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PC pyruvate carboxylase [ Homo sapiens (human) ]

Gene ID: 5091, updated on 5-Mar-2024

Summary

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Official Symbol
PCprovided by HGNC
Official Full Name
pyruvate carboxylaseprovided by HGNC
Primary source
HGNC:HGNC:8636
See related
Ensembl:ENSG00000173599 MIM:608786; AllianceGenome:HGNC:8636
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
PCB
Summary
This gene encodes pyruvate carboxylase, which requires biotin and ATP to catalyse the carboxylation of pyruvate to oxaloacetate. The active enzyme is a homotetramer arranged in a tetrahedron which is located exclusively in the mitochondrial matrix. Pyruvate carboxylase is involved in gluconeogenesis, lipogenesis, insulin secretion and synthesis of the neurotransmitter glutamate. Mutations in this gene have been associated with pyruvate carboxylase deficiency. Alternatively spliced transcript variants with different 5' UTRs, but encoding the same protein, have been found for this gene. [provided by RefSeq, Jul 2008]
Expression
Biased expression in fat (RPKM 30.0), liver (RPKM 19.3) and 13 other tissues See more
Orthologs
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Genomic context

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Location:
11q13.2
Exon count:
31
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (66848420..66958383, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (66844694..66952886, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (66615891..66725854, complement)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene TOP6B like initiator of meiotic double strand breaks Neighboring gene ferritin light chain pseudogene 6 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:66580049-66580832 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:66609109-66609235 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3603 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:66610783-66611489 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:66617715-66618294 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:66618295-66618873 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3605 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3606 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5058 Neighboring gene Ras converting CAAX endopeptidase 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:66644024-66644524 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:66644525-66645025 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:66645752-66646490 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:66649447-66650184 Neighboring gene leucine rich repeat and fibronectin type III domain containing 4 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:66650185-66650922 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5059 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:66672605-66673252 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5060 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:66688620-66689560 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:66690541-66691041 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:66691815-66692466 Neighboring gene RNA, U7 small nuclear 23 pseudogene Neighboring gene microRNA 3163 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5061 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3607 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5062 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3608 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:66743456-66743959 Neighboring gene Sharpr-MPRA regulatory region 11253 Neighboring gene chromosome 11 open reading frame 86 Neighboring gene uncharacterized LOC124902849

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
  • 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. The ubiquitous expression of pyruvate carboxylase among human prostate tumors. Gondas E, et al. Bratisl Lek Listy, 2022. PMID 35907054
  2. Fibroblast pyruvate carboxylase is required for collagen production in the tumour microenvironment. Schwörer S, et al. Nat Metab, 2021 Nov. PMID 34764457, Free PMC Article
  3. Pyruvate carboxylase supports basal ATP-linked respiration in human pluripotent stem cell-derived brown adipocytes. Lao-On U, et al. Biochem Biophys Res Commun, 2021 Sep 10. PMID 34245978
  4. Expression of pyruvate carboxylase in cultured human astrocytoma, glioblastoma and neuroblastoma cells. Gondáš E, et al. Gen Physiol Biophys, 2021 Mar. PMID 33880999
  5. Integrated analysis of transcriptomic and metabolomic data demonstrates the significant role of pyruvate carboxylase in the progression of ovarian cancer. Shang H, et al. Aging (Albany NY), 2020 Nov 7. PMID 33177242, Free PMC Article

