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Pdxdc1 pyridoxal-dependent decarboxylase domain containing 1 [ Mus musculus (house mouse) ]

Gene ID: 94184, updated on 5-Mar-2024

Summary

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Official Symbol
Pdxdc1provided by MGI
Official Full Name
pyridoxal-dependent decarboxylase domain containing 1provided by MGI
Primary source
MGI:MGI:1920909
See related
Ensembl:ENSMUSG00000022680 AllianceGenome:MGI:1920909
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
Kiaa0251-hp; 2210010A19Rik
Summary
Predicted to enable carboxy-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. Is expressed in central nervous system and retina. Orthologous to human PDXDC1 (pyridoxal dependent decarboxylase domain containing 1). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in testis adult (RPKM 34.6), colon adult (RPKM 34.4) and 28 other tissues See more
Orthologs
human all
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Genomic context

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Location:
16 A1; 16 9.64 cM
Exon count:
24
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 16 NC_000082.7 (13651025..13721018, complement)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 16 NC_000082.6 (13833145..13903176, complement)

Chromosome 16 - NC_000082.7Genomic Context describing neighboring genes Neighboring gene elongin-B pseudogene Neighboring gene RRN3 RNA polymerase I transcription factor homolog (yeast) Neighboring gene N-terminal Asn amidase Neighboring gene nudix (nucleoside diphosphate linked moiety X)-type motif 4 pseudogene Neighboring gene STARR-seq mESC enhancer starr_40163 Neighboring gene STARR-positive B cell enhancer ABC_E8619 Neighboring gene Mpv17 transgene, kidney disease mutant-like Neighboring gene STARR-seq mESC enhancer starr_40164 Neighboring gene laminin, gamma 1 pseudogene Neighboring gene STARR-seq mESC enhancer starr_40165 Neighboring gene STARR-seq mESC enhancer starr_40166 Neighboring gene STARR-seq mESC enhancer starr_40168 Neighboring gene STARR-seq mESC enhancer starr_40169 Neighboring gene STARR-seq mESC enhancer starr_40170 Neighboring gene interferon induced transmembrane protein 7 Neighboring gene bMERB domain containing 1

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: Mouse ENCODE transcriptome data
  • Description: RNA profiling data sets generated by the Mouse ENCODE project.
  • BioProject: PRJNA66167
  • Publication: PMID 25409824
  • Analysis date: n/a

Bibliography

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Related articles in PubMed

  1. Identification of PDXDC1 as a novel pleiotropic susceptibility locus shared between lumbar spine bone mineral density and birth weight. Song YQ, et al. J Mol Med (Berl), 2022 May. PMID 35314877, Free PMC Article
  2. Irisin Mediates Effects on Bone and Fat via αV Integrin Receptors. Kim H, et al. Cell, 2018 Dec 13. PMID 30550785, Free PMC Article
  3. BioID screening of biotinylation sites using the avidin-like protein Tamavidin 2-REV identifies global interactors of stimulator of interferon genes (STING). Motani K, et al. J Biol Chem, 2020 Aug 7. PMID 32554809, Free PMC Article
  4. The central role of EED in the orchestration of polycomb group complexes. Cao Q, et al. Nat Commun, 2014. PMID 24457600, Free PMC Article
  5. EUCOMM--the European conditional mouse mutagenesis program. Friedel RH, et al. Brief Funct Genomic Proteomic, 2007 Sep. PMID 17967808

See all (22) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Identification of PDXDC1 as a novel pleiotropic susceptibility locus shared between lumbar spine bone mineral density and birth weight.
    Title: Identification of PDXDC1 as a novel pleiotropic susceptibility locus shared between lumbar spine bone mineral density and birth weight.
Submit: New GeneRIF Correction

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Endonuclease-mediated (3) 

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • MGC8182

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables carbon-carbon lyase activity IEA
Inferred from Electronic Annotation
more info
  
enables carboxy-lyase activity IEA
Inferred from Electronic Annotation
more info
  
enables 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
NP_001034622.1
NP_001277946.1
NP_001344154.1
NP_444411.2
XP_011244355.1
XP_011244356.1
XP_011244357.1
XP_036016092.1
XP_036016093.1

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_001039533.2 → NP_001034622.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform 3

    See identical proteins and their annotated locations for NP_001034622.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) lacks an internal exon in the 3' coding region, which results in a frameshift, compared to variant 4. It encodes isoform 3 which is shorter and has a distinct C-terminus, compared to isoform 4.
    Source sequence(s)
    AC107769, AK004611, AK054329
    Consensus CDS
    CCDS37261.1
    UniProtKB/Swiss-Prot
    Q99K01
    Related
    ENSMUSP00000111471.3, ENSMUST00000115804.9
    Conserved Domains (1) summary
    cl18945
    Location:172 → 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 ...

  2. NM_001291017.1 → NP_001277946.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform 4

    See identical proteins and their annotated locations for NP_001277946.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) encodes the longest isoform (4).
    Source sequence(s)
    AC107769, AK054329
    Consensus CDS
    CCDS70685.1
    UniProtKB/TrEMBL
    A0A0R4J034
    Related
    ENSMUSP00000023361.6, ENSMUST00000023361.12
    Conserved Domains (1) summary
    cl18945
    Location:172 → 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 ...

  3. NM_001357225.1 → NP_001344154.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform 5

    Status: VALIDATED

    Source sequence(s)
    AC107769
    Conserved Domains (1) summary
    cl18945
    Location:171 → 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 ...

  4. NM_053181.3 → NP_444411.2  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform 1

    See identical proteins and their annotated locations for NP_444411.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) lacks the terminal exon used in variant 4 and its 3' terminal exon extends past a splice site that is used in variant 4. This results in a novel 3' coding region and 3' UTR, compared to variant 4. It encodes isoform 1 which is shorter and has a distinct C-terminus, compared to isoform 4.
    Source sequence(s)
    AC107769, AK030613, AK033107, AK054329, BY469248
    UniProtKB/Swiss-Prot
    Q3TCL3, Q3TN13, Q8BMK9, Q8BW02, Q8BW51, Q8BZZ4, Q99K01, Q9DC25
    Related
    ENSMUST00000154150.8
    Conserved Domains (1) summary
    cl18945
    Location:172 → 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_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000082.7 Reference GRCm39 C57BL/6J

    Range
    13651025..13721018 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011246054.4 → XP_011244356.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X2

    Conserved Domains (1) summary
    cl18945
    Location:171 → 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_011246053.3 → XP_011244355.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X1

    Conserved Domains (1) summary
    cl18945
    Location:172 → 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 ...

  3. XM_011246055.4 → XP_011244357.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X3

    Conserved Domains (1) summary
    cl18945
    Location:150 → 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 ...

  4. XM_036160199.1 → XP_036016092.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X4

    Conserved Domains (1) summary
    cl18945
    Location:171 → 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 ...

  5. XM_036160200.1 → XP_036016093.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X5

    Conserved Domains (1) summary
    cl18945
    Location:172 → 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 ...

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_178853.2: Suppressed sequence

    Description
    NM_178853.2: This RefSeq was temporarily suppressed because the splicing pattern of AK075829.1, which was used as its source, does not occur in any other transcripts.
Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q99K01.2 GenPept UniProtKB/Swiss-Prot:Q99K01

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