Pcca (propionyl-CoA carboxylase subunit alpha) - Rat Genome Database

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Gene: Pcca (propionyl-CoA carboxylase subunit alpha) Rattus norvegicus
Analyze
Symbol: Pcca
Name: propionyl-CoA carboxylase subunit alpha
RGD ID: 3264
Description: Predicted to have enzyme binding activity and propionyl-CoA carboxylase activity. Predicted to be involved in cellular amino acid catabolic process and fatty acid catabolic process. Localizes to mitochondrion. Human ortholog(s) of this gene implicated in amino acid metabolic disorder and propionic acidemia. Orthologous to human PCCA (propionyl-CoA carboxylase subunit alpha); PARTICIPATES IN 3-hydroxy-3-methylglutaryl-CoA lyase deficiency pathway; 3-hydroxyisobutyric aciduria pathway; 3-methylcrotonyl CoA carboxylase 1 deficiency pathway; INTERACTS WITH 2,4-dinitrotoluene; 2,6-dinitrotoluene; 3-chloropropane-1,2-diol.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: LOC687008; PCCase alpha subunit; PCCase subunit alpha; propanoyl-CoA:carbon dioxide ligase alpha subunit; propanoyl-CoA:carbon dioxide ligase subunit alpha; propionyl CoA carboxylase, alpha polypeptide; Propionyl Coenzyme A carboxylase alpha polypeptide; propionyl-CoA carboxylase alpha chain, mitochondrial; propionyl-CoA carboxylase alpha subunit; propionyl-coenzyme A carboxylase, alpha polypeptide; similar to Propionyl-CoA carboxylase alpha chain, mitochondrial precursor (PCCase alpha subunit) (Propanoyl-CoA:carbon dioxide ligase alpha subunit)
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
mRatBN7.21599,627,955 - 99,969,555 (+)NCBI
Rnor_6.0 Ensembl15108,960,562 - 109,306,603 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.015108,960,509 - 109,306,879 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.015112,502,385 - 112,687,789 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Rnor_5.015112,346,155 - 112,477,427 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.415107,659,723 - 108,028,929 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.115107,675,589 - 108,044,696 (+)NCBI
Celera1598,401,724 - 98,738,731 (+)NCBICelera
RH 3.4 Map15692.11RGD
Cytogenetic Map15q25NCBI
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

Biological Process

Cellular Component
mitochondrial matrix  (IEA,ISO,ISS)
mitochondrion  (IBA,IDA,ISO)

Molecular Function

References

Additional References at PubMed
PMID:6765947   PMID:8434582   PMID:8889548   PMID:11461925   PMID:13752080   PMID:14651853   PMID:15060005   PMID:16023992   PMID:18614015   PMID:19157941   PMID:19699272   PMID:26316108  
PMID:31505169  


Genomics

Comparative Map Data
Pcca
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21599,627,955 - 99,969,555 (+)NCBI
Rnor_6.0 Ensembl15108,960,562 - 109,306,603 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.015108,960,509 - 109,306,879 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.015112,502,385 - 112,687,789 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Rnor_5.015112,346,155 - 112,477,427 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.415107,659,723 - 108,028,929 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.115107,675,589 - 108,044,696 (+)NCBI
Celera1598,401,724 - 98,738,731 (+)NCBICelera
RH 3.4 Map15692.11RGD
Cytogenetic Map15q25NCBI
PCCA
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl13100,089,015 - 100,530,437 (+)EnsemblGRCh38hg38GRCh38
GRCh3813100,089,020 - 100,530,435 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh3713100,741,347 - 101,182,689 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361399,539,338 - 99,980,690 (+)NCBINCBI36hg18NCBI36
Build 341399,539,402 - 99,980,687NCBI
Celera1381,585,804 - 82,027,260 (+)NCBI
Cytogenetic Map13q32.3NCBI
HuRef1381,336,606 - 81,778,760 (+)NCBIHuRef
CHM1_113100,711,146 - 101,152,990 (+)NCBICHM1_1
Pcca
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3914122,721,752 - 123,127,356 (+)NCBIGRCm39mm39
GRCm39 Ensembl14122,771,736 - 123,128,512 (+)Ensembl
GRCm3814122,484,365 - 122,889,944 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl14122,534,324 - 122,891,100 (+)EnsemblGRCm38mm10GRCm38
MGSCv3714122,933,550 - 123,289,166 (+)NCBIGRCm37mm9NCBIm37
MGSCv3614121,669,524 - 122,025,008 (+)NCBImm8
Celera14121,094,262 - 121,448,288 (+)NCBICelera
Cytogenetic Map14E5NCBI
cM Map1465.99NCBI
Pcca
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540410,317,640 - 10,661,496 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495540410,317,640 - 10,719,148 (-)NCBIChiLan1.0ChiLan1.0
PCCA
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.113100,390,959 - 100,837,772 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl13100,390,959 - 100,837,772 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01381,259,313 - 81,699,117 (+)NCBIMhudiblu_PPA_v0panPan3
PCCA
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12249,965,134 - 50,428,025 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2250,023,369 - 50,428,027 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2249,745,683 - 50,208,149 (+)NCBI
ROS_Cfam_1.02250,406,847 - 50,870,032 (+)NCBI
UMICH_Zoey_3.12250,114,652 - 50,516,893 (+)NCBI
UNSW_CanFamBas_1.02250,090,509 - 50,553,146 (+)NCBI
UU_Cfam_GSD_1.02250,127,751 - 50,590,508 (+)NCBI
Pcca
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404945185,393,912 - 185,784,766 (+)NCBI
SpeTri2.0NW_00493647210,167,387 - 10,501,824 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PCCA
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1168,920,929 - 69,301,533 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11168,920,923 - 69,286,431 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21176,363,099 - 76,547,559 (+)NCBISscrofa10.2Sscrofa10.2susScr3
PCCA
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1378,722,186 - 79,156,049 (+)NCBI
ChlSab1.1 Ensembl378,722,286 - 79,156,863 (+)Ensembl
Pcca
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462479310,691,224 - 11,099,905 (-)NCBI