See all (138) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Leat-associated seizures the possible role of EAAT2, pyruvate carboxylase and glutamine synthetase.
    Title: Leat-associated seizures the possible role of EAAT2, pyruvate carboxylase and glutamine synthetase.
  2. In silico Analysis of Two Novel Variants in the Pyruvate Carboxylase (PC) Gene Associated with the Severe Form of PC Deficiency.
    Title: In silico Analysis of Two Novel Variants in the Pyruvate Carboxylase (PC) Gene Associated with the Severe Form of PC Deficiency.
  3. The ubiquitous expression of pyruvate carboxylase among human prostate tumors.
    Title: The ubiquitous expression of pyruvate carboxylase among human prostate tumors.
  4. Protective effects of all-trans retinoic acid against gastric premalignant lesions by repressing exosomal LncHOXA10-pyruvate carboxylase axis.
    Title: Protective effects of all-trans retinoic acid against gastric premalignant lesions by repressing exosomal LncHOXA10-pyruvate carboxylase axis.
  5. Fibroblast pyruvate carboxylase is required for collagen production in the tumour microenvironment.
    Title: Fibroblast pyruvate carboxylase is required for collagen production in the tumour microenvironment.
  6. Pyruvate carboxylase supports basal ATP-linked respiration in human pluripotent stem cell-derived brown adipocytes.
    Title: Pyruvate carboxylase supports basal ATP-linked respiration in human pluripotent stem cell-derived brown adipocytes.
  7. Rethinking the Citric Acid Cycle: Connecting Pyruvate Carboxylase and Citrate Synthase to the Flow of Energy and Material.
    Title: Rethinking the Citric Acid Cycle: Connecting Pyruvate Carboxylase and Citrate Synthase to the Flow of Energy and Material.
  8. Integrated analysis of transcriptomic and metabolomic data demonstrates the significant role of pyruvate carboxylase in the progression of ovarian cancer.
    Title: Integrated analysis of transcriptomic and metabolomic data demonstrates the significant role of pyruvate carboxylase in the progression of ovarian cancer.
  9. Expression of pyruvate carboxylase in cultured human astrocytoma, glioblastoma and neuroblastoma cells.
    Title: Expression of pyruvate carboxylase in cultured human astrocytoma, glioblastoma and neuroblastoma cells.
  10. Overexpression of Pyruvate Carboxylase Is Correlated With Colorectal Cancer Progression and Supports Growth of Invasive Colon Cancer HT-29 Cell Line.
    Title: Overexpression of Pyruvate Carboxylase Is Correlated With Colorectal Cancer Progression and Supports Growth of Invasive Colon Cancer HT-29 Cell Line.
Submit: New GeneRIF Correction See all GeneRIFs (28)

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

Associated conditions

Description Tests
Pyruvate carboxylase deficiency
MedGen: C0034341 OMIM: 266150 GeneReviews: Pyruvate Carboxylase Deficiency
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EBI GWAS Catalog

Description
Genomewide association study for determinants of HIV-1 acquisition and viral set point in HIV-1 serodiscordant couples with quantified virus exposure.
EBI GWAS Catalog
Large-scale genome-wide association analysis of bipolar disorder identifies a new susceptibility locus near ODZ4.
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

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables ATP binding IEA
Inferred from Electronic Annotation
more info
  
enables biotin binding TAS
Traceable Author Statement
more info
 PubMed 
enables identical protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables pyruvate carboxylase activity EXP
Inferred from Experiment
more info
 PubMed 
enables pyruvate carboxylase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables pyruvate carboxylase activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Process Evidence Code Pubs
involved_in NADH metabolic process IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in NADP metabolic process IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in gluconeogenesis IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in gluconeogenesis IEA
Inferred from Electronic Annotation
more info
  
involved_in gluconeogenesis TAS
Traceable Author Statement
more info
  
involved_in lipid metabolic process IEA
Inferred from Electronic Annotation
more info
  
involved_in negative regulation of gene expression IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation by host of viral process IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in pyruvate metabolic process IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in viral RNA genome packaging IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in viral release from host cell IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
is_active_in cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in cytoplasm IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytosol TAS
Traceable Author Statement
more info
  
located_in mitochondrial matrix TAS
Traceable Author Statement
more info
  
located_in mitochondrion IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
pyruvate carboxylase, mitochondrial
Names
pyruvic carboxylase
NP_000911.2
NP_001035806.1
NP_071504.2
XP_005274088.1
XP_005274089.1
XP_006718641.1
XP_006718642.1
XP_011543388.1
XP_011543389.1
XP_016873357.1
XP_016873358.1
XP_016873359.1
XP_016873360.1
XP_016873361.1
XP_047283014.1
XP_054224998.1
XP_054224999.1
XP_054225000.1
XP_054225001.1
XP_054225002.1
XP_054225003.1
XP_054225004.1
XP_054225005.1
XP_054225006.1
XP_054225007.1

NCBI Reference Sequences (RefSeq)

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NEW Try the new Transcript table

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.

