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HLCS holocarboxylase synthetase [ Homo sapiens (human) ]

Gene ID: 3141, updated on 17-May-2023

Summary

Official Symbol
HLCSprovided by HGNC
Official Full Name
holocarboxylase synthetaseprovided by HGNC
Primary source
HGNC:HGNC:4976
See related
Ensembl:ENSG00000159267 MIM:609018; AllianceGenome:HGNC:4976
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
HCS
Summary
This gene encodes an enzyme that catalyzes the binding of biotin to carboxylases and histones. The protein plays an important role in gluconeogenesis, fatty acid synthesis and branched chain amino acid catabolism. Defects in this gene are the cause of holocarboxylase synthetase deficiency. Multiple alternatively spliced variants, encoding the same protein, have been identified.[provided by RefSeq, Jun 2011]
Expression
Ubiquitous expression in thyroid (RPKM 4.3), prostate (RPKM 3.3) and 25 other tissues See more
Orthologs
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Genomic context

See HLCS in Genome Data Viewer
Location:
21q22.13
Exon count:
19
Annotation release Status Assembly Chr Location
RS_2023_03 current GRCh38.p14 (GCF_000001405.40) 21 NC_000021.9 (36748625..36990211, complement)
RS_2023_03 current T2T-CHM13v2.0 (GCF_009914755.1) 21 NC_060945.1 (35130819..35372426, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 21 NC_000021.8 (38120926..38362511, complement)

Chromosome 21 - NC_000021.9Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:38081463-38082292 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:38091813-38092599 Neighboring gene SIM bHLH transcription factor 2 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr21:38121986-38122511 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr21:38122512-38123036 Neighboring gene NANOG hESC enhancer GRCh37_chr21:38128709-38129210 Neighboring gene uncharacterized LOC105369305 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:38158985-38159520 Neighboring gene Sharpr-MPRA regulatory region 9348 Neighboring gene HLCS intron CAGE-defined mid-level expression enhancer Neighboring gene RNA, 5S ribosomal pseudogene 491 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr21:38281839-38283038 Neighboring gene Sharpr-MPRA regulatory region 2954 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:38312167-38312666 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr21:38319174-38319727 Neighboring gene divergent-paired related homeobox pseudogene 5 Neighboring gene HLCS antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:38378343-38378843 Neighboring gene mitochondrial ribosomal protein L20 pseudogene 1 Neighboring gene ripply transcriptional repressor 3

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables ATP binding IEA
Inferred from Electronic Annotation
more info
 
enables biotin binding IDA
Inferred from Direct Assay
more info
PubMed 
enables biotin-[acetyl-CoA-carboxylase] ligase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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 IDA
Inferred from Direct Assay
more info
PubMed 
enables biotin-protein ligase activity IDA
Inferred from Direct Assay
more info
PubMed 
enables biotin-protein ligase activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
enables biotin-protein ligase activity TAS
Traceable Author Statement
more info
 
enables enzyme binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
involved_in biotin metabolic process TAS
Traceable Author Statement
more info
 
involved_in post-translational protein modification IDA
Inferred from Direct Assay
more info
PubMed 
involved_in response to biotin IDA
Inferred from Direct Assay
more info
PubMed 
Component Evidence Code Pubs
part_of chromatin IDA
Inferred from Direct Assay
more info
PubMed 
is_active_in cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
located_in cytosol HDA PubMed 
located_in cytosol IDA
Inferred from Direct Assay
more info
PubMed 
located_in cytosol TAS
Traceable Author Statement
more info
 
located_in mitochondrion IEA
Inferred from Electronic Annotation
more info
 
located_in nuclear lamina IDA
Inferred from Direct Assay
more info
PubMed 
located_in nuclear matrix IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
biotin--protein ligase
Names
biotin apo-protein ligase
biotin--[acetyl-CoA-carboxylase] ligase
biotin--[methylcrotonoyl-CoA-carboxylase] ligase
biotin--[methylmalonyl-CoA-carboxytransferase] ligase
holocarboxylase synthetase (biotin-(proprionyl-CoA-carboxylase (ATP-hydrolysing)) ligase)
holocarboxylase synthetase (biotin-(proprionyl-Coenzyme A-carboxylase (ATP-hydrolysing)) ligase)
NP_000402.3
NP_001229713.1
NP_001229714.1
NP_001339443.1
NP_001339444.1
NP_001339445.1
NP_001339446.1
NP_001339447.1
XP_011527842.1
XP_024307833.1
XP_047296708.1
XP_047296709.1
XP_047296710.1
XP_047296711.1
XP_047296712.1
XP_054180425.1
XP_054180426.1
XP_054180427.1
XP_054180428.1
XP_054180429.1
XP_054180430.1
XP_054180431.1

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.

