Human Gene PNPO (uc010wlb.2) Description and Page Index
  Description: Homo sapiens pyridoxamine 5'-phosphate oxidase (PNPO), mRNA.
RefSeq Summary (NM_018129): The enzyme encoded by this gene catalyzes the terminal, rate-limiting step in the synthesis of pyridoxal 5'-phosphate, also known as vitamin B6. Vitamin B6 is a required co-factor for enzymes involved in both homocysteine metabolism and synthesis of neurotransmitters such as catecholamine. Mutations in this gene result in pyridoxamine 5'-phosphate oxidase (PNPO) deficiency, a form of neonatal epileptic encephalopathy. [provided by RefSeq, Oct 2008]. Publication Note: This RefSeq record includes a subset of the publications that are available for this gene. Please see the Gene record to access additional publications. ##Evidence-Data-START## Transcript exon combination :: AK001397.1, SRR7346977.1085016.1 [ECO:0000332] RNAseq introns :: single sample supports all introns SAMEA1965299, SAMEA1966682 [ECO:0000348] ##Evidence-Data-END## ##RefSeq-Attributes-START## RefSeq Select criteria :: based on manual assertion, conservation, expression, longest protein ##RefSeq-Attributes-END##
Transcript (Including UTRs)
   Position: hg19 chr17:46,018,889-46,026,674 Size: 7,786 Total Exon Count: 6 Strand: +
Coding Region
   Position: hg19 chr17:46,019,042-46,024,148 Size: 5,107 Coding Exon Count: 6 

Page IndexSequence and LinksGenetic AssociationsMalaCardsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesmRNA Descriptions
PathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr17:46,018,889-46,026,674)mRNA (may differ from genome)Protein (218 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblExonPrimerGeneCardsGeneNetwork
H-INVHGNCLynxMGIPubMedStanford SOURCE
TreefamUniProtKBWikipedia

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): PNPO
CDC HuGE Published Literature: PNPO

-  MalaCards Disease Associations
  MalaCards Gene Search: PNPO
Diseases sorted by gene-association score: pyridoxamine 5'-phosphate oxidase deficiency* (1550), pyridoxal 5'-phosphate-dependent epilepsy* (500), seizure disorder* (241), visual epilepsy* (121), encephalopathy (11), hypophosphatasia, infantile (8), benign familial infantile epilepsy (5), epileptic encephalopathy, early infantile, 15 (4), epileptic encephalopathy, early infantile, 6 (1)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 24.68 RPKM in Liver
Total median expression: 348.48 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -58.40153-0.382 Picture PostScript Text
3' UTR -872.442526-0.345 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR000659 - Pyridox_Oxase
IPR019740 - Pyridox_Oxase_CS
IPR011576 - Pyridox_Oxase_FMN-bd
IPR019576 - Pyridoxamine_oxidase_dimer_C
IPR012349 - Split_barrel_FMN-bd
IPR009002 - Split_barrel_FMN-bd-related

Pfam Domains:
PF01243 - Pyridoxamine 5'-phosphate oxidase
PF10590 - Pyridoxine 5'-phosphate oxidase C-terminal dimerisation region

SCOP Domains:
50475 - FMN-binding split barrel

ModBase Predicted Comparative 3D Structure on B4E152
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
      
      
      

