109977 - Sequence 91001 from Patent EP1572962.
JD562883 - Sequence 543907 from Patent EP1572962.
JD234461 - Sequence 215485 from Patent EP1572962.
JD563692 - Sequence 544716 from Patent EP1572962.
JD357731 - Sequence 338755 from Patent EP1572962.
JD327321 - Sequence 308345 from Patent EP1572962.
JD165748 - Sequence 146772 from Patent EP1572962.
JD091284 - Sequence 72308 from Patent EP1572962.
JD525471 - Sequence 506495 from Patent EP1572962.
JD308439 - Sequence 289463 from Patent EP1572962.
JD185226 - Sequence 166250 from Patent EP1572962.
JD162849 - Sequence 143873 from Patent EP1572962.
JD170339 - Sequence 151363 from Patent EP1572962.
LF358644 - JP 2014500723-A/166147: Polycomb-Associated Non-Coding RNAs.
MA594221 - JP 2018138019-A/166147: Polycomb-Associated Non-Coding RNAs.
LF358645 - JP 2014500723-A/166148: Polycomb-Associated Non-Coding RNAs.
MA594222 - JP 2018138019-A/166148: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q29RF7 (Reactome details) participates in the following event(s):

R-HSA-2468040 Cohesin binds PDS5 and WAPAL
R-HSA-2545203 Deacetylation of cleaved cohesin
R-HSA-2470935 Cohesin binding to decondensed chromatin is facilitated by NIPBL:MAU2
R-HSA-1638821 PP2A-B56 dephosphorylates centromeric cohesin
R-HSA-1638803 Phosphorylation of cohesin by PLK1 at centromeres
R-HSA-2467811 Separation of sister chromatids
R-HSA-2467809 ESPL1 (Separase) cleaves centromeric cohesin
R-HSA-2468287 CDK1 phosphorylates CDCA5 (Sororin) at centromeres
R-HSA-2545253 Deacetylation of cohesin
R-HSA-2467794 Resolution of sister chromatids
R-HSA-2468293 CDK1 phosphorylates CDCA5 (Sororin) at chromosomal arms
R-HSA-2468041 CDCA5 (Sororin) enables cohesion of sister chromosomal arms
R-HSA-2466068 Phosphorylation of cohesin by PLK1 at chromosomal arms
R-HSA-2473152 Acetylation of SMC3 subunit of centromeric chromatin associated cohesin by ESCO1 or ESCO2
R-HSA-2468039 Acetylation of SMC3 subunit of chromosomal arm associated cohesin by ESCO1 or ESCO2
R-HSA-2473151 CDCA5 (Sororin) enables cohesion of sister centromeres
R-HSA-2470946 Cohesin Loading onto Chromatin
R-HSA-2467813 Separation of Sister Chromatids
R-HSA-68884 Mitotic Telophase/Cytokinesis
R-HSA-2500257 Resolution of Sister Chromatid Cohesion
R-HSA-68882 Mitotic Anaphase
R-HSA-2468052 Establishment of Sister Chromatid Cohesion
R-HSA-68886 M Phase
R-HSA-68877 Mitotic Prometaphase
R-HSA-2555396 Mitotic Metaphase and Anaphase
R-HSA-69242 S Phase
R-HSA-69278 Cell Cycle (Mitotic)
R-HSA-1640170 Cell Cycle

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000303538.1, ENST00000303538.10, ENST00000303538.11, ENST00000303538.12, ENST00000303538.2, ENST00000303538.3, ENST00000303538.4, ENST00000303538.5, ENST00000303538.6, ENST00000303538.7, ENST00000303538.8, ENST00000303538.9, KIAA0648 , NM_001100399, PDS5 , PDS5A , PDS5A_HUMAN, PIG54, Q29RF7, Q2TTR5, Q68DF7, Q8N7J4, Q8NG14, Q9Y4D4, uc317ngf.1, uc317ngf.2
UCSC ID: ENST00000303538.13_7
RefSeq Accession: NM_001100399.2
Protein: Q29RF7 (aka PDS5A_HUMAN)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.