Aliases for NGEF Gene

Aliases for NGEF Gene

  • Neuronal Guanine Nucleotide Exchange Factor 2 3 4 5
  • Eph-Interacting Exchange Protein 3 4
  • Ephexin-1 3 4
  • Ephexin1 2 3
  • ARHGEF27 2 3
  • Ephexin 2
  • EPHEXIN 3
  • NGEF 5

External Ids for NGEF Gene

Previous GeneCards Identifiers for NGEF Gene

  • GC02M231800
  • GC02M232472
  • GC02M233707
  • GC02M233945
  • GC02M233568
  • GC02M233451
  • GC02M225592

Summaries for NGEF Gene

GeneCards Summary for NGEF Gene

NGEF (Neuronal Guanine Nucleotide Exchange Factor) is a Protein Coding gene. Among its related pathways are p75 NTR receptor-mediated signalling and Signaling by GPCR. Gene Ontology (GO) annotations related to this gene include guanyl-nucleotide exchange factor activity and Rho guanyl-nucleotide exchange factor activity. An important paralog of this gene is ARHGEF5.

UniProtKB/Swiss-Prot Summary for NGEF Gene

  • Acts as a guanine nucleotide exchange factor (GEF) which differentially activates the GTPases RHOA, RAC1 and CDC42. Plays a role in axon guidance regulating ephrin-induced growth cone collapse and dendritic spine morphogenesis. Upon activation by ephrin through EPHA4, the GEF activity switches toward RHOA resulting in its activation. Activated RHOA promotes cone retraction at the expense of RAC1- and CDC42-stimulated growth cone extension (By similarity).

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for NGEF Gene

Genomics for NGEF Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for NGEF 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
GH02J233011 Promoter/Enhancer 1.6 EPDnew Ensembl ENCODE 256.7 +0.5 476 1.8 ZMYM3 CEBPA BRCA1 YY1 MXD4 FOXA1 KLF11 HOMEZ KMT2B THAP11 NGEF LOC101928881 SCARNA6 EEF1B2P7 GIGYF2 PPFIA1P1 SNORC
GH02J232926 Promoter 1 EPDnew Ensembl 315.6 +85.6 85555 2.2 ZIC2 ZNF341 KLF1 EZH2 EP300 ZBTB20 ZBTB26 NGEF HQ292143 LOC101928881 HSALNG0023062 SNORC
GH02J233013 Promoter 0.3 Ensembl 250.7 +1.6 1555 0.2 LOC101928881 NGEF RF00017-3122 SNORC
GH02J233012 Enhancer 0.2 FANTOM5 252.4 +1.7 1664 0 NGEF LOC101928881 NEU2 RF00017-3122 SNORC
GH02J232900 Enhancer 1.4 FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 27.6 +111.4 111411 2.3 JUND ZIC2 CEBPB EP300 SMC3 FOSL2 SPI1 ZNF189 MAX POLR2A NGEF SNORC LOC101928881 INPP5D piR-56088-018 lnc-SNORC-2
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around NGEF on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for NGEF

Top Transcription factor binding sites by QIAGEN in the NGEF gene promoter:
  • AhR
  • aMEF-2
  • Arnt
  • Brachyury
  • MEF-2A
  • N-Myc
  • POU3F2
  • POU3F2 (N-Oct-5a)
  • POU3F2 (N-Oct-5b)

Genomic Locations for NGEF Gene

Latest Assembly
chr2:232,878,686-233,013,256
(GRCh38/hg38)
Size:
134,571 bases
Orientation:
Minus strand

Previous Assembly
chr2:233,743,411-233,877,966
(GRCh37/hg19 by Entrez Gene)
Size:
134,556 bases
Orientation:
Minus strand

chr2:233,743,396-233,877,982
(GRCh37/hg19 by Ensembl)
Size:
134,587 bases
Orientation:
Minus strand

Genomic View for NGEF Gene

Genes around NGEF on UCSC Golden Path with GeneCards custom track

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

RefSeq DNA sequence for NGEF Gene

Proteins for NGEF Gene

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

    Protein Symbol:
    Q8N5V2-NGEF_HUMAN
    Recommended name:
    Ephexin-1
    Protein Accession:
    Q8N5V2
    Secondary Accessions:
    • B4DMB8
    • B9A045
    • E9PC42
    • Q53QQ4
    • Q53ST7
    • Q6GMQ5
    • Q9NQD6

