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

Gene ID: 25903, updated on 2-Nov-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
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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: 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. 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)

Genotypes

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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