-  Descriptions from all associated GenBank mRNAs
  LF209297 - JP 2014500723-A/16800: Polycomb-Associated Non-Coding RNAs.
AK303792 - Homo sapiens cDNA FLJ59601 complete cds, highly similar to Pyridoxine-5'-phosphate oxidase (EC 1.4.3.5).
AK303665 - Homo sapiens cDNA FLJ59599 complete cds, highly similar to Pyridoxine-5'-phosphate oxidase (EC 1.4.3.5).
AK001397 - Homo sapiens cDNA FLJ10535 fis, clone NT2RP2001070, weakly similar to PUTATIVE PYRIDOXAMINE 5'-PHOSPHATE OXIDASE (EC 1.4.3.5).
JD554813 - Sequence 535837 from Patent EP1572962.
AK223242 - Homo sapiens mRNA for pyridoxine 5'-phosphate oxidase variant, clone: STM03705.
AK303536 - Homo sapiens cDNA FLJ59109 complete cds, highly similar to Pyridoxine-5'-phosphate oxidase (EC 1.4.3.5).
BC006525 - Homo sapiens pyridoxamine 5'-phosphate oxidase, mRNA (cDNA clone MGC:953 IMAGE:2966366), complete cds.
GQ900985 - Homo sapiens clone HEL-T-97 epididymis secretory sperm binding protein mRNA, complete cds.
JD408363 - Sequence 389387 from Patent EP1572962.
KJ899086 - Synthetic construct Homo sapiens clone ccsbBroadEn_08480 PNPO gene, encodes complete protein.
KR709978 - Synthetic construct Homo sapiens clone CCSBHm_00008609 PNPO (PNPO) mRNA, encodes complete protein.
KR709979 - Synthetic construct Homo sapiens clone CCSBHm_00008610 PNPO (PNPO) mRNA, encodes complete protein.
KR709980 - Synthetic construct Homo sapiens clone CCSBHm_00008612 PNPO (PNPO) mRNA, encodes complete protein.
KR712208 - Synthetic construct Homo sapiens clone CCSBHm_00900160 PNPO (PNPO) mRNA, encodes complete protein.
AF468030 - Homo sapiens pyridoxine-5'-phosphate oxidase mRNA, complete cds.
FJ224333 - Homo sapiens epididymis secretory protein Li 302 (HEL-S-302) mRNA, complete cds.
JD511664 - Sequence 492688 from Patent EP1572962.
JD153836 - Sequence 134860 from Patent EP1572962.
JD259686 - Sequence 240710 from Patent EP1572962.
JD152884 - Sequence 133908 from Patent EP1572962.
JD038724 - Sequence 19748 from Patent EP1572962.
JD422823 - Sequence 403847 from Patent EP1572962.
JD521517 - Sequence 502541 from Patent EP1572962.
JD071922 - Sequence 52946 from Patent EP1572962.
JD411274 - Sequence 392298 from Patent EP1572962.
JD285402 - Sequence 266426 from Patent EP1572962.
JD373646 - Sequence 354670 from Patent EP1572962.
JD455299 - Sequence 436323 from Patent EP1572962.
JD184143 - Sequence 165167 from Patent EP1572962.
JD505236 - Sequence 486260 from Patent EP1572962.
JD117383 - Sequence 98407 from Patent EP1572962.
JD138054 - Sequence 119078 from Patent EP1572962.
JD441771 - Sequence 422795 from Patent EP1572962.
JD329861 - Sequence 310885 from Patent EP1572962.
JD103138 - Sequence 84162 from Patent EP1572962.
JD130473 - Sequence 111497 from Patent EP1572962.
JD049745 - Sequence 30769 from Patent EP1572962.
JD470451 - Sequence 451475 from Patent EP1572962.
JD363061 - Sequence 344085 from Patent EP1572962.
JD340609 - Sequence 321633 from Patent EP1572962.
JD202811 - Sequence 183835 from Patent EP1572962.
JD244058 - Sequence 225082 from Patent EP1572962.
JD053376 - Sequence 34400 from Patent EP1572962.
AB209036 - Homo sapiens mRNA for proteasome 26S ATPase subunit 5 variant protein.
MA444874 - JP 2018138019-A/16800: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa00750 - Vitamin B6 metabolism
hsa01100 - Metabolic pathways

-  Other Names for This Gene
  Alternate Gene Symbols: AK303665, B4E152, B4E152_HUMAN
UCSC ID: uc010wlb.2
RefSeq Accession: NM_018129
Protein: B4E152

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: AK303665.1
exon count: 6CDS single in 3' UTR: no RNA size: 1210
ORF size: 657CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 1414.00frame shift in genome: no % Coverage: 100.00
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.