Plpbp (pyridoxal phosphate binding protein) - Rat Genome Database

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Gene: Plpbp (pyridoxal phosphate binding protein) Rattus norvegicus
Analyze
Symbol: Plpbp
Name: pyridoxal phosphate binding protein
RGD ID: 1308962
Description: Predicted to enable pyridoxal phosphate binding activity. Predicted to be located in cytosol. Human ortholog(s) of this gene implicated in early-onset vitamin B6-dependent epilepsy 1. Orthologous to human PLPBP (pyridoxal phosphate binding protein); INTERACTS WITH 17beta-estradiol; 2,3,7,8-tetrachlorodibenzodioxine; 2,4-dinitrotoluene.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC306544; proline synthase co-transcribed bacterial homolog protein; proline synthetase co-transcribed; proline synthetase co-transcribed homolog; proline synthetase co-transcribed homolog (bacterial); Prosc
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81671,705,064 - 71,717,726 (-)NCBIGRCr8
mRatBN7.21665,003,292 - 65,014,886 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1665,002,223 - 65,014,886 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1670,286,586 - 70,298,189 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01673,692,919 - 73,704,520 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01668,938,687 - 68,950,281 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01669,164,654 - 69,176,245 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1669,163,577 - 69,176,036 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01668,838,027 - 68,849,618 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41669,330,481 - 69,342,072 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11669,329,617 - 69,342,033 (-)NCBI
Celera1662,922,672 - 62,934,263 (-)NCBICelera
Cytogenetic Map16q12.3NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
cytosol  (IEA,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. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
3. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
5. Comprehensive gene review and curation RGD comprehensive gene curation
Additional References at PubMed
PMID:18614015   PMID:23376485  


