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Sphk1 sphingosine kinase 1 [ Rattus norvegicus (Norway rat) ]

Gene ID: 170897, updated on 9-Dec-2024

Summary

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Official Symbol: Sphk1provided by RGD
Official Full Name: sphingosine kinase 1provided by RGD
Primary source: RGD:620048
See related: EnsemblRapid:ENSRNOG00000010626 AllianceGenome:RGD:620048
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
Summary: Enables D-erythro-sphingosine kinase activity. Involved in several processes, including cellular response to hydrogen peroxide; cyclooxygenase pathway; and regulation of gene expression. Located in axon and synaptic vesicle. Biomarker of adenocarcinoma and high grade glioma. Human ortholog(s) of this gene implicated in type 2 diabetes mellitus. Orthologous to human SPHK1 (sphingosine kinase 1). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Biased expression in Thymus (RPKM 63.0), Kidney (RPKM 34.3) and 7 other tissues See more
Orthologs: human mouse all
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Genomic context

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See Sphk1 in Genome Data Viewer

Location:: 10q32.1-q32.2

Exon count:: 8

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	10	NC_086028.1 (102257413..102263086)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	10	NC_051345.1 (101758567..101764240)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	10	NC_005109.4 (105498728..105504401)

Chromosome 10 - NC_086028.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

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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?

Role of Sphingosine Kinase 1 in Glucolipotoxicity-Induced Early Activation of Autophagy in INS-1 Pancreatic beta Cells.
Title: Role of Sphingosine Kinase 1 in Glucolipotoxicity-Induced Early Activation of Autophagy in INS-1 Pancreatic β Cells.
Sphk1-induced autophagy in microglia promotes neuronal injury following cerebral ischaemia-reperfusion.
Title: Sphk1-induced autophagy in microglia promotes neuronal injury following cerebral ischaemia-reperfusion.
Critical roles of sphingosine kinase 1 in the regulation of neuroinflammation and neuronal injury after spinal cord injury.
Title: Critical roles of sphingosine kinase 1 in the regulation of neuroinflammation and neuronal injury after spinal cord injury.
The Sphkl/SlP pathway regulates angiogenesis via NOS/NO synthesis following cerebral ischemia-reperfusion.
Title: The Sphkl/SlP pathway regulates angiogenesis via NOS/NO synthesis following cerebral ischemia-reperfusion.
Sphingosine kinase 1 regulates HMGB1 translocation by directly interacting with calcium/calmodulin protein kinase II-delta in sepsis-associated liver injury.
Title: Sphingosine kinase 1 regulates HMGB1 translocation by directly interacting with calcium/calmodulin protein kinase II-δ in sepsis-associated liver injury.
MiR-124 promotes ischemia-reperfusion induced cardiomyocyte apoptosis by targeting sphingosine kinase 1.
Title: MiR-124 promotes ischemia-reperfusion induced cardiomyocyte apoptosis by targeting sphingosine kinase 1.
Sphingosine kinase 1-associated autophagy differs between neurons and astrocytes.
Title: Sphingosine kinase 1-associated autophagy differs between neurons and astrocytes.
Pre-silencing of SphK1 with siRNA reversed PDGF-induced S1P production, miR-21 up-regulation, BMPRII and Id1 down-regulation, as well as pulmonary arterial smooth muscle cell proliferation.
Title: SphK1/S1P Mediates PDGF-Induced Pulmonary Arterial Smooth Muscle Cell Proliferation via miR-21/BMPRII/Id1 Signaling Pathway.
Extracellular vesicles from human-induced pluripotent stem cell-derived mesenchymal stromal cells protect against renal ischemia/reperfusion injury via delivering SP1 and transcriptionally activating sphingosine kinase 1 and inhibiting necroptosis.
Title: Extracellular vesicles from human-induced pluripotent stem cell-derived mesenchymal stromal cells (hiPSC-MSCs) protect against renal ischemia/reperfusion injury via delivering specificity protein (SP1) and transcriptional activating of sphingosine kinase 1 and inhibiting necroptosis.
SPHK1 mediated autophagy is different in neurons and neuroblastoma cells
Title: SPHK1/sphingosine kinase 1-mediated autophagy differs between neurons and SH-SY5Y neuroblastoma cells.