Position Markers
D15Rat63  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.015109,133,729 - 109,133,904NCBIRnor6.0
Rnor_5.015112,515,664 - 112,515,839UniSTSRnor5.0
RGSC_v3.415107,849,474 - 107,849,649UniSTSRGSC3.4
RGSC_v3.415107,849,473 - 107,849,649RGDRGSC3.4
RGSC_v3.115107,865,254 - 107,865,429RGD
Celera1598,564,878 - 98,565,053UniSTS
RH 3.4 Map15710.8RGD
RH 3.4 Map15710.8UniSTS
RH 2.0 Map15611.6RGD
FHH x ACI Map1573.9699RGD
Cytogenetic Map15q25UniSTS
D15Got102  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.015109,287,130 - 109,287,299NCBIRnor6.0
Rnor_5.015112,668,040 - 112,668,209UniSTSRnor5.0
RGSC_v3.415108,008,043 - 108,008,212UniSTSRGSC3.4
RGSC_v3.415108,008,042 - 108,008,212RGDRGSC3.4
RGSC_v3.115108,023,823 - 108,023,992RGD
Celera1598,718,982 - 98,719,151UniSTS
RH 3.4 Map15726.3RGD
RH 3.4 Map15726.3UniSTS
RH 2.0 Map15628.0RGD
Cytogenetic Map15q25UniSTS
RH94721  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.015109,306,616 - 109,306,768NCBIRnor6.0
Rnor_5.015112,687,526 - 112,687,678UniSTSRnor5.0
RGSC_v3.415108,028,666 - 108,028,818UniSTSRGSC3.4
Celera1598,738,468 - 98,738,620UniSTS
RH 3.4 Map15692.11UniSTS
Cytogenetic Map15q25UniSTS
RH144434  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.015108,994,717 - 108,994,991NCBIRnor6.0
Rnor_5.015112,380,733 - 112,381,007UniSTSRnor5.0
RGSC_v3.415107,694,050 - 107,694,324UniSTSRGSC3.4
Celera1598,435,849 - 98,436,123UniSTS
RH 3.4 Map15710.3UniSTS
Cytogenetic Map15q25UniSTS
BE107713  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.015109,081,293 - 109,081,448NCBIRnor6.0
Rnor_5.015112,464,083 - 112,464,238UniSTSRnor5.0
Celera1598,517,236 - 98,517,391UniSTS
RH 3.4 Map15708.6UniSTS
Cytogenetic Map15q25UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
631655Bp126Blood pressure QTL 1264arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1565520564110520564Rat
731177Uae26Urinary albumin excretion QTL 262.40.025urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)1575527634111246239Rat
2300326Plaw1Placental weight QTL 1150.005placenta mass (VT:0004257)placenta wet weight (CMO:0002088)1575761024109400896Rat
1641889Colcr6Colorectal carcinoma resistance QTL 62.90.0126intestine integrity trait (VT:0010554)benign colorectal tumor surface area measurement (CMO:0001799)1581255292109133904Rat
70155Gcs1Gastric cancer susceptibility QTL13.8stomach morphology trait (VT:0000470)stomach tumor susceptibility score (CMO:0002043)1583947714111246239Rat
1549844Bss7Bone structure and strength QTL 76.4femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)1584050550111246239Rat
2317055Aia10Adjuvant induced arthritis QTL 103.41joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)1584050550111246239Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:250
Count of miRNA genes:135
Interacting mature miRNAs:146
Transcripts:ENSRNOT00000019144, ENSRNOT00000057429
Prediction methods:Microtar, 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.


