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    Hlcs holocarboxylase synthetase (biotin- [propriony-Coenzyme A-carboxylase (ATP-hydrolysing)] ligase) [ Mus musculus (house mouse) ]

    Gene ID: 110948, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Hlcsprovided by MGI
    Official Full Name
    holocarboxylase synthetase (biotin- [propriony-Coenzyme A-carboxylase (ATP-hydrolysing)] ligase)provided by MGI
    Primary source
    MGI:MGI:894646
    See related
    Ensembl:ENSMUSG00000040820 AllianceGenome:MGI:894646
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    D16Jhu34; 410I21.SP6
    Summary
    Enables biotin--[biotin carboxyl-carrier protein] ligase activity. Involved in biotin metabolic process. Located in mitochondrion. Is expressed in several structures, including genitourinary system; gut; nervous system; sensory organ; and thymus. 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
    Ubiquitous expression in subcutaneous fat pad adult (RPKM 3.4), ovary adult (RPKM 3.1) and 28 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See Hlcs in Genome Data Viewer
    Location:
    16 C4; 16 55.12 cM
    Exon count:
    16
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 16 NC_000082.7 (93930054..94116098, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 16 NC_000082.6 (94129306..94315239, complement)

    Chromosome 16 - NC_000082.7Genomic Context describing neighboring genes Neighboring gene RIKEN cDNA 2410003I16 gene Neighboring gene STARR-seq mESC enhancer starr_41557 Neighboring gene predicted gene, 31175 Neighboring gene single-minded family bHLH transcription factor 2 Neighboring gene STARR-seq mESC enhancer starr_41560 Neighboring gene STARR-seq mESC enhancer starr_41561 Neighboring gene predicted gene, 41502 Neighboring gene STARR-seq mESC enhancer starr_41562 Neighboring gene CapStarr-seq enhancer MGSCv37_chr16:94462926-94463127 Neighboring gene STARR-seq mESC enhancer starr_41563 Neighboring gene CapStarr-seq enhancer MGSCv37_chr16:94476325-94476540 Neighboring gene STARR-positive B cell enhancer ABC_E8648 Neighboring gene heterogeneous nuclear ribonucleoprotein A3 pseudogene Neighboring gene CapStarr-seq enhancer MGSCv37_chr16:94491341-94491450 Neighboring gene STARR-seq mESC enhancer starr_41566 Neighboring gene STARR-seq mESC enhancer starr_41568 Neighboring gene ripply transcriptional repressor 3 Neighboring gene predicted gene, 31259

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

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    Related articles in PubMed

    1. Assignment of holocarboxylase synthetase gene (HLCS) to human chromosome band 21q22.1 and to mouse chromosome band 16C4 by in situ hybridization. Zhang XX, et al. Cytogenet Cell Genet, 1997. PMID 9186515
    2. Holocarboxylase synthetase knockout is embryonic lethal in mice. Sadri M, et al. PLoS One, 2022. PMID 35385533, Free PMC Article
    3. Cloning and tissue-specific expression of mouse macrophage colony-stimulating factor mRNA. Rajavashisth TB, et al. Proc Natl Acad Sci U S A, 1987 Mar. PMID 3493488, Free PMC Article
    4. Physical and comparative mapping of distal mouse chromosome 16. 5 p5. Cabin DE, et al. Genome Res, 1998 Sep. PMID 9750193, Free PMC Article
    5. Nuclear-encoded mitochondrial ribosomal proteins are required to initiate gastrulation. Cheong A, et al. Development, 2020 May 26. PMID 32376682, Free PMC Article

    See all (28) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Endonuclease-mediated (2) 
    • Gene trapped (1) 
    • Targeted (2)  1 citation

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables ATP binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables biotin binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables biotin binding ISS
    Inferred from Sequence or Structural Similarity
    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 IMP
    Inferred from Mutant Phenotype
    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 enzyme binding ISS
    Inferred from Sequence or Structural Similarity
    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
    		  
    Process Evidence Code Pubs
    involved_in biotin metabolic process IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in post-translational protein modification ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in protein modification process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in response to biotin ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in response to biotin ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Component Evidence Code Pubs
    located_in chromatin ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in chromatin ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytoplasm ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in cytosol ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in cytosol ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in mitochondrion HDA PubMed 
    located_in nuclear lamina ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nuclear lamina ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in nuclear matrix ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nuclear matrix ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  

    General protein information

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    Preferred Names
    biotin--protein ligase
    Names
    biotin apo-protein ligase
    biotin- [propriony-Coenzyme A-carboxylase (ATP-hydrolysing)] ligase
    NP_001346974.1
    NP_631884.1
    XP_006522915.1
    XP_006522916.1
    XP_006522917.1
    XP_006522918.1
    XP_006522919.1
    XP_030104779.1
    XP_030104780.1
    XP_030104781.1
    XP_036015630.1

    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_001360045.2 → NP_001346974.1  biotin--protein ligase isoform 1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longer isoform (1).
      Source sequence(s)
      CT573086, CU207273
      Consensus CDS
      CCDS88973.1
      UniProtKB/TrEMBL
      A0A2I3BPG4
      Related
      ENSMUSP00000153773.2, ENSMUST00000227141.2
      Conserved Domains (2) summary
      COG0340
      Location:614 → 859
      BirA2; Biotin-(acetyl-CoA carboxylase) ligase [Coenzyme transport and metabolism]
      cl00020
      Location:459 → 603
      GAT_1; Type 1 glutamine amidotransferase (GATase1)-like domain

