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EFR3B Gene(Protein Coding)

EFR3 Homolog B

GCID:
GC02P025002
GIFtS:
40
Genes Participants
UDN Logo

Aliases for EFR3B Gene

Aliases for EFR3B Gene

  • EFR3 Homolog B 2 3 5
  • KIAA0953 2 3 4
  • EFR3 Homolog B (S. Cerevisiae) 2
  • Protein EFR3 Homolog B 3

External Ids for EFR3B Gene

Previous HGNC Symbols for EFR3B Gene

  • KIAA0953

Previous GeneCards Identifiers for EFR3B Gene

  • GC02P025118
  • GC02P025264

Summaries for EFR3B Gene

GeneCards Summary for EFR3B Gene

EFR3B (EFR3 Homolog B) is a Protein Coding gene. Gene Ontology (GO) annotations related to this gene include binding. An important paralog of this gene is EFR3A.

UniProtKB/Swiss-Prot for EFR3B Gene

  • Component of a complex required to localize phosphatidylinositol 4-kinase (PI4K) to the plasma membrane (PubMed:23229899, PubMed:25608530, PubMed:26571211). The complex acts as a regulator of phosphatidylinositol 4-phosphate (PtdIns(4)P) synthesis (Probable). In the complex, EFR3B probably acts as the membrane-anchoring component (PubMed:23229899). Also involved in responsiveness to G-protein-coupled receptors; it is however unclear whether this role is direct or indirect (PubMed:25380825).

Additional gene information for EFR3B Gene

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for EFR3B Gene

Genomics for EFR3B Gene

Products:

  1. Regulatory Element

GeneHancer (GH) Regulatory Elements for EFR3B Gene

Promoters and enhancers for EFR3B Gene
GeneHancer (GH) Identifier GH Type GH
Score		 GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites		 Gene Targets
GH02I025041 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE dbSUPER 550.8 +0.4 433 2.8 SIN3A GLIS2 ZNF213 FOS SP3 SP5 MXD4 REST GLIS1 SP7 EFR3B ADCY3 RN7SL856P
GH02I024970 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 11.4 -69.9 -69869 3.6 CLOCK ZFP64 DMAP1 YY1 ZNF213 SP3 NFYC GLIS1 RCOR2 NBN DNAJC27 DNAJC27-AS1 ADCY3 ASXL2 WDCP EFR3B LINC01381 POMC PTRHD1 ENSG00000207069
GH02I024975 Enhancer 1 Ensembl ENCODE 11.2 -66.5 -66503 0.4 ELF3 FOXA2 ARID4B ZNF2 ZSCAN9 RAD21 ARID2 ZSCAN5C ZNF143 RCOR1 EFR3B LINC01381 POMC ADCY3 DNAJC27 DNAJC27-AS1 ENSG00000207069 GC02M025008
GH02I025061 Enhancer 0.6 dbSUPER 11.9 +21.4 21424 3.4 ZBED1 JUNB BATF ATF2 JUND BCL11A POLR2A NFATC1 IKZF2 MAFK ADCY3 EFR3B POMC RPS13P5 DNAJC27 DNAJC27-AS1 ENSG00000202479 NCOA1 RN7SL856P SUCLA2P3
GH02I024984 Enhancer 0.5 ENCODE 11.4 -57.0 -57020 1 MXI1 RFX1 POLR2A NRF1 ADCY3 EFR3B POMC LINC01381 DNAJC27-AS1 DNAJC27 ENSG00000207069 GC02M025008
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around EFR3B on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the EFR3B gene promoter:

Genomic Locations for EFR3B Gene

Genomic Locations for EFR3B Gene
chr2:25,042,104-25,159,137
(GRCh38/hg38)
Size:
117,034 bases
Orientation:
Plus strand
chr2:25,264,973-25,382,004
(GRCh37/hg19)

Genomic View for EFR3B Gene

Genes around EFR3B on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
EFR3B Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for EFR3B Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for EFR3B Gene

