FB2024_04 , released June 25, 2024
Gene: Dmel\Urod
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General Information
Symbol
Dmel\Urod
Species
D. melanogaster
Name
Uroporphyrinogen decarboxylase
Annotation Symbol
CG1818
Feature Type
protein_coding_gene
FlyBase ID
FBgn0033428
Gene Model Status
Current
Stock Availability
5 publicly available
Enzyme Name (EC)
uroporphyrinogen decarboxylase (4.1.1.37)
Gene Summary
Catalyzes the decarboxylation of four acetate groups of uroporphyrinogen-III to yield coproporphyrinogen-III. (UniProt, Q9V595)
Contribute a Gene Snapshot for this gene.
All Summaries
Also Known As

Updo

Key Links
Genomic Location
Cytogenetic map
45F5-45F5
Sequence location
Recombination map
2-61
RefSeq locus
NT_033778 REGION:9584643..9586126
Sequence
Get Decorated FASTA
Genomic Maps
Other Genome Views
The following external sites may use different assemblies or annotations than FlyBase.
NCBI
UCSC
Ensembl
PopFly
Function
Gene Ontology (GO) Annotations (4 terms)
Molecular Function (1 term)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
enables uroporphyrinogen decarboxylase activity
inferred from electronic annotation with InterPro:IPR000257, InterPro:IPR006361
(InterPro Project Members, 2004-)
inferred from biological aspect of ancestor with PANTHER:PTN000472929
(GO Reference Genome Project, 2011-)
Biological Process (2 terms)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (2 terms)
CV Term
Evidence
References
involved_in heme biosynthetic process
inferred from biological aspect of ancestor with PANTHER:PTN000472929
(GO Reference Genome Project, 2011-)
involved_in porphyrin-containing compound biosynthetic process
inferred from electronic annotation with InterPro:IPR000257, InterPro:IPR006361
(InterPro Project Members, 2004-)
Cellular Component (1 term)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
is_active_in cytosol
inferred from biological aspect of ancestor with PANTHER:PTN000472929
(GO Reference Genome Project, 2011-)
Gene Group (FlyBase)
Protein Family (UniProt)
Belongs to the uroporphyrinogen decarboxylase family. (Q9V595)
Protein Signatures (InterPro)
Catalytic Activity (EC/Rhea)
uroporphyrinogen decarboxylase activity
4 H(+) + uroporphyrinogen III = 4 CO2 + coproporphyrinogen III (4.1.1.37)
RHEA 19865:
Summaries
Gene Group (FlyBase)
CARBOXY-LYASES -
Carboxy-lyases are involved in the the addition of a carboxyl group to a compound (carboxylases) or the removal of a carboxyl group from a compound (decarboxylases). (Adapted from FBrf0238856).
Protein Function (UniProtKB)
Catalyzes the decarboxylation of four acetate groups of uroporphyrinogen-III to yield coproporphyrinogen-III.
(UniProt, Q9V595)
Gene Model and Products
Number of Transcripts
1
Number of Unique Polypeptides
1

Please see the JBrowse view of Dmel\Urod for information on other features

To submit a correction to a gene model please use the Contact FlyBase form

Protein Domains (via Pfam)
Isoform displayed:
Pfam protein domains
InterPro name
classification
start
end
Protein Domains (via SMART)
Isoform displayed:
SMART protein domains
InterPro name
classification
start
end
Structure
Protein 3D structure   (Predicted by AlphaFold)   (AlphaFold entry Q9V595)

If you don't see a structure in the viewer, refresh your browser.
Model Confidence:
  • Very high (pLDDT > 90)
  • Confident (90 > pLDDT > 70)
  • Low (70 > pLDDT > 50)
  • Very low (pLDDT < 50)

AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Some regions with low pLDDT may be unstructured in isolation.

Experimentally Determined Structures
Crossreferences
Comments on Gene Model

Low-frequency RNA-Seq exon junction(s) not annotated.

Gene model reviewed during 5.49

Sequence Ontology: Class of Gene
nuclear_gene
protein_coding_gene
Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
Urod-RA
FBtr0088524
NM_136657
1299
356
Additional Transcript Data and Comments
Reported size (kB)
Comments
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Name
FlyBase ID
Predicted MW (kDa)
Length (aa)
Theoretical pI
UniProt
RefSeq ID
GenBank
Urod-PA
FBpp0087607
40.0
356
6.52
Q9V595
NP_610501
AAF58922
Polypeptides with Identical Sequences

There is only one protein coding transcript and one polypeptide associated with this gene

Additional Polypeptide Data and Comments
Reported size (kDa)
Comments
External Data
Subunit Structure (UniProtKB)

Homodimer.

