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Aliases for SEMA5A Gene

Aliases for SEMA5A Gene

  • Semaphorin 5A 2 3 5
  • Sema Domain, Seven Thrombospondin Repeats (Type 1 And Type 1-Like), Transmembrane Domain (TM) And Short Cytoplasmic Domain, (Semaphorin) 5A 2 3
  • Sema F 3 4
  • SEMAF 3 4
  • Semaphorin-5A 3
  • Semaphorin F 3
  • Semaphorin-F 4
  • SemF 3

External Ids for SEMA5A Gene

Previous HGNC Symbols for SEMA5A Gene

  • SEMAF

Previous GeneCards Identifiers for SEMA5A Gene

  • GC05M009206
  • GC05M009071
  • GC05M009091

Summaries for SEMA5A Gene

Entrez Gene Summary for SEMA5A Gene

  • This gene belongs to the semaphorin gene family that encodes membrane proteins containing a semaphorin domain and several thrombospondin type-1 repeats. Members of this family are involved in axonal guidance during neural development. This gene has been implicated as an autism susceptibility gene.[provided by RefSeq, Jan 2010]

GeneCards Summary for SEMA5A Gene

SEMA5A (Semaphorin 5A) is a Protein Coding gene. Diseases associated with SEMA5A include Cri-Du-Chat Syndrome. Among its related pathways are O-glycosylation of TSR domain-containing proteins and Activation of cAMP-Dependent PKA. GO annotations related to this gene include receptor activity and semaphorin receptor binding. An important paralog of this gene is SEMA5B.

UniProtKB/Swiss-Prot for SEMA5A Gene

  • Bifunctional axonal guidance cue regulated by sulfated proteoglycans; attractive effects result from interactions with heparan sulfate proteoglycans (HSPGs), while the inhibitory effects depend on interactions with chondroitin sulfate proteoglycans (CSPGs) (By similarity). Ligand for receptor PLXNB3. In glioma cells, SEMA5A stimulation of PLXNB3 results in the disassembly of F-actin stress fibers, disruption of focal adhesions and cellular collapse as well as inhibition of cell migration and invasion through ARHGDIA-mediated inactivation of RAC1. May promote angiogenesis by increasing endothelial cell proliferation and migration and inhibiting apoptosis.

Gene Wiki entry for SEMA5A Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SEMA5A Gene

Genomics for SEMA5A Gene

Regulatory Elements for SEMA5A Gene

Enhancers for SEMA5A Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH05F009437 0.7 Ensembl ENCODE 17.3 +106.8 106838 4.0 JUND SPI1 SEMA5A ENSG00000248537 GC05P009389 ENSG00000279698
GH05F009347 0.8 Ensembl ENCODE 12.1 +197.4 197381 1.9 HDAC1 PKNOX1 SMARCA4 POLR2A SEMA5A GC05P009360 GC05M008903
GH05F009284 0.5 Ensembl ENCODE 17.5 +261.0 261032 1.5 SEMA5A SNORD123 GC05M009285 GC05P009281
GH05F009483 0.5 Ensembl ENCODE 15.6 +62.3 62339 1.5 SNHG18 SEMA5A SNORD123 ENSG00000272417 ENSG00000279698 GC05P009389
GH05F009408 0.6 ENCODE 9.8 +135.7 135664 3.6 ATF3 ZBTB33 RAD21 YY1 NR2F2 ENSG00000248537 SEMA5A SNORD123 GC05P009389 ENSG00000279698
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around SEMA5A on UCSC Golden Path with GeneCards custom track

Promoters for SEMA5A Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00001407366 221 5001 TBL1XR1 SIN3A ZNF2 RAD21 RFX5 EGR1 SCRT2 ZNF143 EGR2 ZNF654

Genomic Location for SEMA5A Gene

Chromosome:
5
Start:
9,035,026 bp from pter
End:
9,546,121 bp from pter
Size:
511,096 bases
Orientation:
Minus strand

Genomic View for SEMA5A Gene

Genes around SEMA5A on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SEMA5A Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SEMA5A Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SEMA5A Gene

Proteins for SEMA5A Gene

  • Protein details for SEMA5A Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q13591-SEM5A_HUMAN
    Recommended name:
    Semaphorin-5A
    Protein Accession:
    Q13591
    Secondary Accessions:
    • D3DTC6
    • O60408
    • Q1RLL9

