Pcbd2 (pterin-4 alpha-carbinolamine dehydratase 2) - Rat Genome Database

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Gene: Pcbd2 (pterin-4 alpha-carbinolamine dehydratase 2) Rattus norvegicus
Analyze
Symbol: Pcbd2 (Ensembl: Txndc15)
Name: pterin-4 alpha-carbinolamine dehydratase 2 (Ensembl:thioredoxin domain containing 15)
RGD ID: 1590239
Description: Predicted to enable identical protein binding activity and phenylalanine 4-monooxygenase activity. Predicted to be involved in positive regulation of DNA-templated transcription. Predicted to be located in mitochondrion and nucleus. Orthologous to human PCBD2 (pterin-4 alpha-carbinolamine dehydratase 2); INTERACTS WITH (+)-schisandrin B; 2,3,7,8-tetrachlorodibenzodioxine; 4,4'-sulfonyldiphenol.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: dimerization cofactor of hepatocyte nuclear factor 1 alpha 2; LOC102555972; pterin 4 alpha carbinolamine dehydratase/dimerization cofactor of hepatocyte nuclear factor 1 alpha (TCF1) 2; pterin-4 alpha-carbinolamine dehydratase/dimerization cofactor of hepatocyte nuclear factor 1 alpha (TCF1) 2; pterin-4-alpha-carbinolamine dehydratase 2; similar to dimerization cofactor of hepatocyte nuclear factor 1 (HNF1) from muscle; uncharacterized LOC102555972
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8178,850,349 - 8,902,420 (-)NCBIGRCr8
mRatBN7.2178,845,161 - 8,896,343 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl178,845,084 - 8,910,539 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx178,860,830 - 8,911,884 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01710,390,105 - 10,441,472 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0178,857,211 - 8,908,265 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0178,929,675 - 8,980,712 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl178,929,810 - 8,980,571 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01711,094,438 - 11,145,446 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera178,927,317 - 8,977,982 (-)NCBICelera
Cytogenetic Map17p14NCBI
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
mitochondrion  (ISO)
nucleus  (ISO)

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:11980910   PMID:12477932   PMID:15182178   PMID:18614015   PMID:34800366  