(UniProt, Q9V595)
Crossreferences
InterPro - A database of protein families, domains and functional sites
Linkouts
Sequences Consistent with the Gene Model
Mapped Features

Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dmel\Urod using the Feature Mapper tool.

External Data
Crossreferences
Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
Linkouts
Expression Data
Testis-specificity index

The testis specificity index was calculated from modENCODE tissue expression data by Vedelek et al., 2018 to indicate the degree of testis enrichment compared to other tissues. Scores range from -2.52 (underrepresented) to 5.2 (very high testis bias).

2.56

Transcript Expression
Polypeptide Expression
mass spectroscopy
Stage
Tissue/Position (including subcellular localization)
Reference
adult stage
adult head
• membrane
(Aradska et al., 2015)
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Evidence
References
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\Urod in JBrowse
RNA-Seq by Region - Search RNA-Seq expression levels by exon or genomic region
Bulk Downloads
RNA-Seq RPKM values for all genes
Reference
See Gelbart and Emmert, 2013 for analysis details and data files for all genes.
Developmental Proteome: Life Cycle
Developmental Proteome: Embryogenesis
External Data and Images
Linkouts
BDGP expression data - Patterns of gene expression in Drosophila embryogenesis
DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species
EMBL-EBI Single Cell Expression Atlas - Single cell expression across species
FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data
Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
Flygut - An atlas of the Drosophila adult midgut
Images
FlyBase Wiki
Image Based Resources
Alleles, Insertions, Transgenic Constructs, and Aberrations
Classical and Insertion Alleles ( 1 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 7 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of Urod
Transgenic constructs containing regulatory region of Urod
Aberrations (Deficiencies and Duplications) ( 1 )
Inferred from experimentation ( 1 )
Gene disrupted in
Df(2R)Exel8049
(Ryder, 2004.4.26)
Inferred from location ( 0 )
    Variants
    Variant Molecular Consequences
    Alleles Representing Disease-Implicated Variants
    Phenotypes
    For more details about a specific phenotype click on the relevant allele symbol.
    Other Phenotypes
    Allele
    increased size | third instar larval stage, with Scer\GAL4phtm.PO
    Phenotype manifest in
    Allele
    ring gland | third instar larval stage, with Scer\GAL4phtm.PO
    Orthologs
    Downloads
    Download All DIOPT Orthologs
    Human Orthologs (via DIOPT v9.1)
    Species\Gene Symbol
    Score
    Best Score
    Best Reverse Score
    Source
    Compara
    Domainoid
    eggNOG
    Hieranoid
    Homologene
    Inparanoid
    OMA
    OrthoDB
    OrthoFinder
    OrthoInspector
    orthoMCL
    Panther
    Phylome
    SonicParanoid
    Alignment
    Complementation?
    Transgene?
    Homo sapiens (Human) (1)
    Hsap\UROD
    13 of 14
    Yes
    Yes
    Model Organism Orthologs (via DIOPT v9.1)
    Species\Gene Symbol
    Score
    Best Score
    Best Reverse Score
    Source
    Compara
    Domainoid
    eggNOG
    Hieranoid
    Homologene
    Inparanoid
    OMA
    OrthoDB
    OrthoFinder
    OrthoInspector
    orthoMCL
    Panther
    Phylome
    SonicParanoid
    Alignment
    Complementation?
    Transgene?
    Rattus norvegicus (Norway rat) (1)
    Rnor\Urod
    13 of 14
    Yes
    Yes
    Mus musculus (laboratory mouse) (1)
    Mmus\Urod
    12 of 14
    Yes
    Yes
    Xenopus tropicalis (Western clawed frog) (2)
    Xtro\urod
    8 of 13
    Yes
    Yes
    Xtro\tti1
    1 of 13
    No
    No
    Danio rerio (Zebrafish) (1)
    Drer\urod
    13 of 14
    Yes
    Yes
    Caenorhabditis elegans (Nematode, roundworm) (0)
    Anopheles gambiae (African malaria mosquito) (1)
    Agam\AgaP_AGAP011895
    11 of 12
    Yes
    Yes
    Arabidopsis thaliana (thale-cress) (2)
    Atha\HEME2
    10 of 13
    Yes
    Yes
    Atha\HEME1
    8 of 13
    No
    Yes
    Saccharomyces cerevisiae (Brewer's yeast) (1)
    Scer\HEM12
    12 of 13
    Yes
    Yes
    Schizosaccharomyces pombe (Fission yeast) (1)
    Spom\hem12
