Human Gene CERK (uc003bia.3)
  Description: Homo sapiens ceramide kinase (CERK), mRNA.
RefSeq Summary (NM_022766): CERK converts ceramide to ceramide 1-phosphate (C1P), a sphingolipid metabolite. Both CERK and C1P have been implicated in various cellular processes, including proliferation, apoptosis, phagocytosis, and inflammation (Kim et al., 2006 [PubMed 16488390]).[supplied by OMIM, Mar 2008]. Sequence Note: The RefSeq transcript and protein were derived from genomic sequence to make the sequence consistent with the reference genome assembly. The genomic coordinates used for the transcript record were based on alignments.
Transcript (Including UTRs)
   Position: hg19 chr22:47,080,307-47,134,152 Size: 53,846 Total Exon Count: 13 Strand: -
Coding Region
   Position: hg19 chr22:47,083,031-47,134,045 Size: 51,015 Coding Exon Count: 13 

Page IndexSequence and LinksUniProtKB CommentsPrimersGenetic AssociationsMalaCards
CTDGene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein Structure
Other SpeciesGO AnnotationsmRNA DescriptionsPathwaysOther NamesModel Information
Methods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr22:47,080,307-47,134,152)mRNA (may differ from genome)Protein (537 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMalacards
MGIneXtProtOMIMPubMedReactomeTreefam
UniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: CERK1_HUMAN
DESCRIPTION: RecName: Full=Ceramide kinase; Short=hCERK; EC=2.7.1.138; AltName: Full=Acylsphingosine kinase; AltName: Full=Lipid kinase 4; Short=LK4;
FUNCTION: Catalyzes specifically the phosphorylation of ceramide to form ceramide 1-phosphate. Acts efficiently on natural and analog ceramides (C6, C8, C16 ceramides, and C8-dihydroceramide), to a lesser extent on C2-ceramide and C6-dihydroceramide, but not on other lipids, such as various sphingosines. Binds phosphoinositides.
CATALYTIC ACTIVITY: ATP + ceramide = ADP + ceramide 1-phosphate.
COFACTOR: Calcium.
COFACTOR: Magnesium.
ENZYME REGULATION: Inhibited by sulfatide.
BIOPHYSICOCHEMICAL PROPERTIES: pH dependence: Optimum pH is 6.0-7.5;
SUBCELLULAR LOCATION: Cytoplasm. Membrane; Peripheral membrane protein.
TISSUE SPECIFICITY: High level expression in heart, brain, skeletal muscle, kidney and liver; moderate in peripheral blood leukocytes and thymus; very low in spleen, small intestine, placenta and lung.
SIMILARITY: Contains 1 DAGKc domain.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): CERK
CDC HuGE Published Literature: CERK

-  MalaCards Disease Associations
  MalaCards Gene Search: CERK
Diseases sorted by gene-association score: retinitis pigmentosa 26 (13), retinitis pigmentosa (2)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 47.28 RPKM in Pituitary
Total median expression: 716.86 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -62.20107-0.581 Picture PostScript Text
3' UTR -969.852724-0.356 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR001206 - Diacylglycerol_kinase_cat_dom
IPR001849 - Pleckstrin_homology

Pfam Domains:
PF00781 - Diacylglycerol kinase catalytic domain

ModBase Predicted Comparative 3D Structure on Q8TCT0
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologGenome BrowserGenome BrowserGenome BrowserNo ortholog
Gene Details  Gene DetailsGene Details 
Gene Sorter  Gene SorterGene Sorter 
  EnsemblFlyBaseWormBase 
  Protein SequenceProtein SequenceProtein Sequence 
  AlignmentAlignmentAlignment 

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000166 nucleotide binding
GO:0000287 magnesium ion binding
GO:0001729 ceramide kinase activity
GO:0003951 NAD+ kinase activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0016301 kinase activity
GO:0016740 transferase activity

Biological Process:
GO:0006672 ceramide metabolic process
GO:0006687 glycosphingolipid metabolic process
GO:0008152 metabolic process
GO:0016310 phosphorylation
GO:0046834 lipid phosphorylation

