Human Gene PLXNA1 (ENST00000393409.3_3) from GENCODE V47lift37

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Description: plexin A1 (from RefSeq NM_032242.4)
Gencode Transcript: ENST00000393409.3_3
Gencode Gene: ENSG00000114554.12_11
Transcript (Including UTRs)
Position: hg19 chr3:126,701,958-126,756,232 Size: 54,275 Total Exon Count: 32 Strand: +
Coding Region
Position: hg19 chr3:126,707,437-126,752,860 Size: 45,424 Coding Exon Count: 31

Page Index	Sequence and Links	UniProtKB Comments	Primers	MalaCards	CTD
Gene Alleles	RNA-Seq Expression	Microarray Expression	RNA Structure	Protein Structure	Other Species
GO Annotations	mRNA Descriptions	Pathways	Other Names	Model Information	Methods

Data last updated at UCSC: 2024-08-22 23:36:26

Sequence and Links to Tools and Databases

Genomic Sequence (chr3:126,701,958-126,756,232)			mRNA (may differ from genome)		Protein (1896 aa)
Gene Sorter	Genome Browser	Other Species FASTA	VisiGene	Gene interactions	Table Schema
AlphaFold	BioGPS	Ensembl	Entrez Gene	ExonPrimer	GeneCards
HGNC	Malacards	MGI	OMIM	PubMed	Reactome
UniProtKB	Wikipedia	BioGrid CRISPR DB

Comments and Description Text from UniProtKB


	ID: PLXA1_HUMAN DESCRIPTION: RecName: Full=Plexin-A1; AltName: Full=Semaphorin receptor NOV; Flags: Precursor; FUNCTION: Coreceptor for SEMA3A, SEMA3C, SEMA3F and SEMA6D. Necessary for signaling by class 3 semaphorins and subsequent remodeling of the cytoskeleton. Plays a role in axon guidance, invasive growth and cell migration. 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). SUBUNIT: Interacts directly with NRP1 and NRP2. Interacts with FARP2, RND1 and KDR/VEGFR2. Binding of SEMA3A leads to dissociation of FARP2 (By similarity). SUBCELLULAR LOCATION: Cell membrane (Probable); Single-pass type I membrane protein (By similarity). TISSUE SPECIFICITY: Detected in fetal brain, lung, liver and kidney. SIMILARITY: Belongs to the plexin family. SIMILARITY: Contains 4 IPT/TIG domains. SIMILARITY: Contains 1 Sema domain.

Primer design for this transcript

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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.
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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: PLXNA1 Diseases sorted by gene-association score: hereditary congenital facial paresis (13), dubowitz syndrome (7)

Comparative Toxicogenomics Database (CTD)


	The following chemicals interact with this gene C472791 3-(4'-hydroxy-3'-adamantylbiphenyl-4-yl)acrylic acid C009505 4,4'-diaminodiphenylmethane D000082 Acetaminophen D003993 Dibutyl Phthalate D004958 Estradiol D018038 Sodium Selenite C008261 lead acetate C061133 tamibarotene C517826 tetrabrominated diphenyl ether 47

Common Gene Haplotype Alleles


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RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)


	Highest median expression: 21.00 RPKM in Brain - Cortex Total median expression: 461.14 RPKM View in GTEx track of Genome Browser View at GTEx portal View GTEx Body Map

Microarray Expression Data


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mRNA Secondary Structure of 3' and 5' UTRs

Region	Fold Energy	Bases	Energy/Base	Display As
5' UTR	-147.50	246	-0.600	Picture	PostScript	Text
3' UTR	-1514.50	3372	-0.449	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
IPR013783 - Ig-like_fold
IPR014756 - Ig_E-set
IPR002909 - IPT_TIG_rcpt
IPR003659 - Plexin-like
IPR016201 - Plexin-like_fold
IPR013548 - Plexin_cytoplasmic_RasGAP_dom
IPR002165 - Plexin_repeat
IPR008936 - Rho_GTPase_activation_prot
IPR001627 - Semaphorin/CD100_Ag
IPR015943 - WD40/YVTN_repeat-like_dom

