Pdxkl1 (pyridoxal kinase like 1) - Rat Genome Database

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Gene: Pdxkl1 (pyridoxal kinase like 1) Rattus norvegicus
Analyze
No known orthologs.
Symbol: Pdxkl1
Name: pyridoxal kinase like 1
RGD ID: 1566085
Description: Enables pyridoxal binding activity and pyridoxal kinase activity. Involved in several processes, including pyridoxal phosphate biosynthetic process; response to X-ray; and response to progesterone. Predicted to be located in cytoplasm. Predicted to be active in cytosol. Orthologous to human PDXK (pyridoxal kinase); PARTICIPATES IN vitamin B6 metabolic pathway; INTERACTS WITH (+)-schisandrin B; 2,2',4,4'-Tetrabromodiphenyl ether; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC361819; pyridoxal kinase; pyridoxal kinase-like; RGD1566085; similar to pyridoxal (pyridoxine, vitamin B6) kinase
RGD Orthologs
Alliance Orthologs
More Info homologs ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr82010,162,634 - 10,192,271 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl2010,162,634 - 10,192,271 (-)EnsemblGRCr8
mRatBN7.22010,162,934 - 10,192,572 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2010,164,099 - 10,192,739 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx2010,863,151 - 10,892,773 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.02010,224,049 - 10,253,678 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.02010,695,137 - 10,724,757 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.02010,883,952 - 10,912,870 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2010,889,573 - 10,912,769 (-)Ensemblrn6Rnor6.0
Rnor_5.02013,055,730 - 13,084,627 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.42010,499,625 - 10,523,744 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera2011,673,992 - 11,703,668 (-)NCBICelera
Cytogenetic Map20p12NCBI
JBrowse:




Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
cytosol  (IBA,IEA)

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
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. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
3. GOA pipeline RGD automated data pipeline
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:212768   PMID:2119399   PMID:2928487   PMID:2988502   PMID:3007703   PMID:3681477   PMID:6255956   PMID:10204830   PMID:17115225  


Genomics

Variants

.
Variants in Pdxkl1
291 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:39
Count of miRNA genes:37
Interacting mature miRNAs:38
Transcripts:ENSRNOT00000051678
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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
4889610Pancm3Pancreatic morphology QTL 33.750.001pancreas mass (VT:0010144)pancreas wet weight (CMO:0000626)20418947649189476Rat
2317057Aia27Adjuvant induced arthritis QTL 272.83joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)20126925056Rat
1641915Colcr9Colorectal carcinoma resistance QTL 92.970.0024intestine integrity trait (VT:0010554)benign colorectal tumor number (CMO:0001795)20133724594Rat
7387283Uae44Urinary albumin excretion QTL 440.1712urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)20126128279Rat
4889870Pur30Proteinuria QTL 30190.005urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)20804392029865039Rat
7411668Foco32Food consumption QTL 3280.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20136600300Rat
2305926Iddm37Insulin dependent diabetes mellitus QTL 376blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)20153308346533083Rat
1354642Despr15Despair related QTL 150.0027locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)20124164241Rat
1558640Prcs2Prostate cancer susceptibility QTL 23.3prostate integrity trait (VT:0010571)percentage of study population developing ventral prostate tumorous lesions during a period of time (CMO:0000943)20134066551Rat
631265Iresp1Immunoglobin response QTL18.3blood anti-double stranded DNA antibody amount (VT:0004762)serum anti-DNA antibody level (CMO:0001533)20904109911115921Rat
8694189Bw153Body weight QTL 1533.130.001body mass (VT:0001259)body weight gain (CMO:0000420)20129193376Rat
4889857Pur27Proteinuria QTL 2712.20.001urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)20127341128Rat
1598870Bp289Blood pressure QTL 2892.4arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)20821635953216359Rat
9590109Sffal8Serum free fatty acids level QTL 85.320.01blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)20129193376Rat
9589155Insul32Insulin level QTL 326.380.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)20129193376Rat
9590275Scort15Serum corticosterone level QTL 153.480.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20129193376Rat
1581577Pur15Proteinuria QTL 154.380.0002urine total protein amount (VT:0000032)urine protein excretion rate (CMO:0000759)20804392015089182Rat
1598858Cm61Cardiac mass QTL 613.6heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)20821635953216359Rat
7411650Foco23Food consumption QTL 2320.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20129193376Rat
61432Cia1Collagen induced arthritis QTL 1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)20114100378Rat
2317851Alcrsp22Alcohol response QTL 223.20.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20127341128Rat
1641893Alcrsp7Alcohol response QTL 7response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20127341128Rat
6893685Bw111Body weight QTL 1112.70.004body mass (VT:0001259)body weight (CMO:0000012)20132578510Rat
9590252Scort12Serum corticosterone level QTL 1220.460.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20136600300Rat

