Hlcs holocarboxylase synthetase [Rattus norvegicus (Norway rat)] - Gene

Summary

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, Nov 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

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_086029.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Submit: New GeneRIF Correction

General gene information

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Markers

G67818 (e-PCR)
- UniSTS:226165

BF397968 (e-PCR)
- UniSTS:246396

STS-Z41140 (e-PCR)
- UniSTS:69782

BE106240 (e-PCR)
- UniSTS:246187

BQ196240 (e-PCR)
- UniSTS:260523

RH138262 (e-PCR)
- UniSTS:220349

D11Got19 (e-PCR)
- UniSTS:114885

D11Got25 (e-PCR)
- UniSTS:112112

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

EC 6.3.4.10

EC 6.3.4.11

EC 6.3.4.15

EC 6.3.4.9

NP_001413954.1

EC 6.3.4.10

EC 6.3.4.11

EC 6.3.4.15

EC 6.3.4.9

XP_038944719.2

EC 6.3.4.10

EC 6.3.4.11

EC 6.3.4.15

EC 6.3.4.9

XP_038944720.2

EC 6.3.4.10

EC 6.3.4.11

EC 6.3.4.15

EC 6.3.4.9

XP_038944722.2

EC 6.3.4.10

EC 6.3.4.11

EC 6.3.4.15

EC 6.3.4.9

XP_038944723.1

EC 6.3.4.10

EC 6.3.4.11

EC 6.3.4.15

EC 6.3.4.9

XP_038944726.1

EC 6.3.4.10

EC 6.3.4.11

EC 6.3.4.15

EC 6.3.4.9

XP_063126482.1

EC 6.3.4.10

EC 6.3.4.11

EC 6.3.4.15

EC 6.3.4.9

XP_063126483.1

EC 6.3.4.10

EC 6.3.4.11

EC 6.3.4.15

EC 6.3.4.9

XP_063126484.1

EC 6.3.4.10

EC 6.3.4.11

EC 6.3.4.15

EC 6.3.4.9

XP_063126485.1

EC 6.3.4.10

EC 6.3.4.11

EC 6.3.4.15

EC 6.3.4.9

XP_063126486.1

EC 6.3.4.10

EC 6.3.4.11

EC 6.3.4.15

EC 6.3.4.9

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)

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

Status: VALIDATED

Source sequence(s)

JAXUCZ010000011

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

NC_086029.1 Reference GRCr8

Range

46925491..47123111 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_063270415.1 → XP_063126485.1 biotin--protein ligase isoform X7
XM_063270414.1 → XP_063126484.1 biotin--protein ligase isoform X7
XM_063270413.1 → XP_063126483.1 biotin--protein ligase isoform X5
XM_039088792.2 → XP_038944720.2 biotin--protein ligase isoform X2
XM_039088794.2 → XP_038944722.2 biotin--protein ligase isoform X4

Related

ENSRNOP00000109168.1, ENSRNOT00000173266.1
XM_039088791.2 → XP_038944719.2 biotin--protein ligase isoform X1

Related

ENSRNOP00000002291.7, ENSRNOT00000002291.8
XM_063270416.1 → XP_063126486.1 biotin--protein ligase isoform X8
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
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
XM_063270412.1 → XP_063126482.1 biotin--protein ligase isoform X3