Pds5b (PDS5 cohesin associated factor B) - Rat Genome Database

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Gene: Pds5b (PDS5 cohesin associated factor B) Rattus norvegicus
Analyze
Symbol: Pds5b
Name: PDS5 cohesin associated factor B
RGD ID: 1310838
Description: Predicted to enable DNA binding activity. Involved in negative regulation of cell population proliferation. Located in nucleus. Orthologous to human PDS5B (PDS5 cohesin associated factor B); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; aconitine; bisphenol A.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: androgen-induced proliferation inhibitor; androgen-induced prostate proliferative shutoff associated protein; androgen-induced prostate proliferative shutoff-associated protein AS3; androgen-induced shutoff 3; Aprin; AS3; CG008; FLJ23236; KIAA0979; LOC304218; PDS5, regulator of cohesion maintenance, homolog B; PDS5, regulator of cohesion maintenance, homolog B (S. cerevisiae); sister chromatid cohesion protein PDS5 homolog B
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.212202,481 - 345,596 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl12255,313 - 345,596 (+)Ensembl
Rnor_6.012659,995 - 794,042 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl12660,011 - 794,042 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.012644,249 - 777,801 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4124,038,430 - 4,128,352 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1124,038,429 - 4,128,343 (-)NCBI
Celera121,961,611 - 2,051,657 (+)NCBICelera
Cytogenetic Map12p12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


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

Cellular Component
chromatin  (IBA,IEA,ISO)
nucleoplasm  (IEA,ISO)
nucleus  (IBA,IDA,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. Mechanism of androgen action on cell proliferation: AS3 protein as a mediator of proliferative arrest in the rat prostate. Maffini MV, etal., Endocrinology. 2002 Jul;143(7):2708-14.
3. GOA pipeline RGD automated data pipeline
4. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
5. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:10963680   PMID:15855230   PMID:16682347   PMID:19412548  


Genomics

Comparative Map Data
Pds5b
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.212202,481 - 345,596 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl12255,313 - 345,596 (+)Ensembl
Rnor_6.012659,995 - 794,042 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl12660,011 - 794,042 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.012644,249 - 777,801 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4124,038,430 - 4,128,352 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1124,038,429 - 4,128,343 (-)NCBI
Celera121,961,611 - 2,051,657 (+)NCBICelera
Cytogenetic Map12p12NCBI
PDS5B
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381332,586,452 - 32,778,019 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl1332,586,452 - 32,778,019 (+)EnsemblGRCh38hg38GRCh38
GRCh371333,160,589 - 33,352,157 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361332,058,624 - 32,250,157 (+)NCBINCBI36hg18NCBI36
Celera1314,227,385 - 14,418,972 (+)NCBI
Cytogenetic Map13q13.1NCBI
HuRef1313,971,711 - 14,163,184 (+)NCBIHuRef
CHM1_11333,128,125 - 33,319,684 (+)NCBICHM1_1
T2T-CHM13v2.01331,803,785 - 31,995,311 (+)NCBI
Pds5b
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm395150,597,178 - 150,734,134 (+)NCBIGRCm39mm39
GRCm39 Ensembl5150,597,204 - 150,734,155 (+)Ensembl
GRCm385150,673,713 - 150,810,669 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl5150,673,739 - 150,810,690 (+)EnsemblGRCm38mm10GRCm38
MGSCv375151,476,402 - 151,613,244 (+)NCBIGRCm37mm9NCBIm37
MGSCv365150,984,792 - 151,077,265 (+)NCBImm8
Celera5148,678,294 - 148,814,947 (+)NCBICelera
Cytogenetic Map5G3NCBI
Pds5b
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495543113,078,726 - 13,197,482 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495543113,083,229 - 13,268,680 (-)NCBIChiLan1.0ChiLan1.0
PDS5B
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11332,337,765 - 32,462,333 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1332,337,765 - 32,462,333 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01313,843,910 - 14,033,043 (+)NCBIMhudiblu_PPA_v0panPan3
PDS5B
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1257,407,533 - 7,587,177 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl257,410,481 - 7,586,563 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha257,437,222 - 7,617,068 (-)NCBI
ROS_Cfam_1.0257,503,195 - 7,683,352 (-)NCBI
ROS_Cfam_1.0 Ensembl257,505,704 - 7,683,280 (-)Ensembl
UMICH_Zoey_3.1257,402,088 - 7,583,594 (-)NCBI
UNSW_CanFamBas_1.0257,401,438 - 7,581,519 (-)NCBI
UU_Cfam_GSD_1.0257,458,932 - 7,638,962 (-)NCBI
Pds5b
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404945168,574,878 - 168,766,999 (-)NCBI
SpeTri2.0NW_00493647227,258,084 - 27,377,278 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PDS5B
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl119,014,377 - 9,223,035 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1119,014,694 - 9,223,035 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2119,020,332 - 9,044,202 (+)NCBISscrofa10.2Sscrofa10.2susScr3
PDS5B
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1311,330,817 - 11,511,411 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl311,389,199 - 11,508,441 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366605732,839,271 - 33,022,073 (-)NCBIVero_WHO_p1.0
Pds5b
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247765,013,796 - 5,244,957 (-)EnsemblHetGla_female_1.0hetGla2
HetGla 1.0NW_0046247765,013,796 - 5,225,743 (-)NCBIHetGla_female_1.0hetGla2

