Gene detail

Detailed information of FUN_003375-T1 in Dendrogyra cylindrus

Genomic Location: contig_3:4899018...4910592
NR annotation: KAJ7382586.1, Sphingosine kinase 1 [Desmophyllum pertusum]
Species Dendrogyra cylindrus · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

FUN_003375-T1

GTAGCGAGGTCTCTAGTGAGCAATCGAATGGAGGTCGTCAGTCAGCCGGTCAGCATATTTTTTTGATAATCATGGCGGATACAGAAGAAGCGGAGATCCTTGGCGGACAATTTGAACTTCTCCCGGCGAAAAAGTTATTCTTCGTTAGCCTTTCGAGGAAATCTTTCACTTACAGGAAGGGCGCAGAAGGTTGTTGTCCGTGTGTTGGAAAGCAGCGCTCCGCGTCAACAGTGACGACGAATTTGACTGATATTTACGGTGCGAAGGCGTATCGAGGAGCGGAGGACGATCCTGCCGCTTATTTTCAAGTGTATTCTTGTCcagtttttgaaaagaaaagggTCAGACAGAAAATTTGCTTTAAAGTTGTATCTTCTGATTGCGAAGCGTCGAATGTCGCCATAGCTGAACAATGGGTTCGAACCATTTTATGGTTGATCAAGGAACCGGAAAAGAATTTCAATGACATTCAAGAAGAGGGGACCTTGCCATCTTCCCGCAAACTGCTGATACTCATCAACCCATTTAGTGGATCTGGGAAAAGTTTAAAAATCTTTTATGACAAAGTAGAGCCAATGTTGAATGAAGCTGAAATTGAATTTAATGCAGTGACGACAGAGTATGCTGGCCATGCAGTTGAGATTATGTTGTCTATGAACCTTCTTCATGTTGACGGGATTGTCATTTGCTCTGGAGATGGTCTAGTCTATGAGGTTATCAATGGCCTGATGAAGCGTCCTGATTGGGAGGCTGCAATAAACATTCCACTGGGCGTCATTCCGACAGGTTCTGGGAATGCACTTTGTCTTTCTGCCCTCCATGCTACTGGGGAGCCATTTGATCTTACAAGTGCAATTTTTGGTGTCATACGTGGAAATCTACTTGATTTGGACATCTGTTCTGTGGTGACACCGACAGAGAAGCTGTATGCATTTCTTTCAGTGACATGGGGATTGGTCTCTGATGTCGACATTGAGTCAGAGAAGTACAGATGTATGGGGGAGACAAGATTTCTTATTGGCACAATAGAAAGAATTATTGGGCTGCGTAAATACCGAGGGCGACTCTCCTATTTGCCAGCAGAAATTACACATAGTGGAGAAAATAATCTGGGTTATGATTCTAGCCCGAAAGAAGTGGGCCGCAGAGATACAGCTGAGGGCAACACGAGCTCCACCGTAGATCACAGGGAAAGCTGTCAAGGTAACAAGACAATCAGTGACCTACACCATAAAGACAGTAATGTAGGTTCACTCTGTAATGGGCCTTCAGATAATTTGCTACCTCCTCTAAGTTCGGAGCTGCCACCCAGCTGGAAGGTGGAGGAAGGCGAGTTCATTCTTGGCTGTCCAGTGTTTCTGAGTCACCTGGGCACTGATCTCATGGCAAACCCTGAAGGAAAGTTCGGAGATGGCTTGATGGGTATCTTTTATGTGAAATCTGGAACTGGTAGAATGGCACTTTTGGATCTGTTTGGAAAAATGAAGGATGGATCTCATGTTCTTAGCCATCACGTTGAGTATGTCAAGGCATTTGCTTTCCGTTTAGAACCAGATACAAGTCAGCCAGGAACCATAGCAGTTGATGGAGAGAAAATCGATTATGTGCCAATTCAAGGTCAAATACACAAATCTCTTGGAAAGTTAATGTGTGTGACACCACCTCAAAGTTAGTGAATGATTTAATTCATAAGTTTAAATTCATTTATGAATATTTGACAGCTGTATGTACTATAAGTACATTATACTCTGTACAAttctttttattaaaatatGTAGTGGAAATTAAAGGGTATCTCAATTTTTATCCTTTGTCATGAACTTATTAGCAAATTGAGGTAATGAACAGagactcataaggagttgaaacgtgtaacacaTGTTCAGTGTTcgcatattcagttttgccaagtaccatatttggcaacacagaGTTTGTACGCAAATGATTTACATACGTAAtgacacgcaacaaaatttcaGTTTTGCGATAACTCACTTGAATTTCGACCAAAATGCCGTAagttactcacagaaactaaagaaattcatttgtatcaagtgaagttctccagactactgaatgacgacgtaacagaagaatttaaccaaatttaactttattcaacccaaattgttcaaaaacaagattatgccatttagcgcgagctagcatgccctgtgaatttaatccaggtgttgcaattttgattggttgatttttttctcgtgattttcctattatggtacttaatgaaaacgaatgttcaaacgctttgtacaatgcgaatcatagggagttacacgtttcaacccttatgggtttttGCAGTGAAATATAAGATACTACTAAAGGTGCAGTTGCTGTAGTTCAATTATCTTAGCGCAGCACAAACAGTCTATTTCTATATATCTTTTAATTCTATAAAATGTTTTGGTTTCCTATAAGAGTAAATTGATTGTAGAGTTTTAGCTATCTACCATGAAAGTTCCTTAGTCTGATCCATATTATGGATCATCTAATCTTGGACAAATGaagtgaaaaattaagaccaccactcccccatttcaatgatggaaAAAATGGCACATTTTGGttttagtgtgaattcatcATTCATTTAGGGGAAGTTCATTTCTCTTTGTATTTTGCTTTTAGGGTTAGTGGTTTCAATAATTAACAAGCCCTCTGCATGCTTTGCTGGCCTgtgtaatttttatttatttggcaTGCCCACACTGAGCGCTATCATACCATAGAGACTGGCATAATGTACCTCAGGCATGCAGGAAGGCAGGTCATCatgataataatttattaaacttaatttattttaattctaatatttaacaattagattatgagctcgagatttctatgaggtgatagttcaGATGAGgtcgcaggccgaatcaactatcacctcatagaaattgagagcgaataatctaattgtttagtagaattctgactgaaataaacgcaaataacggtttctaattattttcctacgcattatcgaacttaacgttttaacaaaatcgcacgcattgaattagccttggtaaatttgcagttgtttacatgcatgcacccgttaatttcaagcttttaaagtcaagaaaccgctaatgtccttcttttagtcttctcgcaaattttattatccatttacatttaaacttccttccaaaacttcgggaAAACGACAAAAacatcgcattttgtggacgaccttcggcaactgcacactaatggctgatagtgttcaatagctcagccaatcacattgcagcatttgcattagtgtactagtagaattctactaataataATAGAGAACAGTGGGAGAACTTCTTGATGTACAAGCATGTAAACATATTTGGTGTTGAAAGCTACTAATTTTTTAAcataatgtgcagttccagaaaatatccatacccaccccatggaaggtcaatggaaattccgagggggtgg

