Pcbd1 (pterin-4 alpha-carbinolamine dehydratase 1) - Rat Genome Database

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Gene: Pcbd1 (pterin-4 alpha-carbinolamine dehydratase 1) Rattus norvegicus
Analyze
Symbol: Pcbd1
Name: pterin-4 alpha-carbinolamine dehydratase 1
RGD ID: 3263
Description: Enables 4-alpha-hydroxytetrahydrobiopterin dehydratase activity. Involved in L-phenylalanine metabolic process. Acts upstream of or within regulation of protein binding activity. Predicted to be located in cytosol and nucleoplasm. Orthologous to human PCBD1 (pterin-4 alpha-carbinolamine dehydratase 1); INTERACTS WITH (+)-schisandrin B; 6-propyl-2-thiouracil; ammonium chloride.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: 4-alpha-hydroxy-tetrahydropterin dehydratase; 6-pyruvoyl-tetrahydropterin synthase/dimerization cofactor of hepatocyte nuclear factor 1 alpha; 6-pyruvoyl-tetrahydropterin synthase/dimerization cofactor of hepatocyte nuclear factor 1 alpha (TCF1); DCOH; dimerization cofactor of hepatocyte nuclear factor 1-alpha; dimerization cofactor of hepatocyte nuclear factor-1-alpha; dimerization cofactor of HNF1; PCBD; PCD; phenylalanine hydroxylase-stimulating protein; PHS; pterin 4 alpha carbinolamine dehydratase/dimerization cofactor of hepatocyte nuclear factor 1 alpha (TCF1) 1; pterin carbinolamine dehydratase; pterin-4 alpha-carbinolamine dehydratase/dimerization cofactor of hepatocyte nuclear factor 1 alpha; pterin-4-alpha-carbinolamine dehydratase; TCF1
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
mRatBN7.22029,037,545 - 29,044,322 (+)NCBI
Rnor_6.0 Ensembl2030,690,810 - 30,696,476 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.02030,689,690 - 30,696,465 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.02032,484,965 - 32,491,740 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42028,448,703 - 28,454,184 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.12028,462,435 - 28,467,964 (+)NCBI
Celera2030,472,263 - 30,477,776 (+)NCBICelera
Cytogenetic Map20q11NCBI
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

Cellular Component
cellular_component  (ND)
cytosol  (IEA,ISO)
nucleoplasm  (IEA,ISO)
nucleus  (IPI,ISO)

References

Additional References at PubMed
PMID:7744010   PMID:8444860   PMID:8897596   PMID:9865610   PMID:15182178   PMID:16189514   PMID:19056867   PMID:21047120   PMID:21516116   PMID:23376485   PMID:23533145   PMID:25416956  