Pfam Domains:
PF01403 - Sema domain
PF01437 - Plexin repeat
PF01833 - IPT/TIG domain
PF08337 - Plexin cytoplasmic RasGAP domain
PF17960 - TIG domain
PF18020 - TIG domain found in plexin

SCOP Domains:
48350 - GTPase activation domain, GAP
81296 - E set domains
50960 - TolB, C-terminal domain
63825 - YWTD domain
63829 - Calcium-dependent phosphotriesterase
75011 - 3-carboxy-cis,cis-mucoante lactonizing enzyme
101912 - Sema domain
50969 - YVTN repeat-like/Quinoprotein amine dehydrogenase
103575 - Plexin repeat

ModBase Predicted Comparative 3D Structure on Q9UIW2


Front	Top	Side

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.

Mouse	Rat	Zebrafish	D. melanogaster	C. elegans	S. cerevisiae
No ortholog	No ortholog	No ortholog	No ortholog	No ortholog	No ortholog
Gene Details	Gene Details
Gene Sorter	Gene Sorter
	RGD	Ensembl

Gene Ontology (GO) Annotations with Structured Vocabulary


	Molecular Function: GO:0017154 semaphorin receptor activity GO:0038023 signaling receptor activity Biological Process: GO:0007165 signal transduction GO:0007275 multicellular organism development GO:0014910 regulation of smooth muscle cell migration GO:0021785 branchiomotor neuron axon guidance GO:0048841 regulation of axon extension involved in axon guidance GO:0060666 dichotomous subdivision of terminal units involved in salivary gland branching GO:0071526 semaphorin-plexin signaling pathway GO:0097485 neuron projection guidance GO:1990138 neuron projection extension Cellular Component: GO:0002116 semaphorin receptor complex GO:0005886 plasma membrane GO:0016020 membrane GO:0016021 integral component of membrane GO:0070062 extracellular exosome

