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    Hmbs hydroxymethylbilane synthase [ Rattus norvegicus (Norway rat) ]

    Gene ID: 25709, updated on 6-Jun-2024

    Summary

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    Official Symbol
    Hmbsprovided by RGD
    Official Full Name
    hydroxymethylbilane synthaseprovided by RGD
    Primary source
    RGD:2801
    See related
    Ensembl:ENSRNOG00000010390 AllianceGenome:RGD:2801
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    PBGD; hemC; PBG-D; URO-S
    Summary
    Enables several functions, including amine binding activity; hydroxymethylbilane synthase activity; and uroporphyrinogen-III synthase activity. Involved in several processes, including cellular response to dexamethasone stimulus; cellular response to lead ion; and response to estradiol. Located in several cellular components, including axon; cytosol; and perinuclear region of cytoplasm. Colocalizes with condensed chromosome. Biomarker of bilirubin metabolic disorder and liver carcinoma. Human ortholog(s) of this gene implicated in acute intermittent porphyria and sickle cell anemia. Orthologous to human HMBS (hydroxymethylbilane synthase). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in Spleen (RPKM 555.0), Heart (RPKM 170.1) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Hmbs in Genome Data Viewer
    Location:
    8q22
    Exon count:
    15
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 8 NC_086026.1 (53570364..53577758, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 8 NC_051343.1 (44673554..44680950, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 8 NC_005107.4 (48667278..48674673, complement)

    Chromosome 8 - NC_086026.1Genomic Context describing neighboring genes Neighboring gene dolichyl-phosphate N-acetylglucosaminephosphotransferase 1 Neighboring gene H2A.X variant histone Neighboring gene VPS11 core subunit of CORVET and HOPS complexes Neighboring gene hypoxia up-regulated 1

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

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    Related articles in PubMed

    1. An Inducible Promoter Responsive to Different Porphyrinogenic Stimuli Improves Gene Therapy Vectors for Acute Intermittent Porphyria. Serrano-Mendioroz I, et al. Hum Gene Ther, 2018 Apr. PMID 28990424
    2. Seven Novel Mutations in Bulgarian Patients with Acute Hepatic Porphyrias (AHP). Dragneva S, et al. JIMD Rep, 2014. PMID 24997713, Free PMC Article
    3. Comparative proteome analysis of TGF-beta1-induced fibrosis processes in normal rat kidney interstitial fibroblast cells in response to ascofuranone. Kang JH, et al. Proteomics, 2009 Oct. PMID 19688726
    4. Detection of DNA variations in the polymorphic hydroxymethylbilane synthase gene by high-resolution melting analysis. Ulbrichova-Douderova D, et al. Anal Biochem, 2009 Dec 1. PMID 19664584
    5. Functional studies of rat hydroxymethylbilane synthase. Li N, et al. Bioorg Chem, 2008 Oct. PMID 18760440

    See all (76) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Pathways from PubChem

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    General gene information

