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Hmbs hydroxymethylbilane synthase [ Rattus norvegicus (Norway rat) ]

Gene ID: 25709, updated on 7-Sep-2023

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:
14
Annotation release Status Assembly Chr Location
RS_2023_06 current 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_051343.1Genomic 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
 PubMed 
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 biosynthetic process IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
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 
colocalizes_with condensed chromosome IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
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_038936830.1

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_015227675.2-RS_2023_06

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

Reference mRatBN7.2 Primary Assembly

Genomic

  1. NC_051343.1 Reference mRatBN7.2 Primary Assembly

    Range
    44673554..44680950 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_039080902.1 → XP_038936830.1  porphobilinogen deaminase isoform X3

    UniProtKB/Swiss-Prot
    O08568, P19356
    Conserved Domains (1) summary
    cd13645
    Location:51 → 358
    PBP2_HuPBGD_like; Human porphobilinogen deaminase possess type 2 periplasmic binding protein fold

  2. XM_008766149.3 → XP_008764371.1  porphobilinogen deaminase isoform X5

    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

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

    UniProtKB/Swiss-Prot
    O08568, P19356

  4. XM_006242897.3 → XP_006242959.2  porphobilinogen deaminase isoform X4

    UniProtKB/TrEMBL
    A0A0G2K1N3

  5. XM_006242896.3 → 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

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