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    ORMDL1 ORMDL sphingolipid biosynthesis regulator 1 [ Homo sapiens (human) ]

    Gene ID: 94101, updated on 2-Nov-2024

    Summary

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    Official Symbol
    ORMDL1provided by HGNC
    Official Full Name
    ORMDL sphingolipid biosynthesis regulator 1provided by HGNC
    Primary source
    HGNC:HGNC:16036
    See related
    Ensembl:ENSG00000128699 MIM:610073; AllianceGenome:HGNC:16036
    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
    Summary
    Involved in ceramide metabolic process. Acts upstream of or within negative regulation of ceramide biosynthetic process. Located in endoplasmic reticulum membrane. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in spleen (RPKM 13.3), lymph node (RPKM 13.0) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See ORMDL1 in Genome Data Viewer
    Location:
    2q32.2
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (189763859..189784339, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (190253126..190273622, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (190628585..190649065, complement)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105373793 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12172 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16852 Neighboring gene ankyrin and armadillo repeat containing Neighboring gene O-sialoglycoprotein endopeptidase like 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16853 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:190627447-190628193 Neighboring gene OSGEPL1 antisense RNA 1 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:190648352-190649238 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16857 Neighboring gene PMS1 homolog 1, mismatch repair system component Neighboring gene glucosamine-phosphate N-acetyltransferase 1 pseudogene Neighboring gene uncharacterized LOC105373796 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:190727824-190728081

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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

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    Related articles in PubMed

    1. A family of membrane proteins associated with presenilin expression and gamma-secretase function. Araki W, et al. FASEB J, 2008 Mar. PMID 17928364
    2. Expression Patterns and Prognostic Values of ORMDL1 in Different Cancers. Zhu T, et al. Biomed Res Int, 2020. PMID 33145351, Free PMC Article
    3. ORMDL proteins regulate ceramide levels during sterile inflammation. Cai L, et al. J Lipid Res, 2016 Aug. PMID 27313060, Free PMC Article
    4. Mammalian ORMDL proteins mediate the feedback response in ceramide biosynthesis. Siow DL, et al. J Biol Chem, 2012 Nov 23. PMID 23066021, Free PMC Article
    5. Expression of the ORMDLS, modulators of serine palmitoyltransferase, is regulated by sphingolipids in mammalian cells. Gupta SD, et al. J Biol Chem, 2015 Jan 2. PMID 25395622, Free PMC Article

    See all (31) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Expression Patterns and Prognostic Values of ORMDL1 in Different Cancers.
      Title: Expression Patterns and Prognostic Values of ORMDL1 in Different Cancers.
    2. ORMDL1 downregulation modestly increased levels of sphingosine, S1P, and ceramide in HepG2 cells.
      Title: ORMDL proteins regulate ceramide levels during sterile inflammation.
    3. Expression of the ORMDLS, modulators of serine palmitoyltransferase, is regulated by sphingolipids in mammalian cells.
      Title: Expression of the ORMDLS, modulators of serine palmitoyltransferase, is regulated by sphingolipids in mammalian cells.
    4. ORMDL1, ORMDL2 and ORMDL3 mediate the feedback response in ceramide biosynthesis.
      Title: Mammalian ORMDL proteins mediate the feedback response in ceramide biosynthesis.
    5. Adoplin-1/ORMDL-1 displays reduced expression in association with presenilin mutations; Adoplin-1 & two highly homologous genes (adoplin-2, -3) are a gene family that encodes transmembrane proteins that may play roles in gamma-secretase complex maturation
      Title: A family of membrane proteins associated with presenilin expression and gamma-secretase function.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    Genome-wide association of serum bilirubin levels in Korean population.
    EBI GWAS Catalog
    Genome-Wide Association Study Identifies Variants in PMS1 Associated with Serum Ferritin in a Chinese Population.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ44364, DKFZp686G141

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in ceramide metabolic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in ceramide metabolic process IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in intracellular sphingolipid homeostasis IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in motor behavior IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in myelination IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within negative regulation of ceramide biosynthetic process IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in sphingolipid biosynthetic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in sphingomyelin biosynthetic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in endoplasmic reticulum IDA
    Inferred from Direct Assay
    more info
    		  
    located_in endoplasmic reticulum membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of serine palmitoyltransferase complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    ORM1-like protein 1
    Names
    adoplin-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_001128150.2 → NP_001121622.1  ORM1-like protein 1 isoform 1

