SPHK2 sphingosine kinase 2 [Homo sapiens (human)] - Gene

Summary

Official Symbol: SPHK2provided by HGNC
Official Full Name: sphingosine kinase 2provided by HGNC
Primary source: HGNC:HGNC:18859
See related: Ensembl:ENSG00000063176 MIM:607092; AllianceGenome:HGNC:18859
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: SK 2; SK-2; SPK 2; SPK-2
Summary: This gene encodes one of two sphingosine kinase isozymes that catalyze the phosphorylation of sphingosine into sphingosine 1-phosphate. Sphingosine 1-phosphate mediates many cellular processes including migration, proliferation and apoptosis, and also plays a role in several types of cancer by promoting angiogenesis and tumorigenesis. The encoded protein may play a role in breast cancer proliferation and chemoresistance. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Aug 2011]
Expression: Ubiquitous expression in kidney (RPKM 6.4), duodenum (RPKM 5.5) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 19q13.33

Exon count:: 8

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	19	NC_000019.10 (48619506..48630405)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	19	NC_060943.1 (51613990..51624887)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	19	NC_000019.9 (49122763..49133662)

Chromosome 19 - NC_000019.10 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
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?

YTHDF1-mediated sphingosine kinase 2 upregulation alleviates bupivacaine-induced neurotoxicity via the PI3K/AKT axis.
Title: YTHDF1-mediated sphingosine kinase 2 upregulation alleviates bupivacaine-induced neurotoxicity via the PI3K/AKT axis.
The accumulation of sphingosine kinase 2 disrupts the DNA damage response and promotes resistance to genotoxic agents.
Title: The accumulation of sphingosine kinase 2 disrupts the DNA damage response and promotes resistance to genotoxic agents.
Accumulation of sphingosine kinase 2 protein induces malignant transformation in oral keratinocytes associated with stemness, autophagy, senescence, and proliferation.
Title: Accumulation of sphingosine kinase 2 protein induces malignant transformation in oral keratinocytes associated with stemness, autophagy, senescence, and proliferation.
Inhibition of Sphingosine Kinase 2 Results in PARK2-Mediated Mitophagy and Induces Apoptosis in Multiple Myeloma.
Title: Inhibition of Sphingosine Kinase 2 Results in PARK2-Mediated Mitophagy and Induces Apoptosis in Multiple Myeloma.
Sphingosine kinase 2 regulates insulin receptor trafficking in hepatocytes.
Title: Sphingosine kinase 2 regulates insulin receptor trafficking in hepatocytes.
miR-153-3p Attenuates the Development of Gastric Cancer by Suppressing SphK2.
Title: miR-153-3p Attenuates the Development of Gastric Cancer by Suppressing SphK2.
Enzymatic independent role of sphingosine kinase 2 in regulating the expression of type I interferon during influenza A virus infection.
Title: Enzymatic independent role of sphingosine kinase 2 in regulating the expression of type I interferon during influenza A virus infection.
Loss of sphingosine kinase 2 protects against cisplatin-induced kidney injury.
Title: Loss of sphingosine kinase 2 protects against cisplatin-induced kidney injury.
Upregulated flotillins and sphingosine kinase 2 derail AXL vesicular traffic to promote epithelial-mesenchymal transition.
Title: Upregulated flotillins and sphingosine kinase 2 derail AXL vesicular traffic to promote epithelial-mesenchymal transition.
METTL3-mediated m(6)A methylation of SPHK2 promotes gastric cancer progression by targeting KLF2.
Title: METTL3-mediated m(6)A methylation of SPHK2 promotes gastric cancer progression by targeting KLF2.

Submit: New GeneRIF Correction See all GeneRIFs (83)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease. EBI GWAS Catalog EBI GWAS CatalogPubMed
Large-scale genome-wide association analysis of bipolar disorder identifies a new susceptibility locus near ODZ4. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH47213 (e-PCR)
- UniSTS:52739

