Human Gene PDXDC1 (ENST00000396410.9_10) from GENCODE V47lift37
  Description: pyridoxal dependent decarboxylase domain containing 1, transcript variant 1 (from RefSeq NM_015027.4)
Gencode Transcript: ENST00000396410.9_10
Gencode Gene: ENSG00000179889.21_17
Transcript (Including UTRs)
   Position: hg19 chr16:15,068,883-15,132,189 Size: 63,307 Total Exon Count: 23 Strand: +
Coding Region
   Position: hg19 chr16:15,069,057-15,130,132 Size: 61,076 Coding Exon Count: 23 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr16:15,068,883-15,132,189)mRNA (may differ from genome)Protein (788 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
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HGNCMGIOMIMPubMedUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: PDXD1_HUMAN
DESCRIPTION: RecName: Full=Pyridoxal-dependent decarboxylase domain-containing protein 1; EC=4.1.1.-;
COFACTOR: Pyridoxal phosphate (By similarity).
PTM: Phosphorylated upon DNA damage, probably by ATM or ATR.
SIMILARITY: Belongs to the group II decarboxylase family.
SEQUENCE CAUTION: Sequence=AAH33748.1; Type=Frameshift; Positions=369; Sequence=AAZ14099.1; Type=Frameshift; Positions=369; Sequence=BAA19780.1; Type=Erroneous initiation;

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  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: 59.19 RPKM in Testis
Total median expression: 974.90 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 -85.90174-0.494 Picture PostScript Text
3' UTR -561.902057-0.273 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
IPR002129 - PyrdxlP-dep_de-COase
IPR015424 - PyrdxlP-dep_Trfase_major_dom
IPR015421 - PyrdxlP-dep_Trfase_major_sub1
IPR015422 - PyrdxlP-dep_Trfase_major_sub2

Pfam Domains:
PF00282 - Pyridoxal-dependent decarboxylase conserved domain

SCOP Domains:
53383 - PLP-dependent transferases

ModBase Predicted Comparative 3D Structure on Q6P996
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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 DetailsGene Details    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003824 catalytic activity
GO:0016829 lyase activity
GO:0016831 carboxy-lyase activity
GO:0030170 pyridoxal phosphate binding
GO:0045296 cadherin binding

Biological Process:
GO:0019752 carboxylic acid metabolic process

Cellular Component:
GO:0005794 Golgi apparatus
GO:0043231 intracellular membrane-bounded organelle


-  Descriptions from all associated GenBank mRNAs
  AK295168 - Homo sapiens cDNA FLJ59515 complete cds.
AK299799 - Homo sapiens cDNA FLJ59412 complete cds.
BC045554 - Homo sapiens pyridoxal-dependent decarboxylase domain containing 1, mRNA (cDNA clone MGC:57233 IMAGE:5295351), complete cds.
BC053946 - Homo sapiens pyridoxal-dependent decarboxylase domain containing 1, mRNA (cDNA clone IMAGE:5295921).
BC033748 - Homo sapiens pyridoxal-dependent decarboxylase domain containing 1, mRNA (cDNA clone IMAGE:5196034), complete cds.
D87438 - Homo sapiens mRNA for KIAA0251 gene.
BC036520 - Homo sapiens pyridoxal-dependent decarboxylase domain containing 1, mRNA (cDNA clone MGC:33287 IMAGE:5270048), complete cds.
BX647809 - Homo sapiens mRNA; cDNA DKFZp686N0796 (from clone DKFZp686N0796).
BX648066 - Homo sapiens mRNA; cDNA DKFZp686A07210 (from clone DKFZp686A07210).
AK299111 - Homo sapiens cDNA FLJ53168 complete cds.
BC060871 - Homo sapiens pyridoxal-dependent decarboxylase domain containing 1, mRNA (cDNA clone MGC:71824 IMAGE:30347972), complete cds.
AY203955 - Homo sapiens LP8165 mRNA, complete cds.
AB383820 - Synthetic construct DNA, clone: pF1KSDA0251, Homo sapiens PDXDC1 gene for pyridoxal-dependent decarboxylase domain-containing protein 1, complete cds, without stop codon, in Flexi system.
HQ257954 - Synthetic construct Homo sapiens clone IMAGE:100072263 Unknown protein gene, encodes complete protein.
KJ902269 - Synthetic construct Homo sapiens clone ccsbBroadEn_11663 PDXDC1 gene, encodes complete protein.
DQ111782 - Homo sapiens chromosome 16 unknown mRNA.
JD158591 - Sequence 139615 from Patent EP1572962.
JD408861 - Sequence 389885 from Patent EP1572962.
JD217529 - Sequence 198553 from Patent EP1572962.
JD217530 - Sequence 198554 from Patent EP1572962.
DQ578691 - Homo sapiens piRNA piR-46803, complete sequence.
BC025366 - Homo sapiens pyridoxal-dependent decarboxylase domain containing 1, mRNA (cDNA clone IMAGE:3939623), partial cds.
DQ597358 - Homo sapiens piRNA piR-35424, complete sequence.
DQ597465 - Homo sapiens piRNA piR-35531, complete sequence.
AK090552 - Homo sapiens cDNA FLJ33233 fis, clone ASTRO2002035.
AX746506 - Sequence 31 from Patent EP1308459.
AK025504 - Homo sapiens cDNA: FLJ21851 fis, clone HEP01962.
BC042104 - Homo sapiens pyridoxal-dependent decarboxylase domain containing 1, mRNA (cDNA clone IMAGE:5114403), partial cds.
CU675949 - Synthetic construct Homo sapiens gateway clone IMAGE:100018104 3' read NTAN1 mRNA.

-  Other Names for This Gene
  Alternate Gene Symbols: B4DR55, B4DSL3, E7EMH5, E7EPL4, ENST00000396410.1, ENST00000396410.2, ENST00000396410.3, ENST00000396410.4, ENST00000396410.5, ENST00000396410.6, ENST00000396410.7, ENST00000396410.8, H3BNZ1, KIAA0251, NM_015027, O00236, PDXD1_HUMAN, Q4F6X7, Q6P996, Q6PID7, Q86YF1, Q8N4Q9, Q8TBS5, uc318yft.1, uc318yft.2
UCSC ID: ENST00000396410.9_10
RefSeq Accession: NM_015027.4
Protein: Q6P996 (aka PDXD1_HUMAN)

-  Gene Model Information
  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.