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OLFM3 olfactomedin 3 [ Homo sapiens (human) ]

Gene ID: 118427, updated on 2-Nov-2024

Summary

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Official Symbol
OLFM3provided by HGNC
Official Full Name
olfactomedin 3provided by HGNC
Primary source
HGNC:HGNC:17990
See related
Ensembl:ENSG00000118733 MIM:607567; AllianceGenome:HGNC:17990
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
NOE3; NOELIN3; OPTIMEDIN
Summary
Predicted to be involved in signal transduction. Predicted to be located in Golgi apparatus; extracellular region; and synapse. Predicted to be part of AMPA glutamate receptor complex. Predicted to be active in extracellular space. [provided by Alliance of Genome Resources, Nov 2024]
Expression
Biased expression in brain (RPKM 5.4) and adrenal (RPKM 0.4) See more
Orthologs
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Genomic context

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See OLFM3 in Genome Data Viewer
Location:
1p21.1
Exon count:
10
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (101802560..101996926, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (101651747..101846150, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (102268116..102462482, complement)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 1709 Neighboring gene RNA, U6 small nuclear 965, pseudogene Neighboring gene ribosomal protein SA pseudogene 19 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr1:102308332-102309235 Neighboring gene NANOG hESC enhancer GRCh37_chr1:102312328-102312832 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:102334091-102334592 Neighboring gene RNA, U6 small nuclear 352, pseudogene Neighboring gene DnaJ heat shock protein family (Hsp40) member A1 pseudogene 5 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr1:102372718-102373384 Neighboring gene meiotic recombination hotspot Q Neighboring gene uncharacterized LOC107985095 Neighboring gene uncharacterized LOC124904645

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 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. Olfactomedin III expression contributes to anoikis-resistance in clonal variants of a human lung squamous carcinoma cell line. Keenan J, et al. Exp Cell Res, 2012 Mar 10. PMID 22281030
  2. An integrative study of the genetic, social and environmental determinants of chronic kidney disease characterized by tubulointerstitial damages in the North Central Region of Sri Lanka. Nanayakkara S, et al. J Occup Health, 2014. PMID 24351856
  3. Optimedin: a novel olfactomedin-related protein that interacts with myocilin. Torrado M, et al. Hum Mol Genet, 2002 May 15. PMID 12019210
  4. The Optimedin gene is a downstream target of Pax6. Grinchuk O, et al. J Biol Chem, 2005 Oct 21. PMID 16115881
  5. Molecular genetics of successful smoking cessation: convergent genome-wide association study results. Uhl GR, et al. Arch Gen Psychiatry, 2008 Jun. PMID 18519826, Free PMC Article

See all (20) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. This is the first instance of OLFM3 being linked with anoikis resistance in a human cancer cell line
    Title: Olfactomedin III expression contributes to anoikis-resistance in clonal variants of a human lung squamous carcinoma cell line.
  2. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
    Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
  3. Clinical trial and genome-wide association study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
    Title: Molecular genetics of successful smoking cessation: convergent genome-wide association study results.
  4. Pax6 regulation of Optimedin in the eye and brain may directly affect multiple developmental processes, including cell migration and axon growth
    Title: The Optimedin gene is a downstream target of Pax6.
  5. identification of a novel olfactomedin-related gene, named optimedin, located on chromosome 1p21 in humans, expressed in brain and retina; may be a candidate gene for disorders involving the anterior segment of the eye and the retina (optimedin)
    Title: Optimedin: a novel olfactomedin-related protein that interacts with myocilin.
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
An integrative study of the genetic, social and environmental determinants of chronic kidney disease characterized by tubulointerstitial damages in the North Central Region of Sri Lanka.
EBI GWAS Catalog
Parent-of-origin-specific allelic associations among 106 genomic loci for age at menarche.
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)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

