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    Hlcs holocarboxylase synthetase [ Rattus norvegicus (Norway rat) ]

    Gene ID: 288240, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Hlcsprovided by RGD
    Official Full Name
    holocarboxylase synthetaseprovided by RGD
    Primary source
    RGD:1565360
    See related
    EnsemblRapid:ENSRNOG00000001686 AllianceGenome:RGD:1565360
    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
    RGD1565360
    Summary
    Enables biotin--[biotin carboxyl-carrier protein] ligase activity and identical protein binding activity. Involved in response to biotin. Predicted to be located in chromatin; cytosol; and nuclear periphery. Predicted to be active in cytoplasm. Human ortholog(s) of this gene implicated in holocarboxylase synthetase deficiency. Orthologous to human HLCS (holocarboxylase synthetase). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Adrenal (RPKM 59.5), Brain (RPKM 52.3) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Hlcs in Genome Data Viewer
    Location:
    11q11
    Exon count:
    14
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 11 NC_086029.1 (46925491..47123111, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 11 NC_051346.1 (33455806..33635197, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 11 NC_005110.4 (34357372..34537798, complement)

    Chromosome 11 - NC_086029.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC102546699 Neighboring gene SIM bHLH transcription factor 2 Neighboring gene uncharacterized LOC134481059 Neighboring gene small nuclear ribonucleoprotein F-like Neighboring gene ripply transcriptional repressor 3 Neighboring gene phosphatidylinositol glycan anchor biosynthesis, class P Neighboring gene tetratricopeptide repeat domain 3 Neighboring gene U1 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. From an inborn error patient to a search for regulatory meaning: a biotin conducted voyage. Velázquez-Arellano A. Mol Genet Metab, 2006 Mar. PMID 16359899
    2. Biotin holocarboxylase synthetase: purification from rat liver cytosol and some properties. Xia WL, et al. Biochem Mol Biol Int, 1994 Sep. PMID 7849632
    3. Reduced half-life of holocarboxylase synthetase from patients with severe multiple carboxylase deficiency. Bailey LM, et al. Hum Mutat, 2008 Jun. PMID 18429047
    4. Reduced histone biotinylation in multiple carboxylase deficiency patients: a nuclear role for holocarboxylase synthetase. Narang MA, et al. Hum Mol Genet, 2004 Jan 1. PMID 14613969
    5. Identification of holocarboxylase synthetase (HCS) proteins in human placenta. Hiratsuka M, et al. Biochim Biophys Acta, 1998 Jun 11. PMID 9630604

    See all (12) citations in PubMed

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables biotin binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables biotin--[biotin carboxyl-carrier protein] ligase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables biotin--[biotin carboxyl-carrier protein] ligase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables biotin--[biotin carboxyl-carrier protein] ligase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables enzyme binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables identical protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in biotin metabolic process ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in post-translational protein modification ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in response to biotin IEP
    Inferred from Expression Pattern
    more info
    		 PubMed 
    involved_in response to biotin ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    located_in chromatin ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytosol ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nuclear lamina ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nuclear matrix ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    biotin--protein ligase
    Names
    holocarboxylase synthetase (biotin- [propriony-Coenzyme A-carboxylase (ATP-hydrolysing)] ligase)
    holocarboxylase synthetase (biotin-(proprionyl-CoA-carboxylase (ATP-hydrolysing)) ligase)
    holocarboxylase synthetase (biotin-(proprionyl-Coenzyme A-carboxylase (ATP-hydrolysing)) ligase)
    NP_001413953.1
    NP_001413954.1
    XP_038944719.2
    XP_038944720.2
    XP_038944722.2
    XP_038944723.1
    XP_038944726.1
    XP_063126482.1
    XP_063126483.1
    XP_063126484.1
    XP_063126485.1
    XP_063126486.1

    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_001427024.1 → NP_001413953.1  biotin--protein ligase isoform 1

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000011
      UniProtKB/TrEMBL
      A0A8I6A968, A6KPY1
      Related
      ENSRNOP00000090797.2, ENSRNOT00000099969.2

    2. NM_001427025.1 → NP_001413954.1  biotin--protein ligase isoform 2

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000011
      UniProtKB/TrEMBL
      A0A8I6AAD0

    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
      46925491..47123111 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_063270415.1 → XP_063126485.1  biotin--protein ligase isoform X7

      UniProtKB/TrEMBL
      A0A8I6AAD0

    2. XM_063270414.1 → XP_063126484.1  biotin--protein ligase isoform X7

      UniProtKB/TrEMBL
      A0A8I6AAD0

    3. XM_063270413.1 → XP_063126483.1  biotin--protein ligase isoform X5

      UniProtKB/TrEMBL
      A0A8I6AAD0

    4. XM_039088792.2 → XP_038944720.2  biotin--protein ligase isoform X2

    5. XM_039088794.2 → XP_038944722.2  biotin--protein ligase isoform X4

      UniProtKB/TrEMBL
      A0A8I6AAD0
      Related
      ENSRNOP00000109168.1, ENSRNOT00000173266.1

    6. XM_039088791.2 → XP_038944719.2  biotin--protein ligase isoform X1

      Related
      ENSRNOP00000002291.7, ENSRNOT00000002291.8

    7. XM_063270416.1 → XP_063126486.1  biotin--protein ligase isoform X8

      UniProtKB/TrEMBL
      A0A8I6AAD0

    8. XM_039088798.2 → XP_038944726.1  biotin--protein ligase isoform X7

      UniProtKB/TrEMBL
      A0A8I6AAD0
      Conserved Domains (3) summary
      cd16442
      Location:464 → 648
      BPL; biotin protein ligase
      pfam02237
      Location:666 → 713
      BPL_C; Biotin protein ligase C terminal domain
      cl00020
      Location:163 → 457
      GAT_1; Type 1 glutamine amidotransferase (GATase1)-like domain

    9. XM_039088795.1 → XP_038944723.1  biotin--protein ligase isoform X6

      UniProtKB/TrEMBL
      A0A8I6AAD0
      Related
      ENSRNOP00000089138.2, ENSRNOT00000099472.2
      Conserved Domains (3) summary
      cd16442
      Location:566 → 750
      BPL; biotin protein ligase
      pfam02237
      Location:768 → 815
      BPL_C; Biotin protein ligase C terminal domain
      cl00020
      Location:265 → 559
      GAT_1; Type 1 glutamine amidotransferase (GATase1)-like domain

    10. XM_063270412.1 → XP_063126482.1  biotin--protein ligase isoform X3

    RNA

    1. XR_010055942.1 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version

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