    Protein attributes for SEMA5A Gene

    Size:
    1074 amino acids
    Molecular mass:
    120615 Da
    Quaternary structure:
    • Binds PLXNB3.

neXtProt entry for SEMA5A Gene

Post-translational modifications for SEMA5A Gene

  • Ubiquitination at Lys 1035
  • Glycosylation at Asn 142, Asn 168, Asn 227, Asn 277, Asn 323, Asn 367, Asn 437, Asn 536, Asn 591, Asn 717, and Asn 933
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for SEMA5A Gene

Domains & Families for SEMA5A Gene

Gene Families for SEMA5A Gene

Suggested Antigen Peptide Sequences for SEMA5A Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q13591

UniProtKB/Swiss-Prot:

SEM5A_HUMAN :
  • Contains 1 PSI domain.
  • Belongs to the semaphorin family.
Domain:
  • Contains 1 PSI domain.
  • Contains 1 Sema domain.
  • Contains 7 TSP type-1 domains.
Family:
  • Belongs to the semaphorin family.
genes like me logo Genes that share domains with SEMA5A: view

Function for SEMA5A Gene

Molecular function for SEMA5A Gene

GENATLAS Biochemistry:
semaphorin 5A,located in the cri-du-chat critical region repellent of the nerve growth cone guidance
UniProtKB/Swiss-Prot Function:
Bifunctional axonal guidance cue regulated by sulfated proteoglycans; attractive effects result from interactions with heparan sulfate proteoglycans (HSPGs), while the inhibitory effects depend on interactions with chondroitin sulfate proteoglycans (CSPGs) (By similarity). Ligand for receptor PLXNB3. In glioma cells, SEMA5A stimulation of PLXNB3 results in the disassembly of F-actin stress fibers, disruption of focal adhesions and cellular collapse as well as inhibition of cell migration and invasion through ARHGDIA-mediated inactivation of RAC1. May promote angiogenesis by increasing endothelial cell proliferation and migration and inhibiting apoptosis.

Gene Ontology (GO) - Molecular Function for SEMA5A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0030215 semaphorin receptor binding ISS,IBA --
GO:0035373 chondroitin sulfate proteoglycan binding ISS --
GO:0043395 heparan sulfate proteoglycan binding ISS --
GO:0045499 chemorepellent activity IBA --
GO:0045545 syndecan binding ISS --
genes like me logo Genes that share ontologies with SEMA5A: view
genes like me logo Genes that share phenotypes with SEMA5A: view

Human Phenotype Ontology for SEMA5A Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for SEMA5A Gene

MGI Knock Outs for SEMA5A:

Animal Model Products

Inhibitory RNA Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for SEMA5A Gene

Localization for SEMA5A Gene

Subcellular locations from UniProtKB/Swiss-Prot for SEMA5A Gene

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 SEMA5A gene
Compartment Confidence
plasma membrane 5
extracellular 5
mitochondrion 1
peroxisome 1
endoplasmic reticulum 1
cytosol 1
lysosome 1
golgi apparatus 1

Gene Ontology (GO) - Cellular Components for SEMA5A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane TAS --
GO:0016020 membrane ISS --
GO:0016021 integral component of membrane IEA,IBA --
GO:0070062 extracellular exosome IDA 23376485
genes like me logo Genes that share ontologies with SEMA5A: view

Pathways & Interactions for SEMA5A Gene

genes like me logo Genes that share pathways with SEMA5A: view

Gene Ontology (GO) - Biological Process for SEMA5A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001755 neural crest cell migration IBA --
GO:0001938 positive regulation of endothelial cell proliferation ISS --
GO:0002043 blood vessel endothelial cell proliferation involved in sprouting angiogenesis ISS --
GO:0007155 cell adhesion TAS 9049630
GO:0007162 negative regulation of cell adhesion ISS --
genes like me logo Genes that share ontologies with SEMA5A: view

No data available for SIGNOR curated interactions for SEMA5A Gene

Transcripts for SEMA5A Gene

Unigene Clusters for SEMA5A Gene

Sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5A:
Representative Sequences:

Inhibitory RNA Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for SEMA5A Gene

No ASD Table

Relevant External Links for SEMA5A Gene

GeneLoc Exon Structure for
SEMA5A
ECgene alternative splicing isoforms for
SEMA5A

Expression for SEMA5A Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for SEMA5A Gene

