SPHK1 sphingosine kinase 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: SPHK1provided by HGNC
Official Full Name: sphingosine kinase 1provided by HGNC
Primary source: HGNC:HGNC:11240
See related: Ensembl:ENSG00000176170 MIM:603730; AllianceGenome:HGNC:11240
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: SPHK
Summary: The protein encoded by this gene catalyzes the phosphorylation of sphingosine to form sphingosine-1-phosphate (S1P), a lipid mediator with both intra- and extracellular functions. Intracellularly, S1P regulates proliferation and survival, and extracellularly, it is a ligand for cell surface G protein-coupled receptors. This protein, and its product S1P, play a key role in TNF-alpha signaling and the NF-kappa-B activation pathway important in inflammatory, antiapoptotic, and immune processes. Phosphorylation of this protein alters its catalytic activity and promotes its translocation to the plasma membrane. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Sep 2017]
Expression: Ubiquitous expression in gall bladder (RPKM 4.9), esophagus (RPKM 4.2) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 17q25.1

Exon count:: 7

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	17	NC_000017.11 (76383204..76387855)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	17	NC_060941.1 (77279777..77284428)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	17	NC_000017.10 (74379285..74383936)

Chromosome 17 - NC_000017.11 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: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

SphK1 deficiency ameliorates the development of atherosclerosis by inhibiting the S1P/S1PR3/Rhoa/ROCK pathway.
Title: SphK1 deficiency ameliorates the development of atherosclerosis by inhibiting the S1P/S1PR3/Rhoa/ROCK pathway.
Interference with sphingosine kinase-1 reduces the hydrogen peroxide-induced oxidative stress damage in melanocytes through four and a half LIM domains 2.
Title: Interference with sphingosine kinase-1 reduces the hydrogen peroxide-induced oxidative stress damage in melanocytes through four and a half LIM domains 2.
SPHK1 potentiates colorectal cancer progression and metastasis via regulating autophagy mediated by TRAF6-induced ULK1 ubiquitination.
Title: SPHK1 potentiates colorectal cancer progression and metastasis via regulating autophagy mediated by TRAF6-induced ULK1 ubiquitination.
Targeting the SphK1/S1P/PFKFB3 axis suppresses hepatocellular carcinoma progression by disrupting glycolytic energy supply that drives tumor angiogenesis.
Title: Targeting the SphK1/S1P/PFKFB3 axis suppresses hepatocellular carcinoma progression by disrupting glycolytic energy supply that drives tumor angiogenesis.
The role of SphK/S1P/S1PR signaling pathway in bone metabolism.
Title: The role of SphK/S1P/S1PR signaling pathway in bone metabolism.
Kruppel-like factor 12 regulates aging ovarian granulosa cell apoptosis by repressing SPHK1 transcription and sphingosine-1-phosphate (S1P) production.
Title: Krüppel-like factor 12 regulates aging ovarian granulosa cell apoptosis by repressing SPHK1 transcription and sphingosine-1-phosphate (S1P) production.
Sphingosine kinase 1 regulates lipid metabolism to promote progression of kidney renal clear cell carcinoma.
Title: Sphingosine kinase 1 regulates lipid metabolism to promote progression of kidney renal clear cell carcinoma.
DNA methylation status of the SPHK1 and LTB genes underlies the clinicopathological diversity of non-alcoholic steatohepatitis-related hepatocellular carcinomas.
Title: DNA methylation status of the SPHK1 and LTB genes underlies the clinicopathological diversity of non-alcoholic steatohepatitis-related hepatocellular carcinomas.
HOXC11 drives lung adenocarcinoma progression through transcriptional regulation of SPHK1.
Title: HOXC11 drives lung adenocarcinoma progression through transcriptional regulation of SPHK1.
Targeting SPHK1/S1PR3-regulated S-1-P metabolic disorder triggers autophagic cell death in pulmonary lymphangiomyomatosis (LAM).
Title: Targeting SPHK1/S1PR3-regulated S-1-P metabolic disorder triggers autophagic cell death in pulmonary lymphangiomyomatosis (LAM).