Cellular Component:
GO:0005737 cytoplasm
GO:0005886 plasma membrane
GO:0016020 membrane
GO:0016021 integral component of membrane


-  Descriptions from all associated GenBank mRNAs
  BC008382 - Homo sapiens, clone IMAGE:3827158, mRNA.
AL137600 - Homo sapiens mRNA; cDNA DKFZp434E0211 (from clone DKFZp434E0211).
AK026892 - Homo sapiens cDNA: FLJ23239 fis, clone COL01248.
AL832794 - Homo sapiens mRNA; cDNA DKFZp667I1123 (from clone DKFZp667I1123).
BC004278 - Homo sapiens ceramide kinase, mRNA (cDNA clone IMAGE:3615986), complete cds.
AB051433 - Homo sapiens mRNA for KIAA1646 protein, partial cds.
AK025083 - Homo sapiens cDNA: FLJ21430 fis, clone COL04210.
AB079066 - Homo sapiens cerk mRNA for ceramide kinase, complete cds.
JD541491 - Sequence 522515 from Patent EP1572962.
JD363535 - Sequence 344559 from Patent EP1572962.
JD478882 - Sequence 459906 from Patent EP1572962.
JD349294 - Sequence 330318 from Patent EP1572962.
JD457901 - Sequence 438925 from Patent EP1572962.
JD215387 - Sequence 196411 from Patent EP1572962.
BC108712 - Homo sapiens ceramide kinase, mRNA (cDNA clone IMAGE:6140739), complete cds.
JD117013 - Sequence 98037 from Patent EP1572962.
JD117014 - Sequence 98038 from Patent EP1572962.
JD117015 - Sequence 98039 from Patent EP1572962.
JD517516 - Sequence 498540 from Patent EP1572962.
JD240824 - Sequence 221848 from Patent EP1572962.
JD366386 - Sequence 347410 from Patent EP1572962.
JD169115 - Sequence 150139 from Patent EP1572962.
JD385136 - Sequence 366160 from Patent EP1572962.
JD143503 - Sequence 124527 from Patent EP1572962.
JD456404 - Sequence 437428 from Patent EP1572962.
JD157098 - Sequence 138122 from Patent EP1572962.
JD105443 - Sequence 86467 from Patent EP1572962.
JD514224 - Sequence 495248 from Patent EP1572962.
JD558537 - Sequence 539561 from Patent EP1572962.
JD564573 - Sequence 545597 from Patent EP1572962.
JD070918 - Sequence 51942 from Patent EP1572962.
JD027862 - Sequence 8886 from Patent EP1572962.
JD076579 - Sequence 57603 from Patent EP1572962.
JD467374 - Sequence 448398 from Patent EP1572962.
JD424328 - Sequence 405352 from Patent EP1572962.
JD342536 - Sequence 323560 from Patent EP1572962.
JD246714 - Sequence 227738 from Patent EP1572962.
JD427289 - Sequence 408313 from Patent EP1572962.
JD270399 - Sequence 251423 from Patent EP1572962.
JD162445 - Sequence 143469 from Patent EP1572962.
JD163338 - Sequence 144362 from Patent EP1572962.
JD528747 - Sequence 509771 from Patent EP1572962.
JD200697 - Sequence 181721 from Patent EP1572962.
JD479932 - Sequence 460956 from Patent EP1572962.
JD043293 - Sequence 24317 from Patent EP1572962.
DQ579200 - Homo sapiens piRNA piR-47312, complete sequence.
JD279498 - Sequence 260522 from Patent EP1572962.
JD064159 - Sequence 45183 from Patent EP1572962.
JD085756 - Sequence 66780 from Patent EP1572962.
JD535030 - Sequence 516054 from Patent EP1572962.
JD476418 - Sequence 457442 from Patent EP1572962.
JD088790 - Sequence 69814 from Patent EP1572962.
CR457365 - Homo sapiens full open reading frame cDNA clone RZPDo834B1210D for gene CERK, ceramide kinase; complete cds, incl. stopcodon.
