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    OLFML3 olfactomedin like 3 [ Homo sapiens (human) ]

    Gene ID: 56944, updated on 2-Nov-2024

    Summary

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    Official Symbol
    OLFML3provided by HGNC
    Official Full Name
    olfactomedin like 3provided by HGNC
    Primary source
    HGNC:HGNC:24956
    See related
    Ensembl:ENSG00000116774 MIM:610088; AllianceGenome:HGNC:24956
    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
    OLF44; HNOEL-iso
    Summary
    This gene encodes a member of the olfactomedin-like gene family which also includes genes encoding noelin, tiarin, myocilin, amassin, optimedin, photomedin, and latrophilin. The encoded protein is a secreted extracellular matrix glycoprotein with a C-terminal olfactomedin domain that facilitates protein-protein interactions, cell adhesion, and intercellular interactions. It serves as both a scaffold protein that recruits bone morphogenetic protein 1 to its substrate chordin, and as a vascular tissue remodeler with pro-angiogenic properties. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2017]
    Expression
    Broad expression in ovary (RPKM 65.9), endometrium (RPKM 56.6) and 23 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See OLFML3 in Genome Data Viewer
    Location:
    1p13.2
    Exon count:
    4
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (113979474..113982253)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (113991135..113993914)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (114522096..114524875)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1540 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1541 Neighboring gene GATA motif-containing MPRA enhancer 196 Neighboring gene adaptor related protein complex 4 subunit beta 1 Neighboring gene DNA cross-link repair 1B Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1542 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1217 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1218 Neighboring gene HIPK1 antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:114480377-114480904 Neighboring gene MPRA-validated peak375 silencer Neighboring gene homeodomain interacting protein kinase 1 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr1:114519457-114520034 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr1:114521340-114522173 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:114523841-114524673 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:114525929-114526892 Neighboring gene ribosomal protein L13a pseudogene 10 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:114557741-114558940 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:114573243-114573826 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr1:114574411-114574994 Neighboring gene Sharpr-MPRA regulatory region 7982 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:114579664-114580246 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr1:114580831-114581413 Neighboring gene NANOG hESC enhancer GRCh37_chr1:114592578-114593255 Neighboring gene NANOG hESC enhancer GRCh37_chr1:114600776-114601630 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:114621064-114621564 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:114634493-114634994 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr1:114647517-114648164 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1543 Neighboring gene synaptotagmin 6 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:114667021-114667808 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:114688166-114688878

    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. Surfaceome CRISPR screen identifies OLFML3 as a rhinovirus-inducible IFN antagonist. Mei H, et al. Genome Biol, 2021 Oct 22. PMID 34686207, Free PMC Article
    2. hOLF44, a secreted glycoprotein with distinct expression pattern, belongs to an uncharacterized olfactomedin-like subfamily newly identified by phylogenetic analysis. Zeng LC, et al. FEBS Lett, 2004 Jul 30. PMID 15280020
    3. Elucidation of subfamily segregation and intramolecular coevolution of the olfactomedin-like proteins by comprehensive phylogenetic analysis and gene expression pattern assessment. Zeng LC, et al. FEBS Lett, 2005 Oct 24. PMID 16212957
    4. Biodegradable and plasma-treated electrospun scaffolds coated with recombinant Olfactomedin-like 3 for accelerating wound healing and tissue regeneration. Dunn LL, et al. Wound Repair Regen, 2016 Nov. PMID 27684720
    5. Olfactomedin proteins: central players in development and disease. Anholt RR. Front Cell Dev Biol, 2014. PMID 25364714, Free PMC Article

