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    ODC1 ornithine decarboxylase 1 [ Homo sapiens (human) ]

    Gene ID: 4953, updated on 27-May-2024

    Summary

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    Official Symbol
    ODC1provided by HGNC
    Official Full Name
    ornithine decarboxylase 1provided by HGNC
    Primary source
    HGNC:HGNC:8109
    See related
    Ensembl:ENSG00000115758 MIM:165640; AllianceGenome:HGNC:8109
    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
    ODC; BABS; NEDBA; NEDBIA
    Summary
    This gene encodes the rate-limiting enzyme of the polyamine biosynthesis pathway which catalyzes ornithine to putrescine. The activity level for the enzyme varies in response to growth-promoting stimuli and exhibits a high turnover rate in comparison to other mammalian proteins. Originally localized to both chromosomes 2 and 7, the gene encoding this enzyme has been determined to be located on 2p25, with a pseudogene located on 7q31-qter. Multiple alternatively spliced transcript variants encoding distinct isoforms have been identified. [provided by RefSeq, Dec 2013]
    Expression
    Broad expression in testis (RPKM 67.6), bone marrow (RPKM 54.4) and 24 other tissues See more
    Orthologs
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    Genomic context

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    See ODC1 in Genome Data Viewer
    Location:
    2p25.1
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (10439968..10448327, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (10469577..10477937, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (10580094..10588453, complement)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene hippocalcin like 1 Neighboring gene uncharacterized LOC124905972 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr2:10547784-10548983 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:10559385-10559972 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:10559973-10560560 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:10564889-10565701 Neighboring gene uncharacterized LOC124907732 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:10572745-10573710 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:10573711-10574675 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15303 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:10586390-10586619 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15304 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11165 Neighboring gene small nucleolar RNA, H/ACA box 80B Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:10600271-10600772 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:10600773-10601272 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:10606558-10607058 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:10607059-10607559 Neighboring gene ODC1 divergent transcript Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:10609230-10609744 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:10609745-10610259 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:10616917-10617620 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:10617621-10618324 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:10618316-10618506 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:10627262-10627772 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:10627773-10628281 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15305 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15306 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15307 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15308 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:10637679-10638211 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:10662988-10663488 Neighboring gene uncharacterized LOC105373426 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:10679827-10680338 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:10686337-10687208

    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. Bachmann-Bupp Syndrome. Adam MP, et al. , 1993. PMID 36007106
    2. Evaluation of the Influence of Biosurface Design on the Interaction between the Regulatory Peptide RS1-reg and ODC1 Reveals a Membrane-Dependent Affinity Increase. Keller T, et al. Adv Biol (Weinh), 2022 Oct. PMID 35735188
    3. Structural basis of binding and inhibition of ornithine decarboxylase by 1-amino-oxy-3-aminopropane. Zhou XE, et al. Biochem J, 2021 Dec 10. PMID 34796899, Free PMC Article
    4. Expanding the phenotype: Four new cases and hope for treatment in Bachmann-Bupp syndrome. VanSickle EA, et al. Am J Med Genet A, 2021 Nov. PMID 34477286, Free PMC Article
    5. Ornithine decarboxylase (ODC1) gene variant (rs2302615) is associated with gastric cancer independently of Helicobacter pylori CagA serostatus. Miller AK, et al. Oncogene, 2021 Oct. PMID 34376808, Free PMC Article

    See all (113) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Pirin Promotes the Progression of Non-Small-Cell Lung Cancer by Increasing ODC1 to Suppress Autophagy.
      Title: Pirin Promotes the Progression of Non-Small-Cell Lung Cancer by Increasing ODC1 to Suppress Autophagy.
    2. Effects of Spermine Synthase Deficiency in Mesenchymal Stromal Cells Are Rescued by Upstream Inhibition of Ornithine Decarboxylase.
      Title: Effects of Spermine Synthase Deficiency in Mesenchymal Stromal Cells Are Rescued by Upstream Inhibition of Ornithine Decarboxylase.
    3. Evaluation of the Influence of Biosurface Design on the Interaction between the Regulatory Peptide RS1-reg and ODC1 Reveals a Membrane-Dependent Affinity Increase.
      Title: Evaluation of the Influence of Biosurface Design on the Interaction between the Regulatory Peptide RS1-reg and ODC1 Reveals a Membrane-Dependent Affinity Increase.
    4. Expanding the phenotype: Four new cases and hope for treatment in Bachmann-Bupp syndrome.
      Title: Expanding the phenotype: Four new cases and hope for treatment in Bachmann-Bupp syndrome.
    5. Ornithine decarboxylase (ODC1) gene variant (rs2302615) is associated with gastric cancer independently of Helicobacter pylori CagA serostatus.
      Title: Ornithine decarboxylase (ODC1) gene variant (rs2302615) is associated with gastric cancer independently of Helicobacter pylori CagA serostatus.
    6. Structural basis of binding and inhibition of ornithine decarboxylase by 1-amino-oxy-3-aminopropane.
      Title: Structural basis of binding and inhibition of ornithine decarboxylase by 1-amino-oxy-3-aminopropane.
    7. Repurposing eflornithine to treat a patient with a rare ODC1 gain-of-function variant disease.
      Title: Repurposing eflornithine to treat a patient with a rare ODC1 gain-of-function variant disease.
    8. Emerging Role of ODC1 in Neurodevelopmental Disorders and Brain Development.
      Title: Emerging Role of ODC1 in Neurodevelopmental Disorders and Brain Development.
    9. SKP2, positively regulated by circ_ODC1/miR-422a axis, promotes the proliferation of retinoblastoma.
      Title: SKP2, positively regulated by circ_ODC1/miR-422a axis, promotes the proliferation of retinoblastoma.
    10. Oesophageal squamous cell carcinoma-associated IL-33 rewires macrophage polarization towards M2 via activating ornithine decarboxylase.
      Title: Oesophageal squamous cell carcinoma-associated IL-33 rewires macrophage polarization towards M2 via activating ornithine decarboxylase.
    Submit: New GeneRIF Correction See all GeneRIFs (69)