Proteins for EFR3B Gene

Products:

  1. Antibody
  2. Protein
  3. Assay

  • Protein details for EFR3B Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9Y2G0-EFR3B_HUMAN
    Recommended name:
    Protein EFR3 homolog B
    Protein Accession:
    Q9Y2G0
    Secondary Accessions:
    • B7WPL8
    • Q86XU6

    Protein attributes for EFR3B Gene

    Size:
    817 amino acids
    Molecular mass:
    92487 Da
    Quaternary structure:
    • Component of a phosphatidylinositol 4-kinase (PI4K) complex, composed of PI4KA, EFR3 (EFR3A or EFR3B), TTC7 (TTC7A or TTC7B) and FAM126 (FAM126A or FAM126B).
    SequenceCaution:
    • Sequence=BAA76797.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Alternative splice isoforms for EFR3B Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for EFR3B Gene

Protein Expression for EFR3B Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for EFR3B Gene

  • Palmitoylated at its N-terminus, anchoring the protein to the plasma membrane.
  • Ubiquitination at posLast=3838
  • Modification sites at PhosphoSitePlus

Other Protein References for EFR3B Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for EFR3B Gene

Domains & Families for EFR3B Gene

Gene Families for EFR3B Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for EFR3B Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for EFR3B Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q9Y2G0

UniProtKB/Swiss-Prot:

EFR3B_HUMAN :
  • Belongs to the EFR3 family.
Family:
  • Belongs to the EFR3 family.
genes like me logo Genes that share domains with EFR3B: view

Function for EFR3B Gene

Products:

  1. Animal Model
  2. CRISPR
  3. miRNA
  4. Inhibitory RNA
  5. Clone
  6. Cell Line

Molecular function for EFR3B Gene

UniProtKB/Swiss-Prot Function:
Component of a complex required to localize phosphatidylinositol 4-kinase (PI4K) to the plasma membrane (PubMed:23229899, PubMed:25608530, PubMed:26571211). The complex acts as a regulator of phosphatidylinositol 4-phosphate (PtdIns(4)P) synthesis (Probable). In the complex, EFR3B probably acts as the membrane-anchoring component (PubMed:23229899). Also involved in responsiveness to G-protein-coupled receptors; it is however unclear whether this role is direct or indirect (PubMed:25380825).

Phenotypes From GWAS Catalog for EFR3B Gene

Gene Ontology (GO) - Molecular Function for EFR3B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 23229899
genes like me logo Genes that share ontologies with EFR3B: view
genes like me logo Genes that share phenotypes with EFR3B: view

Animal Model Products

CRISPR Products

miRNA for EFR3B Gene

miRTarBase miRNAs that target EFR3B

Inhibitory RNA Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for EFR3B Gene

Localization for EFR3B Gene

Subcellular locations from UniProtKB/Swiss-Prot for EFR3B Gene

Cell membrane; Lipid-anchor. Cytoplasm, cytosol. Note=Palmitoylation anchors the protein to the plasma membrane (PubMed:23229899, PubMed:25380825). A small amount is observed in the cytosol (PubMed:25380825). {ECO:0000269 PubMed:23229899, ECO:0000269 PubMed:25380825}.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for EFR3B gene
Compartment Confidence
plasma membrane 5
cytosol 4
nucleus 2
extracellular 1
peroxisome 1

Gene Ontology (GO) - Cellular Components for EFR3B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IEA --
GO:0005829 cytosol IEA --
GO:0005886 plasma membrane IEA,IDA 23229899
GO:0016020 membrane IEA --
genes like me logo Genes that share ontologies with EFR3B: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for EFR3B Gene

