OLFM3 olfactomedin 3 [Homo sapiens (human)] - Gene

Summary

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: mouse all
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Genomic context

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_000001.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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.
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.
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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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 EBI GWAS CatalogPubMed
Parent-of-origin-specific allelic associations among 106 genomic loci for age at menarche. EBI GWAS Catalog EBI GWAS CatalogPubMed

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

AL033695 (e-PCR)
- UniSTS:93554

AL033929 (e-PCR)
- UniSTS:93812

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)

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
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
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

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
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
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