Sptlc2 serine palmitoyltransferase, long chain base subunit 2 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Sptlc2provided by RGD
Official Full Name: serine palmitoyltransferase, long chain base subunit 2provided by RGD
Primary source: RGD:1305447
See related: Ensembl:ENSRNOG00000012210 AllianceGenome:RGD:1305447
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: LCB 2; Pomt2; SPT 2
Summary: Predicted to enable serine C-palmitoyltransferase activity. Predicted to be involved in adipose tissue development; ceramide biosynthetic process; and sphingosine biosynthetic process. Predicted to act upstream of or within positive regulation of lipophagy; sphinganine biosynthetic process; and sphingomyelin biosynthetic process. Predicted to be integral component of membrane. Predicted to be part of serine C-palmitoyltransferase complex. Human ortholog(s) of this gene implicated in hereditary sensory and autonomic neuropathy type 1C. Orthologous to human SPTLC2 (serine palmitoyltransferase long chain base subunit 2). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Kidney (RPKM 197.2), Lung (RPKM 163.1) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 6q31

Exon count:: 12

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	6	NC_086024.1 (112679623..112762470, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	6	NC_051341.1 (106948682..107031532, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	6	NC_005105.4 (111334408..111417960, complement)

Chromosome 6 - NC_086024.1 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?

SPTLC2 ameliorates chondrocyte dysfunction and extracellular matrix metabolism disturbance in vitro and in vivo in osteoarthritis.
Title: SPTLC2 ameliorates chondrocyte dysfunction and extracellular matrix metabolism disturbance in vitro and in vivo in osteoarthritis.
Data suggest that expression of enzymes involved in sphingolipid metabolism in skeletal muscle are regulated by dietary factors; here, caloric restriction down-regulates expression of Spt1 and Spt2 but up-regulates ceramide synthases (Cers1, Cers2).
Title: Modulation of sphingolipid metabolism with calorie restriction enhances insulin action in skeletal muscle.
marked upregulation of expression of both SPT subunits in actively proliferating cells in balloon-injured vessels(serine palmitoyltransferase 1)(serine palmitoyltransferase 2)
Title: Increased expression of serine palmitoyltransferase (SPT) in balloon-injured rat carotid artery.

Submit: New GeneRIF Correction

General gene information

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Markers

RH134867 (e-PCR)
- UniSTS:218145

BE115266 (e-PCR)
- UniSTS:261467

D19271 (e-PCR)
- UniSTS:124799

RH131889 (e-PCR)
- UniSTS:215172

RH138750 (e-PCR)
- UniSTS:220837

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables pyridoxal phosphate binding	IEA Inferred from Electronic Annotation more info
enables serine C-palmitoyltransferase activity	IBA Inferred from Biological aspect of Ancestor more info
enables serine C-palmitoyltransferase activity	IEA Inferred from Electronic Annotation more info
contributes_to serine C-palmitoyltransferase activity	ISO Inferred from Sequence Orthology more info
enables serine C-palmitoyltransferase activity	ISO Inferred from Sequence Orthology more info
enables serine C-palmitoyltransferase activity	ISS Inferred from Sequence or Structural Similarity more info

Process	Evidence Code	Pubs
involved_in adipose tissue development	IEA Inferred from Electronic Annotation more info
involved_in adipose tissue development	ISO Inferred from Sequence Orthology more info
involved_in adipose tissue development	ISS Inferred from Sequence or Structural Similarity more info
involved_in ceramide biosynthetic process	IBA Inferred from Biological aspect of Ancestor more info
involved_in ceramide biosynthetic process	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within ceramide biosynthetic process	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of lipophagy	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within positive regulation of lipophagy	ISO Inferred from Sequence Orthology more info
involved_in response to immobilization stress	IEP Inferred from Expression Pattern more info	PubMed
involved_in sphinganine biosynthetic process	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within sphinganine biosynthetic process	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within sphingolipid biosynthetic process	ISO Inferred from Sequence Orthology more info
involved_in sphingolipid biosynthetic process	ISO Inferred from Sequence Orthology more info
involved_in sphingolipid biosynthetic process	ISS Inferred from Sequence or Structural Similarity more info
involved_in sphingomyelin biosynthetic process	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within sphingomyelin biosynthetic process	ISO Inferred from Sequence Orthology more info
involved_in sphingosine biosynthetic process	IBA Inferred from Biological aspect of Ancestor more info
involved_in sphingosine biosynthetic process	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within sphingosine biosynthetic process	ISO Inferred from Sequence Orthology more info
involved_in sphingosine biosynthetic process	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in endoplasmic reticulum membrane	IEA Inferred from Electronic Annotation more info
part_of serine C-palmitoyltransferase complex	IBA Inferred from Biological aspect of Ancestor more info
part_of serine C-palmitoyltransferase complex	IEA Inferred from Electronic Annotation more info
part_of serine C-palmitoyltransferase complex	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: serine palmitoyltransferase 2

Names: long chain base biosynthesis protein 2; protein-O-mannosyltransferase 2; serine-palmitoyl-CoA transferase 2

NP_001032174.1

EC 2.3.1.50

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_001037097.3 → NP_001032174.1 serine palmitoyltransferase 2

See identical proteins and their annotated locations for NP_001032174.1

Status: VALIDATED

Source sequence(s)

JAXUCZ010000006

UniProtKB/Swiss-Prot

F1LSV4, Q3B7D2

UniProtKB/TrEMBL

A6JEA2

Related

ENSRNOP00000071651.2, ENSRNOT00000085458.2

Conserved Domains (1) summary

cl18945
Location:65 → 542

AAT_I; Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the ...