Protein differential expression in normal tissues from HIPED for SEMA5A Gene

This gene is overexpressed in Urine (62.6) and Fetal testis (6.4).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for SEMA5A Gene



Protein tissue co-expression partners for SEMA5A Gene

NURSA nuclear receptor signaling pathways regulating expression of SEMA5A Gene:

SEMA5A

SOURCE GeneReport for Unigene cluster for SEMA5A Gene:

Hs.27621
genes like me logo Genes that share expression patterns with SEMA5A: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and mRNA Expression by UniProt/SwissProt for SEMA5A Gene

Orthologs for SEMA5A Gene

This gene was present in the common ancestor of animals.

Orthologs for SEMA5A Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SEMA5A 34 35
  • 99.26 (n)
oppossum
(Monodelphis domestica)
Mammalia SEMA5A 35
  • 92 (a)
OneToOne
dog
(Canis familiaris)
Mammalia SEMA5A 34 35
  • 89.44 (n)
cow
(Bos Taurus)
Mammalia SEMA5A 34 35
  • 88.16 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia SEMA5A 35
  • 88 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Sema5a 34 16 35
  • 87.74 (n)
rat
(Rattus norvegicus)
Mammalia Sema5a 34
  • 86.56 (n)
chicken
(Gallus gallus)
Aves SEMA5A 34 35
  • 79.4 (n)
lizard
(Anolis carolinensis)
Reptilia SEMA5A 35
  • 84 (a)
OneToOne
zebrafish
(Danio rerio)
Actinopterygii sema5a 34 35
  • 74.45 (n)
fruit fly
(Drosophila melanogaster)
Insecta Sema-1a 36
  • 39 (a)
CG4383 36
  • 36 (a)
Sema-1b 36
  • 35 (a)
Sema-2a 36
  • 35 (a)
Sema-5c 36 35
  • 35 (a)
worm
(Caenorhabditis elegans)
Secernentea C36B7.5a 36
  • 32 (a)
C36B7.5b 36
  • 32 (a)
mab-20 36
  • 27 (a)
Species where no ortholog for SEMA5A was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya 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)
  • 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 squirt (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)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)

Evolution for SEMA5A Gene

ENSEMBL:
Gene Tree for SEMA5A (if available)
TreeFam:
Gene Tree for SEMA5A (if available)

Paralogs for SEMA5A Gene

Paralogs for SEMA5A Gene

(9) SIMAP similar genes for SEMA5A Gene using alignment to 4 proteins:

Pseudogenes.org Pseudogenes for SEMA5A Gene

genes like me logo Genes that share paralogs with SEMA5A: view

Variants for SEMA5A Gene

Sequence variations from dbSNP and Humsavar for SEMA5A Gene

SNP ID Clin Chr 05 pos Sequence Context AA Info Type
rs386352358 Uncertain significance 9,044,550(-) GGGCT(A/C/G)AGCAG reference, synonymous-codon
rs10036184 -- 9,421,178(+) CTCCA(C/T)GTTTC intron-variant
rs10036254 -- 9,306,214(+) taatt(A/C)ccagg intron-variant
rs10037308 -- 9,081,797(+) TCCAT(G/T)AAAAC intron-variant
rs10037453 -- 9,258,066(+) AATAC(A/T)GAAAA intron-variant