    2. NM_139145.6 → NP_631884.1  biotin--protein ligase isoform 2

      See identical proteins and their annotated locations for NP_631884.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) contains an alternate exon in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (2) has a distinct N-terminus and is shorter than isoform 1.
      Source sequence(s)
      CT573086, CU207273
      Consensus CDS
      CCDS28346.1
      UniProtKB/Swiss-Prot
      Q920N2
      UniProtKB/TrEMBL
      Q3TZ03
      Related
      ENSMUSP00000130981.2, ENSMUST00000163193.9
      Conserved Domains (2) summary
      COG0340
      Location:467 → 712
      BirA2; Biotin-(acetyl-CoA carboxylase) ligase [Coenzyme transport and metabolism]
      cl00020
      Location:312 → 384
      GAT_1; Type 1 glutamine amidotransferase (GATase1)-like domain

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000082.7 Reference GRCm39 C57BL/6J

      Range
      93930054..94116098 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_030248919.2 → XP_030104779.1  biotin--protein ligase isoform X4

      UniProtKB/Swiss-Prot
      Q920N2
      UniProtKB/TrEMBL
      Q3TZ03
      Conserved Domains (2) summary
      COG0340
      Location:467 → 712
      BirA2; Biotin-(acetyl-CoA carboxylase) ligase [Coenzyme transport and metabolism]
      cl00020
      Location:312 → 384
      GAT_1; Type 1 glutamine amidotransferase (GATase1)-like domain

    2. XM_006522856.3 → XP_006522919.1  biotin--protein ligase isoform X4

      See identical proteins and their annotated locations for XP_006522919.1

      UniProtKB/Swiss-Prot
      Q920N2
      UniProtKB/TrEMBL
      Q3TZ03
      Conserved Domains (2) summary
      COG0340
      Location:467 → 712
      BirA2; Biotin-(acetyl-CoA carboxylase) ligase [Coenzyme transport and metabolism]
      cl00020
      Location:312 → 384
      GAT_1; Type 1 glutamine amidotransferase (GATase1)-like domain

    3. XM_006522852.5 → XP_006522915.1  biotin--protein ligase isoform X1

      Conserved Domains (2) summary
      COG0340
      Location:581 → 826
      BirA2; Biotin-(acetyl-CoA carboxylase) ligase [Coenzyme transport and metabolism]
      cl00020
      Location:426 → 498
      GAT_1; Type 1 glutamine amidotransferase (GATase1)-like domain

    4. XM_030248920.2 → XP_030104780.1  biotin--protein ligase isoform X4

      UniProtKB/Swiss-Prot
      Q920N2
      UniProtKB/TrEMBL
      Q3TZ03
      Conserved Domains (2) summary
      COG0340
      Location:467 → 712
      BirA2; Biotin-(acetyl-CoA carboxylase) ligase [Coenzyme transport and metabolism]
      cl00020
      Location:312 → 384
      GAT_1; Type 1 glutamine amidotransferase (GATase1)-like domain

    5. XM_006522855.3 → XP_006522918.1  biotin--protein ligase isoform X4

      See identical proteins and their annotated locations for XP_006522918.1

      UniProtKB/Swiss-Prot
      Q920N2
      UniProtKB/TrEMBL
      Q3TZ03
      Conserved Domains (2) summary
      COG0340
      Location:467 → 712
      BirA2; Biotin-(acetyl-CoA carboxylase) ligase [Coenzyme transport and metabolism]
      cl00020
      Location:312 → 384
      GAT_1; Type 1 glutamine amidotransferase (GATase1)-like domain

    6. XM_036159737.1 → XP_036015630.1  biotin--protein ligase isoform X4

      UniProtKB/Swiss-Prot
      Q920N2
      UniProtKB/TrEMBL
      Q3TZ03
      Conserved Domains (2) summary
      COG0340
      Location:467 → 712
      BirA2; Biotin-(acetyl-CoA carboxylase) ligase [Coenzyme transport and metabolism]
      cl00020
      Location:312 → 384
      GAT_1; Type 1 glutamine amidotransferase (GATase1)-like domain

    7. XM_006522853.5 → XP_006522916.1  biotin--protein ligase isoform X2

      Conserved Domains (1) summary
      cl00020
      Location:601 → 673
      GAT_1; Type 1 glutamine amidotransferase (GATase1)-like domain

    8. XM_030248921.1 → XP_030104781.1  biotin--protein ligase isoform X5

      Conserved Domains (1) summary
      cl00020
      Location:471 → 543
      GAT_1; Type 1 glutamine amidotransferase (GATase1)-like domain

    9. XM_006522854.5 → XP_006522917.1  biotin--protein ligase isoform X3

      Conserved Domains (1) summary
      cl00020
      Location:601 → 673
      GAT_1; Type 1 glutamine amidotransferase (GATase1)-like domain
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q920N2.1 GenPept UniProtKB/Swiss-Prot:Q920N2

    Gene LinkOut

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

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