Genomics

Comparative Map Data
Pcbd1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.22029,037,545 - 29,044,322 (+)NCBI
Rnor_6.0 Ensembl2030,690,810 - 30,696,476 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.02030,689,690 - 30,696,465 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.02032,484,965 - 32,491,740 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42028,448,703 - 28,454,184 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.12028,462,435 - 28,467,964 (+)NCBI
Celera2030,472,263 - 30,477,776 (+)NCBICelera
Cytogenetic Map20q11NCBI
PCBD1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1070,882,280 - 70,888,565 (-)EnsemblGRCh38hg38GRCh38
GRCh381070,882,280 - 70,888,565 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371072,642,037 - 72,648,322 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361072,313,273 - 72,318,547 (-)NCBINCBI36hg18NCBI36
Celera1065,925,552 - 65,930,826 (-)NCBI
Cytogenetic Map10q22.1NCBI
HuRef1066,637,269 - 66,642,544 (-)NCBIHuRef
CHM1_11072,926,052 - 72,931,326 (-)NCBICHM1_1
Pcbd1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391060,925,110 - 60,930,108 (+)NCBIGRCm39mm39
GRCm39 Ensembl1060,925,110 - 60,930,103 (+)Ensembl
GRCm381061,089,331 - 61,094,329 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1061,089,331 - 61,094,324 (+)EnsemblGRCm38mm10GRCm38
MGSCv371060,552,091 - 60,557,077 (+)NCBIGRCm37mm9NCBIm37
MGSCv361060,484,716 - 60,489,676 (+)NCBImm8
Celera1062,189,905 - 62,194,954 (+)NCBICelera
Cytogenetic Map10B4NCBI
cM Map1032.14NCBI
Pcbd1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495543720,482,589 - 20,488,249 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495543720,482,589 - 20,487,337 (+)NCBIChiLan1.0ChiLan1.0
PCBD1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11069,877,545 - 69,884,030 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1069,878,773 - 69,881,174 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01067,353,903 - 67,359,073 (-)NCBIMhudiblu_PPA_v0panPan3
PCBD1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1421,719,863 - 21,723,493 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl421,719,863 - 21,721,574 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha421,854,056 - 21,858,488 (-)NCBI
ROS_Cfam_1.0421,997,912 - 22,002,345 (-)NCBI
UMICH_Zoey_3.1421,893,535 - 21,897,967 (-)NCBI
UNSW_CanFamBas_1.0422,098,728 - 22,103,182 (-)NCBI
UU_Cfam_GSD_1.0422,451,020 - 22,455,453 (-)NCBI
Pcbd1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440721359,351,220 - 59,355,096 (+)NCBI
SpeTri2.0NW_0049365217,843,945 - 7,847,827 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PCBD1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1473,772,835 - 73,807,281 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11473,769,339 - 73,807,278 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21479,648,886 - 79,655,375 (-)NCBISscrofa10.2Sscrofa10.2susScr3
PCBD1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1960,417,301 - 60,422,313 (+)NCBI
Vero_WHO_p1.0NW_02366604821,141,594 - 21,146,607 (+)NCBI
Pcbd1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247544,893,868 - 4,898,410 (-)NCBI

Position Markers
RH128638  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22029,044,003 - 29,044,188 (+)MAPPER
Rnor_6.02030,696,147 - 30,696,331NCBIRnor6.0
Rnor_5.02032,491,422 - 32,491,606UniSTSRnor5.0
RGSC_v3.42028,453,876 - 28,454,060UniSTSRGSC3.4
Celera2030,477,459 - 30,477,643UniSTS
Cytogenetic Map20q11UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
6893685Bw111Body weight QTL 1112.70.004body mass (VT:0001259)body weight (CMO:0000012)20133300419Rat
9590252Scort12Serum corticosterone level QTL 1220.460.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20137550487Rat
7411668Foco32Food consumption QTL 3280.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20137550487Rat
2305926Iddm37Insulin dependent diabetes mellitus QTL 376blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)20201865447018654Rat
1641915Colcr9Colorectal carcinoma resistance QTL 92.970.0024intestine integrity trait (VT:0010554)benign colorectal tumor number (CMO:0001795)20299970747999707Rat
1598816Memor12Memory QTL 122.4exploratory behavior trait (VT:0010471)average horizontal distance in proximity to the target during voluntary locomotion in an experimental apparatus (CMO:0002674)20410895649108956Rat
4889870Pur30Proteinuria QTL 30190.005total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)20865434130991290Rat
9590092Insglur9Insulin/glucose ratio QTL 918.380.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)201383430956205956Rat
7411652Foco24Food consumption QTL 240.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)201383430956205956Rat
2317880Alcrsp25Alcohol response QTL 252.3response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)201782709656205956Rat
4889610Pancm3Pancreatic morphology QTL 33.750.001pancreas mass (VT:0010144)pancreas wet weight (CMO:0000626)201887215049108956Rat
2303626Vencon10Ventilatory control QTL 100.001respiration trait (VT:0001943)respiration rate (CMO:0000289)202085847056205956Rat
2303578Gluco50Glucose level QTL 502blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)202660884356205956Rat
2303587Bw93Body weight QTL 9313body mass (VT:0001259)body weight (CMO:0000012)202660884356205956Rat
2300188Bmd68Bone mineral density QTL 686.40.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)202660884356205956Rat
1331747Hrtrt16Heart rate QTL 163.163heart pumping trait (VT:2000009)heart rate (CMO:0000002)202671232356205956Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:199
Count of miRNA genes:133
Interacting mature miRNAs:150
Transcripts:ENSRNOT00000000687
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 3 10 41 41 41 42 35 20 3
Low 33 16 19 8 11 32 21 8 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000000687   ⟹   ENSRNOP00000000687
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl2030,690,810 - 30,696,476 (+)Ensembl
RefSeq Acc Id: NM_001007601   ⟹   NP_001007602
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22029,038,806 - 29,044,321 (+)NCBI
Rnor_6.02030,690,951 - 30,696,464 (+)NCBI
Rnor_5.02032,484,965 - 32,491,740 (+)NCBI
RGSC_v3.42028,448,703 - 28,454,184 (+)RGD
Celera2030,472,263 - 30,477,776 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006256414   ⟹   XP_006256476
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22029,037,545 - 29,044,322 (+)NCBI
Rnor_6.02030,689,690 - 30,696,465 (+)NCBI
Rnor_5.02032,484,965 - 32,491,740 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001007602 (Get FASTA)   NCBI Sequence Viewer  
  XP_006256476 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAA40609 (Get FASTA)   NCBI Sequence Viewer  
  CAA06587 (Get FASTA)   NCBI Sequence Viewer  
  EDL93037 (Get FASTA)   NCBI Sequence Viewer  
  P61459 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001007602   ⟸   NM_001007601
- UniProtKB: P61459 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006256476   ⟸   XM_006256414
- Peptide Label: isoform X1
- UniProtKB: P61459 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000000687   ⟸   ENSRNOT00000000687

