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ACER3 alkaline ceramidase 3 [ Homo sapiens (human) ]

Gene ID: 55331, updated on 4-Jan-2025

Summary

Official Symbol
ACER3provided by HGNC
Official Full Name
alkaline ceramidase 3provided by HGNC
Primary source
HGNC:HGNC:16066
See related
Ensembl:ENSG00000078124 MIM:617036; AllianceGenome:HGNC:16066
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
APHC; PHCA; PLDECO
Summary
Enables N-acylsphingosine amidohydrolase activity; calcium ion binding activity; and zinc ion binding activity. Involved in several processes, including myelination; positive regulation of cell population proliferation; and sphingolipid metabolic process. Located in Golgi membrane and endoplasmic reticulum membrane. Biomarker of hepatocellular carcinoma and metabolic dysfunction-associated steatohepatitis. [provided by Alliance of Genome Resources, Jan 2025]
Expression
Ubiquitous expression in fat (RPKM 8.3), brain (RPKM 5.5) and 24 other tissues See more
Orthologs
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Genomic context

See ACER3 in Genome Data Viewer
Location:
11q13.5
Exon count:
16
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (76860918..77026797)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (76791211..76957150)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (76571962..76737841)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5299 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:76494061-76494705 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:76497093-76498015 Neighboring gene Sharpr-MPRA regulatory region 10511 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:76505429-76506334 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:76506335-76507240 Neighboring gene TSKU antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3790 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5300 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5301 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5302 Neighboring gene tsukushi, small leucine rich proteoglycan Neighboring gene uncharacterized LOC124902720 Neighboring gene CRISPRi-validated cis-regulatory element chr11.4478 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr11:76550011-76551210 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3791 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3792 Neighboring gene Sharpr-MPRA regulatory region 1403 Neighboring gene NANOG hESC enhancer GRCh37_chr11:76653242-76653743 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:76656496-76657284 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:76657285-76658073 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3793 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr11:76674446-76675645 Neighboring gene ACER antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3794 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3795 Neighboring gene uncharacterized LOC105369399 Neighboring gene UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 6

Genomic regions, transcripts, and products

Expression

  • Project title: Tissue-specific circular RNA induction during human fetal development
  • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
  • BioProject: PRJNA270632
  • Publication: PMID 26076956
  • Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Alkaline ceramidase 3 deficiency
MedGen: C4540358 OMIM: 617762 GeneReviews: Not available
Compare labs

Pathways from PubChem

Interactions

General gene information

Clone Names

  • FLJ11238

Gene Ontology Provided by GOA

Component Evidence Code Pubs
located_in Golgi membrane PubMed 
is_active_in endoplasmic reticulum membrane  
located_in endoplasmic reticulum membrane PubMed 
located_in endoplasmic reticulum membrane  
located_in membrane PubMed 

General protein information

Preferred Names
alkaline ceramidase 3
Names
alkCDase 3
alkaline CDase 3
alkaline dihydroceramidase SB89
alkaline phytoceramidase
phytoceramidase, alkaline
NP_001287882.1
NP_001287883.1
NP_001287884.1
NP_060837.3
XP_011543453.1
XP_011543454.1
XP_016873476.1
XP_047283191.1
XP_054225268.1
XP_054225269.1
XP_054225270.1
XP_054225271.1

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)

  1. NM_001300953.2NP_001287882.1  alkaline ceramidase 3 isoform b

    See identical proteins and their annotated locations for NP_001287882.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks an alternate in-frame exon compared to variant 1. The resulting isoform (b) has the same N- and C-termini but is shorter compared to isoform a.
    Source sequence(s)
    AI885537, AK294978, AP000752, AP002498, BG702017
    Consensus CDS
    CCDS76454.1
    UniProtKB/TrEMBL
    A0A7P0T912, B7Z2Q2
    Related
    ENSP00000436252.1, ENST00000533873.1
    Conserved Domains (1) summary
    pfam05875
    Location:9222
    Ceramidase; Ceramidase
  2. NM_001300954.2NP_001287883.1  alkaline ceramidase 3 isoform c

