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

    Gene ID: 304721, updated on 9-Dec-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
    EnsemblRapid: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 several human genes including PDXDC1 (pyridoxal dependent decarboxylase domain containing 1). [provided by Alliance of Genome Resources, Dec 2024]
    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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    See Pdxdc1 in Genome Data Viewer
    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 carboxy-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, ENSRNOT00000003284.7
      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
      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

      UniProtKB/TrEMBL
      A0A0G2K7V9

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

      UniProtKB/TrEMBL
      A0A0G2K7V9
      Related
      ENSRNOP00000074368.2, ENSRNOT00000089118.3

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

      UniProtKB/TrEMBL
      A0A1W2Q6L1
      Related
      ENSRNOP00000110783.1, ENSRNOT00000168918.1
      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

      UniProtKB/TrEMBL
      B5DFK8
      Related
      ENSRNOP00000079536.2, ENSRNOT00000101094.2
    Nucleotide Protein Strain
    Heading Accession and Version

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