Genomic

  1. NG_016193.2 RefSeqGene

    Range
    28726..246769
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_000411.8NP_000402.3  biotin--protein ligase isoform 1

    See identical proteins and their annotated locations for NP_000402.3

    Status: REVIEWED

    Source sequence(s)
    AP000697, D23672, D87328
    Consensus CDS
    CCDS13647.1
    UniProtKB/Swiss-Prot
    P50747, Q99451
    Related
    ENSP00000338387.3, ENST00000336648.8
    Conserved Domains (3) summary
    pfam02237
    Location:669716
    BPL_C; Biotin protein ligase C terminal domain
    cd16442
    Location:467647
    BPL; biotin protein ligase
    cl00020
    Location:202460
    GAT_1; Type 1 glutamine amidotransferase (GATase1)-like domain
  2. NM_001242784.3NP_001229713.1  biotin--protein ligase isoform 1

    See identical proteins and their annotated locations for NP_001229713.1

    Status: REVIEWED

    Source sequence(s)
    AP000697, AP000698, AP000704, D87328, DB290499
    Consensus CDS
    CCDS13647.1
    UniProtKB/Swiss-Prot
    P50747, Q99451
    Related
    ENSP00000382071.1, ENST00000399120.5
    Conserved Domains (3) summary
    pfam02237
    Location:669716
    BPL_C; Biotin protein ligase C terminal domain
    cd16442
    Location:467647
    BPL; biotin protein ligase
    cl00020
    Location:202460
    GAT_1; Type 1 glutamine amidotransferase (GATase1)-like domain
  3. NM_001242785.2NP_001229714.1  biotin--protein ligase isoform 1

    See identical proteins and their annotated locations for NP_001229714.1

    Status: REVIEWED

    Source sequence(s)
    AP000697, AP000698, AP000702, AP000703, AP000704
    Consensus CDS
    CCDS13647.1
    UniProtKB/Swiss-Prot
    P50747, Q99451
    Related
    ENSP00000479939.1, ENST00000612277.4
    Conserved Domains (3) summary
    pfam02237
    Location:669716
    BPL_C; Biotin protein ligase C terminal domain
    cd16442
    Location:467647
    BPL; biotin protein ligase
    cl00020
    Location:202460
    GAT_1; Type 1 glutamine amidotransferase (GATase1)-like domain
  4. NM_001352514.2NP_001339443.1  biotin--protein ligase isoform 2

    Status: REVIEWED

    Source sequence(s)
    AP000697, AP000698, AP000702, AP000703, AP000704
    Consensus CDS
    CCDS93094.1
    UniProtKB/TrEMBL
    A0A8C8QSB1
    Related
    ENSP00000502087.2, ENST00000674895.3
    Conserved Domains (3) summary
    pfam02237
    Location:816863
    BPL_C; Biotin protein ligase C terminal domain
    cd16442
    Location:614794
    BPL; biotin protein ligase
    cl00020
    Location:349607
    GAT_1; Type 1 glutamine amidotransferase (GATase1)-like domain
  5. NM_001352515.2NP_001339444.1  biotin--protein ligase isoform 1

    Status: REVIEWED

    Source sequence(s)
    AP000697, AP000698, AP000702, AP000703, AP000704
    Consensus CDS
    CCDS13647.1
    UniProtKB/Swiss-Prot
    Q99451
    Related
    ENSP00000501832.1, ENST00000675057.1
    Conserved Domains (3) summary
    pfam02237
    Location:669716
    BPL_C; Biotin protein ligase C terminal domain
    cd16442
    Location:467647
    BPL; biotin protein ligase
    cl00020
    Location:202460
    GAT_1; Type 1 glutamine amidotransferase (GATase1)-like domain
  6. NM_001352516.2NP_001339445.1  biotin--protein ligase isoform 1

