Human Gene ACER3 (ENST00000532485.6_4) from GENCODE V47lift37
  Description: alkaline ceramidase 3, transcript variant 1 (from RefSeq NM_018367.7)
Gencode Transcript: ENST00000532485.6_4
Gencode Gene: ENSG00000078124.13_9
Transcript (Including UTRs)
   Position: hg19 chr11:76,571,962-76,737,841 Size: 165,880 Total Exon Count: 11 Strand: +
Coding Region
   Position: hg19 chr11:76,572,021-76,731,371 Size: 159,351 Coding Exon Count: 11 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr11:76,571,962-76,737,841)mRNA (may differ from genome)Protein (267 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: ACER3_HUMAN
DESCRIPTION: RecName: Full=Alkaline ceramidase 3; Short=AlkCDase 3; Short=Alkaline CDase 3; EC=3.5.1.-; AltName: Full=Alkaline dihydroceramidase SB89; AltName: Full=Alkaline phytoceramidase; Short=aPHC;
FUNCTION: Hydrolyzes only phytoceramide into phytosphingosine and free fatty acid. Does not have reverse activity.
ENZYME REGULATION: Activated by Ca(2+) and inhibited by Zn(2+).
SUBCELLULAR LOCATION: Endoplasmic reticulum membrane; Multi-pass membrane protein. Golgi apparatus membrane; Multi-pass membrane protein.
TISSUE SPECIFICITY: Ubiquitously expressed. Highest expression in placenta.
SIMILARITY: Belongs to the alkaline ceramidase family.

-  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


-  MalaCards Disease Associations
  MalaCards Gene Search: ACER3
Diseases sorted by gene-association score: farber lipogranulomatosis (12), partial fetal alcohol syndrome (12), corneal dystrophy, posterior amorphous (8)

-  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: 7.56 RPKM in Brain - Spinal cord (cervical c-1)
Total median expression: 169.08 RPKM



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

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -27.5059-0.466 Picture PostScript Text
3' UTR -1837.706470-0.284 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
IPR008901 - Ceramidase

Pfam Domains:
PF05875 - Ceramidase

ModBase Predicted Comparative 3D Structure on Q9NUN7
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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 orthologNo orthologNo orthologNo orthologGenome Browser
Gene DetailsGene Details   Gene Details
Gene SorterGene Sorter   Gene Sorter
 RGDEnsembl  SGD
     Protein Sequence
     Alignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0016787 hydrolase activity
GO:0016811 hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides
GO:0070774 phytoceramidase activity

Biological Process:
GO:0006672 ceramide metabolic process
GO:0008284 positive regulation of cell proliferation
GO:0030148 sphingolipid biosynthetic process
GO:0046512 sphingosine biosynthetic process
GO:0071602 phytosphingosine biosynthetic process

Cellular Component:
GO:0000139 Golgi membrane
GO:0005783 endoplasmic reticulum
GO:0005789 endoplasmic reticulum membrane
GO:0005794 Golgi apparatus
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0030173 integral component of Golgi membrane
GO:0030176 integral component of endoplasmic reticulum membrane