    Protein attributes for NGEF Gene

    Size:
    710 amino acids
    Molecular mass:
    82496 Da
    Quaternary structure:
    • Interacts with CDK5R1 and EPHA4; activated by EPHA4 through the CDK5 kinase.
    SequenceCaution:
    • Sequence=AAH73962.1; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=AAX93288.1; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=CAC00686.1; Type=Frameshift; Evidence={ECO:0000305};

    Alternative splice isoforms for NGEF Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for NGEF Gene

Post-translational modifications for NGEF Gene

  • Src-dependent phosphorylation at Tyr-179 upon EPHA4 activation increases the guanine exchange factor activity toward RHOA. Phosphorylation by CDK5 upon EPHA4 activation by EFNA1 may regulate dendritic spine morphogenesis (By similarity).
  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for NGEF Gene

Domains & Families for NGEF Gene

Gene Families for NGEF Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for NGEF Gene

InterPro:
Blocks:
  • SH3 domain signature
  • Pleckstrin-like
  • DH domain

Suggested Antigen Peptide Sequences for NGEF Gene

GenScript: Design optimal peptide antigens:
  • cDNA FLJ59455, highly similar to Homo sapiens neuronal guanine nucleotide exchange factor (NGEF), mRNA (B4DDI2_HUMAN)
  • Neuronal guanine nucleotide exchange factor (NGEF_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q8N5V2

UniProtKB/Swiss-Prot:

NGEF_HUMAN :
  • The DH domain and the PH domain are both required to mediate interaction with EPHA4.
Domain:
  • The DH domain and the PH domain are both required to mediate interaction with EPHA4.
genes like me logo Genes that share domains with NGEF: view

Function for NGEF Gene

Molecular function for NGEF Gene

UniProtKB/Swiss-Prot Function:
Acts as a guanine nucleotide exchange factor (GEF) which differentially activates the GTPases RHOA, RAC1 and CDC42. Plays a role in axon guidance regulating ephrin-induced growth cone collapse and dendritic spine morphogenesis. Upon activation by ephrin through EPHA4, the GEF activity switches toward RHOA resulting in its activation. Activated RHOA promotes cone retraction at the expense of RAC1- and CDC42-stimulated growth cone extension (By similarity).

Phenotypes From GWAS Catalog for NGEF Gene

Gene Ontology (GO) - Molecular Function for NGEF Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005085 guanyl-nucleotide exchange factor activity EXP 15848799
GO:0005515 protein binding IPI 32814053
genes like me logo Genes that share ontologies with NGEF: view
genes like me logo Genes that share phenotypes with NGEF: view

Animal Models for NGEF Gene

MGI Knock Outs for NGEF:

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for NGEF

Clone products for research

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , miRNA , Transcription Factor Targets and HOMER Transcription for NGEF Gene

Localization for NGEF Gene

Subcellular locations from UniProtKB/Swiss-Prot for NGEF Gene

Cytoplasm. Membrane. Cell projection, growth cone. Note=Associated with membranes. Localizes to axonal growth cones (By similarity). {ECO:0000250}.

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 NGEF gene
Compartment Confidence
cytosol 5
plasma membrane 3
nucleus 3
cytoskeleton 2
extracellular 1
mitochondrion 1
endoplasmic reticulum 1
endosome 1
lysosome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (2)
  • Plasma membrane (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for NGEF Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IEA --
GO:0005829 cytosol TAS --
GO:0016020 membrane IEA --
GO:0030426 growth cone IEA --
GO:0042995 cell projection IEA --
genes like me logo Genes that share ontologies with NGEF: view

Pathways & Interactions for NGEF Gene

genes like me logo Genes that share pathways with NGEF: view

Pathways by source for NGEF Gene

3 GeneGo (Thomson Reuters) pathways for NGEF Gene
  • Cell adhesion Ephrins signaling
  • G-protein signaling_RhoA regulation pathway
  • Neurophysiological process Receptor-mediated axon growth repulsion
4 Qiagen pathways for NGEF Gene
  • EphrinA-EphR Signaling
  • Ephrin-Eph Signaling
  • Guidance Cues and Growth Cone Motility
  • RhoA Pathway

