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    PDXDC1 pyridoxal dependent decarboxylase domain containing 1 [ Homo sapiens (human) ]

    Gene ID: 23042, updated on 30-Oct-2024

    Summary

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    Official Symbol
    PDXDC1provided by HGNC
    Official Full Name
    pyridoxal dependent decarboxylase domain containing 1provided by HGNC
    Primary source
    HGNC:HGNC:28995
    See related
    Ensembl:ENSG00000179889 MIM:614244; AllianceGenome:HGNC:28995
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    LP8165
    Summary
    Enables cadherin binding activity. Predicted to be involved in carboxylic acid metabolic process. Located in Golgi apparatus. [provided by Alliance of Genome Resources, Oct 2024]
    Expression
    Ubiquitous expression in testis (RPKM 42.5), duodenum (RPKM 33.1) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See PDXDC1 in Genome Data Viewer
    Location:
    16p13.11
    Exon count:
    30
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (14974735..15153218)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (14975789..15144257)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (15068592..15233267)

    Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene PKD1P3-NPIPA1 readthrough Neighboring gene polycystin 1, transient receptor potential channel interacting pseudogene 3 Neighboring gene microRNA 6770-1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:15041221-15041722 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:15041723-15042222 Neighboring gene nuclear pore complex interacting protein family member A1 Neighboring gene Sharpr-MPRA regulatory region 4661 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:15068201-15068964 Neighboring gene KIAA2013 pseudogene Neighboring gene ReSE screen-validated silencer GRCh37_chr16:15106867-15106972 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:15109763-15110264 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:15110265-15110764 Neighboring gene microRNA 1972-1 Neighboring gene Sharpr-MPRA regulatory region 1947 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:15121593-15122216 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:15120969-15121592 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:15122498-15123030 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:15149302-15149486 Neighboring gene MPRA-validated peak2507 silencer Neighboring gene N-terminal asparagine amidase Neighboring gene RRN3 homolog, RNA polymerase I transcription factor Neighboring gene Sharpr-MPRA regulatory region 13846 Neighboring gene uncharacterized LOC100505915 Neighboring gene PKD1P6-NPIPP1 readthrough Neighboring gene nuclear pore complex interacting protein pseudogene 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:15231552-15232159 Neighboring gene microRNA 6511b-2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:15240089-15241062 Neighboring gene polycystin 1, transient receptor potential channel interacting pseudogene 6 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:15243079-15243774 Neighboring gene microRNA 3180-4 Neighboring gene uncharacterized LOC105371096

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. Genome-wide analysis of high-risk primary brain cancer pedigrees identifies PDXDC1 as a candidate brain cancer predisposition gene. Cannon-Albright LA, et al. Neuro Oncol, 2021 Feb 25. PMID 32644145, Free PMC Article
    2. Pdxdc1 modulates prepulse inhibition of acoustic startle in the mouse. Feldcamp LA, et al. Transl Psychiatry, 2017 May 9. PMID 28485732, Free PMC Article
    3. Proteome-wide Identification of HtrA2/Omi Substrates. Vande Walle L, et al. J Proteome Res, 2007 Mar. PMID 17266347
    4. Genetic loci associated with plasma phospholipid n-3 fatty acids: a meta-analysis of genome-wide association studies from the CHARGE Consortium. Lemaitre RN, et al. PLoS Genet, 2011 Jul. PMID 21829377, Free PMC Article
    5. A genome-wide association study in 19 633 Japanese subjects identified LHX3-QSOX2 and IGF1 as adult height loci. Okada Y, et al. Hum Mol Genet, 2010 Jun 1. PMID 20189936

    See all (75) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    A genome-wide association study in 19 633 Japanese subjects identified LHX3-QSOX2 and IGF1 as adult height loci.
    EBI GWAS Catalog
    An atlas of genetic influences on human blood metabolites.
    EBI GWAS Catalog
    Discovery and refinement of loci associated with lipid levels.
    EBI GWAS Catalog
    Genetic loci associated with plasma phospholipid n-3 fatty acids: a meta-analysis of genome-wide association studies from the CHARGE Consortium.
    EBI GWAS Catalog
    Genome-wide association study identifies multiple loci influencing human serum metabolite levels.
    EBI GWAS Catalog
    Genome-wide association study identifies novel loci associated with circulating phospho- and sphingolipid concentrations.
    EBI GWAS Catalog
    Genome-wide association study of plasma N6 polyunsaturated fatty acids within the cohorts for heart and aging research in genomic epidemiology consortium.
    EBI GWAS Catalog
    Genome-wide meta-analysis identifies 56 bone mineral density loci and reveals 14 loci associated with risk of fracture.
    EBI GWAS Catalog
    Human metabolic individuality in biomedical and pharmaceutical research.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • KIAA0251

