Aliases for PLXNA4 Gene

Aliases for PLXNA4 Gene

  • Plexin A4 2 3 5
  • Plexin-A4 3 4
  • FAYV2820 2 3
  • KIAA1550 2 4
  • PLXNA4A 3 4
  • PLXNA4B 3 4
  • Epididymis Secretory Sperm Binding Protein 3
  • DKFZp434G0625PRO34003 2
  • Plexin A4, A 2
  • Plexin A4, B 2
  • PRO34003 3
  • PLEXA4 3
  • PLXNA4 5

External Ids for PLXNA4 Gene

Previous HGNC Symbols for PLXNA4 Gene

  • PLXNA4A
  • PLXNA4B

Previous GeneCards Identifiers for PLXNA4 Gene

  • GC07U990159
  • GC07M131215
  • GC07M131228
  • GC07M131269
  • GC07M131467
  • GC07M131720
  • GC07M126124

Summaries for PLXNA4 Gene

GeneCards Summary for PLXNA4 Gene

PLXNA4 (Plexin A4) is a Protein Coding gene. Diseases associated with PLXNA4 include Polycystic Kidney Disease 4 With Or Without Polycystic Liver Disease. Among its related pathways are Semaphorin interactions and Developmental Biology. Gene Ontology (GO) annotations related to this gene include semaphorin receptor activity. An important paralog of this gene is PLXNA2.

UniProtKB/Swiss-Prot Summary for PLXNA4 Gene

  • Coreceptor for SEMA3A. Necessary for signaling by class 3 semaphorins and subsequent remodeling of the cytoskeleton. Plays a role in axon guidance in the developing nervous system. Class 3 semaphorins bind to a complex composed of a neuropilin and a plexin. The plexin modulates the affinity of the complex for specific semaphorins, and its cytoplasmic domain is required for the activation of down-stream signaling events in the cytoplasm (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 PLXNA4 Gene

Genomics for PLXNA4 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for PLXNA4 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
GH07J132575 Promoter/Enhancer 2 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas 258.6 +72.6 72588 3.8 ZNF654 ZIC2 ZNF341 ZEB1 CTCF CTBP1 ZNF610 SIN3A ZBTB48 ZNF2 PLXNA4 LOC100506937 RF00017-6112 HSALNG0061451
GH07J132650 Enhancer 0.7 Ensembl ENCODE 250.7 -1.7 -1729 1.2 ZNF217 CTBP1 RXRA SIN3A REST DPF2 SP1 MNT ZNF592 FLJ40288 PLXNA4 HSALNG0061456 CHCHD3
GH07J132410 Enhancer 1.3 FANTOM5 Ensembl ENCODE dbSUPER 12.5 +238.4 238387 1.8 ZNF600 ZNF580 ATF2 ZIC2 FEZF1 ZNF341 ZNF843 ATF1 ATF4 ZNF518A LOC102724906 PLXNA4 lnc-EXOC4-8 LOC105375511 PODXL
GH07J132614 Promoter/Enhancer 0.9 ENCODE CraniofacialAtlas 11.9 +33.9 33881 0.3 EZH2 POLR2A SIN3A SPI1 TAF1 CTCF RAD21 IKZF1 PLXNA4 FLJ40288 RF00017-6112 HSALNG0061451
GH07J132580 Enhancer 0.9 Ensembl ENCODE 10.6 +68.0 67994 1 ZNF654 ATF2 REST TRIM22 CTCF RAD21 SMC3 SKIL ZNF2 ZNF143 FLJ40288 PLXNA4 RF00017-6112 HSALNG0061451
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around PLXNA4 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for PLXNA4

Top Transcription factor binding sites by QIAGEN in the PLXNA4 gene promoter:
  • AhR
  • C/EBPalpha
  • E47
  • Oct-B1
  • oct-B2
  • oct-B3
  • p300
  • POU2F1
  • STAT5A
  • Tal-1beta

Genomic Locations for PLXNA4 Gene

Latest Assembly
chr7:132,123,332-132,648,688
(GRCh38/hg38)
Size:
525,357 bases
Orientation:
Minus strand