    See identical proteins and their annotated locations for NP_001287883.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) lacks an internal exon and has another exon in its place compared to variant 1. The resulting isoform (c) is shorter at the N-terminus compared to isoform a. Variants 3 and 4 both encode the same isoform (c).
    Source sequence(s)
    AI885537, AP000752, BC049837, BG702017
    Consensus CDS
    CCDS73352.1
    UniProtKB/TrEMBL
    B7Z2V2
    Related
    ENSP00000431149.1, ENST00000526597.5
    Conserved Domains (1) summary
    pfam05875
    Location:1164
    Ceramidase
  3. NM_001300955.2NP_001287884.1  alkaline ceramidase 3 isoform c

    See identical proteins and their annotated locations for NP_001287884.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) lacks an alternate exon and uses a downstream translation start codon compared to variant 1. The resulting isoform (c) is shorter at the N-terminus compared to isoform a. Variants 3 and 4 both encode the same isoform (c).
    Source sequence(s)
    AI885537, AK316120, AP000752, BG702017
    Consensus CDS
    CCDS73352.1
    UniProtKB/TrEMBL
    B7Z2V2
    Related
    ENSP00000505842.1, ENST00000680583.1
    Conserved Domains (1) summary
    pfam05875
    Location:1164
    Ceramidase
  4. NM_018367.7NP_060837.3  alkaline ceramidase 3 isoform a

    See identical proteins and their annotated locations for NP_060837.3

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (a).
    Source sequence(s)
    AI885537, AK315000, AP000752, AP002498, DB461413
    Consensus CDS
    CCDS8247.1
    UniProtKB/Swiss-Prot
    B2RC99, Q9NUN7
    UniProtKB/TrEMBL
    A0A7P0T912
    Related
    ENSP00000434480.1, ENST00000532485.6
    Conserved Domains (1) summary
    pfam05875
    Location:9259
    Ceramidase

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    76860918..77026797
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011545151.3XP_011543453.1  alkaline ceramidase 3 isoform X1

    UniProtKB/TrEMBL
    A0A7P0T912
    Conserved Domains (1) summary
    pfam05875
    Location:9225
    Ceramidase; Ceramidase
  2. XM_047427235.1XP_047283191.1  alkaline ceramidase 3 isoform X4

    UniProtKB/TrEMBL
    A0A7P0T8K3, E9PLZ9
    Related
    ENSP00000505175.1, ENST00000679866.1
  3. XM_017017987.2XP_016873476.1  alkaline ceramidase 3 isoform X3

    UniProtKB/TrEMBL
    A0A7P0TAD8
    Related
    ENSP00000506160.1, ENST00000681257.1
  4. XM_011545152.3XP_011543454.1  alkaline ceramidase 3 isoform X2

    See identical proteins and their annotated locations for XP_011543454.1

    UniProtKB/TrEMBL
    E9PIN9
    Related
    ENSP00000435733.1, ENST00000534206.5
    Conserved Domains (1) summary
    pfam05875
    Location:1217
    Ceramidase; Ceramidase

RNA

  1. XR_007062489.1 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    76791211..76957150
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054369293.1XP_054225268.1  alkaline ceramidase 3 isoform X1

    UniProtKB/TrEMBL
    A0A7P0T912
  2. XM_054369296.1XP_054225271.1  alkaline ceramidase 3 isoform X4

    UniProtKB/TrEMBL
    E9PLZ9
  3. XM_054369295.1XP_054225270.1  alkaline ceramidase 3 isoform X3

    UniProtKB/TrEMBL
    A0A7P0TAD8
  4. XM_054369294.1XP_054225269.1  alkaline ceramidase 3 isoform X2

    UniProtKB/TrEMBL
    B7Z1R2, E9PIN9

RNA

  1. XR_008488417.1 RNA Sequence

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