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q9NRA0	Sphingosine kinase 2 OS=Homo sapiens OX=9606 GN=SPHK2 PE=1 SV=2
Q9JIA7	Sphingosine kinase 2 OS=Mus musculus OX=10090 GN=Sphk2 PE=1 SV=2
Q9NYA1	Sphingosine kinase 1 OS=Homo sapiens OX=9606 GN=SPHK1 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0007176 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF19279 all species →	YegS_C	YegS C-terminal NAD kinase beta sandwich-like domain	Domain	Interproscan
PF00781 all species →	DAGK_cat	Diacylglycerol kinase catalytic domain	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR017438 all species →	Homologous_superfamily	Inorganic polyphosphate/ATP-NAD kinase, N-terminal	Interproscan
IPR001206 all species →	Domain	Diacylglycerol kinase, catalytic domain	Interproscan
IPR045540 all species →	Domain	YegS/DAGK, C-terminal domain	Interproscan
IPR050187 all species →	Family	Lipid Phosphate Formation and Regulation	Interproscan
IPR016064 all species →	Homologous_superfamily	NAD kinase/diacylglycerol kinase-like domain superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR12358 all species →	SPHINGOSINE KINASE	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0016301 all species →	Molecular Function	kinase activity	Interproscan
GO:0001727 all species →	Molecular Function	lipid kinase activity	Interproscan
GO:0005737 all species →	Cellular Component	cytoplasm	Interproscan
GO:0006665 all species →	Biological Process	sphingolipid metabolic process	Interproscan
GO:0016020 all species →	Cellular Component	membrane	Interproscan
GO:0016310 all species →	Biological Process	phosphorylation	Interproscan
GO:0017050 all species →	Molecular Function	D-erythro-sphingosine kinase activity	Interproscan
GO:0043231 all species →	Cellular Component	intracellular membrane-bounded organelle	Interproscan
GO:0046512 all species →	Biological Process	sphingosine biosynthetic process	Interproscan