RH75877 (e-PCR)
- UniSTS:91408

SHGC-36947 (e-PCR)
- UniSTS:39707

D15S1477 (e-PCR)
- UniSTS:474482

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables ATP binding	IEA Inferred from Electronic Annotation 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 histone binding	IDA Inferred from Direct Assay more info	PubMed
enables lipid kinase activity	TAS Traceable Author Statement more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables small GTPase binding	NAS Non-traceable Author Statement more info	PubMed
enables sphinganine 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 blood vessel development	IEA Inferred from Electronic Annotation more info
involved_in brain development	IEA Inferred from Electronic Annotation more info
involved_in cell population proliferation	IEA Inferred from Electronic Annotation more info
involved_in cellular response to phorbol 13-acetate 12-myristate	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of cell growth	ISS Inferred from Sequence or Structural Similarity more info
involved_in phosphorylation	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of apoptotic process	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of apoptotic process	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of calcium ion import	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of cell population proliferation	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of ceramide biosynthetic process	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of cytokine production involved in immune response	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of interleukin-13 production	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of interleukin-6 production	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of mast cell activation involved in immune response	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of mast cell degranulation	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of protein kinase C signaling	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of tumor necrosis factor production	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of ATP biosynthetic process	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of canonical NF-kappaB signal transduction	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of cytochrome-c oxidase activity	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of reactive oxygen species biosynthetic process	ISS Inferred from Sequence or Structural Similarity more info
involved_in sphinganine-1-phosphate biosynthetic process	IBA Inferred from Biological aspect of Ancestor more info
involved_in sphinganine-1-phosphate biosynthetic process	IDA Inferred from Direct Assay 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	ISS Inferred from Sequence or Structural Similarity more info
involved_in sphingosine-1-phosphate receptor signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in transcription initiation-coupled chromatin remodeling	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
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	PubMed
located_in cytosol	TAS Traceable Author Statement more info
located_in endoplasmic reticulum	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
located_in lysosomal membrane	HDA more info	PubMed
is_active_in membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in membrane	IDA Inferred from Direct Assay more info	PubMed
located_in mitochondrial inner membrane	IEA Inferred from Electronic Annotation more info
located_in mitochondrion	ISS Inferred from Sequence or Structural Similarity more info
located_in nucleoplasm	IDA Inferred from Direct Assay more info
part_of nucleosome	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: sphingosine kinase 2

NP_001191087.1

EC 2.7.1.91

NP_001191088.1

EC 2.7.1.91

NP_001191089.1

EC 2.7.1.91

NP_001230805.1

EC 2.7.1.91

NP_064511.2

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.

Genomic

NG_029867.1 RefSeqGene

Range

5216..16115

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001204158.3 → NP_001191087.1 sphingosine kinase 2 isoform b

See identical proteins and their annotated locations for NP_001191087.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) uses an alternate in-frame splice site in the coding region, compared to variant 1. The encoded isoform (b) is shorter than isoform a.

Source sequence(s)

AK122735, AK300541, DB367710

Consensus CDS

CCDS59404.1

UniProtKB/TrEMBL

B3KV83

Related

ENSP00000470092.1, ENST00000600537.5

Conserved Domains (1) summary

pfam00781
Location:128 → 262

DAGK_cat; Diacylglycerol kinase catalytic domain
NM_001204159.3 → NP_001191088.1 sphingosine kinase 2 isoform a

See identical proteins and their annotated locations for NP_001191088.1

Status: REVIEWED

Description

Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. Variants 1 and 3 both encode the same isoform (a).

Source sequence(s)

AC022154, AF245447, AL136701, DB053266

Consensus CDS

CCDS12727.1

UniProtKB/Swiss-Prot

A0T4C8, B4DU87, Q9BRN1, Q9H0Q2, Q9NRA0, Q9NWU7

UniProtKB/TrEMBL

B3KV83

Related

ENSP00000469158.1, ENST00000598088.5

Conserved Domains (1) summary

pfam00781
Location:187 → 321

DAGK_cat; Diacylglycerol kinase catalytic domain
NM_001204160.3 → NP_001191089.1 sphingosine kinase 2 isoform c

See identical proteins and their annotated locations for NP_001191089.1

Status: REVIEWED

Description

Transcript Variant: This variant (4) differs in the 5' UTR, lacks a portion of the 5' coding region and initiates translation at a downstream, in-frame start codon, compared to variant 1. The encoded isoform (c) has a shorter N-terminus, compared to isoform a.

Source sequence(s)

BC010671

Consensus CDS

CCDS59405.1

UniProtKB/TrEMBL

M0R344

Related

ENSP00000471205.1, ENST00000599748.5

Conserved Domains (1) summary

pfam00781
Location:151 → 285

DAGK_cat; Diacylglycerol kinase catalytic domain
NM_001243876.2 → NP_001230805.1 sphingosine kinase 2 isoform d

See identical proteins and their annotated locations for NP_001230805.1

Status: REVIEWED

Description

Transcript Variant: This variant (5) lacks an exon in the coding region and initiates translation at a downstream, in-frame start codon, compared to variant 1. The encoded isoform (d) has a shorter N-terminus, compared to isoform a.

Source sequence(s)

AK122735, DA926908, DB367710

Consensus CDS

CCDS74414.1

UniProtKB/TrEMBL

E9PCV4

Related

ENSP00000341091.4, ENST00000340932.7

Conserved Domains (2) summary

PLN02958
Location:1 → 175

PLN02958; diacylglycerol kinase/D-erythro-sphingosine kinase

PHA03247
Location:149 → 310

PHA03247; large tegument protein UL36; Provisional
NM_020126.5 → NP_064511.2 sphingosine kinase 2 isoform a

See identical proteins and their annotated locations for NP_064511.2

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a). Variants 1 and 3 both encode the same isoform (a).

Source sequence(s)

BC006161

Consensus CDS

CCDS12727.1

UniProtKB/Swiss-Prot

A0T4C8, B4DU87, Q9BRN1, Q9H0Q2, Q9NRA0, Q9NWU7

UniProtKB/TrEMBL

B3KV83

Related

ENSP00000245222.3, ENST00000245222.9

Conserved Domains (1) summary

pfam00781
Location:187 → 321

DAGK_cat; Diacylglycerol kinase catalytic domain