SIGNOR curated interactions for NGEF Gene

Activates:

Gene Ontology (GO) - Biological Process for NGEF Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007186 G protein-coupled receptor signaling pathway TAS --
GO:0007275 multicellular organism development IEA --
GO:0007399 nervous system development IEA --
GO:0030154 cell differentiation IEA --
GO:0043065 positive regulation of apoptotic process TAS --
genes like me logo Genes that share ontologies with NGEF: view

Drugs & Compounds for NGEF Gene

(3) Drugs for NGEF Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Guanosine diphosphate Experimental Pharma 0
Guanosine monophosphate Experimental Pharma 0
Guanosine triphosphate Experimental Pharma 0
genes like me logo Genes that share compounds with NGEF: view

Transcripts for NGEF Gene

mRNA/cDNA for NGEF Gene

2 REFSEQ mRNAs :
11 NCBI additional mRNA sequence :
9 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for NGEF

Clone products for research

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

No ASD Table

Relevant External Links for NGEF Gene

GeneLoc Exon Structure for
NGEF

Expression for NGEF Gene

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

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

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

This gene is overexpressed in Brain - Cortex (x8.2), Brain - Putamen (basal ganglia) (x8.0), Brain - Nucleus accumbens (basal ganglia) (x6.5), Brain - Frontal Cortex (BA9) (x6.5), Brain - Caudate (basal ganglia) (x6.0), and Brain - Anterior cingulate cortex (BA24) (x4.2).

Protein differential expression in normal tissues from HIPED for NGEF Gene

This gene is overexpressed in Frontal cortex (43.3), Plasma (13.2), and Liver (6.4).

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



Protein tissue co-expression partners for NGEF Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for NGEF

SOURCE GeneReport for Unigene cluster for NGEF Gene:

Hs.97316

mRNA Expression by UniProt/SwissProt for NGEF Gene:

Q8N5V2-NGEF_HUMAN
Tissue specificity: Highly expressed in brain specifically in caudate nucleus and to a lower extent in amygdala and hippocampus. Also detected in lung.

Evidence on tissue expression from TISSUES for NGEF Gene

  • Nervous system(4.8)
  • Liver(4.3)
  • Skin(2.1)
genes like me logo Genes that share expression patterns with NGEF: view

Primer products for research

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for NGEF Gene

Orthologs for NGEF Gene

This gene was present in the common ancestor of animals.

Orthologs for NGEF Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia NGEF 29 30
  • 98.32 (n)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia NGEF 30
  • 91 (a)
OneToOne
Dog
(Canis familiaris)
Mammalia NGEF 29 30
  • 90.49 (n)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia NGEF 30
  • 90 (a)
OneToOne
Cow
(Bos Taurus)
Mammalia NGEF 29 30
  • 88.74 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Ngef 29
  • 88.41 (n)
Mouse
(Mus musculus)
Mammalia Ngef 29 16 30
  • 83.62 (n)
OneToOne
Chicken
(Gallus gallus)
Aves NGEF 29 30
  • 82.05 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia NGEF 30
  • 67 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia ngef 29
  • 66.97 (n)
Zebrafish
(Danio rerio)
Actinopterygii LOC569090 29
  • 58.19 (n)
NGEF 30
  • 45 (a)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP007452 29
  • 51.39 (n)
Fruit Fly
(Drosophila melanogaster)
Insecta BcDNA:GH03693 31
  • 33 (a)
Exn 30
  • 10 (a)
OneToMany
Worm
(Caenorhabditis elegans)
Secernentea K07D4.7a 31
  • 37 (a)
K07D4.7b 31
  • 37 (a)
ephx-1 30
  • 17 (a)
OneToMany
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 30
  • 34 (a)
OneToMany
Species where no ortholog for NGEF was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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 Vase (Ciona intestinalis)
  • 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 NGEF Gene

ENSEMBL:
Gene Tree for NGEF (if available)
TreeFam:
Gene Tree for NGEF (if available)
Aminode:
Evolutionary constrained regions (ECRs) for NGEF: view image
Alliance of Genome Resources:
Additional Orthologs for NGEF

