Pds5a (PDS5 cohesin associated factor A) - Rat Genome Database

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Gene: Pds5a (PDS5 cohesin associated factor A) Rattus norvegicus
Analyze
Symbol: Pds5a
Name: PDS5 cohesin associated factor A
RGD ID: 1307094
Description: Predicted to enable cohesin unloader activity. Predicted to be involved in mitotic sister chromatid cohesion and negative regulation of DNA replication. Predicted to act upstream of or within several processes, including embryonic skeletal system morphogenesis; enteric nervous system development; and neuroblast migration. Predicted to be active in chromatin and nucleus. Orthologous to human PDS5A (PDS5 cohesin associated factor A); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; acetamide; acrylamide.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC305343; PDS5, regulator of cohesion maintenance, homolog A; PDS5, regulator of cohesion maintenance, homolog A (S. cerevisiae); RGD1307094; Scc-112; similar to KIAA0648 protein; sister chromatid cohesion protein PDS5 homolog A
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81442,905,734 - 43,004,740 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1442,905,328 - 43,004,740 (+)EnsemblGRCr8
mRatBN7.21442,551,653 - 42,651,074 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1442,552,647 - 42,648,669 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1442,906,546 - 43,002,317 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01444,206,586 - 44,302,356 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01442,686,563 - 42,782,330 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01444,185,445 - 44,282,308 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1444,185,446 - 44,280,079 (+)Ensemblrn6Rnor6.0
Rnor_5.01444,002,786 - 44,101,920 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41445,242,856 - 45,339,943 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1441,703,489 - 41,799,690 (+)NCBICelera
RGSC_v3.11445,245,210 - 45,332,348 (+)NCBI
Cytogenetic Map14p11NCBI
JBrowse:




Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
chromatin  (IBA,ISO)
nucleoplasm  (ISO)
nucleus  (IBA,IEA)

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:16682347   PMID:19412548   PMID:19907496   PMID:21069257   PMID:21111234  