Genomics

Comparative Map Data
Pcbd2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8178,850,349 - 8,902,420 (-)NCBIGRCr8
mRatBN7.2178,845,161 - 8,896,343 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl178,845,084 - 8,910,539 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx178,860,830 - 8,911,884 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01710,390,105 - 10,441,472 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0178,857,211 - 8,908,265 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0178,929,675 - 8,980,712 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl178,929,810 - 8,980,571 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01711,094,438 - 11,145,446 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera178,927,317 - 8,977,982 (-)NCBICelera
Cytogenetic Map17p14NCBI
PCBD2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh385134,905,131 - 134,962,644 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl5134,905,120 - 135,007,959 (+)EnsemblGRCh38hg38GRCh38
GRCh375134,240,821 - 134,298,334 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 365134,268,709 - 134,326,235 (+)NCBINCBI36Build 36hg18NCBI36
Build 345134,268,708 - 134,333,243NCBI
Celera5130,369,123 - 130,422,077 (+)NCBICelera
Cytogenetic Map5q31.1NCBI
HuRef5129,426,903 - 129,486,276 (+)NCBIHuRef
CHM1_15133,673,459 - 133,730,983 (+)NCBICHM1_1
T2T-CHM13v2.05135,432,093 - 135,489,611 (+)NCBIT2T-CHM13v2.0
Pcbd2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391355,874,957 - 55,924,643 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1355,875,181 - 55,924,643 (+)EnsemblGRCm39 Ensembl
GRCm381355,727,097 - 55,776,830 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1355,727,368 - 55,776,830 (+)EnsemblGRCm38mm10GRCm38
MGSCv371355,828,729 - 55,878,191 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361355,736,990 - 55,786,452 (+)NCBIMGSCv36mm8
Celera1356,782,245 - 56,831,727 (+)NCBICelera
Cytogenetic Map13B1NCBI
cM Map1330.06NCBI
Pcbd2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540830,090,808 - 30,137,964 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495540830,090,808 - 30,137,894 (+)NCBIChiLan1.0ChiLan1.0
PCBD2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v24130,199,520 - 130,260,300 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan15128,338,958 - 128,399,860 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v05130,303,900 - 130,364,899 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.15136,446,464 - 136,497,528 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl5136,446,730 - 136,497,011 (+)Ensemblpanpan1.1panPan2
PCBD2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11122,998,005 - 23,015,572 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1122,951,201 - 23,015,572 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1121,711,021 - 21,765,150 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01123,768,358 - 23,822,149 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1123,768,124 - 23,822,149 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11122,467,615 - 22,521,350 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01122,333,522 - 22,387,288 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01122,976,012 - 23,030,046 (+)NCBIUU_Cfam_GSD_1.0
Pcbd2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024407213123,089,793 - 123,136,422 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365972,119,136 - 2,161,379 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365972,113,428 - 2,161,329 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PCBD2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.12137,082,920 - 137,135,175 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
PCBD2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12337,689,451 - 37,737,997 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2337,689,506 - 37,738,161 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366603440,178,570 - 40,227,682 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Pcbd2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462473312,113,915 - 12,162,222 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462473312,113,915 - 12,162,224 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Pcbd2
310 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:100
Count of miRNA genes:90
Interacting mature miRNAs:95
Transcripts:ENSRNOT00000071426
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.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1354581Bp247Blood pressure QTL 2474.5arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)17169599340Rat
1354613Kidm14Kidney mass QTL 146.2kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)17429913035837242Rat
631499Stl1Serum triglyceride level QTL 13.6blood triglyceride amount (VT:0002644)blood triglyceride level (CMO:0000118)17327139827389946Rat
2293664Bmd28Bone mineral density QTL 285.10.0001femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)17435448727028127Rat
1300123Bp194Blood pressure QTL 1942.82arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)17211514934551001Rat
2324619Coatc4Coat color QTL 40.001coat/hair pigmentation trait (VT:0010463)pigmented dorsal coat/hair area to total dorsal coat/hair area ratio (CMO:0001811)17429913021293263Rat
2303627Vencon8Ventilatory control QTL 80.001respiration trait (VT:0001943)tidal volume (CMO:0000222)17452803849528038Rat
70184BpQTLcluster14Blood pressure QTL cluster 143.38arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)17131990913Rat
1581553Pur14Proteinuria QTL 145.30.0001urine total protein amount (VT:0000032)urine protein excretion rate (CMO:0000759)17797996816317111Rat
2303561Bw91Body weight QTL 912body mass (VT:0001259)body weight (CMO:0000012)17886846253868462Rat
631207Niddm41Non-insulin dependent diabetes mellitus QTL 41blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)17137830672Rat
1354651Lmblg2Limb length QTL 26tibia length (VT:0004357)tibia length (CMO:0000450)17429913069599340Rat
1354596Bw32Body weight QTL 324.5body mass (VT:0001259)body weight (CMO:0000012)17429913060781592Rat
10401807Kidm52Kidney mass QTL 52kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)17131701463Rat
10054088Scort28Serum corticosterone level QTL 282.040.0102blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)17452803849528038Rat
1354662Rf49Renal function QTL 492.9blood creatinine amount (VT:0005328)plasma creatinine level (CMO:0000537)17169599340Rat
1354630Cm34Cardiac mass QTL 348.7heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)17429913069599340Rat
2293648Bmd31Bone mineral density QTL 314.50.0001femur size trait (VT:1000369)femoral neck cortical cross-sectional area (CMO:0001702)17435448727028127Rat
1354658Spl8Serum phospholipid level QTL 83.8blood VLDL phospholipid amount (VT:0010507)blood very low density lipoprotein phospholipid level (CMO:0001571)17160781592Rat
1641902Colcr7Colorectal carcinoma resistance QTL 73.350.0044intestine integrity trait (VT:0010554)benign colorectal tumor surface area measurement (CMO:0001799)17211514921881669Rat
1354638Insul1Insulin level QTL 14.8blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)17429913069599340Rat
9590316Scort21Serum corticosterone level QTL 214.750.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)17122871563Rat

Markers in Region
BF390454  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_5.01711,098,001 - 11,098,211NCBIRnor5.0
RGSC_v3.41714,888,664 - 14,888,876UniSTSRGSC3.4
Celera178,930,904 - 8,931,116UniSTS
RH 3.4 Map1777.9UniSTS
Cytogenetic Map17p14UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
nervous system
renal system
reproductive system
respiratory system
9 11 49 113 91 90 59 25 59 6 218 97 93 45 60 31

