Pcsk4 (proprotein convertase subtilisin/kexin type 4) - Rat Genome Database

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Gene: Pcsk4 (proprotein convertase subtilisin/kexin type 4) Rattus norvegicus
Analyze
Symbol: Pcsk4
Name: proprotein convertase subtilisin/kexin type 4
RGD ID: 620325
Description: Predicted to have serine-type endopeptidase activity. Predicted to be involved in peptide hormone processing; single fertilization; and sperm capacitation. Predicted to localize to acrosomal membrane; integral component of Golgi membrane; and trans-Golgi network. Orthologous to human PCSK4 (proprotein convertase subtilisin/kexin type 4); INTERACTS WITH 2,2',4,4'-Tetrabromodiphenyl ether; 2,2',5,5'-tetrachlorobiphenyl; 2,4-dinitrotoluene.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: KEX2-like endoprotease 3; NEC 3; neuroendocrine convertase 3; PC4; prohormone convertase 3
RGD Orthologs
Human
Mouse
Chinchilla
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
mRatBN7.279,381,366 - 9,389,589 (+)NCBI
Rnor_6.0 Ensembl712,247,498 - 12,255,719 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0712,247,498 - 12,255,721 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0712,417,102 - 12,425,518 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4710,892,705 - 10,900,928 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1710,892,704 - 10,900,926 (+)NCBI
Celera77,558,158 - 7,566,382 (+)NCBICelera
Cytogenetic Map7q11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

References

Additional References at PubMed
PMID:9192653   PMID:12477932   PMID:16040806   PMID:16371590   PMID:19342015   PMID:21080038   PMID:21302280  


Genomics

Comparative Map Data
Pcsk4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.279,381,366 - 9,389,589 (+)NCBI
Rnor_6.0 Ensembl712,247,498 - 12,255,719 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0712,247,498 - 12,255,721 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0712,417,102 - 12,425,518 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4710,892,705 - 10,900,928 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1710,892,704 - 10,900,926 (+)NCBI
Celera77,558,158 - 7,566,382 (+)NCBICelera
Cytogenetic Map7q11NCBI
PCSK4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl191,481,428 - 1,490,752 (-)EnsemblGRCh38hg38GRCh38
GRCh38191,481,428 - 1,490,874 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37191,481,427 - 1,490,449 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36191,432,427 - 1,441,407 (-)NCBINCBI36hg18NCBI36
Build 34191,432,426 - 1,434,843NCBI
Celera191,415,419 - 1,424,399 (-)NCBI
Cytogenetic Map19p13.3NCBI
HuRef191,255,223 - 1,264,091 (-)NCBIHuRef
CHM1_1191,481,431 - 1,490,453 (-)NCBICHM1_1
Pcsk4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391080,157,117 - 80,165,583 (-)NCBIGRCm39mm39
GRCm39 Ensembl1080,157,117 - 80,165,332 (-)Ensembl
GRCm381080,321,283 - 80,329,748 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1080,321,283 - 80,329,498 (-)EnsemblGRCm38mm10GRCm38
MGSCv371079,784,028 - 79,792,218 (-)NCBIGRCm37mm9NCBIm37
MGSCv361079,724,431 - 79,732,602 (-)NCBImm8
Celera1081,336,155 - 81,344,348 (-)NCBICelera
Cytogenetic Map10C1NCBI
cM Map1039.72NCBI
Pcsk4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554956,453,991 - 6,459,744 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554956,424,426 - 6,460,252 (+)NCBIChiLan1.0ChiLan1.0
PCSK4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12057,370,035 - 57,376,207 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2057,369,328 - 57,375,590 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2057,162,069 - 57,168,223 (+)NCBI
ROS_Cfam_1.02058,101,329 - 58,107,483 (+)NCBI
UMICH_Zoey_3.12057,157,552 - 57,163,690 (+)NCBI
UNSW_CanFamBas_1.02057,637,009 - 57,643,163 (+)NCBI
UU_Cfam_GSD_1.02057,839,018 - 57,845,172 (+)NCBI
Pcsk4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118217,035,019 - 217,041,168 (+)NCBI
SpeTri2.0NW_004936588793,615 - 800,038 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PCSK4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl276,989,641 - 76,996,509 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1276,982,806 - 76,996,507 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2277,881,928 - 77,888,794 (+)NCBISscrofa10.2Sscrofa10.2susScr3
PCSK4
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.161,253,729 - 1,264,114 (-)NCBI
ChlSab1.1 Ensembl61,254,276 - 1,263,847 (-)Ensembl
Pcsk4
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248287,208,995 - 7,216,188 (+)NCBI