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables cadherin binding HDA PubMed 
    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 IDA
    Inferred from Direct Assay
    more info
    		  
    is_active_in intracellular membrane-bounded organelle IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in intracellular membrane-bounded organelle IDA
    Inferred from Direct Assay
    more info
    		  

    General protein information

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    Preferred Names
    pyridoxal-dependent decarboxylase domain-containing protein 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_001285444.2 → NP_001272373.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform 2

      See identical proteins and their annotated locations for NP_001272373.1

      Status: VALIDATED

      Source sequence(s)
      AC138932, BC042104, BC053946, BC060871, BM997114, BX647809, HY036748
      Consensus CDS
      CCDS66954.1
      UniProtKB/TrEMBL
      B4DHL7
      Related
      ENSP00000455070.1, ENST00000569715.5
      Conserved Domains (1) summary
      cl18945
      Location:145 → 367
      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_001285445.2 → NP_001272374.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform 3

      Status: VALIDATED

      Source sequence(s)
      AC138932, AK299111, BC042104, BC053946, BC060871, BM997114, D87438, HY036748
      Consensus CDS
      CCDS66955.1
      UniProtKB/TrEMBL
      B4DHL7
      Related
      ENSP00000486662.1, ENST00000627450.2
      Conserved Domains (1) summary
      cl18945
      Location:144 → 366
      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_001285447.1 → NP_001272376.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform 4

      See identical proteins and their annotated locations for NP_001272376.1

      Status: VALIDATED

      Source sequence(s)
      AK295168, BC033748, BC042104, BC060871, BM997114, DA775396
      UniProtKB/TrEMBL
      B4DHL7
      Related
      ENSP00000454791.1, ENST00000563679.5
      Conserved Domains (1) summary
      cl18945
      Location:157 → 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 ...

    4. NM_001285448.1 → NP_001272377.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform 5

      Status: VALIDATED

      Source sequence(s)
      AK299799, BC042104, BC060871, BM997114, DA321929
      Consensus CDS
      CCDS66957.1
      UniProtKB/TrEMBL
      B4DHL7
      Related
      ENSP00000391147.3, ENST00000450288.3
      Conserved Domains (1) summary
      cl18945
      Location:81 → 303
      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. NM_001285449.2 → NP_001272378.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform 6

      See identical proteins and their annotated locations for NP_001272378.1

      Status: VALIDATED

      Source sequence(s)
      AC139256, BC045554, CD370048
      Consensus CDS
      CCDS73830.1
      UniProtKB/Swiss-Prot
      A8K9Z5, Q6P474
      UniProtKB/TrEMBL
      Q86XE2
      Related
      ENSP00000437835.2, ENST00000535621.6
      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 ...

    6. NM_001285450.2 → NP_001272379.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform 7

      Status: VALIDATED

      Source sequence(s)
      AC138932, BC033748, BC053946, CA423507, HY036748
      Consensus CDS
      CCDS73831.1
      UniProtKB/Swiss-Prot
      A8K9Z5, Q6P474
      Related
      ENSP00000406703.2, ENST00000455313.6
      Conserved Domains (1) summary
      cl18945
      Location:172 → 371
      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 ...

    7. NM_001324019.2 → NP_001310948.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform 8

      Status: VALIDATED

      Source sequence(s)
      AC138932
      UniProtKB/TrEMBL
      B4DHL7

    8. NM_001324020.2 → NP_001310949.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform 9

      Status: VALIDATED

      Source sequence(s)
      AC138932, AC139256
      UniProtKB/Swiss-Prot
      A8K9Z5, Q6P474

    9. NM_001324021.2 → NP_001310950.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform 10

      Status: VALIDATED

      Source sequence(s)
      AC138932, AC139256
      UniProtKB/Swiss-Prot
      A8K9Z5, Q6P474

    10. NM_015027.4 → NP_055842.2  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform 1

      See identical proteins and their annotated locations for NP_055842.2

      Status: VALIDATED

      Source sequence(s)
      AC138932, AY203955, BC042104, BC060871, BM997114, DB019664
      Consensus CDS
      CCDS32393.1
      UniProtKB/Swiss-Prot
      B4DR55, B4DSL3, E7EMH5, E7EPL4, H3BNZ1, O00236, Q4F6X7, Q6P996, Q6PID7, Q86YF1, Q8N4Q9, Q8TBS5
      UniProtKB/TrEMBL
      B4DHL7
      Related
      ENSP00000379691.4, ENST00000396410.9
      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 ...