Position Markers
RH131564  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.212345,190 - 345,400 (+)MAPPERmRatBN7.2
Rnor_6.012793,637 - 793,846NCBIRnor6.0
Rnor_5.012777,396 - 777,605UniSTSRnor5.0
RGSC_v3.4124,038,626 - 4,038,835UniSTSRGSC3.4
Celera122,051,252 - 2,051,461UniSTS
Cytogenetic Map12p12UniSTS
RH140226  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.212343,139 - 343,333 (+)MAPPERmRatBN7.2
Rnor_6.012791,586 - 791,779NCBIRnor6.0
Rnor_5.012775,345 - 775,538UniSTSRnor5.0
RGSC_v3.4124,040,693 - 4,040,886UniSTSRGSC3.4
Celera122,049,201 - 2,049,394UniSTS
Cytogenetic Map12p12UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1300174Bw15Body weight QTL 152.93body mass (VT:0001259)body weight loss (CMO:0001399)1219318387Rat
2312418Kidm41Kidney mass QTL 413.70.0001kidney mass (VT:0002707)single kidney wet weight to body weight ratio (CMO:0000622)12119611090Rat
10755457Coatc14Coat color QTL 140.01759coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)12122591684Rat
6893681Bw109Body weight QTL 1092.30.004body mass (VT:0001259)body weight (CMO:0000012)12123297788Rat
1581516Cm56Cardiac mass QTL 564.20.05heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)12129333307Rat
1598855Bp294Blood pressure QTL 2943.5arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)12134851688Rat
7411660Foco28Food consumption QTL 2810.90.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12142110980Rat
9590086Insglur6Insulin/glucose ratio QTL 618.970.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)12142110980Rat
8694179Bw150Body weight QTL 1502.90.001body mass (VT:0001259)body weight gain (CMO:0000420)12142110980Rat
7411586Foco5Food consumption QTL 55.40.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12142110980Rat
7411595Foco9Food consumption QTL 940.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12142110980Rat
7411545Bw128Body weight QTL 1285.20.001body mass (VT:0001259)body weight gain (CMO:0000420)12142110980Rat
9590147Scort7Serum corticosterone level QTL 713.610.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)12142110980Rat
2303575Insul14Insulin level QTL 144blood insulin amount (VT:0001560)blood insulin level (CMO:0000349)12142450532Rat
737979Pia22Pristane induced arthritis QTL 2253.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)12144465750Rat
634351Apr5Acute phase response QTL 56.7blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)12144503507Rat
2302042Pia38Pristane induced arthritis QTL 383.50.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G1 level (CMO:0002115)12144503507Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:3028
Count of miRNA genes:317
Interacting mature miRNAs:410
Transcripts:ENSRNOT00000001464, ENSRNOT00000040830, ENSRNOT00000050733, ENSRNOT00000064951, ENSRNOT00000074682
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
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.