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 eye photoreceptor cell development IEA
Inferred from Electronic Annotation
more info
  
involved_in signal transduction IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
part_of AMPA glutamate receptor complex IEA
Inferred from Electronic Annotation
more info
  
located_in Golgi apparatus IEA
Inferred from Electronic Annotation
more info
  
is_active_in extracellular space IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in synapse IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
noelin-3
Names
olfactomedin related ER localized protein 3

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_001288821.2 → NP_001275750.1  noelin-3 isoform 1 precursor

    See identical proteins and their annotated locations for NP_001275750.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1).
    Source sequence(s)
    AF397392, AK095551, AK300870, AL359760, HY346025
    Consensus CDS
    CCDS72832.1
    UniProtKB/Swiss-Prot
    Q5T3V6, Q6IMI7, Q6IMI8, Q6IMI9, Q6IMJ1, Q8TBG1, Q96PB2, Q96PB3, Q96PB4, Q96PB5, Q96PB6, Q96PB7
    UniProtKB/TrEMBL
    Q6IMJ0
    Related
    ENSP00000345192.5, ENST00000338858.9
    Conserved Domains (3) summary
    PRK03918
    Location:81 → 217
    PRK03918; DNA double-strand break repair ATPase Rad50
    pfam02191
    Location:222 → 466
    OLF; Olfactomedin-like domain
    pfam12308
    Location:46 → 145
    Noelin-1; Neurogenesis glycoprotein

  2. NM_001288823.2 → NP_001275752.1  noelin-3 isoform 3

    See identical proteins and their annotated locations for NP_001275752.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR, lacks a portion of the 5' coding region and initiates translation at a downstream start codon, compared to variant 1. It encodes isoform 3, which is shorter at the N-terminus, compared to isoform 1.
    Source sequence(s)
    AF397396, AK095551, AL359760, DA528521, HY346025
    UniProtKB/Swiss-Prot
    Q96PB7
    UniProtKB/TrEMBL
    B3KTG9
    Conserved Domains (3) summary
    PRK03918
    Location:19 → 122
    PRK03918; DNA double-strand break repair ATPase Rad50
    pfam02191
    Location:127 → 371
    OLF; Olfactomedin-like domain
    pfam12308
    Location:1 → 49
    Noelin-1; Neurogenesis glycoprotein

  3. NM_058170.4 → NP_477518.2  noelin-3 isoform 2 precursor

    See identical proteins and their annotated locations for NP_477518.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) contains an alternate 5' terminal exon and initiates translation at an alternate start codon, compared to variant 1. It encodes isoform 2, which is shorter and has a distinct N-terminus, compared to isoform 1.
    Source sequence(s)
    AF397393, AK095551, AL359760, BC022531, HY346025
    Consensus CDS
    CCDS30781.1
    UniProtKB/Swiss-Prot
    Q96PB7
    UniProtKB/TrEMBL
    B3KTG9
    Related
    ENSP00000359121.5, ENST00000370103.9
    Conserved Domains (2) summary
    pfam02191
    Location:202 → 446
    OLF; Olfactomedin-like domain
    pfam12308
    Location:26 → 124
    Noelin-1; Neurogenesis glycoprotein

RNA

  1. NR_110210.2 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) contains an alternate 5' exon structure and includes an alternate internal exon in the 3' region, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 2, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AF397397, AK095551, AL359760, DA528521, HY346025

  2. NR_110211.2 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5) contains an alternate 5' terminal exon and an alternate internal exon in the 3' region, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 2, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AF397395, AK095551, AL359760, DA528521, HY346025

  3. NR_110212.2 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (6) contains an alternate internal exon in the 3' region, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AF397393, AK095551, AK300870, AL359760, HY346025

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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    101802560..101996926 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047444385.1 → XP_047300341.1  noelin-3 isoform X1

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    101651747..101846150 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q96PB7.1 GenPept UniProtKB/Swiss-Prot:Q96PB7

Gene LinkOut

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