    See all (29) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Surfaceome CRISPR screen identifies OLFML3 as a rhinovirus-inducible IFN antagonist.
      Title: Surfaceome CRISPR screen identifies OLFML3 as a rhinovirus-inducible IFN antagonist.
    2. Microglia-Derived Olfactomedin-like 3 Promotes Pro-Tumorigenic Microglial Function and Malignant Features of Glioma Cells.
      Title: Microglia-Derived Olfactomedin-like 3 Promotes Pro-Tumorigenic Microglial Function and Malignant Features of Glioma Cells.
    3. Circadian Regulator CLOCK Recruits Immune-Suppressive Microglia into the GBM Tumor Microenvironment.
      Title: Circadian Regulator CLOCK Recruits Immune-Suppressive Microglia into the GBM Tumor Microenvironment.
    4. This paper reports OLFML3 expression in human and baboon eye. The full coding DNA sequence has 1221 bp, from which an open reading frame of 406 amino acid was obtained.
      Title: Olfactomedin-like 3 (OLFML3) gene expression in baboon and human ocular tissues: cornea, lens, uvea, and retina.
    5. may have matrix-related function involved in human placental and embryonic development, or play a similar role in other physiological processes
      Title: hOLF44, a secreted glycoprotein with distinct expression pattern, belongs to an uncharacterized olfactomedin-like subfamily newly identified by phylogenetic analysis.
    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
    Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic 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)

    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

    Process Evidence Code Pubs
    involved_in signal transduction IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    is_active_in extracellular space IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in extracellular vesicle HDA PubMed 

    General protein information

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    Preferred Names
    olfactomedin-like protein 3
    Names
    olfactomedin, 44-kd

    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.

    Genomic

    1. NG_053036.1 RefSeqGene

      Range
      5084..7863
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001286352.3 → NP_001273281.1  olfactomedin-like protein 3 isoform 2

      See identical proteins and their annotated locations for NP_001273281.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternate exon in the 5' UTR and coding region and initiates translation from an alternate start codon compared to variant 1. The encoded isoform (2) is shorter and has a distinct N-terminus compared to isoform 1.
      Source sequence(s)
      AA576955, AK092766, AL731797
      Consensus CDS
      CCDS65618.1
      UniProtKB/Swiss-Prot
      Q9NRN5
      Related
      ENSP00000358564.1, ENST00000369551.5
      Conserved Domains (1) summary
      pfam02191
      Location:119 → 377
      OLF; Olfactomedin-like domain

    2. NM_001286353.3 → NP_001273282.1  olfactomedin-like protein 3 isoform 3

      See identical proteins and their annotated locations for NP_001273282.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) uses an an alternate splice site in the 5' UTR which results in the use of a downstream start codon compared to variant 1. The encoded isoform (3) has a shorter N-terminus compared to isoform 1.
      Source sequence(s)
      AA576955, AL731797, BP201458
      Consensus CDS
      CCDS72839.1
      UniProtKB/TrEMBL
      B4DNG0
      Related
      ENSP00000376977.3, ENST00000393300.6
      Conserved Domains (1) summary
      pfam02191
      Location:78 → 336
      OLF; Olfactomedin-like domain

    3. NM_020190.5 → NP_064575.1  olfactomedin-like protein 3 isoform 1 precursor

      See identical proteins and their annotated locations for NP_064575.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      AY464015
      Consensus CDS
      CCDS870.1
      UniProtKB/Swiss-Prot
      Q53FR1, Q53HV9, Q5SQL6, Q69AX9, Q8NBJ2, Q9NRN5
      UniProtKB/TrEMBL
      M1LAK4
      Related
      ENSP00000322273.4, ENST00000320334.5
      Conserved Domains (2) summary
      pfam02191
      Location:139 → 397
      OLF; Olfactomedin-like domain
      cl28015
      Location:25 → 100
      PspA_IM30; PspA/IM30 family

    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
      113979474..113982253
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017001848.3 → XP_016857337.1  olfactomedin-like protein 3 isoform X1

      UniProtKB/Swiss-Prot
      Q9NRN5
      Conserved Domains (1) summary
      pfam02191
      Location:119 → 377
      OLF; Olfactomedin-like domain

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      113991135..113993914
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054337755.1 → XP_054193730.1  olfactomedin-like protein 3 isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9NRN5.1 GenPept UniProtKB/Swiss-Prot:Q9NRN5

    Gene LinkOut

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

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