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 3 43 57 41 15 41 1 4 70 35 34 11 1
Low 4 7 7 4 7 7
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000077482   ⟹   ENSRNOP00000072844
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl15108,960,562 - 109,306,603 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000081906   ⟹   ENSRNOP00000073510
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl15108,960,562 - 109,306,603 (+)Ensembl
RefSeq Acc Id: NM_019330   ⟹   NP_062203
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21599,627,986 - 99,968,269 (+)NCBI
Rnor_6.015108,960,530 - 109,306,879 (+)NCBI
Rnor_5.015112,346,155 - 112,477,427 (+)NCBI
Rnor_5.015112,502,385 - 112,687,789 (+)NCBI
RGSC_v3.415107,659,723 - 108,028,929 (+)RGD
Celera1598,401,724 - 98,738,731 (+)RGD
Sequence:
RefSeq Acc Id: XM_017599802   ⟹   XP_017455291
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.015108,960,509 - 109,306,879 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039093662   ⟹   XP_038949590
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21599,627,955 - 99,969,555 (+)NCBI
RefSeq Acc Id: XM_039093663   ⟹   XP_038949591
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21599,627,955 - 99,968,269 (+)NCBI
RefSeq Acc Id: XM_039093664   ⟹   XP_038949592
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21599,627,955 - 99,968,269 (+)NCBI
RefSeq Acc Id: XM_039093665   ⟹   XP_038949593
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21599,655,374 - 99,968,269 (+)NCBI
Protein Sequences
Protein RefSeqs NP_062203 (Get FASTA)   NCBI Sequence Viewer  
  XP_038949590 (Get FASTA)   NCBI Sequence Viewer  
  XP_038949591 (Get FASTA)   NCBI Sequence Viewer  
  XP_038949592 (Get FASTA)   NCBI Sequence Viewer  
  XP_038949593 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein P14882 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_062203   ⟸   NM_019330
- UniProtKB: P14882 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_017455291   ⟸   XM_017599802
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000072844   ⟸   ENSRNOT00000077482
RefSeq Acc Id: ENSRNOP00000073510   ⟸   ENSRNOT00000081906
RefSeq Acc Id: XP_038949590   ⟸   XM_039093662
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038949591   ⟸   XM_039093663
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038949592   ⟸   XM_039093664
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038949593   ⟸   XM_039093665
- Peptide Label: isoform X4
Transcriptome

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

Promoters
RGD ID:13699893
Promoter ID:EPDNEW_R10408
Type:single initiation site
Name:AC123185_1
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_6.015108,956,394 - 108,956,454EPDNEW
RGD ID:13699885
Promoter ID:EPDNEW_R10409
Type:initiation region
Name:Pcca_1
Description:propionyl-CoA carboxylase alpha subunit
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_6.015108,960,526 - 108,960,586EPDNEW

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)
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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
LN/MavRrrc (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
M520/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
MHS/Gib (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
MNS/Gib (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
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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:3264 AgrOrtholog
Ensembl Genes ENSRNOG00000057042 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000072844 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000073510 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000077482 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000081906 UniProtKB/TrEMBL
Gene3D-CATH 3.30.1490.20 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro ATP-grasp UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ATP_grasp_subdomain_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  BC-like_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Biotin_BS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Biotin_carboxylation_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Biotin_COase_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Biotin_lipoyl UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CbamoylP_synth_lsu-like_ATP-bd UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PCC_BT UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PreATP-grasp_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Rudment_hybrid_motif UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Single_hybrid_motif UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:687008 UniProtKB/Swiss-Prot
NCBI Gene 687008 ENTREZGENE
Pfam Biotin_carb_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Biotin_carb_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Biotin_lipoyl UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CPSase_L_D2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PCC_BT UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Pcca PhenoGen
PROSITE ATP_GRASP UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  BIOTIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  BIOTINYL_LIPOYL UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CPSASE_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CPSASE_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PS50979 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART Biotin_carb_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF51230 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF51246 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF52440 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGR TC205059
UniProt A0A0G2K401_RAT UniProtKB/TrEMBL
  A0A0G2K5P9_RAT UniProtKB/TrEMBL
  P14882 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2018-05-04 Pcca  propionyl-CoA carboxylase subunit alpha  Pcca  propionyl-CoA carboxylase alpha subunit  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2015-11-20 Pcca  propionyl-CoA carboxylase alpha subunit  Pcca  propionyl CoA carboxylase, alpha polypeptide  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2013-04-01 Pcca  propionyl CoA carboxylase, alpha polypeptide  Pcca  propionyl-coenzyme A carboxylase, alpha polypeptide  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-05-05 Pcca  propionyl-coenzyme A carboxylase, alpha polypeptide  LOC687008  similar to Propionyl-CoA carboxylase alpha chain, mitochondrial precursor (PCCase alpha subunit) (Propanoyl-CoA:carbon dioxide ligase alpha subunit)  Data Merged 737654 APPROVED
2006-11-20 LOC687008  similar to Propionyl-CoA carboxylase alpha chain, mitochondrial precursor (PCCase alpha subunit) (Propanoyl-CoA:carbon dioxide ligase alpha subunit)      Symbol and Name status set to provisional 70820 PROVISIONAL
2002-06-10 Pcca  Propionyl Coenzyme A carboxylase, alpha polypeptide      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_protein may contain a biotinylated lysine residue 633579