Submit: New GeneRIF Correction See all GeneRIFs (42)

General gene information

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Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables ATP binding	IEA Inferred from Electronic Annotation more info
enables ATP binding	ISO Inferred from Sequence Orthology more info
enables D-erythro-sphingosine kinase activity	IBA Inferred from Biological aspect of Ancestor more info
enables D-erythro-sphingosine kinase activity	IDA Inferred from Direct Assay more info	PubMed
enables D-erythro-sphingosine kinase activity	IEA Inferred from Electronic Annotation more info
enables D-erythro-sphingosine kinase activity	ISO Inferred from Sequence Orthology more info
enables D-erythro-sphingosine kinase activity	ISS Inferred from Sequence or Structural Similarity more info
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables DNA binding	ISO Inferred from Sequence Orthology more info
enables acetyltransferase activity	ISO Inferred from Sequence Orthology more info
enables acetyltransferase activity	ISS Inferred from Sequence or Structural Similarity more info
enables calmodulin binding	IEA Inferred from Electronic Annotation more info
enables calmodulin binding	ISO Inferred from Sequence Orthology more info
enables kinase activity	IEA Inferred from Electronic Annotation more info
enables lipid binding	IEA Inferred from Electronic Annotation more info
enables lipid binding	ISO Inferred from Sequence Orthology more info
enables lipid binding	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 magnesium ion binding	ISS Inferred from Sequence or Structural Similarity more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein phosphatase 2A binding	IEA Inferred from Electronic Annotation more info
enables protein phosphatase 2A binding	ISO Inferred from Sequence Orthology more info
enables sphingosine kinase activity	ISO Inferred from Sequence Orthology more info
enables sphingosine kinase activity	ISS Inferred from Sequence or Structural Similarity more info
enables sphingosine-1-phosphate receptor activity	IEA Inferred from Electronic Annotation more info
enables sphingosine-1-phosphate receptor activity	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within DNA biosynthetic process	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within blood vessel development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within brain development	ISO Inferred from Sequence Orthology more info
involved_in calcium-mediated signaling	IEA Inferred from Electronic Annotation more info
involved_in calcium-mediated signaling	ISO Inferred from Sequence Orthology more info
acts_upstream_of cell population proliferation	ISO Inferred from Sequence Orthology more info
involved_in cellular response to growth factor stimulus	IBA Inferred from Biological aspect of Ancestor more info
involved_in cellular response to growth factor stimulus	IEP Inferred from Expression Pattern more info	PubMed
involved_in cellular response to hydrogen peroxide	IEP Inferred from Expression Pattern more info	PubMed
acts_upstream_of_or_within cellular response to hydrogen peroxide	ISO Inferred from Sequence Orthology more info
involved_in cellular response to starvation	IEP Inferred from Expression Pattern more info	PubMed
involved_in cellular response to vascular endothelial growth factor stimulus	IEA Inferred from Electronic Annotation more info
involved_in cellular response to vascular endothelial growth factor stimulus	ISO Inferred from Sequence Orthology more info
involved_in cellular response to vascular endothelial growth factor stimulus	ISS Inferred from Sequence or Structural Similarity more info
involved_in cyclooxygenase pathway	IDA Inferred from Direct Assay more info	PubMed
involved_in female pregnancy	IEP Inferred from Expression Pattern more info	PubMed
acts_upstream_of_or_within inflammatory response	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of apoptotic process	IBA Inferred from Biological aspect of Ancestor more info
involved_in negative regulation of apoptotic process	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of apoptotic process	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within negative regulation of apoptotic process	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of apoptotic process	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of apoptotic process	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of ceramide biosynthetic process	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of ceramide biosynthetic process	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of ceramide biosynthetic process	ISS Inferred from Sequence or Structural Similarity more info
involved_in phosphorylation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of NF-kappaB transcription factor activity	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of NF-kappaB transcription factor activity	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of NF-kappaB transcription factor activity	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of angiogenesis	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of angiogenesis	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of cell growth	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of cell growth	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of cell migration	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of cell migration	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of cell migration	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of cell population proliferation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of fibroblast proliferation	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within positive regulation of fibroblast proliferation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of interleukin-17 production	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of mitotic cell cycle	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of mitotic cell cycle	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of mitotic nuclear division	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of