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 2 29 34 18 19 18 3 3 74 27 40 11 3
Low 1 14 23 23 23 5 8 8 1 5
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001101805 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001102383 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008768957 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017598313 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017598314 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039089319 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039089320 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039089321 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039089322 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039089323 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039089324 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039089325 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039089328 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AY388627 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY820182 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY820183 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY831451 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY831452 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY836673 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH474108 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CK357543 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000223 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000001464   ⟹   ENSRNOP00000001464
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl12255,323 - 345,596 (+)Ensembl
Rnor_6.0 Ensembl12703,281 - 794,042 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000040830   ⟹   ENSRNOP00000041874
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl12255,313 - 334,077 (+)Ensembl
Rnor_6.0 Ensembl12660,011 - 783,122 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000050733   ⟹   ENSRNOP00000040297
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl12255,323 - 345,596 (+)Ensembl
Rnor_6.0 Ensembl12703,290 - 791,222 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000064951   ⟹   ENSRNOP00000063199
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl12255,313 - 341,484 (+)Ensembl
Rnor_6.0 Ensembl12703,290 - 791,222 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000107387   ⟹   ENSRNOP00000083511
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl12255,323 - 345,596 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000112327   ⟹   ENSRNOP00000092974
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl12255,323 - 345,596 (+)Ensembl
RefSeq Acc Id: NM_001101805   ⟹   NP_001095275
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.212255,323 - 345,596 (+)NCBI
Rnor_6.012703,281 - 794,042 (+)NCBI
Rnor_5.012644,249 - 777,801 (+)NCBI
RGSC_v3.4124,038,430 - 4,128,352 (-)RGD
Celera121,961,611 - 2,051,657 (+)RGD
Sequence:
RefSeq Acc Id: NM_001102383   ⟹   NP_001095853
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.212255,323 - 345,596 (+)NCBI
Rnor_6.012703,281 - 794,042 (+)NCBI
Rnor_5.012644,249 - 777,801 (+)NCBI
RGSC_v3.4124,038,430 - 4,128,352 (-)RGD
Celera121,961,611 - 2,051,657 (+)RGD
Sequence:
RefSeq Acc Id: XM_017598313   ⟹   XP_017453802
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.212255,313 - 331,001 (+)NCBI
Rnor_6.012703,271 - 779,444 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039089319   ⟹   XP_038945247
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.212255,313 - 345,561 (+)NCBI
RefSeq Acc Id: XM_039089320   ⟹   XP_038945248
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.212255,313 - 345,561 (+)NCBI
RefSeq Acc Id: XM_039089321   ⟹   XP_038945249
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.212255,313 - 345,561 (+)NCBI
RefSeq Acc Id: XM_039089322   ⟹   XP_038945250
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.212209,608 - 345,561 (+)NCBI
RefSeq Acc Id: XM_039089323   ⟹   XP_038945251
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.212202,481 - 345,561 (+)NCBI
RefSeq Acc Id: XM_039089324   ⟹   XP_038945252
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.212202,502 - 345,561 (+)NCBI
RefSeq Acc Id: XM_039089325   ⟹   XP_038945253
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.212255,313 - 345,561 (+)NCBI
RefSeq Acc Id: XM_039089328   ⟹   XP_038945256
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.212255,313 - 345,561 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_001095275   ⟸   NM_001101805
- Peptide Label: isoform 2
- UniProtKB: D3ZU56 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: NP_001095853   ⟸   NM_001102383
- Peptide Label: isoform 1
- UniProtKB: D3ZXE2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017453802   ⟸   XM_017598313
- Peptide Label: isoform X7
- Sequence:
RefSeq Acc Id: ENSRNOP00000001464   ⟸   ENSRNOT00000001464
RefSeq Acc Id: ENSRNOP00000041874   ⟸   ENSRNOT00000040830
RefSeq Acc Id: ENSRNOP00000063199   ⟸   ENSRNOT00000064951
RefSeq Acc Id: ENSRNOP00000040297   ⟸   ENSRNOT00000050733
RefSeq Acc Id: XP_038945251   ⟸   XM_039089323
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038945252   ⟸   XM_039089324
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038945250   ⟸   XM_039089322
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038945247   ⟸   XM_039089319
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038945253   ⟸   XM_039089325
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038945248   ⟸   XM_039089320
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038945249   ⟸   XM_039089321
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038945256   ⟸   XM_039089328
- Peptide Label: isoform X6
RefSeq Acc Id: ENSRNOP00000083511   ⟸   ENSRNOT00000107387
RefSeq Acc Id: ENSRNOP00000092974   ⟸   ENSRNOT00000112327

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q6TRW4-F1-model_v2 AlphaFold Q6TRW4 1-1447 view protein structure