Genomic

  1. NG_008319.1 RefSeqGene

    Range
    4994..114957
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_000920.4 → NP_000911.2  pyruvate carboxylase, mitochondrial precursor

    See identical proteins and their annotated locations for NP_000911.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) results from the use of a more distal promoter. Transcript variants 1-3 encode the same protein.
    Source sequence(s)
    AP000485, AP003176, BC011617, DA542083
    Consensus CDS
    CCDS8152.1
    UniProtKB/Swiss-Prot
    B4DN00, P11498, Q16705
    Related
    ENSP00000377530.2, ENST00000393958.7
    Conserved Domains (1) summary
    PRK12999
    Location:33 → 1178
    PRK12999; pyruvate carboxylase; Reviewed

  2. NM_001040716.2 → NP_001035806.1  pyruvate carboxylase, mitochondrial precursor

    See identical proteins and their annotated locations for NP_001035806.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) also results from the use of a more distal promoter, however, it contains an additional 5' non-coding exon, hence has a longer 5' UTR compared to transcript variant 1. Transcript variants 1-3 encode the same protein.
    Source sequence(s)
    AP000485, AP003176, BC011617, CN267865, DA542083
    Consensus CDS
    CCDS8152.1
    UniProtKB/Swiss-Prot
    B4DN00, P11498, Q16705
    Related
    ENSP00000377532.1, ENST00000393960.7
    Conserved Domains (1) summary
    PRK12999
    Location:33 → 1178
    PRK12999; pyruvate carboxylase; Reviewed

  3. NM_022172.3 → NP_071504.2  pyruvate carboxylase, mitochondrial precursor

    See identical proteins and their annotated locations for NP_071504.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) contains an alternate 5' non-coding exon resulting from the use of a more proximal promoter, hence has a distinct 5' UTR compared to transcript variant 1. Transcript variants 1-3 encode the same protein.
    Source sequence(s)
    AP000485, AP003176, S72370, U30891
    Consensus CDS
    CCDS8152.1
    UniProtKB/Swiss-Prot
    B4DN00, P11498, Q16705
    Related
    ENSP00000377527.2, ENST00000393955.6
    Conserved Domains (1) summary
    PRK12999
    Location:33 → 1178
    PRK12999; pyruvate carboxylase; Reviewed

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    66848420..66958383 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006718578.4 → XP_006718641.1  pyruvate carboxylase, mitochondrial isoform X1

    See identical proteins and their annotated locations for XP_006718641.1

    UniProtKB/Swiss-Prot
    B4DN00, P11498, Q16705
    Conserved Domains (1) summary
    PRK12999
    Location:33 → 1178
    PRK12999; pyruvate carboxylase; Reviewed

  2. XM_017017871.2 → XP_016873360.1  pyruvate carboxylase, mitochondrial isoform X1

    UniProtKB/Swiss-Prot
    B4DN00, P11498, Q16705
    Related
    ENSP00000435905.2, ENST00000529047.6
    Conserved Domains (1) summary
    PRK12999
    Location:33 → 1178
    PRK12999; pyruvate carboxylase; Reviewed

  3. XM_017017869.2 → XP_016873358.1  pyruvate carboxylase, mitochondrial isoform X1

    UniProtKB/Swiss-Prot
    B4DN00, P11498, Q16705
    Conserved Domains (1) summary
    PRK12999
    Location:33 → 1178
    PRK12999; pyruvate carboxylase; Reviewed

  4. XM_017017870.2 → XP_016873359.1  pyruvate carboxylase, mitochondrial isoform X1

    UniProtKB/Swiss-Prot
    B4DN00, P11498, Q16705
    Related
    ENSP00000498302.1, ENST00000652125.1
    Conserved Domains (1) summary
    PRK12999
    Location:33 → 1178
    PRK12999; pyruvate carboxylase; Reviewed

  5. XM_017017868.2 → XP_016873357.1  pyruvate carboxylase, mitochondrial isoform X1

    UniProtKB/Swiss-Prot
    B4DN00, P11498, Q16705
    Related
    ENSP00000498406.1, ENST00000651036.1
    Conserved Domains (1) summary
    PRK12999
    Location:33 → 1178
    PRK12999; pyruvate carboxylase; Reviewed

  6. XM_017017872.3 → XP_016873361.1  pyruvate carboxylase, mitochondrial isoform X1

    UniProtKB/Swiss-Prot
    B4DN00, P11498, Q16705
    Conserved Domains (1) summary
    PRK12999
    Location:33 → 1178
    PRK12999; pyruvate carboxylase; Reviewed

  7. XM_011545086.3 → XP_011543388.1  pyruvate carboxylase, mitochondrial isoform X1

    See identical proteins and their annotated locations for XP_011543388.1

    UniProtKB/Swiss-Prot
    B4DN00, P11498, Q16705
    Conserved Domains (1) summary
    PRK12999
    Location:33 → 1178
    PRK12999; pyruvate carboxylase; Reviewed

  8. XM_005274031.5 → XP_005274088.1  pyruvate carboxylase, mitochondrial isoform X1

    See identical proteins and their annotated locations for XP_005274088.1

    UniProtKB/Swiss-Prot
    B4DN00, P11498, Q16705
    Conserved Domains (1) summary
    PRK12999
    Location:33 → 1178
    PRK12999; pyruvate carboxylase; Reviewed