Previous Assembly
chr7:131,808,099-132,333,447
(GRCh37/hg19 by Entrez Gene)
Size:
525,349 bases
Orientation:
Minus strand

chr7:131,808,091-132,333,447
(GRCh37/hg19 by Ensembl)
Size:
525,357 bases
Orientation:
Minus strand

Genomic View for PLXNA4 Gene

Genes around PLXNA4 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PLXNA4 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PLXNA4 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PLXNA4 Gene

Proteins for PLXNA4 Gene

  • Protein details for PLXNA4 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9HCM2-PLXA4_HUMAN
    Recommended name:
    Plexin-A4
    Protein Accession:
    Q9HCM2
    Secondary Accessions:
    • A4D1N6
    • E9PAM2
    • Q6UWC6
    • Q6ZW89
    • Q8N969
    • Q8ND00
    • Q8NEN3
    • Q9NTD4

    Protein attributes for PLXNA4 Gene

    Size:
    1894 amino acids
    Molecular mass:
    212455 Da
    Quaternary structure:
    • Interacts with NRP1 and NRP2.
    SequenceCaution:
    • Sequence=AAQ89209.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for PLXNA4 Gene

    Alternative splice isoforms for PLXNA4 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for PLXNA4 Gene

Post-translational modifications for PLXNA4 Gene

  • Glycosylation at Asn655, Asn1007, Asn1132, and Asn1180
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for PLXNA4 Gene

Domains & Families for PLXNA4 Gene

Gene Families for PLXNA4 Gene

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

Suggested Antigen Peptide Sequences for PLXNA4 Gene

GenScript: Design optimal peptide antigens:
  • Plexin A4 (A4D1N7_HUMAN)
  • Plexin-A4 (PLXA4_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q9HCM2

UniProtKB/Swiss-Prot:

PLXA4_HUMAN :
  • Belongs to the plexin family.
Family:
  • Belongs to the plexin family.
genes like me logo Genes that share domains with PLXNA4: view

Function for PLXNA4 Gene

Molecular function for PLXNA4 Gene

UniProtKB/Swiss-Prot Function:
Coreceptor for SEMA3A. Necessary for signaling by class 3 semaphorins and subsequent remodeling of the cytoskeleton. Plays a role in axon guidance in the developing nervous system. Class 3 semaphorins bind to a complex composed of a neuropilin and a plexin. The plexin modulates the affinity of the complex for specific semaphorins, and its cytoplasmic domain is required for the activation of down-stream signaling events in the cytoplasm (By similarity).
GENATLAS Biochemistry:
plexin A4,calcium-dependent cell adhesion molecule at the neuronal cell surface,receptor for the semaphorin 7A (SEMA7A)

Phenotypes From GWAS Catalog for PLXNA4 Gene

Gene Ontology (GO) - Molecular Function for PLXNA4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI --
GO:0017154 semaphorin receptor activity IBA 21873635
genes like me logo Genes that share ontologies with PLXNA4: view
genes like me logo Genes that share phenotypes with PLXNA4: view

Animal Models for PLXNA4 Gene

MGI Knock Outs for PLXNA4:

Animal Models for research

  • Taconic Biosciences Mouse Models for PLXNA4

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PLXNA4

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for PLXNA4 Gene

Localization for PLXNA4 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PLXNA4 Gene

Cell membrane. Single-pass type I membrane protein.

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 PLXNA4 gene
Compartment Confidence
plasma membrane 5
extracellular 2
cytoskeleton 2
mitochondrion 2
nucleus 2
cytosol 2
peroxisome 1
endoplasmic reticulum 1
endosome 1
lysosome 1
golgi apparatus 1

Subcellular locations from the

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

Gene Ontology (GO) - Cellular Components for PLXNA4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0002116 semaphorin receptor complex IBA,TAS 19909241
GO:0005886 plasma membrane TAS --
GO:0005887 integral component of plasma membrane IBA 21873635
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with PLXNA4: view

Pathways & Interactions for PLXNA4 Gene

genes like me logo Genes that share pathways with PLXNA4: view

Pathways by source for PLXNA4 Gene

1 Cell Signaling Technology pathway for PLXNA4 Gene

SIGNOR curated interactions for PLXNA4 Gene

Is activated by:

Gene Ontology (GO) - Biological Process for PLXNA4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007162 negative regulation of cell adhesion IBA 21873635
GO:0007165 signal transduction IEA --
GO:0007399 nervous system development IEA --
GO:0007411 axon guidance IEA --
GO:0008045 motor neuron axon guidance IEA --
genes like me logo Genes that share ontologies with PLXNA4: view

Drugs & Compounds for PLXNA4 Gene

No Compound Related Data Available

Transcripts for PLXNA4 Gene

mRNA/cDNA for PLXNA4 Gene

4 REFSEQ mRNAs :
15 NCBI additional mRNA sequence :
5 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 PLXNA4

Alternative Splicing Database (ASD) splice patterns (SP) for PLXNA4 Gene

No ASD Table

Relevant External Links for PLXNA4 Gene

GeneLoc Exon Structure for
PLXNA4

Expression for PLXNA4 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for PLXNA4 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for PLXNA4 Gene

This gene is overexpressed in Fetal Brain (25.1), Brain (17.7), Frontal cortex (12.0), and Peripheral blood mononuclear cells (7.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for PLXNA4 Gene



Protein tissue co-expression partners for PLXNA4 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for PLXNA4

SOURCE GeneReport for Unigene cluster for PLXNA4 Gene:

Hs.511454

Evidence on tissue expression from TISSUES for PLXNA4 Gene

  • Nervous system(4.9)
  • Kidney(4.3)
  • Eye(2.3)
  • Heart(2.2)
  • Blood(2.1)
genes like me logo Genes that share expression patterns with PLXNA4: view

Primer products for research

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for PLXNA4 Gene

Orthologs for PLXNA4 Gene

This gene was present in the common ancestor of chordates.

Orthologs for PLXNA4 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia PLXNA4 29 30
  • 99.54 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia PLEX2 30
  • 97 (a)
OneToOne
PLXNA4 29
  • 91.37 (n)
Dog
(Canis familiaris)
Mammalia PLXNA4 29 30
  • 91.92 (n)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia PLXNA4 30
  • 91 (a)
OneToOne
Mouse
(Mus musculus)
Mammalia Plxna4 29 16 30
  • 89.54 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Plxna4a 29
  • 89.51 (n)
Platypus
(Ornithorhynchus anatinus)
Mammalia -- 30
  • 82 (a)
OneToMany
-- 30
  • 81 (a)
OneToMany
-- 30
  • 68 (a)
OneToMany
Chicken
(Gallus gallus)
Aves PLXNA4 30
  • 92 (a)
OneToOne
PLXNA4B 29
  • 82.24 (n)
Lizard
(Anolis carolinensis)
Reptilia PLXNA4 30
  • 89 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia plxna4 29
  • 73.57 (n)
Zebrafish
(Danio rerio)
Actinopterygii plxna4 29 30
  • 72.64 (n)
OneToOne
Species where no ortholog for PLXNA4 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • 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)
  • Fruit Fly (Drosophila melanogaster)
  • 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 Squirt (Ciona savignyi)
  • 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)
  • Worm (Caenorhabditis elegans)

Evolution for PLXNA4 Gene

ENSEMBL:
Gene Tree for PLXNA4 (if available)
TreeFam:
Gene Tree for PLXNA4 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for PLXNA4: view image
Alliance of Genome Resources:
Additional Orthologs for PLXNA4

Paralogs for PLXNA4 Gene

Paralogs for PLXNA4 Gene

(10) SIMAP similar genes for PLXNA4 Gene using alignment to 2 proteins:

  • PLXA4_HUMAN
  • A4D1N7_HUMAN
genes like me logo Genes that share paralogs with PLXNA4: view

Variants for PLXNA4 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for PLXNA4 Gene