Descriptions from all associated GenBank mRNAs


	AB385178 - Synthetic construct DNA, clone: pF1KB7014, Homo sapiens PLXNA1 gene for plexin-A1 precursor, complete cds, without stop codon, in Flexi system. JA482209 - Sequence 192 from Patent WO2011072091. JE980501 - Sequence 192 from Patent EP2862929. LF384155 - JP 2014500723-A/191658: Polycomb-Associated Non-Coding RNAs. X87832 - Homo sapiens mRNA for partial NOV/plexin-A1 protein. BC156129 - Synthetic construct Homo sapiens clone IMAGE:100062448, MGC:190517 plexin A1 (PLXNA1) mRNA, encodes complete protein. BC157020 - Synthetic construct Homo sapiens clone IMAGE:100063348, MGC:190752 plexin A1 (PLXNA1) mRNA, encodes complete protein. AK293425 - Homo sapiens cDNA FLJ57256 complete cds, highly similar to Plexin-A1 precursor. AK126101 - Homo sapiens cDNA FLJ44113 fis, clone TESTI4046487, highly similar to Mus musculus plexin A1 (Plxna1). MA619732 - JP 2018138019-A/191658: Polycomb-Associated Non-Coding RNAs. LF212063 - JP 2014500723-A/19566: Polycomb-Associated Non-Coding RNAs. JD216178 - Sequence 197202 from Patent EP1572962. MA447640 - JP 2018138019-A/19566: Polycomb-Associated Non-Coding RNAs. LF364018 - JP 2014500723-A/171521: Polycomb-Associated Non-Coding RNAs. LF364017 - JP 2014500723-A/171520: Polycomb-Associated Non-Coding RNAs. LF364015 - JP 2014500723-A/171518: Polycomb-Associated Non-Coding RNAs. AK128612 - Homo sapiens cDNA FLJ46771 fis, clone TRACH3025828, highly similar to Plexin-A1 precursor. LF364014 - JP 2014500723-A/171517: Polycomb-Associated Non-Coding RNAs. LF364013 - JP 2014500723-A/171516: Polycomb-Associated Non-Coding RNAs. AL162013 - Homo sapiens mRNA; cDNA DKFZp761P19121 (from clone DKFZp761P19121); partial cds. LF364012 - JP 2014500723-A/171515: Polycomb-Associated Non-Coding RNAs. LF364011 - JP 2014500723-A/171514: Polycomb-Associated Non-Coding RNAs. AK127254 - Homo sapiens cDNA FLJ45321 fis, clone BRHIP3006279. AK055605 - Homo sapiens cDNA FLJ31043 fis, clone HSYRA2000248. JD134095 - Sequence 115119 from Patent EP1572962. LF364010 - JP 2014500723-A/171513: Polycomb-Associated Non-Coding RNAs. JD281609 - Sequence 262633 from Patent EP1572962. JD333868 - Sequence 314892 from Patent EP1572962. JD229561 - Sequence 210585 from Patent EP1572962. JD157411 - Sequence 138435 from Patent EP1572962. JD407798 - Sequence 388822 from Patent EP1572962. JD114722 - Sequence 95746 from Patent EP1572962. JD097382 - Sequence 78406 from Patent EP1572962. JD050775 - Sequence 31799 from Patent EP1572962. JD050540 - Sequence 31564 from Patent EP1572962. JD470024 - Sequence 451048 from Patent EP1572962. JD370145 - Sequence 351169 from Patent EP1572962. JD231051 - Sequence 212075 from Patent EP1572962. BC017323 - Homo sapiens plexin A1, mRNA (cDNA clone IMAGE:4551416), partial cds. JD420445 - Sequence 401469 from Patent EP1572962. JD485982 - Sequence 467006 from Patent EP1572962. JD210721 - Sequence 191745 from Patent EP1572962. JD210722 - Sequence 191746 from Patent EP1572962. JD179814 - Sequence 160838 from Patent EP1572962. JD364198 - Sequence 345222 from Patent EP1572962. JD131148 - Sequence 112172 from Patent EP1572962. JD445966 - Sequence 426990 from Patent EP1572962. JD467373 - Sequence 448397 from Patent EP1572962. JD277995 - Sequence 259019 from Patent EP1572962. JD107918 - Sequence 88942 from Patent EP1572962. JD200629 - Sequence 181653 from Patent EP1572962. JD426636 - Sequence 407660 from Patent EP1572962. JD203338 - Sequence 184362 from Patent EP1572962. JD483230 - Sequence 464254 from Patent EP1572962. JD157574 - Sequence 138598 from Patent EP1572962. JD077788 - Sequence 58812 from Patent EP1572962. JD142266 - Sequence 123290 from Patent EP1572962. BC042904 - Homo sapiens plexin A1, mRNA (cDNA clone IMAGE:5258253), partial cds. JD157266 - Sequence 138290 from Patent EP1572962. JD390464 - Sequence 371488 from Patent EP1572962. JD301497 - Sequence 282521 from Patent EP1572962. JD290844 - Sequence 271868 from Patent EP1572962. JD128527 - Sequence 109551 from Patent EP1572962. JD215393 - Sequence 196417 from Patent EP1572962. JD209412 - Sequence 190436 from Patent EP1572962. JD546961 - Sequence 527985 from Patent EP1572962. AK054675 - Homo sapiens cDNA FLJ30113 fis, clone BNGH42000474. LF364007 - JP 2014500723-A/171510: Polycomb-Associated Non-Coding RNAs. JD459924 - Sequence 440948 from Patent EP1572962. LF364005 - JP 2014500723-A/171508: Polycomb-Associated Non-Coding RNAs. JD470674 - Sequence 451698 from Patent EP1572962. LF364004 - JP 2014500723-A/171507: Polycomb-Associated Non-Coding RNAs. AL136663 - Homo sapiens mRNA; cDNA DKFZp564A176 (from clone DKFZp564A176). JD425543 - Sequence 406567 from Patent EP1572962. JD209319 - Sequence 190343 from Patent EP1572962. JD113897 - Sequence 94921 from Patent EP1572962. JD256250 - Sequence 237274 from Patent EP1572962. BC032432 - Homo sapiens plexin A1, mRNA (cDNA clone IMAGE:4517879). DQ594451 - Homo sapiens piRNA piR-60563, complete sequence. JD515599 - Sequence 496623 from Patent EP1572962. JD171469 - Sequence 152493 from Patent EP1572962. JD151332 - Sequence 132356 from Patent EP1572962. JD282360 - Sequence 263384 from Patent EP1572962. JD345493 - Sequence 326517 from Patent EP1572962. KJ901641 - Synthetic construct Homo sapiens clone ccsbBroadEn_11035 PLXNA1 gene, encodes complete protein. JD541680 - Sequence 522704 from Patent EP1572962. JD532544 - Sequence 513568 from Patent EP1572962. JD453228 - Sequence 434252 from Patent EP1572962. JD273496 - Sequence 254520 from Patent EP1572962. JD370032 - Sequence 351056 from Patent EP1572962. JD150170 - Sequence 131194 from Patent EP1572962. JD194272 - Sequence 175296 from Patent EP1572962. JD194273 - Sequence 175297 from Patent EP1572962. JD387416 - Sequence 368440 from Patent EP1572962. JD192850 - Sequence 173874 from Patent EP1572962. LF364000 - JP 2014500723-A/171503: Polycomb-Associated Non-Coding RNAs. JD562729 - Sequence 543753 from Patent EP1572962. JD473765 - Sequence 454789 from Patent EP1572962. JD232154 - Sequence 213178 from Patent EP1572962. LF363999 - JP 2014500723-A/171502: Polycomb-Associated Non-Coding RNAs. JD248479 - Sequence 229503 from Patent EP1572962. JD552281 - Sequence 533305 from Patent EP1572962. JD490714 - Sequence 471738 from Patent EP1572962. JD304303 - Sequence 285327 from Patent EP1572962. MA599595 - JP 2018138019-A/171521: Polycomb-Associated Non-Coding RNAs. MA599594 - JP 2018138019-A/171520: Polycomb-Associated Non-Coding RNAs. MA599592 - JP 2018138019-A/171518: Polycomb-Associated Non-Coding RNAs. MA599591 - JP 2018138019-A/171517: Polycomb-Associated Non-Coding RNAs. MA599590 - JP 2018138019-A/171516: Polycomb-Associated Non-Coding RNAs. MA599589 - JP 2018138019-A/171515: Polycomb-Associated Non-Coding RNAs. MA599588 - JP 2018138019-A/171514: Polycomb-Associated Non-Coding RNAs. MA599587 - JP 2018138019-A/171513: Polycomb-Associated Non-Coding RNAs. MA599584 - JP 2018138019-A/171510: Polycomb-Associated Non-Coding RNAs. MA599582 - JP 2018138019-A/171508: Polycomb-Associated Non-Coding RNAs. MA599581 - JP 2018138019-A/171507: Polycomb-Associated Non-Coding RNAs. MA599577 - JP 2018138019-A/171503: Polycomb-Associated Non-Coding RNAs. MA599576 - JP 2018138019-A/171502: Polycomb-Associated Non-Coding RNAs.