Genomics

Comparative Map Data
Pds5a
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81442,905,734 - 43,004,740 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1442,905,328 - 43,004,740 (+)EnsemblGRCr8
mRatBN7.21442,551,653 - 42,651,074 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1442,552,647 - 42,648,669 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1442,906,546 - 43,002,317 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01444,206,586 - 44,302,356 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01442,686,563 - 42,782,330 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01444,185,445 - 44,282,308 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1444,185,446 - 44,280,079 (+)Ensemblrn6Rnor6.0
Rnor_5.01444,002,786 - 44,101,920 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41445,242,856 - 45,339,943 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1441,703,489 - 41,799,690 (+)NCBICelera
RGSC_v3.11445,245,210 - 45,332,348 (+)NCBI
Cytogenetic Map14p11NCBI
PDS5A
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38439,822,863 - 39,977,911 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl439,822,863 - 39,977,987 (-)Ensemblhg38GRCh38
GRCh37439,824,483 - 39,979,531 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36439,500,878 - 39,655,971 (-)NCBIBuild 36Build 36hg18NCBI36
Celera440,262,836 - 40,418,746 (-)NCBICelera
Cytogenetic Map4p14NCBI
HuRef439,148,123 - 39,303,097 (-)NCBIHuRef
CHM1_1439,824,013 - 39,979,289 (-)NCBICHM1_1
T2T-CHM13v2.0439,792,793 - 39,947,875 (-)NCBIT2T-CHM13v2.0
Pds5a
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39565,763,062 - 65,855,579 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl565,763,064 - 65,855,616 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm38565,605,719 - 65,698,236 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl565,605,721 - 65,698,273 (-)Ensemblmm10GRCm38
MGSCv37566,006,499 - 66,089,095 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv36565,894,395 - 65,976,991 (-)NCBIMGSCv36mm8
Celera562,894,477 - 62,976,070 (-)NCBICelera
Cytogenetic Map5C3.1NCBI
Pds5a
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554437,475,385 - 7,604,714 (+)Ensembl
ChiLan1.0NW_0049554437,475,434 - 7,603,548 (+)NCBIChiLan1.0ChiLan1.0
PDS5A
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2340,010,324 - 40,163,673 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1440,202,307 - 40,355,091 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0434,149,622 - 34,303,065 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1440,002,869 - 40,156,698 (-)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl440,002,869 - 40,156,698 (-)EnsemblpanPan2panpan1.1
PDS5A
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1372,521,839 - 72,673,164 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl372,521,868 - 72,673,164 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha375,069,353 - 75,219,966 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0373,293,527 - 73,445,444 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl373,293,480 - 73,445,444 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1372,561,918 - 72,712,462 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0372,707,576 - 72,858,212 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0373,093,485 - 73,244,844 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Pds5a
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440528538,830,942 - 38,960,760 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049364827,340,236 - 7,467,484 (-)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049364827,337,475 - 7,466,715 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PDS5A
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl830,988,370 - 31,134,331 (-)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1830,988,366 - 31,134,331 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2832,549,363 - 32,553,717 (+)NCBISscrofa10.2Sscrofa10.2susScr3
PDS5A
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12710,333,784 - 10,502,113 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2710,388,334 - 10,487,029 (+)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366604756,716,378 - 56,883,955 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Pds5a
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462476127,030,615 - 27,175,960 (+)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_00462476127,029,420 - 27,186,537 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
Pds5a
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v11122,661,927 - 22,753,151 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Pds5a
328 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:16
Count of miRNA genes:16
Interacting mature miRNAs:16
Transcripts:ENSRNOT00000003437
Prediction methods:Miranda, Rnahybrid
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2313089Bss81Bone structure and strength QTL 813.40.0001body length (VT:0001256)body length, nose to rump (CMO:0000079)143802371083023710Rat
70214Niddm28Non-insulin dependent diabetes mellitus QTL 284.06blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)143900944484009444Rat
1300154Bp189Blood pressure QTL 1893.04arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)143123808072970315Rat
70187Pancm5Pancreatic morphology QTL 516.7pancreas mass (VT:0010144)pancreas weight to body weight ratio (CMO:0000630)143067446985041098Rat
631523Pia13Pristane induced arthritis QTL 133.3joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1433424686102238540Rat
1358296Ael3Aortic elastin QTL 33.70.00051aorta elastin amount (VT:0003905)aortic elastin14862139853621398Rat
2313100Bss82Bone structure and strength QTL 8230.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)143802371083023710Rat
7387267Uae42Urinary albumin excretion QTL 420.61urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)142252151767521517Rat
631839Niddm37Non-insulin dependent diabetes mellitus QTL 373.37blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1411334716100078267Rat
2313397Coatc1Coat color QTL1coat/hair pigmentation trait (VT:0010463)coat/hair color measurement (CMO:0001808)141889519263895192Rat
631262Tcas4Tongue tumor susceptibility QTL 47.29tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)141790672654251504Rat
1300136Rf22Renal function QTL 223.9renal blood flow trait (VT:2000006)absolute change in renal vascular resistance (CMO:0001900)144261625899224555Rat
2313048Bss84Bone structure and strength QTL 843.10.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)143802371083023710Rat
2302045Pia39Pristane induced arthritis QTL 394.90.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G2a level (CMO:0002116)14862139853621398Rat
738037Hcas6Hepatocarcinoma susceptibility QTL 62.93liver integrity trait (VT:0010547)liver nonremodeling tumorous lesion volume to total liver volume ratio (CMO:0001464)143941117087582095Rat
2313084Bss83Bone structure and strength QTL 832.90.0001tibia size trait (VT:0100001)tibia midshaft endosteal cross-sectional area (CMO:0001716)143802371083023710Rat