SNP ID Clinical significance and condition Chr 07 pos Variation AA Info Type
rs10248377 Benign: not provided 132,181,396(-) C/T
NM_020911.1(PLXNA4):c.3477G>A (p.Thr1159=)
SYNONYMOUS
rs112682233 Benign: not provided 132,241,157(-) C/T
NM_020911.1(PLXNA4):c.1513G>A (p.Val505Ile)
MISSENSE
rs113388134 Benign: not provided 132,164,134(-) G/A
NM_020911.1(PLXNA4):c.4500+8C>T
INTRON
rs113830939 Benign: not provided 132,508,612(-) G/A
NM_020911.1(PLXNA4):c.82C>T (p.Arg28Trp)
MISSENSE
rs115629766 Likely Benign: not provided 132,507,661(-) G/A
NM_020911.1(PLXNA4):c.1033C>T (p.Arg345Trp)
MISSENSE

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for PLXNA4 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 PLXNA4 Gene

Variant ID Type Subtype PubMed ID
dgv1961e212 CNV gain 25503493
esv2462922 CNV insertion 19546169
esv2662010 CNV deletion 23128226
esv2665361 CNV deletion 23128226
esv2667603 CNV deletion 23128226
esv2735160 CNV deletion 23290073
esv2735161 CNV deletion 23290073
esv2735163 CNV deletion 23290073
esv2735164 CNV deletion 23290073
esv2735165 CNV deletion 23290073
esv2735166 CNV deletion 23290073
esv2735167 CNV deletion 23290073
esv2735168 CNV deletion 23290073
esv2759564 CNV gain 17122850
esv3386177 CNV duplication 20981092
esv3449281 CNV duplication 20981092
esv3451174 CNV insertion 20981092
esv3542445 CNV deletion 23714750
esv3542447 CNV deletion 23714750
esv3615056 CNV gain 21293372
esv996570 CNV deletion 20482838
nsv1030698 CNV loss 25217958
nsv1032205 CNV gain 25217958
nsv1074552 CNV deletion 25765185
nsv1074553 CNV deletion 25765185
nsv1078598 CNV duplication 25765185
nsv1115009 CNV deletion 24896259
nsv1119552 CNV insertion 24896259
nsv1124979 CNV duplication 24896259
nsv1140204 CNV insertion 24896259
nsv1146570 CNV duplication 26484159
nsv1150041 CNV deletion 26484159
nsv1151159 CNV insertion 26484159
nsv464724 CNV loss 19166990
nsv476543 CNV novel sequence insertion 20440878
nsv478331 CNV novel sequence insertion 20440878
nsv478530 CNV novel sequence insertion 20440878
nsv507418 OTHER sequence alteration 20534489
nsv522425 CNV gain 19592680
nsv525647 CNV loss 19592680
nsv526514 CNV loss 19592680
nsv526523 CNV loss 19592680
nsv608438 CNV loss 21841781
nsv608439 CNV loss 21841781
nsv820471 CNV deletion 20802225
nsv824308 CNV loss 20364138
nsv831135 CNV loss 17160897
nsv831136 CNV loss 17160897
nsv831138 CNV gain 17160897
nsv831139 CNV loss 17160897
nsv831140 CNV loss 17160897
nsv831141 CNV loss 17160897

Variation tolerance for PLXNA4 Gene

Residual Variation Intolerance Score: 3.84% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.46; 64.18% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PLXNA4 Gene

Human Gene Mutation Database (HGMD)
PLXNA4
SNPedia medical, phenotypic, and genealogical associations of SNPs for
PLXNA4
Leiden Open Variation Database (LOVD)
PLXNA4

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PLXNA4 Gene

Disorders for PLXNA4 Gene

MalaCards: The human disease database

(1) MalaCards diseases for PLXNA4 Gene - From: COP

- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for PLXNA4

Human Genome Epidemiology Navigator
(HuGE)
Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
genes like me logo Genes that share disorders with PLXNA4: view

No data available for UniProtKB/Swiss-Prot and Genatlas for PLXNA4 Gene

Publications for PLXNA4 Gene

  1. Genome-wide association study of lung function decline in adults with and without asthma. (PMID: 22424883) Imboden M … Probst-Hensch NM (The Journal of allergy and clinical immunology 2012) 3 40
  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. Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study. (PMID: 20628086) Bailey SD … DREAM investigators (Diabetes care 2010) 3 40
  4. 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
  5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4

Products for PLXNA4 Gene

Sources for PLXNA4 Gene