Submit: New GeneRIF Correction See all GeneRIFs (285)

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Protein interactions

Protein	Gene	Interaction	Pubs
Envelope surface glycoprotein gp120	env	HIV-1 gp120 upregulates the expression of sphingosine kinase 1 (SPHK1) in human B cells	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables ATP binding	IDA Inferred from Direct Assay more info	PubMed
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	TAS Traceable Author Statement more info
enables DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables acetyltransferase activity	ISS Inferred from Sequence or Structural Similarity more info
enables calmodulin binding	IDA Inferred from Direct Assay more info	PubMed
enables lipid binding	IDA Inferred from Direct Assay more info	PubMed
enables lipid kinase activity	TAS Traceable Author Statement more info
enables magnesium ion binding	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein phosphatase 2A binding	IPI Inferred from Physical Interaction more info	PubMed
enables sphingosine kinase activity	IDA Inferred from Direct Assay more info	PubMed
enables sphingosine-1-phosphate receptor activity	IMP Inferred from Mutant Phenotype more info	PubMed

Process	Evidence Code	Pubs
involved_in DNA biosynthetic process	IEA Inferred from Electronic Annotation more info
involved_in blood vessel development	IEA Inferred from Electronic Annotation more info
involved_in brain development	IEA Inferred from Electronic Annotation more info
involved_in calcium-mediated signaling	IDA Inferred from Direct Assay more info	PubMed
involved_in cell population proliferation	IEA Inferred from Electronic Annotation more info
involved_in cellular response to growth factor stimulus	IBA Inferred from Biological aspect of Ancestor more info
involved_in cellular response to hydrogen peroxide	IEA Inferred from Electronic Annotation more info
involved_in cellular response to vascular endothelial growth factor stimulus	IDA Inferred from Direct Assay more info	PubMed
involved_in inflammatory response	IEA Inferred from Electronic Annotation more info
involved_in intracellular signal transduction	TAS Traceable Author Statement more info	PubMed
involved_in negative regulation of apoptotic process	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within negative regulation of apoptotic process	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of apoptotic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of apoptotic process	TAS Traceable Author Statement more info	PubMed
involved_in negative regulation of ceramide biosynthetic process	IDA Inferred from Direct Assay more info	PubMed
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	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of angiogenesis	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of cell growth	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of cell migration	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within positive regulation of fibroblast proliferation	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of interleukin-17 production	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of mitotic cell cycle	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of mitotic nuclear division	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of non-canonical NF-kappaB signal transduction	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of p38MAPK cascade	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of peptidyl-threonine phosphorylation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of protein ubiquitination	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of smooth muscle contraction	IDA Inferred from Direct Assay more info	PubMed
involved_in protein acetylation	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of endocytosis	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of endosomal vesicle fusion	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of interleukin-1 beta production	IEA Inferred from Electronic Annotation more info
involved_in regulation of microglial cell activation	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of neuroinflammatory response	ISS Inferred from Sequence or Structural Similarity 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	IDA Inferred from Direct Assay more info	PubMed
involved_in response to tumor necrosis factor	IDA Inferred from Direct Assay more info	PubMed
involved_in sphingoid catabolic process	NAS Non-traceable Author Statement more info	PubMed
involved_in sphingolipid biosynthetic process	TAS Traceable Author Statement more info
involved_in sphingosine biosynthetic process	IBA Inferred from Biological aspect of Ancestor more info
involved_in sphingosine biosynthetic process	IGI Inferred from Genetic Interaction more info	PubMed
involved_in sphingosine biosynthetic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in sphingosine metabolic process	IDA Inferred from Direct Assay more info	PubMed
involved_in sphingosine-1-phosphate receptor signaling pathway	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in clathrin-coated pit	IDA Inferred from Direct Assay more info	PubMed
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in cytosol	IDA Inferred from Direct Assay more info
located_in cytosol	TAS Traceable Author Statement more info	PubMed
located_in early endosome membrane	IDA Inferred from Direct Assay more info	PubMed
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 nucleoplasm	TAS Traceable Author Statement more info
located_in nucleus	ISS Inferred from Sequence or Structural Similarity more info
located_in plasma membrane	IDA Inferred from Direct Assay more info	PubMed
is_active_in presynapse	IDA Inferred from Direct Assay more info	PubMed
is_active_in presynapse	IMP Inferred from Mutant Phenotype more info	PubMed
located_in presynapse	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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Preferred Names: sphingosine kinase 1

Names: SK 1; SPK 1; acetyltransferase SPHK1

NP_001136073.1

EC 2.7.1.91

NP_001136074.1

EC 2.7.1.91

NP_001342068.1

EC 2.7.1.91

NP_068807.2

EC 2.7.1.91

NP_892010.2

EC 2.7.1.91

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_001142601.2 → NP_001136073.1 sphingosine kinase 1 isoform 3

See identical proteins and their annotated locations for NP_001136073.1

Status: REVIEWED

Description

Transcript Variant: This variant (3) contains an alternate in-frame segment in the 5' coding region and uses a downstream start codon, compared to variant 2. Isoform 3 has a shorter N-terminus, compared to isoform 2. Variants 3, 4 and 5 encode the same isoform (3).