Markers in Region
D14Got103  
Rat AssemblyChrPosition (strand)SourceJBrowse
GRCr81442,976,759 - 42,976,990 (+)Marker Load Pipeline
mRatBN7.21442,623,091 - 42,623,324 (+)MAPPERmRatBN7.2
Rnor_6.01444,254,107 - 44,254,337NCBIRnor6.0
Rnor_5.01444,073,719 - 44,073,949UniSTSRnor5.0
RGSC_v3.41445,314,496 - 45,314,726UniSTSRGSC3.4
Celera1441,774,128 - 41,774,380UniSTS
Cytogenetic Map14p11UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
16 12 67 165 91 90 59 92 59 6 356 192 11 144 81 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000003437   ⟹   ENSRNOP00000003437
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1442,906,333 - 43,002,335 (+)Ensembl
mRatBN7.2 Ensembl1442,552,647 - 42,648,669 (+)Ensembl
Rnor_6.0 Ensembl1444,185,446 - 44,280,079 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000143027   ⟹   ENSRNOP00000107870
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1442,905,328 - 43,004,740 (+)Ensembl
RefSeq Acc Id: NM_001083624   ⟹   NP_001077093
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81442,906,333 - 43,002,335 (+)NCBI
mRatBN7.21442,552,647 - 42,648,669 (+)NCBI
Rnor_6.01444,185,479 - 44,279,903 (+)NCBI
Rnor_5.01444,002,786 - 44,101,920 (+)NCBI
RGSC_v3.41445,242,856 - 45,339,943 (+)RGD
Celera1441,703,489 - 41,799,690 (+)RGD
Sequence:
RefSeq Acc Id: XM_039091918   ⟹   XP_038947846
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81442,905,734 - 43,004,740 (+)NCBI
mRatBN7.21442,551,956 - 42,651,074 (+)NCBI
RefSeq Acc Id: XM_063273131   ⟹   XP_063129201
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81442,905,741 - 43,004,740 (+)NCBI
RefSeq Acc Id: XM_063273132   ⟹   XP_063129202
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81442,905,734 - 43,004,740 (+)NCBI
RefSeq Acc Id: XM_063273133   ⟹   XP_063129203
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81442,958,718 - 43,004,740 (+)NCBI
RefSeq Acc Id: NP_001077093   ⟸   NM_001083624
- UniProtKB: A4L9P7 (UniProtKB/Swiss-Prot)
- Sequence:
Ensembl Acc Id: ENSRNOP00000003437   ⟸   ENSRNOT00000003437
RefSeq Acc Id: XP_038947846   ⟸   XM_039091918
- Peptide Label: isoform X1
- UniProtKB: A0A8L2Q0A3 (UniProtKB/TrEMBL),   A6JDD2 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063129202   ⟸   XM_063273132
- Peptide Label: isoform X3
RefSeq Acc Id: XP_063129201   ⟸   XM_063273131
- Peptide Label: isoform X2
- UniProtKB: A4L9P7 (UniProtKB/Swiss-Prot)
RefSeq Acc Id: XP_063129203   ⟸   XM_063273133
- Peptide Label: isoform X4
Ensembl Acc Id: ENSRNOP00000107870   ⟸   ENSRNOT00000143027

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-A4L9P7-F1-model_v2 AlphaFold A4L9P7 1-1333 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1307094 AgrOrtholog
BioCyc Gene G2FUF-15753 BioCyc
Ensembl Genes ENSRNOG00000002541 Ensembl, ENTREZGENE
Ensembl Transcript ENSRNOT00000003437 ENTREZGENE
  ENSRNOT00000143027 ENTREZGENE
Gene3D-CATH 1.25.10.10 UniProtKB/Swiss-Prot
InterPro ARM-like UniProtKB/Swiss-Prot
  ARM-type_fold UniProtKB/Swiss-Prot
  Pds5 UniProtKB/Swiss-Prot
KEGG Report rno:305343 UniProtKB/Swiss-Prot
NCBI Gene 305343 ENTREZGENE
PANTHER PTHR12663 UniProtKB/Swiss-Prot
  SISTER CHROMATID COHESION PROTEIN PDS5 HOMOLOG A UniProtKB/Swiss-Prot
Pfam PDS5 UniProtKB/Swiss-Prot
PhenoGen Pds5a PhenoGen
RatGTEx ENSRNOG00000002541 RatGTEx
Superfamily-SCOP SSF48371 UniProtKB/Swiss-Prot
UniProt A0A8L2Q0A3 ENTREZGENE, UniProtKB/TrEMBL
  A0ABK0LPV4_RAT UniProtKB/TrEMBL
  A4L9P7 ENTREZGENE
  A6JDD2 ENTREZGENE, UniProtKB/TrEMBL
  PDS5A_RAT UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2014-12-01 Pds5a  PDS5 cohesin associated factor A  Pds5a  PDS5, regulator of cohesion maintenance, homolog A (S. cerevisiae)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-07 Pds5a  PDS5, regulator of cohesion maintenance, homolog A (S. cerevisiae)  RGD1307094_predicted  similar to KIAA0648 protein (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-01-20 RGD1307094_predicted  similar to KIAA0648 protein (predicted)  LOC305343_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC305343_predicted  similar to KIAA0648 protein (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL