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Hlcs holocarboxylase synthetase [ Rattus norvegicus (Norway rat) ]

Gene ID: 288240, updated on 13-Jul-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-[propionyl-CoA-carboxylase (ATP-hydrolyzing)] 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, Apr 2022]
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-[acetyl-CoA-carboxylase] ligase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables biotin-[propionyl-CoA-carboxylase (ATP-hydrolyzing)] ligase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables biotin-[propionyl-CoA-carboxylase (ATP-hydrolyzing)] ligase activity ISO
Inferred from Sequence Orthology
more info
  
enables biotin-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
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 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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