Pacs2 (phosphofurin acidic cluster sorting protein 2) - Rat Genome Database
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Gene: Pacs2 (phosphofurin acidic cluster sorting protein 2) Rattus norvegicus
Analyze
Symbol: Pacs2
Name: phosphofurin acidic cluster sorting protein 2
RGD ID: 1597262
Description: Predicted to have ion channel binding activity. Predicted to be involved in several processes, including endoplasmic reticulum calcium ion homeostasis; mitochondrion-endoplasmic reticulum membrane tethering; and protein localization to phagophore assembly site. Predicted to localize to endoplasmic reticulum and mitochondrion. Human ortholog(s) of this gene implicated in early infantile epileptic encephalopathy 66. Orthologous to human PACS2 (phosphofurin acidic cluster sorting protein 2); INTERACTS WITH amphetamine; endosulfan; valproic acid.
Type: protein-coding
RefSeq Status: MODEL
Also known as: hypothetical protein LOC691631; LOC691631
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.06137,824,136 - 137,889,144 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl6137,824,213 - 137,887,418 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.06146,820,318 - 146,884,454 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.46138,023,917 - 138,080,745 (+)NCBIRGSC3.4rn4RGSC3.4
Celera6129,635,451 - 129,694,749 (+)NCBICelera
Cytogenetic Map6q32NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


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

Molecular Function

References

Additional References at PubMed
PMID:15692563   PMID:15692567   PMID:23455425   PMID:24646523   PMID:31210325  


Genomics

Comparative Map Data
Pacs2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.06137,824,136 - 137,889,144 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl6137,824,213 - 137,887,418 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.06146,820,318 - 146,884,454 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.46138,023,917 - 138,080,745 (+)NCBIRGSC3.4rn4RGSC3.4
Celera6129,635,451 - 129,694,749 (+)NCBICelera
Cytogenetic Map6q32NCBI
PACS2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl14105,300,563 - 105,398,147 (+)EnsemblGRCh38hg38GRCh38
GRCh3814105,300,718 - 105,398,147 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh3714105,767,170 - 105,864,484 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 3614104,852,126 - 104,935,529 (+)NCBINCBI36hg18NCBI36
Celera1485,829,098 - 85,913,416 (+)NCBI
Cytogenetic Map14q32.33NCBI
HuRef1485,963,394 - 86,060,744 (+)NCBIHuRef
CHM1_114105,697,018 - 105,802,244 (+)NCBICHM1_1
Pacs2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3912112,977,998 - 113,038,021 (+)NCBIGRCm39mm39
GRCm3812113,014,454 - 113,074,401 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl12113,014,508 - 113,074,401 (+)EnsemblGRCm38mm10GRCm38
MGSCv3712114,252,719 - 114,312,612 (+)NCBIGRCm37mm9NCBIm37
MGSCv3612113,462,316 - 113,522,209 (+)NCBImm8
Celera12114,258,367 - 114,288,553 (+)NCBICelera
Cytogenetic Map12F1NCBI
Pacs2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555383,559,724 - 3,619,649 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049555383,559,738 - 3,616,862 (+)NCBIChiLan1.0ChiLan1.0
PACS2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.114105,749,588 - 105,810,253 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl14105,737,878 - 105,810,349 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01485,935,807 - 86,035,935 (+)NCBIMhudiblu_PPA_v0panPan3
PACS2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl872,673,472 - 72,721,215 (+)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.1872,672,861 - 72,721,655 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Pacs2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_004936621172,727 - 206,803 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PACS2
(Sus scrofa - pig)
No map positions available.
PACS2
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12483,211,766 - 83,292,231 (+)NCBI
ChlSab1.1 Ensembl2483,212,300 - 83,295,233 (+)Ensembl
Pacs2
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_004624734125,190 - 184,690 (-)NCBI

