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    Hacl1 2-hydroxyacyl-CoA lyase 1 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 85255, updated on 6-Jun-2024

    Summary

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    Official Symbol
    Hacl1provided by RGD
    Official Full Name
    2-hydroxyacyl-CoA lyase 1provided by RGD
    Primary source
    RGD:619849
    See related
    Ensembl:ENSRNOG00000019630 AllianceGenome:RGD:619849
    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
    Also known as
    Hpcl2; Phyh2
    Summary
    Enables carbon-carbon lyase activity and thiamine pyrophosphate binding activity. Involved in fatty acid alpha-oxidation and methyl-branched fatty acid metabolic process. Located in peroxisome. Orthologous to human HACL1 (2-hydroxyacyl-CoA lyase 1). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in Liver (RPKM 566.1), Kidney (RPKM 258.0) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Hacl1 in Genome Data Viewer
    Location:
    16p16
    Exon count:
    19
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 16 NC_086034.1 (6831293..6869410, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 16 NC_051351.1 (6826881..6863027, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 16 NC_005115.4 (7720047..7758119, complement)

    Chromosome 16 - NC_086034.1Genomic Context describing neighboring genes Neighboring gene methyltransferase 6, tRNA N3-cytidine Neighboring gene ELL associated factor 1 Neighboring gene collagen like tail subunit of asymmetric acetylcholinesterase Neighboring gene uncharacterized LOC134482450 Neighboring gene biotinidase Neighboring gene ankyrin repeat domain 28 Neighboring gene mitochondrial ribosomal protein L37, pseudogene 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. Phytol-induced pathology in 2-hydroxyacyl-CoA lyase (HACL1) deficient mice. Evidence for a second non-HACL1-related lyase. Mezzar S, et al. Biochim Biophys Acta Mol Cell Biol Lipids, 2017 Sep. PMID 28629946
    2. Role of thiamine pyrophosphate in oligomerisation, functioning and import of peroxisomal 2-hydroxyacyl-CoA lyase. Fraccascia P, et al. Biochim Biophys Acta, 2011 Oct. PMID 21708296
    3. Breakdown of 2-hydroxylated straight chain fatty acids via peroxisomal 2-hydroxyphytanoyl-CoA lyase: a revised pathway for the alpha-oxidation of straight chain fatty acids. Foulon V, et al. J Biol Chem, 2005 Mar 18. PMID 15644336
    4. Purification, molecular cloning, and expression of 2-hydroxyphytanoyl-CoA lyase, a peroxisomal thiamine pyrophosphate-dependent enzyme that catalyzes the carbon-carbon bond cleavage during alpha-oxidation of 3-methyl-branched fatty acids. Foulon V, et al. Proc Natl Acad Sci U S A, 1999 Aug 31. PMID 10468558, Free PMC Article
    5. Phytosphingosine degradation pathway includes fatty acid α-oxidation reactions in the endoplasmic reticulum. Kitamura T, et al. Proc Natl Acad Sci U S A, 2017 Mar 28. PMID 28289220, Free PMC Article

    See all (12) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. 2-hydroxyphytanoyl-CoA lyase has a role in the breakdown of long chain 2-hydroxyfatty acids
      Title: Breakdown of 2-hydroxylated straight chain fatty acids via peroxisomal 2-hydroxyphytanoyl-CoA lyase: a revised pathway for the alpha-oxidation of straight chain fatty acids.
    Submit: New GeneRIF Correction

    Pathways from PubChem

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    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables 2-hydroxyacyl-CoA lyase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables 2-hydroxyacyl-CoA lyase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables 2-hydroxyphytanoyl-CoA lyase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables ATP binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables ATP binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables carbon-carbon lyase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables carbon-carbon lyase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables catalytic activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables identical protein binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables identical protein binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables identical protein binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables lyase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables magnesium ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables magnesium ion binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables thiamine pyrophosphate binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables thiamine pyrophosphate binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables thiamine pyrophosphate binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables thiamine pyrophosphate binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    involved_in fatty acid alpha-oxidation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in fatty acid alpha-oxidation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in fatty acid alpha-oxidation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in fatty acid alpha-oxidation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in fatty acid metabolic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in fatty acid metabolic process ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within lipid metabolic process ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in methyl-branched fatty acid metabolic process IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in methyl-branched fatty acid metabolic process ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in phytanic acid metabolic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in phytanic acid metabolic process ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in phytanic acid metabolic process ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in protein targeting to peroxisome IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in protein targeting to peroxisome ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in protein targeting to peroxisome ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Component Evidence Code Pubs
    located_in intracellular membrane-bounded organelle ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in peroxisome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in peroxisome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in peroxisome IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in peroxisome ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    2-hydroxyacyl-CoA lyase 1
    Names
    2-HPCL
    2-hydroxyphytanoyl-CoA lyase
    2-hydroxyphytanoyl-Coenzyme A lyase
    phytanoyl-CoA 2-hydroxylase 2
    phytanoyl-Coenzyme A 2-hydroxylase 2
    NP_445945.1
    XP_063131860.1
    XP_063131861.1
    XP_063131862.1

    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_053493.1 → NP_445945.1  2-hydroxyacyl-CoA lyase 1

      See identical proteins and their annotated locations for NP_445945.1

      Status: PROVISIONAL

      Source sequence(s)
      AJ517469
      UniProtKB/Swiss-Prot
      Q8CHM7
      UniProtKB/TrEMBL
      A0A8I6ACR4, A6KFY4
      Related
      ENSRNOP00000026588.2, ENSRNOT00000026588.4
      Conserved Domains (4) summary
      cd07035
      Location:22 → 175
      TPP_PYR_POX_like; Pyrimidine (PYR) binding domain of POX and related proteins
      PRK09259
      Location:19 → 564
      PRK09259; putative oxalyl-CoA decarboxylase; Validated
      cd02004
      Location:380 → 563
      TPP_BZL_OCoD_HPCL; Thiamine pyrophosphate (TPP) family, BZL_OCoD_HPCL subfamily, TPP-binding module; composed of proteins similar to benzaldehyde lyase (BZL), oxalyl-CoA decarboxylase (OCoD) and 2-hydroxyphytanoyl-CoA lyase (2-HPCL). Pseudomonas fluorescens biovar I BZL ...
      pfam00205
      Location:206 → 335
      TPP_enzyme_M; Thiamine pyrophosphate enzyme, central domain

    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_086034.1 Reference GRCr8

      Range
      6831293..6869410 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_063275792.1 → XP_063131862.1  2-hydroxyacyl-CoA lyase 1 isoform X3

      UniProtKB/Swiss-Prot
      Q8CHM7
      UniProtKB/TrEMBL
      A0A8I6ACR4, A6KFY4

    2. XM_063275790.1 → XP_063131860.1  2-hydroxyacyl-CoA lyase 1 isoform X1

      UniProtKB/TrEMBL
      A0A8I6ACR4, A0A8I6G9A1

    3. XM_063275791.1 → XP_063131861.1  2-hydroxyacyl-CoA lyase 1 isoform X2

      UniProtKB/TrEMBL
      A0A8I6ACR4

    RNA

    1. XR_010058324.1 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8CHM7.1 GenPept UniProtKB/Swiss-Prot:Q8CHM7

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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