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    Markers

    Homology

    Clone Names

    • MGC108753

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables amine binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables carboxylic acid binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables hydroxymethylbilane synthase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables hydroxymethylbilane synthase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables hydroxymethylbilane synthase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables hydroxymethylbilane synthase activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables hydroxymethylbilane synthase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables uroporphyrinogen-III synthase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in animal organ regeneration IEP
    Inferred from Expression Pattern
    more info
    		 PubMed 
    involved_in astrocyte differentiation IEP
    Inferred from Expression Pattern
    more info
    		 PubMed 
    involved_in cellular response to amine stimulus IEP
    Inferred from Expression Pattern
    more info
    		 PubMed 
    involved_in cellular response to antibiotic IEP
    Inferred from Expression Pattern
    more info
    		 PubMed 
    involved_in cellular response to arsenic-containing substance IEP
    Inferred from Expression Pattern
    more info
    		 PubMed 
    involved_in cellular response to cytokine stimulus IEP
    Inferred from Expression Pattern
    more info
    		 PubMed 
    involved_in cellular response to dexamethasone stimulus IEP
    Inferred from Expression Pattern
    more info
    		 PubMed 
    involved_in cellular response to lead ion IEP
    Inferred from Expression Pattern
    more info
    		 PubMed 
    involved_in heme A biosynthetic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in heme A biosynthetic process ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in heme B biosynthetic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in heme B biosynthetic process ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in heme O biosynthetic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in heme O biosynthetic process ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in heme biosynthetic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in heme biosynthetic process ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in liver development IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in porphyrin-containing compound biosynthetic process IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in porphyrin-containing compound metabolic process IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in protoporphyrinogen IX biosynthetic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in response to amino acid IEP
    Inferred from Expression Pattern
    more info
    		 PubMed 
    involved_in response to carbohydrate IEP
    Inferred from Expression Pattern
    more info
    		 PubMed 
    involved_in response to cobalt ion IEP
    Inferred from Expression Pattern
    more info
    		 PubMed 
    involved_in response to estradiol IEP
    Inferred from Expression Pattern
    more info
    		 PubMed 
    involved_in response to hormone IEP
    Inferred from Expression Pattern
    more info
    		 PubMed 
    involved_in response to hypoxia IEP
    Inferred from Expression Pattern
    more info
    		 PubMed 
    involved_in response to lead ion IEP
    Inferred from Expression Pattern
    more info
    		 PubMed 
    involved_in response to metal ion IEP
    Inferred from Expression Pattern
    more info
    		 PubMed 
    involved_in response to methylmercury IEP
    Inferred from Expression Pattern
    more info
    		 PubMed 
    involved_in response to nutrient levels IEP
    Inferred from Expression Pattern
    more info
    		 PubMed 
    involved_in response to organic cyclic compound IEP
    Inferred from Expression Pattern
    more info
    		 PubMed 
    involved_in response to vitamin IEP
    Inferred from Expression Pattern
    more info
    		 PubMed 
    involved_in response to xenobiotic stimulus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in response to xenobiotic stimulus IEP
    Inferred from Expression Pattern
    more info
    		 PubMed 
    involved_in response to zinc ion IEP
    Inferred from Expression Pattern
    more info
    		 PubMed 
    involved_in tetrapyrrole biosynthetic process IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in tetrapyrrole biosynthetic process IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in axon IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in condensed chromosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytosol IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in cytosol ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in perinuclear region of cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    porphobilinogen deaminase
    Names
    alternative name: porphobilinogen deaminase
    pre-uroporphyrinogen synthase
    uroporphyrinogen I synthase
    NP_037300.2
    XP_006242958.2
    XP_006242959.2
    XP_008764370.2
    XP_008764371.1
    XP_063121048.1

    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_013168.2 → NP_037300.2  porphobilinogen deaminase

      See identical proteins and their annotated locations for NP_037300.2

      Status: VALIDATED

      Source sequence(s)
      BC088162
      UniProtKB/Swiss-Prot
      O08568, P19356
      UniProtKB/TrEMBL
      Q5M893
      Related
      ENSRNOP00000014128.4, ENSRNOT00000014127.6
      Conserved Domains (2) summary
      PRK00072
      Location:17 → 344
      hemC; porphobilinogen deaminase; Reviewed
      cd13645
      Location:20 → 299
      PBP2_HuPBGD_like; Human porphobilinogen deaminase possess type 2 periplasmic binding protein fold

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086026.1 Reference GRCr8

      Range
      53570364..53577758 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_008766149.3 → XP_008764371.1  porphobilinogen deaminase isoform X4

      UniProtKB/Swiss-Prot
      O08568, P19356
      Conserved Domains (2) summary
      PRK00072
      Location:17 → 372
      hemC; porphobilinogen deaminase; Reviewed
      cd13645
      Location:20 → 327
      PBP2_HuPBGD_like; Human porphobilinogen deaminase possess type 2 periplasmic binding protein fold

    2. XM_063264978.1 → XP_063121048.1  porphobilinogen deaminase isoform X5

      UniProtKB/Swiss-Prot
      O08568, P19356
      UniProtKB/TrEMBL
      A0A0G2K1N3

    3. XM_008766148.3 → XP_008764370.2  porphobilinogen deaminase isoform X1

      UniProtKB/Swiss-Prot
      O08568, P19356

    4. XM_006242897.4 → XP_006242959.2  porphobilinogen deaminase isoform X3

      UniProtKB/Swiss-Prot
      O08568, P19356

    5. XM_006242896.4 → XP_006242958.2  porphobilinogen deaminase isoform X2

      UniProtKB/Swiss-Prot
      O08568, P19356
      UniProtKB/TrEMBL
      A6J3X2
      Conserved Domains (2) summary
      PRK00072
      Location:1 → 328
      hemC; porphobilinogen deaminase; Reviewed
      cd13645
      Location:4 → 283
      PBP2_HuPBGD_like; Human porphobilinogen deaminase possess type 2 periplasmic binding protein fold
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P19356.2 GenPept UniProtKB/Swiss-Prot:P19356

    Gene LinkOut

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