Structural Variations from Database of Genomic Variants (DGV) for SEMA5A Gene

Variant ID Type Subtype PubMed ID
nsv956437 CNV deletion 24416366
nsv830200 CNV loss 17160897
nsv597083 CNV loss 21841781
nsv597082 CNV loss 21841781
nsv597081 CNV gain 21841781
nsv597078 CNV loss 21841781
nsv597077 CNV gain 21841781
nsv597073 CNV loss 21841781
nsv597072 CNV loss 21841781
nsv597071 CNV gain 21841781
nsv597070 CNV loss 21841781
nsv597069 CNV gain 21841781
nsv523773 CNV loss 19592680
nsv519704 CNV loss 19592680
nsv509959 OTHER sequence alteration 20534489
nsv4710 CNV insertion 18451855
nsv4708 CNV deletion 18451855
nsv4707 CNV deletion 18451855
nsv330056 CNV insertion 16902084
nsv328692 CNV deletion 16902084
nsv328306 CNV deletion 16902084
nsv1128142 CNV deletion 24896259
nsv1117537 CNV deletion 24896259
nsv1071667 CNV deletion 25765185
nsv1071662 CNV deletion 25765185
nsv1032672 CNV gain 25217958
esv994899 CNV deletion 20482838
esv987627 CNV deletion 20482838
esv9146 CNV loss 19470904
esv6240 CNV loss 19470904
esv5211 CNV loss 18987735
esv4882 CNV loss 18987735
esv3603974 CNV loss 21293372
esv3603973 CNV loss 21293372
esv3603972 CNV loss 21293372
esv3603970 CNV loss 21293372
esv3575815 CNV gain 25503493
esv3569967 CNV loss 25503493
esv3569966 CNV loss 25503493
esv3565504 CNV deletion 23714750
esv3565501 CNV deletion 23714750
esv3565500 CNV deletion 23714750
esv3565496 CNV deletion 23714750
esv3294718 CNV deletion 24192839
esv2762496 CNV loss 21179565
esv2729728 CNV deletion 23290073
esv2729727 CNV deletion 23290073
esv2729726 CNV deletion 23290073
esv2729725 CNV deletion 23290073
esv2729724 CNV deletion 23290073
esv2729723 CNV deletion 23290073
esv2677155 CNV deletion 23128226
esv2673753 CNV deletion 23128226
esv2665092 CNV deletion 23128226
esv2660190 CNV deletion 23128226
esv2592018 CNV deletion 19546169
esv2490802 CNV deletion 19546169
esv2429188 CNV deletion 19546169
esv22711 CNV loss 19812545
esv2017706 CNV deletion 18987734
esv1762654 CNV deletion 17803354
esv1558495 CNV insertion 17803354
esv1400888 CNV deletion 17803354
esv1376619 CNV deletion 17803354
esv1002666 CNV deletion 20482838
dgv9573n54 CNV gain+loss 21841781
dgv9572n54 CNV gain 21841781
dgv5565n100 CNV gain 25217958
dgv3034n106 CNV deletion 24896259
dgv3033n106 CNV deletion 24896259
dgv3032n106 CNV insertion 24896259
dgv28e194 CNV deletion 18987734
dgv1576e212 CNV loss 25503493

Variation tolerance for SEMA5A Gene

Residual Variation Intolerance Score: 11.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.96; 49.44% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for SEMA5A Gene

Human Gene Mutation Database (HGMD)
SEMA5A
SNPedia medical, phenotypic, and genealogical associations of SNPs for
SEMA5A

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SEMA5A Gene

Disorders for SEMA5A Gene

MalaCards: The human disease database

(1) MalaCards diseases for SEMA5A Gene - From: Orphanet, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
cri-du-chat syndrome
  • 5p deletion syndrome
- elite association - COSMIC cancer census association via MalaCards

Relevant External Links for SEMA5A

Genetic Association Database (GAD)
SEMA5A
Human Genome Epidemiology (HuGE) Navigator
SEMA5A
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
SEMA5A
genes like me logo Genes that share disorders with SEMA5A: view

No data available for UniProtKB/Swiss-Prot and Genatlas for SEMA5A Gene

Publications for SEMA5A Gene

  1. Molecular cloning and mapping of human semaphorin F from the Cri-du- chat candidate interval. (PMID: 9464278) Simmons A.D. … Lovett M. (Biochem. Biophys. Res. Commun. 1998) 2 3 4 22 64
  2. [Correlation study of semaphorin 5a with risk of Parkinson's disease in a Chinese Han population]. (PMID: 19957501) Dong H.R. … Ding X.S. (Zhonghua Yi Xue Za Zhi 2009) 3 22 46 64
  3. Association study of semaphorin 5A with risk of Parkinson's disease in a Chinese Han population. (PMID: 18950607) Ding H. … Zhang Q. (Brain Res. 2008) 3 22 46 64
  4. Polymorphism in semaphorin 5A (Sema5A) gene is not a marker of Parkinson's disease risk. (PMID: 16481103) Bialecka M. … Drozdzik M. (Neurosci. Lett. 2006) 3 22 46 64
  5. Plexin-B3 is a functional receptor for semaphorin 5A. (PMID: 15218527) Artigiani S. … Tamagnone L. (EMBO Rep. 2004) 3 4 22 64

Products for SEMA5A Gene

Sources for SEMA5A Gene

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