neuron projection development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of neurotransmitter secretion	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of non-canonical NF-kappaB signal transduction	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of non-canonical NF-kappaB signal transduction	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of non-canonical NF-kappaB signal transduction	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of p38MAPK cascade	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of p38MAPK cascade	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of p38MAPK cascade	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of peptidyl-threonine phosphorylation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of protein phosphorylation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of protein ubiquitination	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of protein ubiquitination	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of protein ubiquitination	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of smooth muscle contraction	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of smooth muscle contraction	ISO Inferred from Sequence Orthology more info
involved_in protein acetylation	ISO Inferred from Sequence Orthology more info
involved_in protein acetylation	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of endocytosis	IEA Inferred from Electronic Annotation more info
involved_in regulation of endocytosis	ISO Inferred from Sequence Orthology more info
involved_in regulation of endocytosis	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of endosomal vesicle fusion	ISO Inferred from Sequence Orthology more info
involved_in regulation of endosomal vesicle fusion	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within regulation of interleukin-1 beta production	ISO Inferred from Sequence Orthology more info
involved_in regulation of microglial cell activation	ISO Inferred from Sequence Orthology more info
involved_in regulation of microglial cell activation	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of neuroinflammatory response	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of neuroinflammatory response	ISO Inferred from Sequence Orthology more info
involved_in regulation of neuroinflammatory response	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of phagocytosis	ISO Inferred from Sequence Orthology more info
involved_in regulation of phagocytosis	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of tumor necrosis factor-mediated signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in regulation of tumor necrosis factor-mediated signaling pathway	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of tumor necrosis factor-mediated signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in regulation of tumor necrosis factor-mediated signaling pathway	ISS Inferred from Sequence or Structural Similarity more info
involved_in response to ATP	IEP Inferred from Expression Pattern more info	PubMed
involved_in response to amine	IEP Inferred from Expression Pattern more info	PubMed
involved_in response to interleukin-1	IEP Inferred from Expression Pattern more info	PubMed
involved_in response to magnesium ion	IEP Inferred from Expression Pattern more info	PubMed
involved_in response to organic cyclic compound	IEP Inferred from Expression Pattern more info	PubMed
involved_in response to progesterone	IEP Inferred from Expression Pattern more info	PubMed
involved_in response to tumor necrosis factor	IEA Inferred from Electronic Annotation more info
involved_in response to tumor necrosis factor	ISO Inferred from Sequence Orthology more info
involved_in response to tumor necrosis factor	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within sphingolipid mediated signaling pathway	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
involved_in sphingosine biosynthetic process	ISO Inferred from Sequence Orthology more info
involved_in sphingosine metabolic process	ISO Inferred from Sequence Orthology more info
involved_in sphingosine metabolic process	ISS Inferred from Sequence or Structural Similarity more info
involved_in sphingosine-1-phosphate receptor signaling pathway	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in axon	IDA Inferred from Direct Assay more info	PubMed
located_in clathrin-coated pit	IEA Inferred from Electronic Annotation more info
located_in clathrin-coated pit	ISO Inferred from Sequence Orthology more info
located_in clathrin-coated pit	ISS Inferred from Sequence or Structural Similarity more info
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
located_in cytoplasm	ISS Inferred from Sequence or Structural Similarity more info
located_in cytosol	IEA Inferred from Electronic Annotation more info
located_in cytosol	ISO Inferred from Sequence Orthology more info
located_in early endosome membrane	IEA Inferred from Electronic Annotation more info
located_in early endosome membrane	ISO Inferred from Sequence Orthology more info
located_in early endosome membrane	ISS Inferred from Sequence or Structural Similarity more info
located_in endocytic vesicle	ISO Inferred from Sequence Orthology more info
located_in endocytic vesicle	ISS Inferred from Sequence or Structural Similarity more info
is_active_in intracellular membrane-bounded organelle	IBA Inferred from Biological aspect of Ancestor more info
is_active_in membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	ISO Inferred from Sequence Orthology more info
located_in nucleus	ISS Inferred from Sequence or Structural Similarity more info
located_in plasma membrane	IEA Inferred from Electronic Annotation more info
located_in plasma membrane	ISO Inferred from Sequence Orthology more info
located_in presynapse	IEA Inferred from Electronic Annotation more info
is_active_in presynapse	ISO Inferred from Sequence Orthology more info
located_in presynapse	ISO Inferred from Sequence Orthology more info
located_in synaptic vesicle	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: sphingosine kinase 1