Sequence


Ensembl Acc Id: ENSRNOT00000000146   ⟹   ENSRNOP00000000146
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl178,898,078 - 8,910,431 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000071426   ⟹   ENSRNOP00000067457
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl178,845,214 - 8,910,539 (-)Ensembl
Rnor_6.0 Ensembl178,929,810 - 8,980,571 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000100127   ⟹   ENSRNOP00000090384
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl178,845,084 - 8,896,398 (-)Ensembl
RefSeq Acc Id: NM_001402494   ⟹   NP_001389423
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8178,850,349 - 8,901,267 (-)NCBI
mRatBN7.2178,845,164 - 8,896,093 (-)NCBI
RefSeq Acc Id: XM_039096452   ⟹   XP_038952380
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8178,889,504 - 8,902,420 (-)NCBI
mRatBN7.2178,883,585 - 8,896,342 (-)NCBI
RefSeq Acc Id: XR_010058946
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8178,887,762 - 8,902,420 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001389423 (Get FASTA)   NCBI Sequence Viewer  
  XP_038952380 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL93956 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000067457.2
  ENSRNOP00000090384.1
Ensembl Acc Id: ENSRNOP00000067457   ⟸   ENSRNOT00000071426
RefSeq Acc Id: XP_038952380   ⟸   XM_039096452
- Peptide Label: isoform X1
Ensembl Acc Id: ENSRNOP00000090384   ⟸   ENSRNOT00000100127
Ensembl Acc Id: ENSRNOP00000000146   ⟸   ENSRNOT00000000146
RefSeq Acc Id: NP_001389423   ⟸   NM_001402494
Protein Domains
Thioredoxin

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-M0RCX0-F1-model_v2 AlphaFold M0RCX0 1-127 view protein structure

Transcriptome

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

Promoters
RGD ID:13700299
Promoter ID:EPDNEW_R10815
Type:multiple initiation site
Name:Pcbd2_1
Description:pterin-4 alpha-carbinolamine dehydratase 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_6.0178,980,536 - 8,980,596EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1590239 AgrOrtholog
BioCyc Gene G2FUF-10223 BioCyc
BioCyc Pathway PWY-8099 [tetrahydropteridine recycling] BioCyc
BioCyc Pathway Image PWY-8099 BioCyc
Ensembl Genes ENSRNOG00000000133 Ensembl, UniProtKB/TrEMBL
  ENSRNOG00000047796 Ensembl
Ensembl Transcript ENSRNOT00000071426.3 UniProtKB/TrEMBL
  ENSRNOT00000100127.1 UniProtKB/TrEMBL
Gene3D-CATH 3.30.1360.20 UniProtKB/TrEMBL
  Glutaredoxin UniProtKB/TrEMBL
InterPro PCD_sf UniProtKB/TrEMBL
  Thioredoxin-like_sf UniProtKB/TrEMBL
  Thioredoxin_domain UniProtKB/TrEMBL
  Trans/pterin_deHydtase UniProtKB/TrEMBL
  TXNDC15 UniProtKB/TrEMBL
NCBI Gene 685729 ENTREZGENE
PANTHER PTERIN-4-ALPHA-CARBINOLAMINE DEHYDRATASE 2 UniProtKB/TrEMBL
  PTHR12599 UniProtKB/TrEMBL
  PTHR14684 UniProtKB/TrEMBL
  THIOREDOXIN DOMAIN-CONTAINING PROTEIN 15 UniProtKB/TrEMBL
Pfam Pterin_4a UniProtKB/TrEMBL
  Thioredoxin UniProtKB/TrEMBL
PhenoGen Pcbd2 PhenoGen
PROSITE THIOREDOXIN_2 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000000133 RatGTEx
  ENSRNOG00000047796 RatGTEx
Superfamily-SCOP SSF52833 UniProtKB/TrEMBL
  Trans_pterinDh UniProtKB/TrEMBL
UniProt A0A8I6AE92_RAT UniProtKB/TrEMBL
  M0RCX0_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2021-03-09 Pcbd2  pterin-4 alpha-carbinolamine dehydratase 2  LOC102555972  uncharacterized LOC102555972  Data merged from RGD:7704908 737654 PROVISIONAL
2016-02-03 Pcbd2  pterin-4 alpha-carbinolamine dehydratase 2  Pcbd2  pterin 4 alpha carbinolamine dehydratase/dimerization cofactor of hepatocyte nuclear factor 1 alpha (TCF1) 2  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2013-12-18 LOC102555972  uncharacterized LOC102555972      Symbol and Name status set to provisional 70820 PROVISIONAL
2006-11-20 LOC685729  similar to dimerization cofactor of hepatocyte nuclear factor 1 (HNF1) from muscle      Symbol and Name status set to provisional 70820 PROVISIONAL