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    Hgd homogentisate 1, 2-dioxygenase [ Rattus norvegicus (Norway rat) ]

    Gene ID: 360719, updated on 5-Mar-2024

    Summary

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    Official Symbol
    Hgdprovided by RGD
    Official Full Name
    homogentisate 1, 2-dioxygenaseprovided by RGD
    Primary source
    RGD:1308757
    See related
    Ensembl:ENSRNOG00000002701 AllianceGenome:RGD:1308757
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Summary
    Predicted to enable homogentisate 1,2-dioxygenase activity and identical protein binding activity. Predicted to be involved in L-phenylalanine catabolic process. Predicted to act upstream of or within cellular amino acid metabolic process. Human ortholog(s) of this gene implicated in alkaptonuria. Orthologous to human HGD (homogentisate 1,2-dioxygenase). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in Liver (RPKM 1183.2) and Kidney (RPKM 1076.5) See more
    Orthologs
    human mouse all
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    Genomic context

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    Location:
    11q21
    Exon count:
    14
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 11 NC_086029.1 (76592202..76643776, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 11 NC_051346.1 (63086750..63138325, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 11 NC_005110.4 (65983221..66034555, complement)

    Chromosome 11 - NC_086029.1Genomic Context describing neighboring genes Neighboring gene keratin, type II cytoskeletal 8-like Neighboring gene NADH:ubiquinone oxidoreductase subunit B4 Neighboring gene RAB, member of RAS oncogene family-like 3 Neighboring gene general transcription factor IIE subunit 1 Neighboring gene syntaxin binding protein 5L Neighboring gene U2 spliceosomal RNA

    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. The molecular basis of alkaptonuria. Fernández-Cañón JM, et al. Nat Genet, 1996 Sep. PMID 8782815
    2. aku, a mutation of the mouse homologous to human alkaptonuria, maps to chromosome 16. Montagutelli X, et al. Genomics, 1994 Jan 1. PMID 8188247
    3. Large-scale proteomics and phosphoproteomics of urinary exosomes. Gonzales PA, et al. J Am Soc Nephrol, 2009 Feb. PMID 19056867, Free PMC Article
    4. In-depth proteomic analyses of exosomes isolated from expressed prostatic secretions in urine. Principe S, et al. Proteomics, 2013 May. PMID 23533145, Free PMC Article
    5. Proteomic analysis of podocyte exosome-enriched fraction from normal human urine. Prunotto M, et al. J Proteomics, 2013 Apr 26. PMID 23376485

    See all (8) citations in PubMed

    GeneRIFs: Gene References Into Functions

    General gene information

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    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables homogentisate 1,2-dioxygenase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables homogentisate 1,2-dioxygenase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables identical protein binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in L-phenylalanine catabolic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in L-phenylalanine catabolic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within amino acid metabolic process ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in biological_process ND
    No biological Data available
    more info
    		  
    involved_in tyrosine metabolic process IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    homogentisate 1,2-dioxygenase
    NP_001012145.1
    XP_038944422.1

    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_001012145.1 → NP_001012145.1  homogentisate 1,2-dioxygenase

      See identical proteins and their annotated locations for NP_001012145.1

      Status: PROVISIONAL

      Source sequence(s)
      BC078948
      UniProtKB/TrEMBL
      A6IR88, G3V6C2, Q6AYR0
      Related
      ENSRNOP00000003645.4, ENSRNOT00000003645.7
      Conserved Domains (1) summary
      TIGR01015
      Location:3 → 434
      hmgA; homogentisate 1,2-dioxygenase

    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_086029.1 Reference GRCr8

      Range
      76592202..76643776 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_039088494.2 → XP_038944422.1  homogentisate 1,2-dioxygenase isoform X1

      Conserved Domains (1) summary
      cl40423
      Location:5 → 258
      cupin_RmlC-like; RmlC-like cupin superfamily
    Nucleotide Protein Strain
    Heading Accession and Version

    Gene LinkOut

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