Human Gene SEMA3A (ENST00000265362.9_7) from GENCODE V47lift37
  Description: semaphorin 3A (from RefSeq NM_006080.3)
Gencode Transcript: ENST00000265362.9_7
Gencode Gene: ENSG00000075213.11_12
Transcript (Including UTRs)
   Position: hg19 chr7:83,585,093-83,824,105 Size: 239,013 Total Exon Count: 17 Strand: -
Coding Region
   Position: hg19 chr7:83,590,687-83,823,902 Size: 233,216 Coding Exon Count: 17 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesGeneReviewsModel Information
Methods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr7:83,585,093-83,824,105)mRNA (may differ from genome)Protein (771 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
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-  Comments and Description Text from UniProtKB
  ID: SEM3A_HUMAN
DESCRIPTION: RecName: Full=Semaphorin-3A; AltName: Full=Semaphorin III; Short=Sema III; Flags: Precursor;
FUNCTION: Induces the collapse and paralysis of neuronal growth cones. Could serve as a ligand that guides specific growth cones by a motility-inhibiting mechanism. Binds to the complex neuropilin-1/plexin-1 (By similarity).
SUBUNIT: Interacts with PLXND1 (By similarity).
SUBCELLULAR LOCATION: Secreted (By similarity).
DOMAIN: Strong binding to neuropilin is mediated by the carboxy third of the protein.
SIMILARITY: Belongs to the semaphorin family.
SIMILARITY: Contains 1 Ig-like C2-type (immunoglobulin-like) domain.
SIMILARITY: Contains 1 PSI domain.
SIMILARITY: Contains 1 Sema domain.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: SEMA3A
Diseases sorted by gene-association score: hypogonadotropic hypogonadism 16 with or without anosmia* (906), kallmann syndrome* (116), sema3a-related isolated gonadotropin-releasing hormone deficiency* (100), spondyloepimetaphyseal dysplasia, sponastrime type (16), angiomatous meningioma (15), spondyloepimetaphyseal dysplasia, missouri type (11), brachyolmia 4 with mild epiphyseal and metaphyseal changes (11), prurigo nodularis (10), cowchock syndrome (10), smed strudwick type (10), kniest dysplasia (9), wallerian degeneration (7), achondrogenesis, type ii or hypochondrogenesis (6), hypochondrogenesis (6), brachial plexus lesion (5), sed congenita (5), brugada syndrome (2), schizophrenia (2), dementia, frontotemporal (1)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 5.84 RPKM in Colon - Sigmoid
Total median expression: 47.55 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -46.60203-0.230 Picture PostScript Text
3' UTR -1247.005594-0.223 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR007110 - Ig-like
IPR013783 - Ig-like_fold
IPR003599 - Ig_sub
IPR003659 - Plexin-like
IPR016201 - Plexin-like_fold
IPR001627 - Semaphorin/CD100_Ag
IPR015943 - WD40/YVTN_repeat-like_dom

Pfam Domains:
PF01403 - Sema domain
PF18452 - Immunoglobulin domain

SCOP Domains:
48726 - Immunoglobulin
101912 - Sema domain
103575 - Plexin repeat

ModBase Predicted Comparative 3D Structure on Q14563
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0030215 semaphorin receptor binding
GO:0038191 neuropilin binding
GO:0045499 chemorepellent activity