Genomics

Comparative Map Data
Plpbp
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81671,705,064 - 71,717,726 (-)NCBIGRCr8
mRatBN7.21665,003,292 - 65,014,886 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1665,002,223 - 65,014,886 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1670,286,586 - 70,298,189 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01673,692,919 - 73,704,520 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01668,938,687 - 68,950,281 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01669,164,654 - 69,176,245 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1669,163,577 - 69,176,036 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01668,838,027 - 68,849,618 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41669,330,481 - 69,342,072 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11669,329,617 - 69,342,033 (-)NCBI
Celera1662,922,672 - 62,934,263 (-)NCBICelera
Cytogenetic Map16q12.3NCBI
PLPBP
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38837,762,546 - 37,779,768 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl837,762,595 - 37,779,768 (+)EnsemblGRCh38hg38GRCh38
GRCh37837,620,064 - 37,637,286 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36837,738,833 - 37,756,444 (+)NCBINCBI36Build 36hg18NCBI36
Build 34837,738,832 - 37,756,443NCBI
Celera836,572,050 - 36,589,221 (+)NCBICelera
Cytogenetic Map8p11.23NCBI
HuRef836,154,898 - 36,171,954 (+)NCBIHuRef
CHM1_1837,821,558 - 37,838,742 (+)NCBICHM1_1
T2T-CHM13v2.0838,038,942 - 38,056,164 (+)NCBIT2T-CHM13v2.0
Plpbp
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39827,530,801 - 27,546,160 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl827,532,583 - 27,546,160 (+)EnsemblGRCm39 Ensembl
GRCm38827,041,924 - 27,056,132 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl827,042,555 - 27,056,132 (+)EnsemblGRCm38mm10GRCm38
MGSCv37828,153,027 - 28,166,604 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36828,508,471 - 28,522,235 (+)NCBIMGSCv36mm8
Celera828,531,400 - 28,544,944 (+)NCBICelera
Cytogenetic Map8A2NCBI
cM Map815.91NCBI
Plpbp
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495546313,467,632 - 13,498,640 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495546313,467,965 - 13,498,544 (+)NCBIChiLan1.0ChiLan1.0
PLPBP
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2756,321,157 - 56,341,824 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1832,038,239 - 32,058,898 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0837,060,599 - 37,081,250 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1834,238,372 - 34,258,846 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl834,238,411 - 34,258,846 (+)Ensemblpanpan1.1panPan2
PLPBP
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11627,599,078 - 27,617,902 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1627,599,310 - 27,617,843 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1628,115,774 - 28,134,641 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01629,498,245 - 29,517,118 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1629,498,248 - 29,517,119 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11627,719,694 - 27,738,561 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01628,297,384 - 28,316,235 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01628,336,475 - 28,355,332 (-)NCBIUU_Cfam_GSD_1.0
Plpbp
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494350,223,519 - 50,245,081 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049367101,216,104 - 1,238,153 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049367101,216,142 - 1,236,559 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PLPBP
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1548,624,837 - 48,636,589 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11548,624,790 - 48,636,584 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21555,741,253 - 55,753,025 (-)NCBISscrofa10.2Sscrofa10.2susScr3
PLPBP
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1835,798,067 - 35,817,714 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl835,798,067 - 35,816,054 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660526,187,619 - 6,207,714 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Plpbp
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247805,810,342 - 5,838,775 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247805,811,180 - 5,838,411 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Plpbp
24 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:36
Count of miRNA genes:35
Interacting mature miRNAs:36
Transcripts:ENSRNOT00000018369
Prediction methods: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
1600378Arunc4Aerobic running capacity QTL 40.03exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)1638024580345693Rat
70205Gcr3Gastric cancer resistance QTL 32.3stomach morphology trait (VT:0000470)stomach tumor depth of invasion (CMO:0001888)161769679182635055Rat
70205Gcr3Gastric cancer resistance QTL 32.3stomach morphology trait (VT:0000470)stomach tumor diameter (CMO:0001889)161769679182635055Rat
70205Gcr3Gastric cancer resistance QTL 32.3stomach morphology trait (VT:0000470)stomach tumor depth of invasion (CMO:0001888)161769679182635055Rat
70205Gcr3Gastric cancer resistance QTL 32.3stomach morphology trait (VT:0000470)stomach tumor diameter (CMO:0001889)161769679182635055Rat
70215Niddm29Non-insulin dependent diabetes mellitus QTL 293.54blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)161900443575226532Rat
2302057Pia29Pristane induced arthritis QTL 293.60.001blood autoantibody amount (VT:0003725)serum immunoglobulin M-type rheumatoid factor level relative to an arbitrary reference serum (CMO:0002111)162173597566735975Rat
8694453Bw172Body weight QTL 1728.330.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)162432551369325513Rat
6903294Stl30Serum triglyceride level QTL 302.60.0013blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)162515279370152793Rat
1578768Stresp22Stress response QTL 222.8thymus mass (VT:0004954)thymus wet weight (CMO:0000855)163528887080288870Rat
2293690Bss45Bone structure and strength QTL 455.130.0001lumbar vertebra morphology trait (VT:0010494)lumbar vertebra cortical cross-sectional area (CMO:0001690)163775215682752156Rat
2300163Bmd64Bone mineral density QTL 645.30.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)163775215682752156Rat
7205510Activ5Activity QTL 53.780.00028locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)164239634584729064Rat
8694429Bw164Body weight QTL 16450.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)165272646484729064Rat
8694364Abfw7Abdominal fat weight QTL 712.220.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)165272646484729064Rat
7411648Foco22Food consumption QTL 22150.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)165272646484729064Rat
631525Pia14Pristane induced arthritis QTL 144.4joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)165571108783402471Rat

Markers in Region
WI-15099  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21665,012,044 - 65,012,247 (+)MAPPERmRatBN7.2
Rnor_6.01669,173,407 - 69,173,609NCBIRnor6.0
Rnor_5.01668,846,780 - 68,846,982UniSTSRnor5.0
RGSC_v3.41669,339,234 - 69,339,436UniSTSRGSC3.4
Celera1662,931,425 - 62,931,627UniSTS
Cytogenetic Map16q12.4UniSTS
RH127692  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21665,002,354 - 65,002,562 (+)MAPPERmRatBN7.2
Rnor_6.01669,163,717 - 69,163,924NCBIRnor6.0
Rnor_5.01668,837,090 - 68,837,297UniSTSRnor5.0
RGSC_v3.41669,329,544 - 69,329,751UniSTSRGSC3.4
Celera1662,921,735 - 62,921,942UniSTS
RH 3.4 Map16593.9UniSTS
Cytogenetic Map16q12.4UniSTS