      See identical proteins and their annotated locations for NP_001121622.1

      Status: VALIDATED

      Source sequence(s)
      AC013468
      Consensus CDS
      CCDS2301.1
      UniProtKB/Swiss-Prot
      B2R8W3, D3DPH9, Q9P0S3
      Related
      ENSP00000376161.3, ENST00000392350.7
      Conserved Domains (1) summary
      pfam04061
      Location:11 → 146
      ORMDL; ORMDL family

    2. NM_001371384.1 → NP_001358313.1  ORM1-like protein 1 isoform 4

      Status: VALIDATED

      Source sequence(s)
      AC013468
      Conserved Domains (1) summary
      pfam04061
      Location:11 → 144
      ORMDL; ORMDL family

    3. NM_001371385.1 → NP_001358314.1  ORM1-like protein 1 isoform 2

      Status: VALIDATED

      Source sequence(s)
      AC013468
      Conserved Domains (1) summary
      pfam04061
      Location:11 → 146
      ORMDL; ORMDL family

    4. NM_001371386.1 → NP_001358315.1  ORM1-like protein 1 isoform 2

      Status: VALIDATED

      Source sequence(s)
      AC013468
      Related
      ENSP00000520902.1, ENST00000850615.1
      Conserved Domains (1) summary
      pfam04061
      Location:11 → 146
      ORMDL; ORMDL family

    5. NM_001371387.1 → NP_001358316.1  ORM1-like protein 1 isoform 3

      Status: VALIDATED

      Source sequence(s)
      AC013468
      UniProtKB/TrEMBL
      A0A1B0GXE7
      Conserved Domains (1) summary
      pfam04061
      Location:11 → 109
      ORMDL; ORMDL family

    6. NM_001371388.1 → NP_001358317.1  ORM1-like protein 1 isoform 3

      Status: VALIDATED

      Source sequence(s)
      AC013468
      UniProtKB/TrEMBL
      A0A1B0GXE7
      Conserved Domains (1) summary
      pfam04061
      Location:11 → 109
      ORMDL; ORMDL family

    7. NM_016467.5 → NP_057551.1  ORM1-like protein 1 isoform 1

      See identical proteins and their annotated locations for NP_057551.1

      Status: VALIDATED

      Source sequence(s)
      AA603217, AC013468, AF395704, AI674061, DB122266
      Consensus CDS
      CCDS2301.1
      UniProtKB/Swiss-Prot
      B2R8W3, D3DPH9, Q9P0S3
      Related
      ENSP00000376160.4, ENST00000392349.9
      Conserved Domains (1) summary
      pfam04061
      Location:11 → 146
      ORMDL; ORMDL family

    RNA

    1. NR_163942.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC013468

    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_000002.12 Reference GRCh38.p14 Primary Assembly

      Range
      189763859..189784339 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047446425.1 → XP_047302381.1  ORM1-like protein 1 isoform X1

      UniProtKB/Swiss-Prot
      B2R8W3, D3DPH9, Q9P0S3

    2. XM_005246970.4 → XP_005247027.1  ORM1-like protein 1 isoform X1

      See identical proteins and their annotated locations for XP_005247027.1

      UniProtKB/Swiss-Prot
      B2R8W3, D3DPH9, Q9P0S3
      Conserved Domains (1) summary
      pfam04061
      Location:11 → 146
      ORMDL; ORMDL family

    3. XM_017005347.2 → XP_016860836.1  ORM1-like protein 1 isoform X1

      UniProtKB/Swiss-Prot
      B2R8W3, D3DPH9, Q9P0S3
      Conserved Domains (1) summary
      pfam04061
      Location:11 → 146
      ORMDL; ORMDL family

    4. XM_047446427.1 → XP_047302383.1  ORM1-like protein 1 isoform X2

      Related
      ENSP00000407234.1, ENST00000442547.5

    5. XM_047446426.1 → XP_047302382.1  ORM1-like protein 1 isoform X2

      Related
      ENSP00000402074.1, ENST00000458355.1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060926.1 Alternate T2T-CHM13v2.0

      Range
      190253126..190273622 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054344633.1 → XP_054200608.1  ORM1-like protein 1 isoform X1

      UniProtKB/Swiss-Prot
      B2R8W3, D3DPH9, Q9P0S3

    2. XM_054344632.1 → XP_054200607.1  ORM1-like protein 1 isoform X1

      UniProtKB/Swiss-Prot
      B2R8W3, D3DPH9, Q9P0S3

    3. XM_054344635.1 → XP_054200610.1  ORM1-like protein 1 isoform X2

    4. XM_054344634.1 → XP_054200609.1  ORM1-like protein 1 isoform X2

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9P0S3.1 GenPept UniProtKB/Swiss-Prot:Q9P0S3

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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