    11 of 12
    Yes
    Yes
    Escherichia coli (enterobacterium) (1)
    Ecol\hemE
    7 of 11
    Yes
    Yes
    Other Organism Orthologs (via OrthoDB)
    Data provided directly from OrthoDB:Urod. Refer to their site for version information.
    Paralogs
    Downloads
    Download All DIOPT Paralogs
    Paralogs (via DIOPT v9.1)
    Gene Symbol
    Score
    Source
    Compara
    Domainoid
    eggNOG
    Homologene
    Inparanoid
    OMA
    OrthoDB
    OrthoFinder
    OrthoInspector
    orthoMCL
    Panther
    Phylome
    SonicParanoid
    Alignment
    Drosophila melanogaster (Fruit fly) (3)
    Bhmt
    1 of 13
    CG7560
    1 of 13
    CG10621
    1 of 13
    Human Disease Associations
    FlyBase Human Disease Model Reports
      Disease Ontology (DO) Annotations
      Models Based on Experimental Evidence ( 1 )
      Allele
      Disease
      Evidence
      References
      UrodRNAi.UAS.cUa
      model of  porphyria
      CEA
      (Huynh et al., 2019)
      Potential Models Based on Orthology ( 1 )
      Human Ortholog
      Disease
      Evidence
      References
      UROD; uroporphyrinogen decarboxylase
      model of  porphyria cutanea tarda
      IEA
      (FlyBase, 2019-)
      Modifiers Based on Experimental Evidence ( 0 )
      Allele
      Disease
      Interaction
      References
      Disease Associations of Human Orthologs (via DIOPT v9.1 and OMIM)
      Note that ortholog calls supported by only 1 or 2 algorithms (DIOPT score < 3) are not shown.
      Homo sapiens (Human)
      Gene name
      Score
      OMIM
      OMIM Phenotype
      DO term
      Complementation?
      Transgene?
      UROD; uroporphyrinogen decarboxylase
      13 of 14
      613521
      Functional Complementation Data
      Functional complementation data is computed by FlyBase using a combination of the orthology data obtained from DIOPT and OrthoDB and the allele-level genetic interaction data curated from the literature.
      Interactions
      Summary of Physical Interactions
      esyN Network Diagram
      Other Interaction Browsers
      Summary of Genetic Interactions
      esyN Network Diagram
      Other Interaction Browsers
      Starting gene(s)
      Interaction type
      Interacting gene(s)
      Reference
      Starting gene(s)
      Interaction type
      Interacting gene(s)
      Reference
      External Data
      Subunit Structure (UniProtKB)
      Homodimer.
      (UniProt, Q9V595 )
      Linkouts
      BioGRID - A database of protein and genetic interactions.
      DroID - A comprehensive database of gene and protein interactions.
      MIST (protein-protein) - An integrated Molecular Interaction Database
      Pathways
      Signaling Pathways (FlyBase)
      Metabolic Pathways
      FlyCyc Pathways - Pathways from a BioCyc PGDB for Dmel
      KEGG Metabolic Pathways - A collection of manually drawn metabolic pathway maps representing knowledge of molecular interaction, reaction and relation networks.
      Reactome Metabolic Pathways - An open-source, open access, manually curated and peer-reviewed metabolic pathway database.
      External Data
      Linkouts
      KEGG Pathways - A collection of manually drawn pathway maps representing knowledge of molecular interaction, reaction and relation networks.
      Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.
      Genomic Location and Detailed Mapping Data
      Chromosome (arm)
      2R
      Recombination map
      2-61
      Cytogenetic map
      45F5-45F5
      Sequence location
      FlyBase Computed Cytological Location
      Cytogenetic map
      Evidence for location
      45F5-45F5
      Limits computationally determined from genome sequence between P{lacW}l(2)k09501k09501 and P{PZ}Mmp202353&P{PZ}Uba105642
      Experimentally Determined Cytological Location
      Cytogenetic map
      Notes
      References
      Experimentally Determined Recombination Data
      Location

      2-61

      (FlyBase, 2016)

      2-59.4

      (Comeron et al., 2012)
      Left of (cM)
      Right of (cM)
      Notes
      Stocks and Reagents
      Stocks (5)
      Genomic Clones (10)
       

      Please Note FlyBase no longer curates genomic clone accessions so this list may not be complete

      cDNA Clones (20)
       