Paralogs for NGEF Gene

Paralogs for NGEF Gene

(7) SIMAP similar genes for NGEF Gene using alignment to 7 proteins:

  • NGEF_HUMAN
  • B4DDI2_HUMAN
  • C9J2D9_HUMAN
  • C9JTV7_HUMAN
  • H7BZ39_HUMAN
  • H7C2C2_HUMAN
  • H7C2S7_HUMAN
genes like me logo Genes that share paralogs with NGEF: view

Variants for NGEF Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for NGEF Gene

SNP ID Clinical significance and condition Chr 02 pos Variation AA Info Type
rs61750834 Benign: not provided 232,891,481(-) C/T
NM_019850.3(NGEF):c.1149G>A (p.Glu383=)
SYNONYMOUS
rs2271703 -- p.Arg78Gly
rs4973588 -- p.Met111Thr

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for NGEF Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

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

Variant ID Type Subtype PubMed ID
dgv2172n106 CNV deletion 24896259
dgv2358e59 CNV duplication 20981092
dgv4188n100 CNV gain 25217958
dgv633e201 CNV deletion 23290073
esv1028910 CNV insertion 17803354
esv1149653 CNV insertion 17803354
esv1438259 CNV deletion 17803354
esv1445847 CNV deletion 17803354
esv1592465 CNV deletion 17803354
esv1761461 CNV insertion 17803354
esv1789642 CNV deletion 17803354
esv23962 CNV gain 19812545
esv2443215 CNV deletion 19546169
esv2662638 CNV deletion 23128226
esv2721633 CNV deletion 23290073
esv2721634 CNV deletion 23290073
esv2721635 CNV deletion 23290073
esv2721637 CNV deletion 23290073
esv2721640 CNV deletion 23290073
esv2721641 CNV deletion 23290073
esv2721642 CNV deletion 23290073
esv2721643 CNV deletion 23290073
esv2721644 CNV deletion 23290073
esv2721645 CNV deletion 23290073
esv2721646 CNV deletion 23290073
esv3194 CNV loss 18987735
esv3389322 CNV insertion 20981092
esv3389683 CNV duplication 20981092
esv3594664 CNV loss 21293372
esv3594665 CNV loss 21293372
esv3594666 CNV loss 21293372
esv8097 CNV loss 19470904
esv8496 CNV loss 19470904
esv8770 CNV loss 19470904
nsv1009825 CNV gain 25217958
nsv1014548 CNV gain 25217958
nsv1071655 CNV deletion 25765185
nsv1073021 CNV deletion 25765185
nsv1110361 CNV duplication 24896259
nsv1114181 CNV deletion 24896259
nsv1116836 CNV deletion 24896259
nsv1132893 CNV insertion 24896259
nsv1142981 CNV tandem duplication 24896259
nsv1143068 CNV deletion 24896259
nsv477463 CNV novel sequence insertion 20440878
nsv518226 CNV loss 19592680
nsv518558 CNV loss 19592680
nsv834570 CNV gain 17160897
nsv953203 CNV deletion 24416366

Variation tolerance for NGEF Gene

Residual Variation Intolerance Score: 6.54% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.97; 36.48% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for NGEF Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
NGEF
Leiden Open Variation Database (LOVD)
NGEF

SNP Genotyping and Copy Number Assays for research

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

Disorders for NGEF Gene

Additional Disease Information for NGEF

Human Genome Epidemiology Navigator
(HuGE)
Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform

No disorders were found for NGEF Gene.

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

Publications for NGEF Gene

  1. Characterization of Ngef, a novel member of the Dbl family of genes expressed predominantly in the caudate nucleus. (PMID: 10777665) Rodrigues NR … Davies KE (Genomics 2000) 2 3 4
  2. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 40
  3. Mutation of ARHGAP9 in patients with coronary spastic angina. (PMID: 19911011) Takefuji M … Kaibuchi K (Journal of human genetics 2010) 3 40
  4. Generation and annotation of the DNA sequences of human chromosomes 2 and 4. (PMID: 15815621) Hillier LW … Wilson RK (Nature 2005) 3 4
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4

Products for NGEF Gene

Sources for NGEF Gene