Biological Process:
GO:0001764 neuron migration
GO:0002027 regulation of heart rate
GO:0006915 apoptotic process
GO:0007275 multicellular organism development
GO:0007399 nervous system development
GO:0007411 axon guidance
GO:0007413 axonal fasciculation
GO:0008045 motor neuron axon guidance
GO:0010633 negative regulation of epithelial cell migration
GO:0010977 negative regulation of neuron projection development
GO:0021612 facial nerve structural organization
GO:0021637 trigeminal nerve structural organization
GO:0021675 nerve development
GO:0021772 olfactory bulb development
GO:0021785 branchiomotor neuron axon guidance
GO:0021828 gonadotrophin-releasing hormone neuronal migration to the hypothalamus
GO:0030154 cell differentiation
GO:0030517 negative regulation of axon extension
GO:0036486 ventral trunk neural crest cell migration
GO:0046330 positive regulation of JNK cascade
GO:0048485 sympathetic nervous system development
GO:0048813 dendrite morphogenesis
GO:0048841 regulation of axon extension involved in axon guidance
GO:0048843 negative regulation of axon extension involved in axon guidance
GO:0048846 axon extension involved in axon guidance
GO:0048880 sensory system development
GO:0050919 negative chemotaxis
GO:0060385 axonogenesis involved in innervation
GO:0060666 dichotomous subdivision of terminal units involved in salivary gland branching
GO:0061549 sympathetic ganglion development
GO:0061551 trigeminal ganglion development
GO:0071526 semaphorin-plexin signaling pathway
GO:0097490 sympathetic neuron projection extension
GO:0097491 sympathetic neuron projection guidance
GO:1901166 neural crest cell migration involved in autonomic nervous system development
GO:1902285 semaphorin-plexin signaling pathway involved in neuron projection guidance
GO:1902287 semaphorin-plexin signaling pathway involved in axon guidance
GO:1903045 neural crest cell migration involved in sympathetic nervous system development
GO:1903375 facioacoustic ganglion development
GO:2000020 positive regulation of male gonad development
GO:2001224 positive regulation of neuron migration

Cellular Component:
GO:0005576 extracellular region
GO:0005615 extracellular space
GO:0030424 axon
GO:0030425 dendrite


-  Descriptions from all associated GenBank mRNAs
  AK289954 - Homo sapiens cDNA FLJ78428 complete cds, highly similar to Homo sapiens sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3A (SEMA3A), mRNA.
L26081 - Homo sapiens semaphorin-III (Hsema-I) mRNA, complete cds.
BC111416 - Homo sapiens sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3A, mRNA (cDNA clone MGC:133243 IMAGE:40034963), complete cds.
JD089551 - Sequence 70575 from Patent EP1572962.
JD113190 - Sequence 94214 from Patent EP1572962.
JD445613 - Sequence 426637 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q14563 (Reactome details) participates in the following event(s):

R-HSA-399931 Activation of Fyn
R-HSA-399933 Sema3A binds Nrp-1 bound to PlexinA
R-HSA-399934 Phosphorylation of Plexin-A
R-HSA-399951 Phosphorylation of CRMPs by GSK3beta
R-HSA-399944 Phosphorylation of CRMPs by Cdk5
R-HSA-399946 Recruitment and activation of Cdk5
R-HSA-399941 Rac1 binds PlexinA
R-HSA-399947 Tyrosine phosphorylation of CRMPs by Fes
R-HSA-399928 Recruitment of Rnd1 to Plexin A
R-HSA-399930 Activation of PAK by Rac1
R-HSA-399939 Autophosphorylation of PAK
R-HSA-399952 Phosphorylation of LIMK-1 by PAK
R-HSA-399935 Inactivation of R-Ras by Sema3A-Plexin-A GAP activity
R-HSA-399956 CRMPs in Sema3A signaling
R-HSA-399955 SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion
R-HSA-373755 Semaphorin interactions
R-HSA-422475 Axon guidance
R-HSA-399954 Sema3A PAK dependent Axon repulsion
R-HSA-1266738 Developmental Biology

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000265362.1, ENST00000265362.2, ENST00000265362.3, ENST00000265362.4, ENST00000265362.5, ENST00000265362.6, ENST00000265362.7, ENST00000265362.8, NM_006080, Q14563, SEM3A_HUMAN, SEMAD, uc317iau.1, uc317iau.2
UCSC ID: ENST00000265362.9_7
RefSeq Accession: NM_006080.3
Protein: Q14563 (aka SEM3A_HUMAN or SM3A_HUMAN)

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene SEMA3A:
brugada (Brugada Syndrome)
kms (Isolated Gonadotropin-Releasing Hormone (GnRH) Deficiency)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.