Pathways & Interactions for EFR3B Gene

SuperPathways for EFR3B Gene

PathCards logo More details on SuperPathways for EFR3B
No Data Available

Interacting Proteins for EFR3B Gene

STRING Interaction Network Preview (showing 5 interactants - click image to see details)
http://version10.5.string-db.org/api/image/networkList?limit=0&targetmode=proteins&caller_identity=gene_cards&network_flavor=evidence&identifiers=9606.ENSP00000384081%0d%0a9606.ENSP00000347714%0d%0a9606.ENSP00000458238%0d%0a9606.ENSP00000336127%0d%0a9606.ENSP00000316699%0d%0a9606.ENSP00000359449%0d%0a
Selected Interacting proteins: Q9Y2G0-EFR3B_HUMAN ENSP00000384081 for EFR3B Gene via IID STRING

Gene Ontology (GO) - Biological Process for EFR3B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0046854 phosphatidylinositol phosphorylation IDA 23229899
GO:0072659 protein localization to plasma membrane IDA 23229899
genes like me logo Genes that share ontologies with EFR3B: view

No data available for Pathways by source and SIGNOR curated interactions for EFR3B Gene

Drugs & Compounds for EFR3B Gene

Products:

  1. Drug
No Compound Related Data Available

Transcripts for EFR3B Gene

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone

mRNA/cDNA for EFR3B Gene

(3) REFSEQ mRNAs :
(4) Additional mRNA sequences :
(15) Selected AceView cDNA sequences:
(5) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for EFR3B Gene

EFR3 homolog B (S. cerevisiae):
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Alternative Splicing Database (ASD) splice patterns (SP) for EFR3B Gene

No ASD Table

Relevant External Links for EFR3B Gene

GeneLoc Exon Structure for
EFR3B
ECgene alternative splicing isoforms for
EFR3B

Expression for EFR3B Gene

Products:

  1. Primer
  2. Gene Expression Assay

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for EFR3B Gene

mRNA expression in normal human tissues for EFR3B Gene
mRNA expression by BioGPS for EFR3B GenemRNA expression by GTEx for EFR3B Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for EFR3B Gene

This gene is overexpressed in Brain - Cerebellar Hemisphere (x4.5) and Brain - Nucleus accumbens (basal ganglia) (x4.2).

Protein differential expression in normal tissues from HIPED for EFR3B Gene

This gene is overexpressed in Frontal cortex (33.8) and Brain (30.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for EFR3B Gene



Protein tissue co-expression partners for EFR3B Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of EFR3B Gene:

EFR3B

SOURCE GeneReport for Unigene cluster for EFR3B Gene:

Hs.4892

Evidence on tissue expression from TISSUES for EFR3B Gene

  • Nervous system(4.6)
genes like me logo Genes that share expression patterns with EFR3B: view

Primer Products

No data available for mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for EFR3B Gene

Orthologs for EFR3B Gene

This gene was present in the common ancestor of animals.

Orthologs for EFR3B Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
 Mammalia EFR3B 33 34
  • 97.76 (n)
oppossum
(Monodelphis domestica)
 Mammalia EFR3B 34
  • 95 (a)
 OneToOne
platypus
(Ornithorhynchus anatinus)
 Mammalia -- 34
  • 92 (a)
 OneToMany
-- 34
  • 68 (a)
 OneToMany
-- 34
  • 51 (a)
 OneToMany
dog
(Canis familiaris)
 Mammalia EFR3B 33 34
  • 91.8 (n)
cow
(Bos Taurus)
 Mammalia EFR3B 33 34
  • 91.55 (n)
rat
(Rattus norvegicus)
 Mammalia Efr3b 33
  • 90.06 (n)
mouse
(Mus musculus)
 Mammalia Efr3b 33 16 34
  • 90.04 (n)
chicken
(Gallus gallus)
 Aves EFR3B 33 34
  • 82.21 (n)
lizard
(Anolis carolinensis)
 Reptilia -- 34
  • 96 (a)
 OneToMany
-- 34
  • 83 (a)
 OneToMany
tropical clawed frog
(Silurana tropicalis)
 Amphibia efr3b 33
  • 78.12 (n)
zebrafish
(Danio rerio)
 Actinopterygii efr3ba 34
  • 75 (a)
 OneToMany
efr3bb 33 34
  • 74.55 (n)
African malaria mosquito
(Anopheles gambiae)
 Insecta AgaP_AGAP012183 33
  • 53.13 (n)
fruit fly
(Drosophila melanogaster)
 Insecta stmA 33 34
  • 51.48 (n)
worm
(Caenorhabditis elegans)
 Secernentea C32D5.3 33 34
  • 50.03 (n)
sea squirt
(Ciona savignyi)
 Ascidiacea -- 34
  • 38 (a)
 OneToMany
Species where no ortholog for EFR3B was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for EFR3B Gene

