Sc5d sterol-C5-desaturase [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Sc5dprovided by RGD
Official Full Name: sterol-C5-desaturaseprovided by RGD
Primary source: RGD:620775
See related: EnsemblRapid:ENSRNOG00000065944 AllianceGenome:RGD:620775
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
Also known as: Sc5dl
Summary: Enables C-5 sterol desaturase activity and delta7-sterol 5(6)-desaturase activity. Involved in cholesterol biosynthetic process via lathosterol. Is active in endoplasmic reticulum membrane. Orthologous to human SC5D (sterol-C5-desaturase). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Biased expression in Liver (RPKM 1112.9), Brain (RPKM 325.5) and 7 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 8q22

Exon count:: 6

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	8	NC_086026.1 (51526669..51538277, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	8	NC_051343.1 (42629649..42641257, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	8	NC_005107.4 (46525406..46537014, complement)

Chromosome 8 - NC_086026.1 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
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?

The effect of dietary plant extracts and vegetable oils on hepatic SREBP-1c, Delta5 and Delta6 desaturases has been reported.
Title: Adding a purple corn extract in rats supplemented with chia oil decreases gene expression of SREBP-1c and retains Δ5 and Δ6 hepatic desaturase activity, unmodified the hepatic lipid profile.
testicular distribution of Delta5- and Delta6-desaturase and stearoyl-CoA desaturase 1 and 2 shows that all four desaturases seem to be localized in the Sertoli cells, with far lower expression in germ cells
Title: Expression and regulation of delta5-desaturase, delta6-desaturase, stearoyl-coenzyme A (CoA) desaturase 1, and stearoyl-CoA desaturase 2 in rat testis.

Submit: New GeneRIF Correction

General gene information

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Markers

RH139703 (e-PCR)
- UniSTS:221787

RH133454 (e-PCR)
- UniSTS:216737

RH136956 (e-PCR)
- UniSTS:219045

Sc5d (e-PCR), detects polymorphism
- UniSTS:546983

AI228309 (e-PCR)
- UniSTS:261583

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables C-5 sterol desaturase activity	IBA Inferred from Biological aspect of Ancestor more info
enables C-5 sterol desaturase activity	IDA Inferred from Direct Assay more info	PubMed
enables C-5 sterol desaturase activity	ISO Inferred from Sequence Orthology more info
enables delta7-sterol 5(6)-desaturase activity	IDA Inferred from Direct Assay more info	PubMed
enables delta7-sterol 5(6)-desaturase activity	ISO Inferred from Sequence Orthology more info
enables delta7-sterol 5(6)-desaturase activity	TAS Traceable Author Statement more info	PubMed
enables iron ion binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in cholesterol biosynthetic process via lathosterol	IBA Inferred from Biological aspect of Ancestor more info
involved_in cholesterol biosynthetic process via lathosterol	IDA Inferred from Direct Assay more info	PubMed
involved_in cholesterol biosynthetic process via lathosterol	ISO Inferred from Sequence Orthology more info
involved_in fatty acid metabolic process	TAS Traceable Author Statement more info	PubMed
involved_in negative regulation of ferroptosis	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of ferroptosis	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
is_active_in endoplasmic reticulum membrane	IDA Inferred from Direct Assay more info	PubMed
is_active_in endoplasmic reticulum membrane	ISO Inferred from Sequence Orthology more info
is_active_in membrane	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: lathosterol oxidase

Names: C-5 sterol desaturase; delta(7)-sterol 5-desaturase; delta(7)-sterol C5(6)-desaturase; lathosterol 5-desaturase; sterol-C5-desaturase (ERG3 delta-5-desaturase homolog, S. cerevisiae)-like; sterol-C5-desaturase (fungal ERG3, delta-5-desaturase) homolog; sterol-C5-desaturase (fungal ERG3, delta-5-desaturase)-like

NP_446094.1

EC 1.14.19.20

XP_017450895.1

EC 1.14.19.20

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_053642.2 → NP_446094.1 lathosterol oxidase

See identical proteins and their annotated locations for NP_446094.1

Status: PROVISIONAL

Source sequence(s)

BC081704

UniProtKB/Swiss-Prot

Q9EQS5

UniProtKB/TrEMBL

A6J3S8

Related

ENSRNOP00000092291.1, ENSRNOT00000106582.2

Conserved Domains (1) summary

COG3000
Location:40 → 257

ERG3; Sterol desaturase/sphingolipid hydroxylase, fatty acid hydroxylase superfamily [Lipid transport and metabolism]

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_086026.1 Reference GRCr8

Range

51526669..51538277 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_017595406.3 → XP_017450895.1 lathosterol oxidase isoform X1

UniProtKB/Swiss-Prot

Q9EQS5

UniProtKB/TrEMBL

A6J3S8

Conserved Domains (1) summary

COG3000
Location:40 → 257

ERG3; Sterol desaturase/sphingolipid hydroxylase, fatty acid hydroxylase superfamily [Lipid transport and metabolism]