Markers in Region
RH126288  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22010,168,469 - 10,168,922 (+)MAPPERmRatBN7.2
mRatBN7.22010,231,575 - 10,232,021 (+)MAPPERmRatBN7.2
Rnor_6.02010,951,833 - 10,952,278NCBIRnor6.0
Rnor_6.02010,889,488 - 10,889,941NCBIRnor6.0
Rnor_5.02013,123,611 - 13,124,056UniSTSRnor5.0
Rnor_5.02013,061,266 - 13,061,719UniSTSRnor5.0
RGSC_v3.42010,562,838 - 10,563,283UniSTSRGSC3.4
RGSC_v3.42010,499,734 - 10,500,186UniSTSRGSC3.4
Celera2011,679,528 - 11,679,980UniSTS
Celera2011,742,341 - 11,742,786UniSTS
Cytogenetic Map20p12UniSTS


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
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
16 12 67 161 91 90 59 92 59 6 356 192 11 140 81 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000051678   ⟹   ENSRNOP00000043021
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl2010,889,573 - 10,912,769 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000097943   ⟹   ENSRNOP00000084402
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl2010,162,634 - 10,192,271 (-)Ensembl
mRatBN7.2 Ensembl2010,164,099 - 10,192,739 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000098080   ⟹   ENSRNOP00000090354
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl2010,162,634 - 10,192,271 (-)Ensembl
mRatBN7.2 Ensembl2010,164,099 - 10,192,739 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000151839   ⟹   ENSRNOP00000099678
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl2010,162,634 - 10,192,271 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000153000   ⟹   ENSRNOP00000102304
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl2010,162,634 - 10,185,921 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000167571   ⟹   ENSRNOP00000099918
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl2010,162,634 - 10,191,438 (-)Ensembl
RefSeq Acc Id: NM_001402486   ⟹   NP_001389415
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82010,162,634 - 10,192,271 (-)NCBI
mRatBN7.22010,162,934 - 10,192,572 (-)NCBI
RefSeq Acc Id: XM_039099174   ⟹   XP_038955102
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82010,162,634 - 10,192,243 (-)NCBI
mRatBN7.22010,162,934 - 10,192,549 (-)NCBI
RefSeq Acc Id: XM_039099175   ⟹   XP_038955103
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82010,162,634 - 10,192,242 (-)NCBI
mRatBN7.22010,162,934 - 10,192,547 (-)NCBI
RefSeq Acc Id: XM_063279232   ⟹   XP_063135302
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82010,162,634 - 10,192,068 (-)NCBI
Ensembl Acc Id: ENSRNOP00000043021   ⟸   ENSRNOT00000051678
RefSeq Acc Id: XP_038955102   ⟸   XM_039099174
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038955103   ⟸   XM_039099175
- Peptide Label: isoform X2
Ensembl Acc Id: ENSRNOP00000090354   ⟸   ENSRNOT00000098080
Ensembl Acc Id: ENSRNOP00000084402   ⟸   ENSRNOT00000097943
RefSeq Acc Id: NP_001389415   ⟸   NM_001402486
- UniProtKB: O35331 (UniProtKB/Swiss-Prot),   A0A8I6AAM1 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063135302   ⟸   XM_063279232
- Peptide Label: isoform X1
Ensembl Acc Id: ENSRNOP00000099918   ⟸   ENSRNOT00000167571
Ensembl Acc Id: ENSRNOP00000102304   ⟸   ENSRNOT00000153000
Ensembl Acc Id: ENSRNOP00000099678   ⟸   ENSRNOT00000151839
Protein Domains
Pyridoxamine kinase/Phosphomethylpyrimidine kinase