    Status: REVIEWED

    Source sequence(s)
    AP000697, AP000698, AP000702, AP000703, AP000704
    Consensus CDS
    CCDS13647.1
    UniProtKB/Swiss-Prot
    Q99451
    Related
    ENSP00000501750.1, ENST00000675307.1
    Conserved Domains (3) summary
    pfam02237
    Location:669716
    BPL_C; Biotin protein ligase C terminal domain
    cd16442
    Location:467647
    BPL; biotin protein ligase
    cl00020
    Location:202460
    GAT_1; Type 1 glutamine amidotransferase (GATase1)-like domain
  7. NM_001352517.1NP_001339446.1  biotin--protein ligase isoform 1

    Status: REVIEWED

    Source sequence(s)
    AP000697, AP000698, AP000702, AP000703, AP000704
    Consensus CDS
    CCDS13647.1
    UniProtKB/Swiss-Prot
    Q99451
    Conserved Domains (3) summary
    pfam02237
    Location:669716
    BPL_C; Biotin protein ligase C terminal domain
    cd16442
    Location:467647
    BPL; biotin protein ligase
    cl00020
    Location:202460
    GAT_1; Type 1 glutamine amidotransferase (GATase1)-like domain
  8. NM_001352518.2NP_001339447.1  biotin--protein ligase isoform 1

    Status: REVIEWED

    Source sequence(s)
    AP000697, AP000698, AP000702, AP000703, AP000704
    Consensus CDS
    CCDS13647.1
    UniProtKB/Swiss-Prot
    Q99451
    Conserved Domains (3) summary
    pfam02237
    Location:669716
    BPL_C; Biotin protein ligase C terminal domain
    cd16442
    Location:467647
    BPL; biotin protein ligase
    cl00020
    Location:202460
    GAT_1; Type 1 glutamine amidotransferase (GATase1)-like domain

RNA

  1. NR_148020.2 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AP000697, AP000698, AP000702, AP000703, AP000704
  2. NR_148021.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AP000697, AP000698, AP000702, AP000703, AP000704

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_03

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000021.9 Reference GRCh38.p14 Primary Assembly

    Range
    36748625..36990211 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_024452065.2XP_024307833.1  biotin--protein ligase isoform X4

    Conserved Domains (3) summary
    pfam02237
    Location:612659
    BPL_C; Biotin protein ligase C terminal domain
    cd16442
    Location:410590
    BPL; biotin protein ligase
    cl00020
    Location:145403
    GAT_1; Type 1 glutamine amidotransferase (GATase1)-like domain
  2. XM_047440752.1XP_047296708.1  biotin--protein ligase isoform X1

  3. XM_047440754.1XP_047296710.1  biotin--protein ligase isoform X3

    UniProtKB/Swiss-Prot
    Q99451
  4. XM_047440753.1XP_047296709.1  biotin--protein ligase isoform X2

  5. XM_047440756.1XP_047296712.1  biotin--protein ligase isoform X7

  6. XM_011529540.3XP_011527842.1  biotin--protein ligase isoform X5

    Conserved Domains (1) summary
    cl00020
    Location:349607
    GAT_1; Type 1 glutamine amidotransferase (GATase1)-like domain
  7. XM_047440755.1XP_047296711.1  biotin--protein ligase isoform X6

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060945.1 Alternate T2T-CHM13v2.0

    Range
    35130819..35372426 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054324453.1XP_054180428.1  biotin--protein ligase isoform X4

  2. XM_054324450.1XP_054180425.1  biotin--protein ligase isoform X1

  3. XM_054324452.1XP_054180427.1  biotin--protein ligase isoform X3

    UniProtKB/Swiss-Prot
    Q99451
  4. XM_054324451.1XP_054180426.1  biotin--protein ligase isoform X2

  5. XM_054324456.1XP_054180431.1  biotin--protein ligase isoform X7

  6. XM_054324454.1XP_054180429.1  biotin--protein ligase isoform X5

  7. XM_054324455.1XP_054180430.1  biotin--protein ligase isoform X6