      Please Note This section lists cDNAs and ESTs that fall within the genomic extent of the gene model, which may include cDNAs and ESTs of genes within introns, or of overlapping genes. Please see JBrowse for alignment of the cDNAs and ESTs to the gene model.

      cDNA clones, fully sequenced
      BDGP DGC clones
      Other clones
      Drosophila Genomics Resource Center cDNA clones

      For each fully sequenced cDNA the DGRC maintains various forms of the cDNA (e.g tagged or untagged) in several different host vectors for subsequent cloning and expression in Drosophila and Drosophila cell lines.

      cDNA Clones, End Sequenced (ESTs)
      BDGP DGC clones
      Other clones
      RNAi and Array Information
      Linkouts
      DRSC - Results frm RNAi screens
      Antibody Information
      Laboratory Generated Antibodies
       
      Commercially Available Antibodies
       
      Cell Line Information
      Publicly Available Cell Lines
       
        Other Stable Cell Lines
         
          Other Comments
          Relationship to Other Genes
          Source for database merge of
          Additional comments

          Source for identity of Updo CG1818 was sequence comparison ( date:000721 ).

          (FlyBase, 1996-)
          Nomenclature History
          Source for database identify of

          Source for identity of: Updo CG1818

          (FlyBase, 1996-)

          Source for identity of: Urod Updo

          (FlyBase, 2017-)
          Nomenclature comments

          Changed symbol from 'Urod' to 'Updo' (and added fullname) to be consistent with nomenclature used for orthologs.

          (FlyBase, 2017-)
          Etymology
          Synonyms and Secondary IDs (4)
          Datasets (0)
          Study focus (0)
          Experimental Role
          Project
          Project Type
          Title
          Study result (0)
          Result
          Result Type
          Title
          External Crossreferences and Linkouts ( 45 )
          Sequence Crossreferences
          NCBI Gene - Gene integrates information from a wide range of species. A record may include nomenclature, Reference Sequences (RefSeqs), maps, pathways, variations, phenotypes, and links to genome-, phenotype-, and locus-specific resources worldwide.
          GenBank Nucleotide - A collection of sequences from several sources, including GenBank, RefSeq, TPA, and PDB.
          GenBank Protein - A collection of sequences from several sources, including translations from annotated coding regions in GenBank, RefSeq and TPA, as well as records from SwissProt, PIR, PRF, and PDB.
          RefSeq - A comprehensive, integrated, non-redundant, well-annotated set of reference sequences including genomic, transcript, and protein.
          UniProt/GCRP - The gene-centric reference proteome (GCRP) provides a 1:1 mapping between genes and UniProt accessions in which a single 'canonical' isoform represents the product(s) of each protein-coding gene.
          UniProt/Swiss-Prot - Manually annotated and reviewed records of protein sequence and functional information
          UniProt/TrEMBL - Automatically annotated and unreviewed records of protein sequence and functional information
          Other crossreferences
          AlphaFold DB - AlphaFold provides open access to protein structure predictions for the human proteome and other key proteins of interest, to accelerate scientific research.
          BDGP expression data - Patterns of gene expression in Drosophila embryogenesis
          DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species
          EMBL-EBI Single Cell Expression Atlas - Single cell expression across species
          FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data
          FlyMine - An integrated database for Drosophila genomics
          InterPro - A database of protein families, domains and functional sites
          KEGG Genes - Molecular building blocks of life in the genomic space.
          MARRVEL_MODEL - MARRVEL (model organism gene)
          Linkouts
          BioGRID - A database of protein and genetic interactions.
          Drosophila Genomics Resource Center - Drosophila Genomics Resource Center (DGRC) cDNA clones
          DroID - A comprehensive database of gene and protein interactions.
          DRSC - Results frm RNAi screens
          Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
          FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
          FlyCyc Genes - Genes from a BioCyc PGDB for Dmel
          FlyCyc Pathways - Pathways from a BioCyc PGDB for Dmel
          Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
          Flygut - An atlas of the Drosophila adult midgut
          FlyMet - A comprehensive tissue-specific metabolomics resource for Drosophila.
          iBeetle-Base - RNAi phenotypes in the red flour beetle (Tribolium castaneum)
          KEGG Metabolic Pathways - A collection of manually drawn metabolic pathway maps representing knowledge of molecular interaction, reaction and relation networks.
          KEGG Pathways - A collection of manually drawn pathway maps representing knowledge of molecular interaction, reaction and relation networks.
          MIST (protein-protein) - An integrated Molecular Interaction Database
          Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.
          Reactome Metabolic Pathways - An open-source, open access, manually curated and peer-reviewed metabolic pathway database.
          References (35)