Transcriptome

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

Promoters
RGD ID:13701599
Promoter ID:EPDNEW_R12122
Type:initiation region
Name:Pcbd1_1
Description:pterin-4 alpha-carbinolamine dehydratase 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_6.02030,690,963 - 30,691,023EPDNEW

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)
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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:3263 AgrOrtholog
Ensembl Genes ENSRNOG00000000566 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000000687 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000000687 ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH 3.30.1360.20 UniProtKB/Swiss-Prot
InterPro PCD_sf UniProtKB/Swiss-Prot
  Pterin_deHydtase UniProtKB/Swiss-Prot
KEGG Report rno:29700 UniProtKB/Swiss-Prot
NCBI Gene 29700 ENTREZGENE
PANTHER PTHR12599 UniProtKB/Swiss-Prot
Pfam Pterin_4a UniProtKB/Swiss-Prot
PhenoGen Pcbd1 PhenoGen
Superfamily-SCOP SSF55248 UniProtKB/Swiss-Prot
UniProt P61459 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary P70519 UniProtKB/Swiss-Prot
  P80095 UniProtKB/Swiss-Prot
  Q9D930 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-02-03 Pcbd1  pterin-4 alpha-carbinolamine dehydratase 1  Pcbd1  pterin-4 alpha-carbinolamine dehydratase/dimerization cofactor of hepatocyte nuclear factor 1 alpha  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2009-02-26 Pcbd1  pterin-4 alpha-carbinolamine dehydratase/dimerization cofactor of hepatocyte nuclear factor 1 alpha  Pcbd1  pterin 4 alpha carbinolamine dehydratase/dimerization cofactor of hepatocyte nuclear factor 1 alpha (TCF1) 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-08-22 Pcbd1  pterin 4 alpha carbinolamine dehydratase/dimerization cofactor of hepatocyte nuclear factor 1 alpha (TCF1) 1  Pcbd  6-pyruvoyl-tetrahydropterin synthase/dimerization cofactor of hepatocyte nuclear factor 1 alpha (TCF1)  Name updated 1299863 APPROVED
2004-09-10 Pcbd  6-pyruvoyl-tetrahydropterin synthase/dimerization cofactor of hepatocyte nuclear factor 1 alpha (TCF1)    6-pyruvoyl-tetrahydropterin synthase/dimerization cofactor of hepatocyte nuclear factor 1 alpha  Name updated 1299863 APPROVED
2002-06-10 Pcbd  6-pyruvoyl-tetrahydropterin synthase/dimerization cofactor of hepatocyte nuclear factor 1 alpha      Name updated 70584 APPROVED