Transcriptome

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

Promoters
RGD ID:13698385
Promoter ID:EPDNEW_R8884
Type:initiation region
Name:Pds5b_1
Description:PDS5 cohesin associated factor B
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.012659,993 - 660,053EPDNEW

Strain Variation

Strain Sequence Variants (MRatBN7.2)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN-Lx/CubMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BUF/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
DA/OlaHsd (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/Stm (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE16/Stm (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/FarMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB10/IpcvMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF10A/StmMcwi (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrcAek (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrcAek (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrcAek (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/NRrrcMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MWF/Hsd (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHR/OlalpcvMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WAG/RijCrl (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/N (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Damaging Variants


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
12 707531 707532 G A snv WKY/N (MCW)


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
12 759978 759979 G C snv F344/Stm (KyushuU), F344/DuCrlCrlj (KyushuU)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1310838 AgrOrtholog
BioCyc Gene G2FUF-20522 BioCyc
Ensembl Genes ENSRNOG00000001098 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000001464 ENTREZGENE
  ENSRNOP00000001464.5 UniProtKB/TrEMBL
  ENSRNOP00000040297 ENTREZGENE
  ENSRNOP00000040297.6 UniProtKB/TrEMBL
  ENSRNOP00000041874.6 UniProtKB/TrEMBL
  ENSRNOP00000063199.2 UniProtKB/TrEMBL
  ENSRNOP00000083511 ENTREZGENE
  ENSRNOP00000083511.1 UniProtKB/TrEMBL
  ENSRNOP00000092974 ENTREZGENE
  ENSRNOP00000092974.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000001464 ENTREZGENE
  ENSRNOT00000001464.8 UniProtKB/TrEMBL
  ENSRNOT00000040830.6 UniProtKB/TrEMBL
  ENSRNOT00000050733 ENTREZGENE
  ENSRNOT00000050733.7 UniProtKB/TrEMBL
  ENSRNOT00000064951.4 UniProtKB/TrEMBL
  ENSRNOT00000107387 ENTREZGENE
  ENSRNOT00000107387.1 UniProtKB/TrEMBL
  ENSRNOT00000112327 ENTREZGENE
  ENSRNOT00000112327.1 UniProtKB/TrEMBL
Gene3D-CATH 1.25.10.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro ARM-like UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ARM-type_fold UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Pds5 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:304218 UniProtKB/TrEMBL
NCBI Gene 304218 ENTREZGENE
PANTHER PTHR12663 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Pds5b PhenoGen
Superfamily-SCOP SSF48371 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A8I6GAU9_RAT UniProtKB/TrEMBL
  A0A8I6GK18_RAT UniProtKB/TrEMBL
  D3ZMU3_RAT UniProtKB/TrEMBL
  D3ZU56 ENTREZGENE, UniProtKB/TrEMBL
  D3ZXE2 ENTREZGENE, UniProtKB/TrEMBL
  F1M797_RAT UniProtKB/TrEMBL
  PDS5B_RAT UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary Q5G5U1 UniProtKB/Swiss-Prot
  Q5G6V7 UniProtKB/Swiss-Prot
  Q5G6V8 UniProtKB/Swiss-Prot
  Q5PY35 UniProtKB/Swiss-Prot
  Q5PY36 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2014-12-01 Pds5b  PDS5 cohesin associated factor B  Pds5b  PDS5, regulator of cohesion maintenance, homolog B (S. cerevisiae)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2013-05-24 Pds5b  PDS5, regulator of cohesion maintenance, homolog B (S. cerevisiae)  RGD1624199  androgen-induced proliferation inhibitor  Data Merged 1643240 APPROVED
2008-01-30 Pds5b  PDS5, regulator of cohesion maintenance, homolog B (S. cerevisiae)  Aprin_predicted  androgen-induced proliferation inhibitor (predicted)  Symbol and Name updated to reflect Human and Mouse nomenclature 1299863 APPROVED
2006-03-07 Aprin_predicted  androgen-induced proliferation inhibitor (predicted)  Aprin  androgen-induced proliferation inhibitor  Symbol and Name status set to approved 1299863 APPROVED
2005-12-06 Aprin  androgen-induced proliferation inhibitor  Aprin_predicted  androgen-induced proliferation inhibitor (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-12 Aprin_predicted  androgen-induced proliferation inhibitor (predicted)      Symbol and Name status set to approved 70820 APPROVED