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    OLFML2B olfactomedin like 2B [ Homo sapiens (human) ]

    Gene ID: 25903, updated on 10-Dec-2024

    Summary

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    Official Symbol
    OLFML2Bprovided by HGNC
    Official Full Name
    olfactomedin like 2Bprovided by HGNC
    Primary source
    HGNC:HGNC:24558
    See related
    Ensembl:ENSG00000162745 AllianceGenome:HGNC:24558
    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
    Summary
    This gene encodes an olfactomedin domain-containing protein. Most olfactomedin domain-containing proteins are secreted glycoproteins. [provided by RefSeq, Dec 2016]
    Expression
    Broad expression in gall bladder (RPKM 9.8), placenta (RPKM 5.9) and 16 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See OLFML2B in Genome Data Viewer
    Location:
    1q23.3
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (161983192..162023869, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (161327500..161368171, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (161952982..161993659, complement)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124904444 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1488 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2008 Neighboring gene activating transcription factor 6 Neighboring gene proteasome activator subunit 3 pseudogene Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_558 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:161972665-161973166 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1489 Neighboring gene Sharpr-MPRA regulatory region 11962 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr1:162025767-162026281 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1491 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1492 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1490 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr1:162061183-162061778 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr1:162061779-162062373 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_577 Neighboring gene uncharacterized LOC105371475 Neighboring gene nitric oxide synthase 1 adaptor protein Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:162106088-162107287 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:162114645-162115359 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:162121700-162122200 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:162150234-162150764 Neighboring gene microRNA 4654 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:162167833-162168469 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr1:162219262-162219923 Neighboring gene uncharacterized LOC124904445

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    1. Bioinformatic exploration of OLFML2B overexpression in gastric cancer base on multiple analyzing tools. Liu J, et al. BMC Cancer, 2019 Mar 13. PMID 30866865, Free PMC Article
    2. Olfactomedin domain-containing proteins: possible mechanisms of action and functions in normal development and pathology. Tomarev SI, et al. Mol Neurobiol, 2009 Oct. PMID 19554483, Free PMC Article
    3. Common genetic variation near the phospholamban gene is associated with cardiac repolarisation: meta-analysis of three genome-wide association studies. Nolte IM, et al. PLoS One, 2009 Jul 9. PMID 19587794, Free PMC Article
    4. Genome-wide association and population genetic analysis of C-reactive protein in African American and Hispanic American women. Reiner AP, et al. Am J Hum Genet, 2012 Sep 7. PMID 22939635, Free PMC Article
    5. Stress-induced NEDDylation promotes cytosolic protein aggregation through HDAC6 in a p62-dependent manner. Kim S, et al. iScience, 2021 Mar 19. PMID 33665565, Free PMC Article

    See all (17) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. The high expression of OLFML2B was associate with a short overall survival in gastric cancer patients.
      Title: Bioinformatic exploration of OLFML2B overexpression in gastric cancer base on multiple analyzing tools.
    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. Observational study of gene-disease association, gene-gene interaction, gene-environment interaction, and genetic testing. (HuGE Navigator)
      Title: Integrative predictive model of coronary artery calcification in atherosclerosis.
    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
    Common genetic variation near the phospholamban gene is associated with cardiac repolarisation: meta-analysis of three genome-wide association studies.
    EBI GWAS Catalog
    Genetic association study of QT interval highlights role for calcium signaling pathways in myocardial repolarization.
    EBI GWAS Catalog
    Genome wide association study (GWAS) of Chagas cardiomyopathy in Trypanosoma cruzi seropositive subjects.
    EBI GWAS Catalog
    Genome-wide association and population genetic analysis of C-reactive protein in African American and Hispanic American women.
    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)

    HIV-1 interactions

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    Replication interactions

    Interaction Pubs
    Knockdown of olfactomedin-like 2B (OLFML2B) by siRNA inhibits HIV-1 replication in HeLa P4/R5 cells PubMed

    Go to the HIV-1, Human Interaction Database

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC51337

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables extracellular matrix binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables identical protein binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in extracellular matrix organization IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in signal transduction IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    located_in extracellular matrix IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in extracellular space IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    olfactomedin-like protein 2B
    Names
    photomedin-2

    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_052853.1 RefSeqGene

      Range
      5597..46274
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001297713.2 → NP_001284642.1  olfactomedin-like protein 2B isoform 1 precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) uses an alternate in-frame splice site in the 5' coding region, compared to variant 3. The encoded isoform (1) is shorter than isoform 3.
      Source sequence(s)
      AK301499, AK316154, AL590408, BC067274
      Consensus CDS
      CCDS72966.1
      UniProtKB/TrEMBL
      B4DWE8, F2Z3N3
      Related
      ENSP00000356917.2, ENST00000367940.2
      Conserved Domains (1) summary
      pfam02191
      Location:499 → 747
      OLF; Olfactomedin-like domain

    2. NM_001347700.2 → NP_001334629.1  olfactomedin-like protein 2B isoform 3 precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) represents the longest transcript and encodes the longest isoform (3).
      Source sequence(s)
      AL391825, AL590408, BC067274
      UniProtKB/TrEMBL
      B4DWE8

    3. NM_015441.3 → NP_056256.1  olfactomedin-like protein 2B isoform 2 precursor

      See identical proteins and their annotated locations for NP_056256.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice site, compared to variant 3. The encoded isoform (2) is shorter than isoform 3.
      Source sequence(s)
      AL391825, AL590408, BC067274
      Consensus CDS
      CCDS1236.1
      UniProtKB/Swiss-Prot
      B7ZA39, Q5VU96, Q68BL8, Q6NX46, Q86X11, Q9Y3X6
      UniProtKB/TrEMBL
      B4DWE8
      Related
      ENSP00000294794.3, ENST00000294794.8
      Conserved Domains (3) summary
      pfam02191
      Location:498 → 746
      OLF; Olfactomedin-like domain
      pfam06785
      Location:125 → 252
      UPF0242; Uncharacterized protein family (UPF0242)
      cl25496
      Location:349 → 481
      Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)

    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
      161983192..162023869 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011509398.3 → XP_011507700.1  olfactomedin-like protein 2B isoform X1

      Conserved Domains (1) summary
      pfam02191
      Location:258 → 506
      OLF; Olfactomedin-like domain

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      161327500..161368171 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054335860.1 → XP_054191835.1  olfactomedin-like protein 2B isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q68BL8.2 GenPept UniProtKB/Swiss-Prot:Q68BL8

    Gene LinkOut

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

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