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CERS3 ceramide synthase 3 [ Homo sapiens (human) ]

Gene ID: 204219, updated on 3-Oct-2020

Summary

Official Symbol
CERS3provided by HGNC
Official Full Name
ceramide synthase 3provided by HGNC
Primary source
HGNC:HGNC:23752
See related
Ensembl:ENSG00000154227 MIM:615276
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
ARCI9; LASS3
Summary
This gene is a member of the ceramide synthase family of genes. The ceramide synthase enzymes regulate sphingolipid synthesis by catalyzing the formation of ceramides from sphingoid base and acyl-coA substrates. This family member is involved in the synthesis of ceramides with ultra-long-chain acyl moieties (ULC-Cers), important to the epidermis in its role in creating a protective barrier from the environment. The protein encoded by this gene has also been implicated in modification of the lipid structures required for spermatogenesis. Mutations in this gene have been associated with male fertility defects, and epidermal defects, including ichthyosis. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Aug 2015]
Expression
Biased expression in skin (RPKM 15.5), esophagus (RPKM 13.5) and 1 other tissue See more
Orthologs

Genomic context

See CERS3 in Genome Data Viewer
Location:
15q26.3
Exon count:
17
Annotation release Status Assembly Chr Location
109.20200815 current GRCh38.p13 (GCF_000001405.39) 15 NC_000015.10 (100400395..100544982, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (100940600..101084925, complement)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene ADAM metallopeptidase with thrombospondin type 1 motif 17 Neighboring gene uncharacterized LOC107984740 Neighboring gene uncharacterized LOC105371021 Neighboring gene spermatogenesis associated 41 Neighboring gene CERS3 antisense RNA 1 Neighboring gene uncharacterized LOC102723335 Neighboring gene RNA, U6 small nuclear 322, pseudogene Neighboring gene PRKX pseudogene 1

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Autosomal recessive congenital ichthyosis 9 Compare labs
The Contribution of Common Genetic Variation to Nicotine and Cotinine Glucuronidation in Multiple Ethnic/Racial Populations.
GeneReviews: Not available

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Tat tat HIV-1 Tat upregulates the expression of ceramide synthase 3 (CERS3) in human primary T cells PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • MGC27091

Gene Ontology Provided by GOA

Function Evidence Code Pubs
DNA binding IEA
Inferred from Electronic Annotation
more info
 
N-acyltransferase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
sphingosine N-acyltransferase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
sphingosine N-acyltransferase activity IDA
Inferred from Direct Assay
more info
PubMed 
Process Evidence Code Pubs
ceramide biosynthetic process IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
ceramide biosynthetic process IDA
Inferred from Direct Assay
more info
PubMed 
ceramide biosynthetic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
cornification ISS
Inferred from Sequence or Structural Similarity
more info
 
epidermis development ISS
Inferred from Sequence or Structural Similarity
more info
 
keratinocyte differentiation IMP
Inferred from Mutant Phenotype
more info
PubMed 
sphingolipid biosynthetic process TAS
Traceable Author Statement
more info
 
Component Evidence Code Pubs
endoplasmic reticulum IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
endoplasmic reticulum ISS
Inferred from Sequence or Structural Similarity
more info
 
endoplasmic reticulum membrane TAS
Traceable Author Statement
more info
 
integral component of membrane IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
ceramide synthase 3
Names
LAG1 homolog, ceramide synthase 3
LAG1 longevity assurance homolog 3
dihydroceramide synthase 3
sphingosine N-acyltransferase CERS3
NP_001277270.1
NP_001277271.1
NP_001277272.1
NP_001365718.1
NP_849164.2
XP_011519657.1
XP_011519659.1
XP_011519660.1
XP_016877491.1
XP_016877492.1
XP_016877493.1

NCBI Reference Sequences (RefSeq)

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

  1. NG_042826.1 RefSeqGene

    Range
    5038..149326
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001290341.2NP_001277270.1  ceramide synthase 3 isoform 1

    See identical proteins and their annotated locations for NP_001277270.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (1).
    Source sequence(s)
    AC015723, AC027020, BC027616, BC034500, HY237628
    UniProtKB/Swiss-Prot
    Q8IU89
    Conserved Domains (2) summary
    cd00086
    Location:93139
    homeodomain; Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
    pfam03798
    Location:142335
    TRAM_LAG1_CLN8; TLC domain
  2. NM_001290342.2NP_001277271.1  ceramide synthase 3 isoform 2