Position Markers
AI576245  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.279,384,203 - 9,384,306 (+)MAPPER
Rnor_6.0712,250,336 - 12,250,438NCBIRnor6.0
Rnor_5.0712,420,131 - 12,420,233UniSTSRnor5.0
RGSC_v3.4710,895,543 - 10,895,645UniSTSRGSC3.4
Celera77,560,997 - 7,561,099UniSTS
RH 3.4 Map725.3UniSTS
Cytogenetic Map7q11UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2298550Neuinf6Neuroinflammation QTL 63.3nervous system integrity trait (VT:0010566)spinal cord RT1-B protein level (CMO:0002132)7134147172Rat
9590142Scort5Serum corticosterone level QTL 524.40.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)7134828535Rat
7411566Bw136Body weight QTL 13610.40.001body mass (VT:0001259)body weight gain (CMO:0000420)7134828535Rat
724560Plsm3Polydactyly-luxate syndrome (PLS) morphotypes QTL 30.0003tibia length (VT:0004357)tibia length (CMO:0000450)7137009673Rat
2317047Wbc4White blood cell count QTL 40.01leukocyte quantity (VT:0000217)white blood cell count (CMO:0000027)7138119654Rat
1300176Hrtrt10Heart rate QTL 103.19heart pumping trait (VT:2000009)heart rate (CMO:0000002)7265313832258115Rat
634336Anxrr17Anxiety related response QTL 173.66locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)72920071124838025Rat
61410Bw19Body weight QTL 196.20.001body mass (VT:0001259)body weight (CMO:0000012)7591147750911477Rat
631503Bp102Blood pressure QTL 1021.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)7595196950951969Rat
10755438Coatc9Coat color QTL 90coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)7975804554758045Rat
9590102Sffal5Serum free fatty acids level QTL 58.620.001blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)71164710256647102Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:179
Count of miRNA genes:111
Interacting mature miRNAs:128
Transcripts:ENSRNOT00000022358
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 8
Low 3 14 37 27 5 27 2 5 74 34 32 11 2
Below cutoff 25 19 14 13 14 6 6 1 1 6

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000022358   ⟹   ENSRNOP00000022358
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl712,247,498 - 12,255,719 (+)Ensembl
RefSeq Acc Id: NM_133559   ⟹   NP_598243
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.279,381,366 - 9,389,589 (+)NCBI
Rnor_6.0712,247,498 - 12,255,721 (+)NCBI
Rnor_5.0712,417,102 - 12,425,518 (+)NCBI
RGSC_v3.4710,892,705 - 10,900,928 (+)RGD
Celera77,558,158 - 7,566,382 (+)RGD
Sequence:
Reference Sequences
RefSeq Acc Id: NP_598243   ⟸   NM_133559
- Peptide Label: precursor
- UniProtKB: Q78EH2 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000022358   ⟸   ENSRNOT00000022358
Protein Domains
P/Homo B   Peptidase S8

Transcriptome

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

Promoters
RGD ID:13695023
Promoter ID:EPDNEW_R5548
Type:multiple initiation site
Name:Pcsk4_1
Description:proprotein convertase subtilisin/kexin type 4
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_6.0712,247,478 - 12,247,538EPDNEW

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)
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
SBH/Ygl (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: SBH/Ygl sequenced by MCW
SBH/Ygl (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
SBN/Ygl (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: SBN/Ygl sequenced by MCW
SBN/Ygl (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
SHR/NHsd (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
SHRSP/Gcrc (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
SR/JrHsd (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: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (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
SS/Jr (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
SS/JrHsdMcwi (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)
SS/JrHsdMcwi (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
WAG/Rij (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
WKY/Gcrc (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
WKY/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
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_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
7 12424914 12424915 C T snv GH/OmrMcwi (MCW), ZFDM (KyushuU), BBDP/WorN (KNAW), WKY/NCrl (KNAW), LE/Stm (Illumina) (KNAW), LE/Stm (SOLiD) (KNAW), LEW/Crl (KNAW), LEW/NCrl (KNAW), MNS/Gib (KNAW), SDLEF7/Barth (UDEL), LE/OrlBarth (UDEL), Crl:SD (UDEL), BUF/MNa (KyushuU), LE/Stm (KyushuU), HTX/Kyo (KyushuU), ZF (KyushuU), MHS/Gib (KNAW)


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
7 12255119 12255120 C T snv GH/OmrMcwi (MCW)


Assembly: RGSC_v3.4

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
7 10900326 10900327 C T snv LE/Stm (KNAW), GH/OmrMcwi (MCW), BBDP/WorN (ICL), LE/Stm (ICL), WKY/NCrl (ICL), LEW/NCrl (ICL), MHS/Gib (ICL), MNS/Gib (ICL), LEW/Crl (ICL)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:620325 AgrOrtholog
Ensembl Genes ENSRNOG00000016405 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000022358 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000022358 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 2.60.120.260 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  3.30.70.850 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  3.40.50.200 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7456182 IMAGE-MGC_LOAD
InterPro Galactose-bd-like_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Kexin/furin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  P_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Peptidase_S8/S53_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Peptidase_S8/S53_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Peptidase_S8_Asp-AS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Peptidase_S8_His-AS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Peptidase_S8_Ser-AS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Peptidase_S8_subtilisin-rel UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  S8_pro-domain UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  S8_pro-domain_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:171085 UniProtKB/Swiss-Prot
MGC_CLONE MGC:114269 IMAGE-MGC_LOAD
NCBI Gene 171085 ENTREZGENE
Pfam P_proprotein UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Peptidase_S8 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  S8_pro-domain UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Pcsk4 PhenoGen
PRINTS SUBTILISIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE P_HOMO_B UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SUBTILASE UniProtKB/Swiss-Prot
  SUBTILASE_ASP UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SUBTILASE_HIS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SUBTILASE_SER UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF49785 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF52743 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt D3ZKU8_RAT UniProtKB/TrEMBL
  PCSK4_RAT UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary A1A4C9 UniProtKB/Swiss-Prot
  Q07213 UniProtKB/Swiss-Prot
  Q07214 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2004-09-10 Pcsk4  proprotein convertase subtilisin/kexin type 4      Symbol and Name status set to approved 1299863 APPROVED
2002-08-07 Pcsk4  proprotein convertase subtilisin/kexin type 4      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_expression enriched in testis; expressed in pachytene spermatocytes and the round spermatids 633734