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

Gene ID: 110948, updated on 11-Apr-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
Predicted to enable biotin binding activity; biotin-protein ligase activity; and enzyme binding activity. Predicted to be involved in histone biotinylation and response to biotin. 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, Apr 2022]
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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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 (27) 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)
  • Gene trapped (1) 
  • Targeted (2)  1 citation
  • Endonuclease-mediated (2) 

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-[acetyl-CoA-carboxylase] ligase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables biotin-[methylcrotonoyl-CoA-carboxylase] ligase activity IEA
Inferred from Electronic Annotation
more info
  
enables biotin-[methylmalonyl-CoA-carboxytransferase] ligase activity IEA
Inferred from Electronic Annotation
more info
  
enables biotin-[propionyl-CoA-carboxylase (ATP-hydrolyzing)] ligase activity ISO
Inferred from Sequence Orthology
more info
  
enables biotin-protein ligase activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
enables biotin-protein ligase activity ISO
Inferred from Sequence Orthology
more info
  
enables catalytic activity IEA
Inferred from Electronic Annotation
more info
  
enables enzyme binding ISO
Inferred from Sequence Orthology
more info
  
enables identical protein binding ISO
Inferred from Sequence Orthology
more info
  
enables ligase activity IEA
Inferred from Electronic Annotation
more info
  
enables nucleotide binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in biotin metabolic process IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within metabolic process IEA
Inferred from Electronic Annotation
more info
  
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
  
Component Evidence Code Pubs
part_of 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 mitochondrion HDA PubMed 
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
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

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