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3Z8P5-F1-model_v2 AlphaFold D3Z8P5 1-319 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1566085 AgrOrtholog
BioCyc Gene G2FUF-4287 BioCyc
BioCyc Pathway PLPSAL-PWY [pyridoxal 5'-phosphate salvage I] BioCyc
BioCyc Pathway Image PLPSAL-PWY BioCyc
Ensembl Genes ENSRNOG00000049970 Ensembl
  ENSRNOG00000068407 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000097943.2 UniProtKB/TrEMBL
  ENSRNOT00000098080 ENTREZGENE
  ENSRNOT00000098080.2 UniProtKB/TrEMBL
  ENSRNOT00000151839.1 UniProtKB/TrEMBL
  ENSRNOT00000153000.1 UniProtKB/TrEMBL
  ENSRNOT00000167571.1 UniProtKB/TrEMBL
Gene3D-CATH 3.40.1190.20 UniProtKB/TrEMBL
InterPro PM/HMP-P_kinase-1 UniProtKB/TrEMBL
  PyrdxlKinase UniProtKB/TrEMBL
  Ribokinase-like UniProtKB/TrEMBL
NCBI Gene 361819 ENTREZGENE
PANTHER PTHR10534 UniProtKB/TrEMBL
  PYRIDOXAL KINASE UniProtKB/TrEMBL
Pfam Phos_pyr_kin UniProtKB/TrEMBL
PhenoGen Pdxkl1 PhenoGen
RatGTEx ENSRNOG00000049970 RatGTEx
  ENSRNOG00000068407 RatGTEx
Superfamily-SCOP SSF53613 UniProtKB/TrEMBL
UniProt A0A8I5ZY09_RAT UniProtKB/TrEMBL
  A0A8I6AAM1 ENTREZGENE, UniProtKB/TrEMBL
  A0ABK0LA87_RAT UniProtKB/TrEMBL
  A0ABK0LEN0_RAT UniProtKB/TrEMBL
  A0ABK0LHK5_RAT UniProtKB/TrEMBL
  O35331 ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2023-09-19 Pdxkl1  pyridoxal kinase like 1  RGD1566085  similar to pyridoxal (pyridoxine, vitamin B6) kinase  Symbol and Name Changed 1299863 APPROVED
2022-06-02 RGD1566085  similar to pyridoxal (pyridoxine, vitamin B6) kinase  RGD1566085  similar to pyridoxal (pyridoxine, vitamin B6) kinase  Data merged from RGD:149736533 737654 PROVISIONAL
2021-08-09 RGD1566085  similar to pyridoxal (pyridoxine, vitamin B6) kinase      Symbol and Name status set to provisional 45752 PROVISIONAL
2008-04-30 RGD1566085  similar to pyridoxal (pyridoxine, vitamin B6) kinase   RGD1566085_predicted  similar to pyridoxal (pyridoxine, vitamin B6) kinase (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-07 RGD1566085_predicted  similar to pyridoxal (pyridoxine, vitamin B6) kinase (predicted)  LOC361819  similar to pyridoxal (pyridoxine, vitamin B6) kinase  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC361819  similar to pyridoxal (pyridoxine, vitamin B6) kinase      Symbol and Name status set to provisional 70820 PROVISIONAL