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000016.10 Reference GRCh38.p14 Primary Assembly

      Range
      14974735..15153218
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_024450194.2 → XP_024305962.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X7

      UniProtKB/Swiss-Prot
      A8K9Z5, Q6P474
      Related
      ENSP00000520890.1, ENST00000850603.1
      Conserved Domains (1) summary
      cl18945
      Location:157 → 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 ...

    2. XM_017023065.2 → XP_016878554.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X6

      UniProtKB/Swiss-Prot
      A8K9Z5, Q6P474

    3. XM_047433790.1 → XP_047289746.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X8

    4. XM_024450195.2 → XP_024305963.2  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X6

    5. XM_017023059.2 → XP_016878548.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X1

      UniProtKB/TrEMBL
      B4DHL7
      Conserved Domains (1) summary
      cl18945
      Location:157 → 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 ...

    6. XM_047433788.1 → XP_047289744.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X2

    7. XM_006720865.3 → XP_006720928.2  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X2

      UniProtKB/TrEMBL
      B4DHL7
      Conserved Domains (1) summary
      cl18945
      Location:130 → 352
      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 ...

    8. XM_017023063.2 → XP_016878552.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X4

      UniProtKB/TrEMBL
      B4DHL7

    9. XM_017023060.2 → XP_016878549.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X3

      UniProtKB/TrEMBL
      B4DHL7
      Conserved Domains (1) summary
      cl18945
      Location:181 → 403
      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 ...

    10. XM_047433789.1 → XP_047289745.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X5

    11. XM_047433791.1 → XP_047289747.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X9

    12. XM_017023061.3 → XP_016878550.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X1

      UniProtKB/TrEMBL
      B4DHL7
      Conserved Domains (1) summary
      cl18945
      Location:157 → 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 ...

    13. XM_024450197.2 → XP_024305965.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X8

      UniProtKB/Swiss-Prot
      A8K9Z5, Q6P474
      Conserved Domains (1) summary
      cl18945
      Location:130 → 352
      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 ...

    Reference GRCh38.p14 ALT_REF_LOCI_1

    Genomic

    1. NT_187607.1 Reference GRCh38.p14 ALT_REF_LOCI_1

      Range
      508761..694938 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054329064.1 → XP_054185039.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X17

    2. XM_054329066.1 → XP_054185041.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X16

    3. XM_054329065.1 → XP_054185040.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X18

    4. XM_054329063.1 → XP_054185038.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X16

    5. XM_054329068.1 → XP_054185043.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X20

    6. XM_054329067.1 → XP_054185042.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X19

    7. XM_054329070.1 → XP_054185045.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X18

    8. XM_054329058.1 → XP_054185033.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X10

    9. XM_054329055.1 → XP_054185030.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X10

    10. XM_054329054.1 → XP_054185029.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X1

    11. XM_054329057.1 → XP_054185032.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X12

    12. XM_054329056.1 → XP_054185031.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X11

    13. XM_054329059.1 → XP_054185034.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X1

    14. XM_054329069.1 → XP_054185044.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X21

    15. XM_054329060.1 → XP_054185035.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X13

    16. XM_054329062.1 → XP_054185037.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X15

    17. XM_054329061.1 → XP_054185036.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X14

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060940.1 Alternate T2T-CHM13v2.0

      Range
      14975789..15144257
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054379826.1 → XP_054235801.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X1

    2. XM_054379827.1 → XP_054235802.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X2

    3. XM_054379829.1 → XP_054235804.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X2

    4. XM_054379831.1 → XP_054235806.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X4

    5. XM_054379828.1 → XP_054235803.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X3

    6. XM_054379832.1 → XP_054235807.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X5

    7. XM_054379833.1 → XP_054235808.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X22

    8. XM_054379830.1 → XP_054235805.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q6P996.2 GenPept UniProtKB/Swiss-Prot:Q6P996

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