CU678652 - Synthetic construct Homo sapiens gateway clone IMAGE:100018548 5' read CERK mRNA.
JD461038 - Sequence 442062 from Patent EP1572962.
JD502520 - Sequence 483544 from Patent EP1572962.
JD296003 - Sequence 277027 from Patent EP1572962.
JD218705 - Sequence 199729 from Patent EP1572962.
JD284335 - Sequence 265359 from Patent EP1572962.
JD467655 - Sequence 448679 from Patent EP1572962.
JD303032 - Sequence 284056 from Patent EP1572962.
JD310925 - Sequence 291949 from Patent EP1572962.
JD550011 - Sequence 531035 from Patent EP1572962.
JD086269 - Sequence 67293 from Patent EP1572962.
JD424221 - Sequence 405245 from Patent EP1572962.
JD479977 - Sequence 461001 from Patent EP1572962.
JD217011 - Sequence 198035 from Patent EP1572962.
JD307634 - Sequence 288658 from Patent EP1572962.
JD287398 - Sequence 268422 from Patent EP1572962.
JD293875 - Sequence 274899 from Patent EP1572962.
JD087279 - Sequence 68303 from Patent EP1572962.
JD429807 - Sequence 410831 from Patent EP1572962.
JD477287 - Sequence 458311 from Patent EP1572962.
AJ457828 - Homo sapiens mRNA for putative lipid kinase (LK4 gene).
JD406150 - Sequence 387174 from Patent EP1572962.
AK291476 - Homo sapiens cDNA FLJ77308 complete cds, highly similar to Homo sapiens ceramide kinase (CERK), transcript variant 1, mRNA.
BC067255 - Homo sapiens ceramide kinase, mRNA (cDNA clone IMAGE:6185601), complete cds.
BC126940 - Homo sapiens ceramide kinase, mRNA (cDNA clone MGC:141854 IMAGE:40084110), complete cds.
CR456404 - Homo sapiens bK29F11.1 full length open reading frame (ORF) cDNA clone (cDNA clone C22ORF:pGEM.bK29F11.1).
CU012949 - Homo sapiens CERK, mRNA (cDNA clone IMAGE:100000113), complete cds, with stop codon, in Gateway system.
AB462977 - Synthetic construct DNA, clone: pF1KA1646, Homo sapiens CERK gene for ceramide kinase, without stop codon, in Flexi system.
CU013237 - Homo sapiens CERK, mRNA (cDNA clone IMAGE:100000017), complete cds, without stop codon, in Gateway system.
LF212623 - JP 2014500723-A/20126: Polycomb-Associated Non-Coding RNAs.
JD405712 - Sequence 386736 from Patent EP1572962.
JD128966 - Sequence 109990 from Patent EP1572962.
JD458351 - Sequence 439375 from Patent EP1572962.
MA448200 - JP 2018138019-A/20126: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa00600 - Sphingolipid metabolism

Reactome (by CSHL, EBI, and GO)

Protein Q8TCT0 (Reactome details) participates in the following event(s):

R-HSA-1638845 CERK phosphorylates CERA to form C1P
R-HSA-1660662 Glycosphingolipid metabolism
R-HSA-428157 Sphingolipid metabolism
R-HSA-556833 Metabolism of lipids
R-HSA-1430728 Metabolism

-  Other Names for This Gene
  Alternate Gene Symbols: A0JNT4, A8K611, CERK1_HUMAN, KIAA1646, NM_022766, NP_073603, Q8TCT0, Q9BYB3, Q9UGE5
UCSC ID: uc003bia.3
RefSeq Accession: NM_022766
Protein: Q8TCT0 (aka CERK1_HUMAN or CEK1_HUMAN)
CCDS: CCDS14077.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_022766.5
exon count: 13CDS single in 3' UTR: no RNA size: 4445
ORF size: 1614CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 3428.00frame shift in genome: no % Coverage: 100.00
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.