-  Descriptions from all associated GenBank mRNAs
  AK315000 - Homo sapiens cDNA, FLJ95927, Homo sapiens phytoceramidase, alkaline (PHCA), mRNA.
AF327353 - Homo sapiens alkaline dihydroceramidase SB89 mRNA, complete cds.
AF214454 - Homo sapiens alkaline phytoceramidase (APHC) mRNA, complete cds.
AK308856 - Homo sapiens cDNA, FLJ98897.
AK002100 - Homo sapiens cDNA FLJ11238 fis, clone PLACE1008532.
AK316120 - Homo sapiens cDNA, FLJ79019 complete cds, highly similar to Alkaline phytoceramidase (EC 3.5.1.-).
AK295327 - Homo sapiens cDNA FLJ57307 complete cds, highly similar to Alkaline phytoceramidase (EC 3.5.1.-).
AK295142 - Homo sapiens cDNA FLJ57303 complete cds, highly similar to Alkaline phytoceramidase (EC 3.5.1.-).
AK294978 - Homo sapiens cDNA FLJ50957 complete cds, highly similar to Alkaline phytoceramidase (EC 3.5.1.-).
BC063034 - Homo sapiens phytoceramidase, alkaline, mRNA (cDNA clone IMAGE:5193732).
BC049837 - Homo sapiens phytoceramidase, alkaline, mRNA (cDNA clone IMAGE:5214265), partial cds.
AK293800 - Homo sapiens cDNA FLJ51673 complete cds, highly similar to Alkaline phytoceramidase (EC 3.5.1.-).
BC073853 - Homo sapiens alkaline ceramidase 3, mRNA (cDNA clone MGC:90228 IMAGE:3867010), complete cds.
CU687264 - Synthetic construct Homo sapiens gateway clone IMAGE:100022762 5' read PHCA mRNA.
HQ447508 - Synthetic construct Homo sapiens clone IMAGE:100070845; CCSB014391_03 phytoceramidase, alkaline (PHCA) gene, encodes complete protein.
KJ899127 - Synthetic construct Homo sapiens clone ccsbBroadEn_08521 ACER3 gene, encodes complete protein.
JD125236 - Sequence 106260 from Patent EP1572962.
AK090589 - Homo sapiens cDNA FLJ33270 fis, clone ASTRO2007643.
JD443656 - Sequence 424680 from Patent EP1572962.
JD090076 - Sequence 71100 from Patent EP1572962.
JD546827 - Sequence 527851 from Patent EP1572962.
JD499297 - Sequence 480321 from Patent EP1572962.
JD241344 - Sequence 222368 from Patent EP1572962.
JD467223 - Sequence 448247 from Patent EP1572962.
JD067846 - Sequence 48870 from Patent EP1572962.
JD091348 - Sequence 72372 from Patent EP1572962.
JD528006 - Sequence 509030 from Patent EP1572962.
JD528086 - Sequence 509110 from Patent EP1572962.
JD197360 - Sequence 178384 from Patent EP1572962.
JD516143 - Sequence 497167 from Patent EP1572962.
JD515644 - Sequence 496668 from Patent EP1572962.
JD052350 - Sequence 33374 from Patent EP1572962.
JD359662 - Sequence 340686 from Patent EP1572962.
JD103768 - Sequence 84792 from Patent EP1572962.
JD197157 - Sequence 178181 from Patent EP1572962.
JD434440 - Sequence 415464 from Patent EP1572962.
JD330207 - Sequence 311231 from Patent EP1572962.
JD506735 - Sequence 487759 from Patent EP1572962.
JD233892 - Sequence 214916 from Patent EP1572962.
JD238762 - Sequence 219786 from Patent EP1572962.
JD088505 - Sequence 69529 from Patent EP1572962.
JD561225 - Sequence 542249 from Patent EP1572962.
JD166333 - Sequence 147357 from Patent EP1572962.
JD285063 - Sequence 266087 from Patent EP1572962.
JD046568 - Sequence 27592 from Patent EP1572962.
JD410797 - Sequence 391821 from Patent EP1572962.
JD370255 - Sequence 351279 from Patent EP1572962.
JD432428 - Sequence 413452 from Patent EP1572962.
JD481446 - Sequence 462470 from Patent EP1572962.
JD212297 - Sequence 193321 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q9NUN7 (Reactome details) participates in the following event(s):

R-HSA-428262 phytoceramide + H2O => stearate + phytosphingosine
R-HSA-1660661 Sphingolipid de novo biosynthesis
R-HSA-428157 Sphingolipid metabolism
R-HSA-556833 Metabolism of lipids
R-HSA-1430728 Metabolism

-  Other Names for This Gene
  Alternate Gene Symbols: ACER3_HUMAN, APHC, B2RC99, ENST00000532485.1, ENST00000532485.2, ENST00000532485.3, ENST00000532485.4, ENST00000532485.5, NM_018367, PHCA, Q9NUN7, uc324kfe.1, uc324kfe.2
UCSC ID: ENST00000532485.6_4
RefSeq Accession: NM_018367.7
Protein: Q9NUN7 (aka ACER3_HUMAN)

-  Gene Model Information
  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.