Source sequence(s)

AK022402, BC030553, DC384776

Consensus CDS

CCDS45785.1

UniProtKB/Swiss-Prot

Q8N632, Q96GK1, Q9HD92, Q9NY70, Q9NYA1, Q9NYL3

UniProtKB/TrEMBL

B3KVB3, Q53ZR5, Q96HV8

Related

ENSP00000465726.2, ENST00000592299.6

Conserved Domains (1) summary

PLN02958
Location:11 → 345

PLN02958; diacylglycerol kinase/D-erythro-sphingosine kinase
NM_001142602.2 → NP_001136074.1 sphingosine kinase 1 isoform 3

See identical proteins and their annotated locations for NP_001136074.1

Status: REVIEWED

Description

Transcript Variant: This variant (4) contains an alternate in-frame segment in the 5' coding region and uses a downstream start codon, compared to variant 2. Isoform 3 has a shorter N-terminus, compared to isoform 2. Variants 3, 4 and 5 encode the same isoform (3).

Source sequence(s)

BC030553, BP304783, DC384776

Consensus CDS

CCDS45785.1

UniProtKB/Swiss-Prot

Q8N632, Q96GK1, Q9HD92, Q9NY70, Q9NYA1, Q9NYL3

UniProtKB/TrEMBL

B3KVB3, Q53ZR5, Q96HV8

Related

ENSP00000376285.2, ENST00000392496.3

Conserved Domains (1) summary

PLN02958
Location:11 → 345

PLN02958; diacylglycerol kinase/D-erythro-sphingosine kinase
NM_001355139.2 → NP_001342068.1 sphingosine kinase 1 isoform 3

Status: REVIEWED

Source sequence(s)

BC030553, DA482243, DC384776

Consensus CDS

CCDS45785.1

UniProtKB/Swiss-Prot

Q8N632, Q96GK1, Q9HD92, Q9NY70, Q9NYA1, Q9NYL3

UniProtKB/TrEMBL

B3KVB3, Q53ZR5, Q96HV8

Conserved Domains (1) summary

PLN02958
Location:11 → 345

PLN02958; diacylglycerol kinase/D-erythro-sphingosine kinase
NM_021972.4 → NP_068807.2 sphingosine kinase 1 isoform 1

See identical proteins and their annotated locations for NP_068807.2

Status: REVIEWED

Description

Transcript Variant: This variant (1) has multiple differences in the coding region, compared to variant 2. The resulting protein (isoform 1) has a shorter N-terminus and contains an additional in-frame portion of the 5' coding region, compared to isoform 2.

Source sequence(s)

AK022402, BC009419, BC030553, DC384776

Consensus CDS

CCDS59297.1

UniProtKB/TrEMBL

B3KVB3, Q96HV8

Related

ENSP00000468547.1, ENST00000590959.5

Conserved Domains (1) summary

cl27661
Location:25 → 359

LCB5; Diacylglycerol kinase family enzyme [Lipid transport and metabolism, General function prediction only]
NM_182965.3 → NP_892010.2 sphingosine kinase 1 isoform 2

Status: REVIEWED

Description

Transcript Variant: This variant (2) represents the longest transcript and encodes the longest isoform (2).

Source sequence(s)

AK022402, BC030553, DC384776

Consensus CDS

CCDS11744.1

UniProtKB/TrEMBL

B3KVB3, Q96HV8

Related

ENSP00000313681.3, ENST00000323374.8

Conserved Domains (2) summary

PLN02958
Location:97 → 431

PLN02958; diacylglycerol kinase/D-erythro-sphingosine kinase

pfam00781
Location:102 → 207

DAGK_cat; Diacylglycerol kinase catalytic domain