ENSEMBL:
Gene Tree for EFR3B (if available)
TreeFam:
Gene Tree for EFR3B (if available)

Paralogs for EFR3B Gene

Paralogs for EFR3B Gene

(1) SIMAP similar genes for EFR3B Gene using alignment to 3 proteins:

genes like me logo Genes that share paralogs with EFR3B: view

Variants for EFR3B Gene

Products:

  1. SNP Genotyping and Copy Number Assay

Sequence variations from dbSNP and Humsavar for EFR3B Gene

SNP ID Clin Chr 02 pos Variation AA Info Type
rs1000016955 -- 25,104,124(+) G/A intron_variant
rs1000026291 -- 25,093,080(+) C/G/T coding_sequence_variant, non_coding_transcript_variant, synonymous_variant
rs1000029553 -- 25,148,754(+) C/G intron_variant
rs1000068924 -- 25,127,404(+) T/C intron_variant
rs1000090370 -- 25,134,283(+) G/C intron_variant

Structural Variations from Database of Genomic Variants (DGV) for EFR3B Gene

Variant ID Type Subtype PubMed ID
dgv57n68 CNV loss 17160897
esv1006182 OTHER inversion 20482838
esv24844 CNV gain 19812545
esv2666849 CNV deletion 23128226
esv2762426 CNV loss 21179565
esv33372 CNV loss 17666407
esv3590085 CNV gain 21293372
esv3590086 CNV loss 21293372
esv3590087 CNV loss 21293372
esv3590089 CNV loss 21293372
nsv1008732 CNV loss 25217958
nsv1133465 CNV deletion 24896259
nsv2647 CNV insertion 18451855
nsv997725 CNV gain 25217958

Variation tolerance for EFR3B Gene

Gene Damage Index Score: 1.72; 32.69% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for EFR3B Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
EFR3B

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for EFR3B Gene

Disorders for EFR3B Gene

Additional Disease Information for EFR3B

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology

No disorders were found for EFR3B Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for EFR3B Gene

Publications for EFR3B Gene

  1. Prediction of the coding sequences of unidentified human genes. XIII. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro. (PMID: 10231032) Nagase T … Ohara O (DNA research : an international journal for rapid publication of reports on genes and genomes 1999) 2 3 4 58
  2. The leukodystrophy protein FAM126A (hyccin) regulates PtdIns(4)P synthesis at the plasma membrane. (PMID: 26571211) Baskin JM … De Camilli P (Nature cell biology 2016) 3 4 58
  3. EFR3s are palmitoylated plasma membrane proteins that control responsiveness to G-protein-coupled receptors. (PMID: 25380825) Bojjireddy N … Balla T (Journal of cell science 2015) 3 4 58
  4. PtdIns4P synthesis by PI4KIIIα at the plasma membrane and its impact on plasma membrane identity. (PMID: 23229899) Nakatsu F … De Camilli P (The Journal of cell biology 2012) 3 4 58
  5. A genome-wide meta-analysis of six type 1 diabetes cohorts identifies multiple associated loci. (PMID: 21980299) Bradfield JP … Hakonarson H (PLoS genetics 2011) 3 44 58

Products for EFR3B Gene

Sources for EFR3B Gene

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