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Pdxdc1 pyridoxal-dependent decarboxylase domain containing 1 [ Rattus norvegicus (Norway rat) ]

Gene ID: 304721, updated on 5-Mar-2024

Summary

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Symbol
Pdxdc1provided by RGD
Full Name
pyridoxal-dependent decarboxylase domain containing 1provided by RGD
Primary source
RGD:1562597
See related
Ensembl:ENSRNOG00000002407 AllianceGenome:RGD:1562597
Gene type
protein coding
RefSeq status
PROVISIONAL
Organism
Rattus norvegicus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as
RGD1562597
Summary
Predicted to enable carbon-carbon lyase activity and pyridoxal phosphate binding activity. Predicted to be involved in carboxylic acid metabolic process. Predicted to be located in Golgi apparatus. Predicted to be active in intracellular membrane-bounded organelle. Orthologous to human PDXDC1 (pyridoxal dependent decarboxylase domain containing 1). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Biased expression in Kidney (RPKM 179.3), Liver (RPKM 166.3) and 9 other tissues See more
Orthologs
human mouse all
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Genomic context

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Location:
10q11
Exon count:
24
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCr8 (GCF_036323735.1) 10 NC_086028.1 (2528989..2620669)
RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 10 NC_051345.1 (2025056..2113712)
106 previous assembly Rnor_6.0 (GCF_000001895.5) 10 NC_005109.4 (3232794..3321438, complement)

Chromosome 10 - NC_086028.1Genomic Context describing neighboring genes Neighboring gene large ribosomal subunit protein uL13-like Neighboring gene bMERB domain containing 1 Neighboring gene nuclear receptor coactivator 4, pseudogene 1 Neighboring gene MPV17 mitochondrial inner membrane protein like Neighboring gene uncharacterized LOC102552514 Neighboring gene N-terminal asparagine amidase Neighboring gene RRN3 homolog, RNA polymerase I transcription factor

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
  • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
  • BioProject: PRJNA238328
  • Publication: PMID 24510058
  • Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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Related articles in PubMed

  1. Gene and alternative splicing annotation with AIR. Florea L, et al. Genome Res, 2005 Jan. PMID 15632090, Free PMC Article
  2. E-cadherin interactome complexity and robustness resolved by quantitative proteomics. Guo Z, et al. Sci Signal, 2014 Dec 2. PMID 25468996, Free PMC Article
  3. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, et al. Proc Natl Acad Sci U S A, 2002 Dec 24. PMID 12477932, Free PMC Article
  4. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

GeneRIFs: Gene References Into Functions

General gene information

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Markers

Homology

Clone Names

  • MGC189517

Gene Ontology Provided by RGD

Function Evidence Code Pubs
enables carbon-carbon lyase activity IEA
Inferred from Electronic Annotation
more info
  
enables pyridoxal phosphate binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in carboxylic acid metabolic process IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in Golgi apparatus ISO
Inferred from Sequence Orthology
more info
  
is_active_in intracellular membrane-bounded organelle IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in intracellular membrane-bounded organelle ISO
Inferred from Sequence Orthology
more info
  

General protein information

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Preferred Names
pyridoxal-dependent decarboxylase domain-containing protein 1
Names
pyridoxal-dependent decarboxylase domain-containing protein 1-like
NP_001128433.1
XP_006245767.1
XP_006245770.2
XP_038942164.1
XP_038942166.1
XP_063125337.1
XP_063125338.1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001134961.1 → NP_001128433.1  pyridoxal-dependent decarboxylase domain-containing protein 1

    See identical proteins and their annotated locations for NP_001128433.1

    Status: PROVISIONAL

    Source sequence(s)
    CH474017
    UniProtKB/TrEMBL
    A6K4F5, B5DFK8, G3V6B0
    Related
    ENSRNOP00000003284.5, ENSRNOT00000003284.6
    Conserved Domains (1) summary
    cl18945
    Location:203 → 394
    AAT_I; Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the ...

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCr8

Genomic

  1. NC_086028.1 Reference GRCr8

    Range
    2528989..2620669
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006245705.5 → XP_006245767.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X2

    UniProtKB/TrEMBL
    B5DFK8
    Conserved Domains (1) summary
    cl18945
    Location:202 → 393
    AAT_I; Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the ...

  2. XM_039086236.2 → XP_038942164.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X4

    UniProtKB/TrEMBL
    A0A0G2K7V9
    Related
    ENSRNOP00000074368.2
    Conserved Domains (1) summary
    cl18945
    Location:188 → 379
    AAT_I; Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the ...

  3. XM_063269268.1 → XP_063125338.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X5

  4. XM_006245708.5 → XP_006245770.2  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X1

  5. XM_039086238.2 → XP_038942166.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X6

    UniProtKB/TrEMBL
    A0A1W2Q6L1
    Related
    ENSRNOP00000076319.2
    Conserved Domains (1) summary
    cl18945
    Location:181 → 372
    AAT_I; Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the ...

  6. XM_063269267.1 → XP_063125337.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X3

Nucleotide Protein Strain
Heading Accession and Version

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