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 19 41 8 11 74 35 41 11 8
Low
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000018369   ⟹   ENSRNOP00000055400
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1665,002,223 - 65,014,657 (-)Ensembl
Rnor_6.0 Ensembl1669,163,577 - 69,176,036 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000098394   ⟹   ENSRNOP00000076766
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1665,002,223 - 65,012,641 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000114627   ⟹   ENSRNOP00000092068
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1665,006,941 - 65,014,886 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000118770   ⟹   ENSRNOP00000095942
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1665,002,223 - 65,014,578 (-)Ensembl
RefSeq Acc Id: NM_001107320   ⟹   NP_001100790
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81671,706,133 - 71,717,726 (-)NCBI
mRatBN7.21665,003,292 - 65,014,886 (-)NCBI
Rnor_6.01669,164,654 - 69,176,245 (-)NCBI
Rnor_5.01668,838,027 - 68,849,618 (-)NCBI
RGSC_v3.41669,330,481 - 69,342,072 (-)RGD
Celera1662,922,672 - 62,934,263 (-)RGD
Sequence:
RefSeq Acc Id: XM_063275442   ⟹   XP_063131512
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81671,705,064 - 71,716,208 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001100790 (Get FASTA)   NCBI Sequence Viewer  
  XP_063131512 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDM09089 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000055400
  ENSRNOP00000055400.2
  ENSRNOP00000076766.1
  ENSRNOP00000092068.1
  ENSRNOP00000095942.1
Reference Protein Sequences
RefSeq Acc Id: NP_001100790   ⟸   NM_001107320
- UniProtKB: D3ZCA0 (UniProtKB/TrEMBL),   A6IVY3 (UniProtKB/TrEMBL),   A0A8I6AQ45 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000055400   ⟸   ENSRNOT00000018369
RefSeq Acc Id: ENSRNOP00000095942   ⟸   ENSRNOT00000118770
RefSeq Acc Id: ENSRNOP00000092068   ⟸   ENSRNOT00000114627
RefSeq Acc Id: ENSRNOP00000076766   ⟸   ENSRNOT00000098394
RefSeq Acc Id: XP_063131512   ⟸   XM_063275442
- Peptide Label: isoform X1
Protein Domains
Alanine racemase N-terminal

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZCA0-F1-model_v2 AlphaFold D3ZCA0 1-275 view protein structure

Transcriptome

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

Promoters
RGD ID:13700156
Promoter ID:EPDNEW_R10679
Type:initiation region
Name:Plpbp_1
Description:pyridoxal phosphate binding protein
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_6.01669,176,012 - 69,176,072EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1308962 AgrOrtholog
BioCyc Gene G2FUF-11029 BioCyc
Ensembl Genes ENSRNOG00000013751 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000018369 ENTREZGENE
  ENSRNOT00000018369.7 UniProtKB/TrEMBL
  ENSRNOT00000098394.1 UniProtKB/TrEMBL
  ENSRNOT00000114627.1 UniProtKB/TrEMBL
  ENSRNOT00000118770.1 UniProtKB/TrEMBL
Gene3D-CATH 3.20.20.10 UniProtKB/TrEMBL
InterPro Ala_racemase_N UniProtKB/TrEMBL
  PLP-binding_barrel UniProtKB/TrEMBL
  Prd-pyrdxlP-dep_enz_YBL036C UniProtKB/TrEMBL
KEGG Report rno:306544 UniProtKB/TrEMBL
NCBI Gene 306544 ENTREZGENE
PANTHER PP_YBL036C UniProtKB/TrEMBL
  PYRIDOXAL PHOSPHATE HOMEOSTASIS PROTEIN UniProtKB/TrEMBL
Pfam Ala_racemase_N UniProtKB/TrEMBL
PhenoGen Plpbp PhenoGen
PIRSF YBL036c_PLPDEIII UniProtKB/TrEMBL
PROSITE UPF0001 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000013751 RatGTEx
Superfamily-SCOP SSF51419 UniProtKB/TrEMBL
UniProt A0A8I5YBG7_RAT UniProtKB/TrEMBL
  A0A8I6AQ45 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I6AV58_RAT UniProtKB/TrEMBL
  A6IVY3 ENTREZGENE, UniProtKB/TrEMBL
  D3ZCA0 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2017-03-27 Plpbp  pyridoxal phosphate binding protein  Prosc  proline synthetase co-transcribed homolog (bacterial)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-10-24 Prosc  proline synthetase co-transcribed homolog (bacterial)  Prosc  proline synthetase co-transcribed   Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Prosc  proline synthetase co-transcribed   Prosc_predicted  proline synthetase co-transcribed (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Prosc_predicted  proline synthetase co-transcribed (predicted)      Symbol and Name status set to approved 70820 APPROVED