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ODC1 ornithine decarboxylase 1 [ Homo sapiens (human) ]

Gene ID: 4953, updated on 2-Nov-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_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (10439968..10448327, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (10469577..10477937, complement)
RS_2024_09 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 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. Genetic polymorphism in ornithine decarboxylase and risk of breast cancer. Brown I, et al. Fam Cancer, 2009. PMID 19225907
  2. Ornithine decarboxylase and ribosomal RNA synthesis during the stimulation of lymphocytes by phytohaemagglutinin. Kay JE, et al. FEBS Lett, 1971 Jul 15. PMID 11945886
  3. Pronounced reduction in adenoma recurrence associated with aspirin use and a polymorphism in the ornithine decarboxylase gene. Martinez ME, et al. Proc Natl Acad Sci U S A, 2003 Jun 24. PMID 12810952, Free PMC Article
  4. Diagnostic impact of ornithine decarboxylase in meningiomas. Stenzel W, et al. J Neurooncol, 2004 Jan. PMID 15015770
  5. Method for targeting protein destruction by using a ubiquitin-independent, proteasome-mediated degradation pathway. Matsuzawa S, et al. Proc Natl Acad Sci U S A, 2005 Oct 18. PMID 16219697, Free PMC Article

See all (116) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. FOXA1 co-activates circODC1 and ODC1 in HPV-positive cervical cancer cell growth.
    Title: FOXA1 co-activates circODC1 and ODC1 in HPV-positive cervical cancer cell growth.
  2. 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.
  3. 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.
  4. 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.
  5. 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.
  6. 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.
  7. 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.
  8. 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.
  9. Emerging Role of ODC1 in Neurodevelopmental Disorders and Brain Development.
    Title: Emerging Role of ODC1 in Neurodevelopmental Disorders and Brain Development.
  10. 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.
Submit: New GeneRIF Correction See all GeneRIFs (70)

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_2024_08

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

Gene LinkOut

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