Biochemical and Signaling Pathways


	Reactome (by CSHL, EBI, and GO) Protein Q9UIW2 (Reactome details) participates in the following event(s): R-HSA-416725 SEMA6D binds to PLXNA1:TREM2:DAP12 R-NUL-421139 Limk1 phosphorylates Cfl1, inactivating it R-HSA-399942 Plexin-A1-4 binds NRP1 R-HSA-399934 Phosphorylation of Plexin-A R-HSA-399933 Sema3A binds Nrp-1 bound to PlexinA R-HSA-399931 Activation of Fyn R-HSA-399946 Recruitment and activation of Cdk5 R-HSA-399951 Phosphorylation of CRMPs by GSK3beta R-HSA-399944 Phosphorylation of CRMPs by 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-416700 Other semaphorin interactions R-HSA-373755 Semaphorin interactions R-HSA-399955 SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion R-HSA-422475 Axon guidance R-HSA-399956 CRMPs in Sema3A signaling R-HSA-1266738 Developmental Biology R-HSA-399954 Sema3A PAK dependent Axon repulsion

Other Names for This Gene


	Alternate Gene Symbols: ENST00000393409.1, ENST00000393409.2, NM_032242, NOV, PLXA1_HUMAN, PLXN1, PLXNA1 , Q9UIW2, uc318vvj.1, uc318vvj.2 UCSC ID: ENST00000393409.3_3 RefSeq Accession: NM_032242.4 Protein: Q9UIW2 (aka PLXA1_HUMAN)

Gene Model Information


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Methods, Credits, and Use Restrictions


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