Search by domain instead of by gene. Any accession above (InterPro, Pfam, PANTHER, GO, KEGG) can be used as a query on the Functional Domain Search page, which searches all 148 annotated genomes at once.

KEGG pathway

KO	Enzyme	Enzyme ID	Pathway	Map ID	Source
K04718	SPHK; sphingosine kinase	EC:2.7.1.91	Tuberculosis	ko05152	deepkoala

Searching by KO or pathway ID across all species is available on the KEGG Pathway page.

Co-expression network

Genes whose expression across the transcriptome samples of Dendrogyra cylindrus tracks this one. Counts are over the whole network; the network view itself draws at most 100 partners per query gene (CNIDO_NET_TOP_K), so a hub gene can show fewer edges than the number below.

No co-expression network has been built for this species, so this gene has no partners to show. Networks are available for the species listed on the Network Analysis page.

Single-cell expression

Whether this gene can be visualised in the single-cell atlases of Dendrogyra cylindrus, and in which cell types it is a marker. Expression is stored per cell, so the violin plot and the cell-type means are computed in the viewer — open a dataset to see them.

No single-cell dataset has been published for this species. The atlases that do exist are listed in the Cell Atlas.

Epigenetic marks

Chromatin and DNA-methylation data covering this gene. Peak calls are listed per sample with the genomic region the peak falls in; DNA methylation is listed as sample availability only, because those tables are queried by the DNA Methylation page itself.

No epigenomic data has been deposited for this species. The assays that exist across the site are described in the Epigenomic Data module.

What you can do with this gene

Every tool below opens with this gene already entered, so you land on the analysis rather than on an empty form. Links open in a new tab.

Analysis	What it does	Status
Primer design	Design PCR / qPCR primers on this gene’s sequence with the published primer3 settings. Opens with the primers already computed.	template found	open →
BLAST	Search this gene’s sequence against the CnidoSite BLAST databases. The query is filled in and the species’ database is preselected — press Run to start.	template found	open →
Expression heatmap	Draw this gene’s expression as a heatmap across all RNA-seq samples, and compare it with the genes you add next to it.	no expression matrix	–
Gene family / orthogroup	Look this gene up in the single-copy orthogroups built from the high-quality cnidarian genomes, and see which other species carry an orthologue.		open →
Gene set analysis	Start a gene-set enrichment analysis with this gene as the seed list. Add more genes on that page before running it.		open →