Names: SK 1; SPK 1; acetyltransferase SPHK1

NP_001257736.1

EC 2.7.1.91

NP_001257737.1

EC 2.7.1.91

NP_001257738.1

EC 2.7.1.91

NP_001257739.1

EC 2.7.1.91

NP_001257740.1

EC 2.7.1.91

NP_596877.2

EC 2.7.1.91

XP_006247849.1

EC 2.7.1.91

NCBI Reference Sequences (RefSeq)

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NEW Try the new Transcript table

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_001270807.1 → NP_001257736.1 sphingosine kinase 1 isoform b

See identical proteins and their annotated locations for NP_001257736.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) uses an alternate first exon compared to variant 1. The resulting isoform (b) is shorter at the N-terminus compared to isoform a. Variants 2, 3, 4, 5, and 6 all encode the same isoform (b).

Source sequence(s)

BC081738, JAXUCZ010000010

UniProtKB/Swiss-Prot

Q642F6, Q91V26

UniProtKB/TrEMBL

A6HKX2

Conserved Domains (1) summary

PLN02958
Location:11 → 344

PLN02958; diacylglycerol kinase/D-erythro-sphingosine kinase
NM_001270808.1 → NP_001257737.1 sphingosine kinase 1 isoform b

See identical proteins and their annotated locations for NP_001257737.1

Status: VALIDATED

Description

Transcript Variant: This variant (3) uses an alternate first exon compared to variant 1. The resulting isoform (b) is shorter at the N-terminus compared to isoform a. Variants 2, 3, 4, 5, and 6 all encode the same isoform (b).

Source sequence(s)

BC081738, JAXUCZ010000010

UniProtKB/Swiss-Prot

Q642F6, Q91V26

UniProtKB/TrEMBL

A6HKX2

Conserved Domains (1) summary

PLN02958
Location:11 → 344

PLN02958; diacylglycerol kinase/D-erythro-sphingosine kinase
NM_001270809.1 → NP_001257738.1 sphingosine kinase 1 isoform b

See identical proteins and their annotated locations for NP_001257738.1

Status: VALIDATED

Description

Transcript Variant: This variant (4) uses an alternate splice junction at the 3' end of the first exon compared to variant 1. The resulting isoform (b) is shorter at the N-terminus compared to isoform a. Variants 2, 3, 4, 5, and 6 all encode the same isoform (b).

Source sequence(s)

BC081738, JAXUCZ010000010

UniProtKB/Swiss-Prot

Q642F6, Q91V26

UniProtKB/TrEMBL

A6HKX2

Conserved Domains (1) summary

PLN02958
Location:11 → 344

PLN02958; diacylglycerol kinase/D-erythro-sphingosine kinase
NM_001270810.1 → NP_001257739.1 sphingosine kinase 1 isoform b

See identical proteins and their annotated locations for NP_001257739.1

Status: VALIDATED

Description

Transcript Variant: This variant (5) uses an alternate splice junction at the 3' end of the first exon compared to variant 1. The resulting isoform (b) is shorter at the N-terminus compared to isoform a. Variants 2, 3, 4, 5, and 6 all encode the same isoform (b).

Source sequence(s)

BC081738, JAXUCZ010000010

UniProtKB/Swiss-Prot

Q642F6, Q91V26

UniProtKB/TrEMBL

A6HKX2

Conserved Domains (1) summary

PLN02958
Location:11 → 344

PLN02958; diacylglycerol kinase/D-erythro-sphingosine kinase
NM_001270811.1 → NP_001257740.1 sphingosine kinase 1 isoform a

Status: VALIDATED

Description

Transcript Variant: This variant (1) encodes the longer isoform (a).

Source sequence(s)

BC081738, JAXUCZ010000010

UniProtKB/TrEMBL

A0A0G2K373, Q1HGK5

Related

ENSRNOP00000072525.1, ENSRNOT00000083593.3

Conserved Domains (2) summary

COG1597
Location:91 → 443

LCB5; Diacylglycerol kinase family enzyme [Lipid transport and metabolism, General function prediction only]

pfam00781
Location:91 → 197

DAGK_cat; Diacylglycerol kinase catalytic domain
NM_133386.3 → NP_596877.2 sphingosine kinase 1 isoform b

See identical proteins and their annotated locations for NP_596877.2

Status: VALIDATED

Description

Transcript Variant: This variant (6) retains an intron compared to variant 1. The resulting isoform (b) is shorter at the N-terminus compared to isoform a. Variants 2, 3, 4, 5, and 6 all encode the same isoform (b).

Source sequence(s)

BC081738, JAXUCZ010000010

UniProtKB/Swiss-Prot

Q642F6, Q91V26

UniProtKB/TrEMBL

A6HKX2

Conserved Domains (1) summary

PLN02958
Location:11 → 344

PLN02958; diacylglycerol kinase/D-erythro-sphingosine kinase

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_086028.1 Reference GRCr8

Range

102257413..102263086

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006247787.4 → XP_006247849.1 sphingosine kinase 1 isoform X1

UniProtKB/Swiss-Prot

Q642F6, Q91V26

UniProtKB/TrEMBL

A0A140TAE3

Conserved Domains (1) summary

PLN02958
Location:10 → 343

PLN02958; diacylglycerol kinase/D-erythro-sphingosine kinase