    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

    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 ornithine decarboxylase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables ornithine decarboxylase activity IDA
    Inferred from Direct Assay
    more info
    		  
    enables ornithine decarboxylase activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables ornithine decarboxylase activity TAS
    Traceable Author Statement
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein homodimerization activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Process Evidence Code Pubs
    involved_in cell population proliferation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in kidney development IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in polyamine metabolic process TAS
    Traceable Author Statement
    more info
    		  
    involved_in positive regulation of cell population proliferation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in putrescine biosynthetic process from ornithine IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in putrescine biosynthetic process from ornithine IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in putrescine biosynthetic process from ornithine ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in regulation of protein catabolic process ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in response to virus IEP
    Inferred from Expression Pattern
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in cellular_component ND
    No biological Data available
    more info
    		  
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytoplasm ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  

    General protein information

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    Preferred Names
    ornithine decarboxylase
    NP_001274117.1
    NP_001274118.1
    NP_001274119.1
    NP_002530.1

    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.

    Genomic

    1. NG_012105.1 RefSeqGene

      Range
      5001..13360
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001287188.2 → NP_001274117.1  ornithine decarboxylase isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) has an alternate splice site, which results in translation initiation at a downstream AUG start codon, compared to variant 1. The resulting isoform (2) has a shorter N-termius, compared to isoform 1.
      Source sequence(s)
      AC007249, AI277727, AK301956, BC014562
      UniProtKB/TrEMBL
      B4DXF8
      Conserved Domains (1) summary
      cd00622
      Location:1 → 279
      PLPDE_III_ODC; Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Ornithine Decarboxylase

    2. NM_001287189.2 → NP_001274118.1  ornithine decarboxylase isoform 1

      See identical proteins and their annotated locations for NP_001274118.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) has an alternate 5' UTR exon, compared to variant 1. Variants 1, 3 and 4 encode the same isoform (1).
      Source sequence(s)
      AC007249, AI277727, AK292352, BC014562, HY044065
      Consensus CDS
      CCDS1672.1
      UniProtKB/Swiss-Prot
      P11926, Q53TU3, Q6LDS9
      Related
      ENSP00000385333.1, ENST00000405333.5
      Conserved Domains (1) summary
      cd00622
      Location:37 → 408
      PLPDE_III_ODC; Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Ornithine Decarboxylase

    3. NM_001287190.2 → NP_001274119.1  ornithine decarboxylase isoform 1

      See identical proteins and their annotated locations for NP_001274119.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) has an alternate 5' UTR exon, compared to variant 1. Variants 1, 3 and 4 encode the same isoform (1).
      Source sequence(s)
      AC007249, AI277727, BC014562, BI463057, HY044065
      Consensus CDS
      CCDS1672.1
      UniProtKB/Swiss-Prot
      P11926, Q53TU3, Q6LDS9
      Related
      ENSP00000390691.2, ENST00000443218.2
      Conserved Domains (1) summary
      cd00622
      Location:37 → 408
      PLPDE_III_ODC; Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Ornithine Decarboxylase

    4. NM_002539.3 → NP_002530.1  ornithine decarboxylase isoform 1

      See identical proteins and their annotated locations for NP_002530.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (1). Variants 1, 3, and 4 encode the same isoform (1).
      Source sequence(s)
      AC007249, AI277727, BC014562, BC025296
      Consensus CDS
      CCDS1672.1
      UniProtKB/Swiss-Prot
      P11926, Q53TU3, Q6LDS9
      Related
      ENSP00000234111.4, ENST00000234111.9
      Conserved Domains (1) summary
      cd00622
      Location:37 → 408
      PLPDE_III_ODC; Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Ornithine Decarboxylase

    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_000002.12 Reference GRCh38.p14 Primary Assembly

      Range
      10439968..10448327 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060926.1 Alternate T2T-CHM13v2.0

      Range
      10469577..10477937 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P11926.2 GenPept UniProtKB/Swiss-Prot:P11926

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