  9. XM_005274032.5 → XP_005274089.1  pyruvate carboxylase, mitochondrial isoform X1

    See identical proteins and their annotated locations for XP_005274089.1

    UniProtKB/Swiss-Prot
    B4DN00, P11498, Q16705
    Conserved Domains (1) summary
    PRK12999
    Location:33 → 1178
    PRK12999; pyruvate carboxylase; Reviewed

  10. XM_047427058.1 → XP_047283014.1  pyruvate carboxylase, mitochondrial isoform X3

  11. XM_006718579.4 → XP_006718642.1  pyruvate carboxylase, mitochondrial isoform X3

    Conserved Domains (4) summary
    cd06850
    Location:604 → 670
    biotinyl_domain; The biotinyl-domain or biotin carboxyl carrier protein (BCCP) domain is present in all biotin-dependent enzymes, such as acetyl-CoA carboxylase, pyruvate carboxylase, propionyl-CoA carboxylase, methylcrotonyl-CoA carboxylase, geranyl-CoA carboxylase, ...
    cd07937
    Location:58 → 341
    DRE_TIM_PC_TC_5S; Pyruvate carboxylase and Transcarboxylase 5S, carboxyltransferase domain
    PRK09282
    Location:60 → 671
    PRK09282; pyruvate carboxylase subunit B; Validated
    pfam02436
    Location:354 → 553
    PYC_OADA; Conserved carboxylase domain

  12. XM_011545087.3 → XP_011543389.1  pyruvate carboxylase, mitochondrial isoform X2

    Conserved Domains (5) summary
    cd06850
    Location:679 → 745
    biotinyl_domain; The biotinyl-domain or biotin carboxyl carrier protein (BCCP) domain is present in all biotin-dependent enzymes, such as acetyl-CoA carboxylase, pyruvate carboxylase, propionyl-CoA carboxylase, methylcrotonyl-CoA carboxylase, geranyl-CoA carboxylase, ...
    cd07937
    Location:133 → 416
    DRE_TIM_PC_TC_5S; Pyruvate carboxylase and Transcarboxylase 5S, carboxyltransferase domain
    PRK09282
    Location:135 → 746
    PRK09282; pyruvate carboxylase subunit B; Validated
    pfam02436
    Location:429 → 628
    PYC_OADA; Conserved carboxylase domain
    cl08365
    Location:24 → 50
    Biotin_carb_C; Biotin carboxylase C-terminal domain

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    66844694..66952886 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054369027.1 → XP_054225002.1  pyruvate carboxylase, mitochondrial isoform X1

    UniProtKB/Swiss-Prot
    B4DN00, P11498, Q16705

  2. XM_054369025.1 → XP_054225000.1  pyruvate carboxylase, mitochondrial isoform X1

    UniProtKB/Swiss-Prot
    B4DN00, P11498, Q16705

  3. XM_054369029.1 → XP_054225004.1  pyruvate carboxylase, mitochondrial isoform X1

    UniProtKB/Swiss-Prot
    B4DN00, P11498, Q16705

  4. XM_054369023.1 → XP_054224998.1  pyruvate carboxylase, mitochondrial isoform X1

    UniProtKB/Swiss-Prot
    B4DN00, P11498, Q16705

  5. XM_054369024.1 → XP_054224999.1  pyruvate carboxylase, mitochondrial isoform X1

    UniProtKB/Swiss-Prot
    B4DN00, P11498, Q16705

  6. XM_054369028.1 → XP_054225003.1  pyruvate carboxylase, mitochondrial isoform X1

    UniProtKB/Swiss-Prot
    B4DN00, P11498, Q16705

  7. XM_054369026.1 → XP_054225001.1  pyruvate carboxylase, mitochondrial isoform X1

    UniProtKB/Swiss-Prot
    B4DN00, P11498, Q16705

  8. XM_054369030.1 → XP_054225005.1  pyruvate carboxylase, mitochondrial isoform X1

    UniProtKB/Swiss-Prot
    B4DN00, P11498, Q16705

  9. XM_054369031.1 → XP_054225006.1  pyruvate carboxylase, mitochondrial isoform X1

    UniProtKB/Swiss-Prot
    B4DN00, P11498, Q16705

  10. XM_054369032.1 → XP_054225007.1  pyruvate carboxylase, mitochondrial isoform X2

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P11498.2 GenPept UniProtKB/Swiss-Prot:P11498

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