    See identical proteins and their annotated locations for NP_001277271.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR and the 5' coding region and initiates translation at a downstream start codon, compared to variant 1. Variants 2, 3 and 4 encode the same isoform (2), which has a shorter N-terminus, compared to isoform 1.
    Source sequence(s)
    AC015723, AC027020, BC028703, BC034500, BC034970, HY022150, HY022670
    Consensus CDS
    CCDS10384.1
    UniProtKB/Swiss-Prot
    Q8IU89
    Related
    ENSP00000437640.2, ENST00000538112.6
    Conserved Domains (2) summary
    cd00086
    Location:82128
    homeodomain; Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
    pfam03798
    Location:131324
    TRAM_LAG1_CLN8; TLC domain
  3. NM_001290343.2NP_001277272.1  ceramide synthase 3 isoform 2

    See identical proteins and their annotated locations for NP_001277272.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR and the 5' coding region and initiates translation at a downstream start codon, compared to variant 1. Variants 2, 3 and 4 encode the same isoform (2), which has a shorter N-terminus, compared to isoform 1.
    Source sequence(s)
    AC015723, AC027020, BC034500, BC034970
    Consensus CDS
    CCDS10384.1
    UniProtKB/Swiss-Prot
    Q8IU89
    Conserved Domains (2) summary
    cd00086
    Location:82128
    homeodomain; Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
    pfam03798
    Location:131324
    TRAM_LAG1_CLN8; TLC domain
  4. NM_001378789.1NP_001365718.1  ceramide synthase 3 isoform 2

    Status: REVIEWED

    Source sequence(s)
    AC015723, AC027020
    Conserved Domains (2) summary
    cd00086
    Location:82128
    homeodomain; Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
    pfam03798
    Location:131324
    TRAM_LAG1_CLN8; TLC domain
  5. NM_178842.5NP_849164.2  ceramide synthase 3 isoform 2

    See identical proteins and their annotated locations for NP_849164.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) differs in the 5' UTR and the 5' coding region and initiates translation at a downstream start codon, compared to variant 1. Variants 2, 3 and 4 encode the same isoform (2), which has a shorter N-terminus, compared to isoform 1.
    Source sequence(s)
    AC015723, AC027020, BC034500, BC034970
    Consensus CDS
    CCDS10384.1
    UniProtKB/Swiss-Prot
    Q8IU89
    Related
    ENSP00000284382.4, ENST00000284382.8
    Conserved Domains (2) summary
    cd00086
    Location:82128
    homeodomain; Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
    pfam03798
    Location:131324
    TRAM_LAG1_CLN8; TLC domain

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20200815

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000015.10 Reference GRCh38.p13 Primary Assembly

    Range
    100400395..100544982 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017022004.1XP_016877493.1  ceramide synthase 3 isoform X2

    UniProtKB/Swiss-Prot
    Q8IU89
    Conserved Domains (2) summary
    cd00086
    Location:82128
    homeodomain; Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
    pfam03798
    Location:131324
    TRAM_LAG1_CLN8; TLC domain
  2. XM_017022003.1XP_016877492.1  ceramide synthase 3 isoform X2

    UniProtKB/Swiss-Prot
    Q8IU89
    Conserved Domains (2) summary
    cd00086
    Location:82128
    homeodomain; Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
    pfam03798
    Location:131324
    TRAM_LAG1_CLN8; TLC domain
  3. XM_011521357.2XP_011519659.1  ceramide synthase 3 isoform X1

    See identical proteins and their annotated locations for XP_011519659.1

    Conserved Domains (2) summary
    cd00086
    Location:93139
    homeodomain; Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
    pfam03798
    Location:142335
    TRAM_LAG1_CLN8; TLC domain
  4. XM_011521355.2XP_011519657.1  ceramide synthase 3 isoform X1

    See identical proteins and their annotated locations for XP_011519657.1

    Conserved Domains (2) summary
    cd00086
    Location:93139
    homeodomain; Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
    pfam03798
    Location:142335
    TRAM_LAG1_CLN8; TLC domain
  5. XM_011521358.1XP_011519660.1  ceramide synthase 3 isoform X1

    See identical proteins and their annotated locations for XP_011519660.1

    Conserved Domains (2) summary
    cd00086
    Location:93139
    homeodomain; Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
    pfam03798
    Location:142335
    TRAM_LAG1_CLN8; TLC domain
  6. XM_017022002.1XP_016877491.1  ceramide synthase 3 isoform X1

    Conserved Domains (2) summary
    cd00086
    Location:93139
    homeodomain; Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
    pfam03798
    Location:142335
    TRAM_LAG1_CLN8; TLC domain
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