Hmgcl 3-hydroxy-3-methylglutaryl-CoA lyase [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Hmgclprovided by RGD
Official Full Name: 3-hydroxy-3-methylglutaryl-CoA lyaseprovided by RGD
Primary source: RGD:620554
See related: EnsemblRapid:ENSRNOG00000009422 AllianceGenome:RGD:620554
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary: Enables carboxylic acid binding activity; fatty-acyl-CoA binding activity; and hydroxymethylglutaryl-CoA lyase activity. Involved in several processes, including ketone body biosynthetic process; liver development; and response to fatty acid. Predicted to be located in peroxisome. Predicted to be part of protein-containing complex. Predicted to be active in mitochondrion. Human ortholog(s) of this gene implicated in 3-hydroxy-3-methylglutaryl-CoA lyase deficiency and amino acid metabolic disorder. Orthologous to human HMGCL (3-hydroxy-3-methylglutaryl-CoA lyase). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in Liver (RPKM 532.5), Kidney (RPKM 407.5) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 5q36

Exon count:: 10

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	5	NC_086023.1 (153461738..153475552)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	5	NC_051340.1 (148178203..148192072)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	5	NC_005104.4 (154294841..154308582)

Chromosome 5 - NC_086023.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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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 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?

Results describe the in vitro effects of 3-hydroxy-3-methylglutarate metabolites in 3-hydroxy-3-methylglutaryl-CoA lyase deficiency on parameters of oxidative stress in striatum and liver.
Title: Striatum is more vulnerable to oxidative damage induced by the metabolites accumulating in 3-hydroxy-3-methylglutaryl-CoA lyase deficiency as compared to liver.

Submit: New GeneRIF Correction

General gene information

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Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables carboxylic acid binding	IPI Inferred from Physical Interaction more info	PubMed
enables fatty-acyl-CoA binding	IPI Inferred from Physical Interaction more info	PubMed
enables hydroxymethylglutaryl-CoA lyase activity	IBA Inferred from Biological aspect of Ancestor more info
enables hydroxymethylglutaryl-CoA lyase activity	IDA Inferred from Direct Assay more info	PubMed
enables hydroxymethylglutaryl-CoA lyase activity	IEA Inferred from Electronic Annotation more info
enables hydroxymethylglutaryl-CoA lyase activity	ISO Inferred from Sequence Orthology more info
enables hydroxymethylglutaryl-CoA lyase activity	ISS Inferred from Sequence or Structural Similarity more info
enables magnesium ion binding	IEA Inferred from Electronic Annotation more info
enables magnesium ion binding	ISO Inferred from Sequence Orthology more info
enables manganese ion binding	IEA Inferred from Electronic Annotation more info
enables manganese ion binding	ISO Inferred from Sequence Orthology more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables metal ion binding	ISO Inferred from Sequence Orthology more info
enables metal ion binding	ISS Inferred from Sequence or Structural Similarity more info
enables structural molecule activity	IEA Inferred from Electronic Annotation more info
enables structural molecule activity	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in L-leucine catabolic process	IBA Inferred from Biological aspect of Ancestor more info
involved_in acyl-CoA metabolic process	IDA Inferred from Direct Assay more info	PubMed
involved_in ketone body biosynthetic process	IBA Inferred from Biological aspect of Ancestor more info
involved_in ketone body biosynthetic process	IDA Inferred from Direct Assay more info	PubMed
involved_in ketone body biosynthetic process	IEA Inferred from Electronic Annotation more info
involved_in ketone body biosynthetic process	ISO Inferred from Sequence Orthology more info
involved_in lipid metabolic process	IEA Inferred from Electronic Annotation more info
involved_in lipid metabolic process	ISO Inferred from Sequence Orthology more info
involved_in liver development	IEP Inferred from Expression Pattern more info	PubMed
involved_in mitochondrion organization	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within mitochondrion organization	ISO Inferred from Sequence Orthology more info
involved_in response to fatty acid	IEP Inferred from Expression Pattern more info	PubMed
involved_in response to nutrient	IEP Inferred from Expression Pattern more info	PubMed
involved_in response to starvation	IEP Inferred from Expression Pattern more info	PubMed

Component	Evidence Code	Pubs
located_in mitochondrial matrix	IEA Inferred from Electronic Annotation more info
is_active_in mitochondrion	IBA Inferred from Biological aspect of Ancestor more info
located_in mitochondrion	ISO Inferred from Sequence Orthology more info
located_in peroxisome	IEA Inferred from Electronic Annotation more info
located_in peroxisome	ISO Inferred from Sequence Orthology more info
part_of protein-containing complex	IEA Inferred from Electronic Annotation more info
part_of protein-containing complex	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: hydroxymethylglutaryl-CoA lyase, mitochondrial

Names: 3-hydroxy-3-methylglutarate-CoA lyase; 3-hydroxy-3-methylglutaryl-Coenzyme A lyase; 3-hydroxymethyl-3-methylglutaryl-CoA lyase; 3-hydroxymethyl-3-methylglutaryl-Coenzyme A lyase; HL; HMG-CoA lyase

NP_077362.1

EC 4.1.3.4

XP_038966760.1

EC 4.1.3.4

XP_063144533.1

EC 4.1.3.4

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_024386.2 → NP_077362.1 hydroxymethylglutaryl-CoA lyase, mitochondrial precursor

See identical proteins and their annotated locations for NP_077362.1

Status: PROVISIONAL

Source sequence(s)

JAXUCZ010000005

UniProtKB/Swiss-Prot

P97519

UniProtKB/TrEMBL

A0A8L2Q6E3, A6IT78

Related

ENSRNOP00000012853.5, ENSRNOT00000012853.8

Conserved Domains (1) summary

cl21457
Location:17 → 325

TIM; TIM-like beta/alpha barrel domains

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_086023.1 Reference GRCr8

Range

153461738..153475552

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_039110832.2 → XP_038966760.1 hydroxymethylglutaryl-CoA lyase, mitochondrial isoform X1

Conserved Domains (1) summary

cl21457
Location:17 → 257

TIM; TIM-like beta/alpha barrel domains
XM_063288463.1 → XP_063144533.1 hydroxymethylglutaryl-CoA lyase, mitochondrial isoform X2