Position Markers
RH135260  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.06137,870,344 - 137,870,545NCBIRnor6.0
Rnor_5.06146,865,654 - 146,865,855UniSTSRnor5.0
RGSC_v3.46138,064,396 - 138,064,597UniSTSRGSC3.4
Celera6129,675,949 - 129,676,150UniSTS
Cytogenetic Map6q32UniSTS
RH 3.4 Map6782.5UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
731173Uae22Urinary albumin excretion QTL 2210.1urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)668781170147991367Rat
2290393Uae37Urinary albumin excretion QTL 370.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)668781170147991367Rat
724513Uae14Urinary albumin excretion QTL 146.5urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)688996335139410483Rat
2303624Vencon5Ventilatory control QTL 54.45respiration trait (VT:0001943)minute ventilation (VE) (CMO:0000132)692879510137879510Rat
12801411Schws8Schwannoma susceptibility QTL 8nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)699273921144273921Rat
61414Pia3Pristane induced arthritis QTL 34.5joint integrity trait (VT:0010548)post-insult time to onset of experimental arthritis (CMO:0001450)699273921144792678Rat
8552796Vie3Viral induced encephalitis QTL 32.6brain integrity trait (VT:0010579)encephalitis incidence/prevalence measurement (CMO:0002361)6101207574147991367Rat
1358355Srcrt4Stress Responsive Cort QTL 46.39blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)6104363890147991367Rat
2313399Anxrr28Anxiety related response QTL 28aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)6104381930138066274Rat
4145118Mcs26Mammary carcinoma susceptibility QTL 260.0001mammary gland integrity trait (VT:0010552)post-insult time to mammary tumor formation (CMO:0000345)6111134524138065254Rat
737976Pia24Pristane induced arthritis QTL 24joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)6117355600147991367Rat
1641917Colcr5Colorectal carcinoma resistance QTL 53.180.0009intestine integrity trait (VT:0010554)benign colorectal tumor number (CMO:0001795)6127286494144745573Rat
2293085Iddm29Insulin dependent diabetes mellitus QTL 297.66blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)6127286494147249902Rat
61329Eae9Experimental allergic encephalomyelitis QTL 93.7body mass (VT:0001259)change in body weight (CMO:0002045)6127286494147991367Rat
2312560Pur20Proteinuria QTL 202.10.005total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)6130561943144745573Rat
71111Iddm8Insulin dependent diabetes mellitus QTL 81.90.002blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)6132652096138068606Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:192
Count of miRNA genes:83
Interacting mature miRNAs:88
Transcripts:ENSRNOT00000020027, ENSRNOT00000056880
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 33 38 22 18 22 8 11 74 35 41 11 8
Low 1 10 19 19 1 19
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts XM_006225889 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006225891 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006240668 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006240670 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017594524 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017594525 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017594526 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017603308 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017603309 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017603310 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017603311 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AABR07065617 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AABR07065618 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AABR07065619 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01046769 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01046770 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ212280 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000056880   ⟹   ENSRNOP00000053720
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl6137,824,213 - 137,887,418 (+)Ensembl
RefSeq Acc Id: XM_006225889   ⟹   XP_006225951
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera6129,635,452 - 129,694,749 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006225891   ⟹   XP_006225953
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera6129,635,452 - 129,694,749 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006240668   ⟹   XP_006240730
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.06137,824,137 - 137,889,144 (+)NCBI
Rnor_5.06146,820,318 - 146,884,454 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006240670   ⟹   XP_006240732
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.06137,824,137 - 137,889,144 (+)NCBI
Rnor_5.06146,820,318 - 146,884,454 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017594524   ⟹   XP_017450013
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.06137,824,136 - 137,889,144 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017594525   ⟹   XP_017450014
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.06137,824,137 - 137,889,144 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017594526   ⟹   XP_017450015
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.06137,847,952 - 137,889,144 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017603308   ⟹   XP_017458797
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera6129,635,451 - 129,694,749 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017603309   ⟹   XP_017458798
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera6129,635,452 - 129,694,749 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017603310   ⟹   XP_017458799
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera6129,658,918 - 129,694,749 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017603311   ⟹   XP_017458800
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera6129,643,875 - 129,694,749 (+)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: XP_006225951   ⟸   XM_006225889
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_006225953   ⟸   XM_006225891
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_006240730   ⟸   XM_006240668
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_006240732   ⟸   XM_006240670
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_017458797   ⟸   XM_017603308
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_017458798   ⟸   XM_017603309
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_017458800   ⟸   XM_017603311
- Peptide Label: isoform X6
- Sequence:
RefSeq Acc Id: XP_017458799   ⟸   XM_017603310
- Peptide Label: isoform X5
- Sequence:
RefSeq Acc Id: XP_017450013   ⟸   XM_017594524
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_017450014   ⟸   XM_017594525
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_017450015   ⟸   XM_017594526
- Peptide Label: isoform X5
- Sequence:
RefSeq Acc Id: ENSRNOP00000053720   ⟸   ENSRNOT00000056880

Transcriptome

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

Promoters
RGD ID:13694864
Promoter ID:EPDNEW_R5384
Type:multiple initiation site
Name:Pacs2_1
Description:phosphofurin acidic cluster sorting protein 2
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_6.06137,824,164 - 137,824,224EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Damaging Variants


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
6 137878865 137878866 G T snv ACI/N (MCW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1597262 AgrOrtholog
Ensembl Genes ENSRNOG00000014744 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000053720 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000056880 ENTREZGENE, UniProtKB/TrEMBL
InterPro Phosphofurin_acidic_CSp-1 UniProtKB/TrEMBL
NCBI Gene 691631 ENTREZGENE
PANTHER PTHR13280 UniProtKB/TrEMBL
Pfam Pacs-1 UniProtKB/TrEMBL
PhenoGen Pacs2 PhenoGen
UniGene Rn.155780 ENTREZGENE
UniProt D3ZJG4_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2012-10-02 Pacs2  phosphofurin acidic cluster sorting protein 2  LOC691631  hypothetical protein LOC691631  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-01-09 LOC691631  hypothetical protein LOC691631  LOC686271  hypothetical protein LOC686271  Data Merged 1643240 APPROVED
2006-11-20 LOC691631  hypothetical protein LOC691631      Symbol and Name status set to provisional 70820 PROVISIONAL
2006-11-19 LOC686271  hypothetical protein LOC686271      Symbol and Name status set to provisional 70820 PROVISIONAL