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

    Gene ID: 94184, updated on 2-Nov-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 several human genes including PDXDC1 (pyridoxal dependent decarboxylase domain containing 1). [provided by Alliance of Genome Resources, Nov 2024]
    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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    See Pdxdc1 in Genome Data Viewer
    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 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 (24) 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 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
    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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