Plxnd1 (plexin D1) - Rat Genome Database

Name: Plxnd1
Creator: Rat Genome Database
License: Creative Commons CC BY 4.0
Keywords: Rat Gene RGD Genome

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Gene: Plxnd1 (plexin D1) Rattus norvegicus

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Symbol:

Plxnd1

Name:

plexin D1

RGD ID:

1310796

Description:

Predicted to enable protein domain specific binding activity and semaphorin receptor activity. Predicted to be involved in several processes, including negative regulation of neuron apoptotic process; nervous system development; and positive regulation of axonogenesis. Predicted to act upstream of or within circulatory system development; dichotomous subdivision of terminal units involved in salivary gland branching; and kidney development. Predicted to be located in axon; cell body; and lamellipodium. Predicted to be part of semaphorin receptor complex. Predicted to be active in glutamatergic synapse and plasma membrane. Used to study transient cerebral ischemia. Orthologous to human PLXND1 (plexin D1); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 6-propyl-2-thiouracil; acrylamide.

Type:

protein-coding

RefSeq Status:

VALIDATED

Previously known as:

LOC312652; plexin-D1

RGD Orthologs

Alliance Orthologs

More Info

more info ...

More Info

Species	Gene symbol and name	Data Source	Assertion derived from	less info ...
Orthologs ¹				less info ...
Homo sapiens (human):	PLXND1 (plexin D1)	HGNC	Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, Panther, PhylomeDB, Treefam
Mus musculus (house mouse):	Plxnd1 (plexin D1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chinchilla lanigera (long-tailed chinchilla):	Plxnd1 (plexin D1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	PLXND1 (plexin D1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	PLXND1 (plexin D1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Plxnd1 (plexin D1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	PLXND1 (plexin D1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	PLXND1 (plexin D1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Plxnd1 (plexin D1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Other homologs ²
Homo sapiens (human):	NFATC3 (nuclear factor of activated T cells 3)	HGNC	OMA
Alliance orthologs ³
Homo sapiens (human):	PLXND1 (plexin D1)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Mus musculus (house mouse):	Plxnd1 (plexin D1)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Danio rerio (zebrafish):	plxnd1 (plexin D1)	Alliance	DIOPT (OrthoFinder\|PhylomeDB)
Drosophila melanogaster (fruit fly):	PlexB	Alliance	DIOPT (Hieranoid\|OrthoFinder\|PANTHER)
Xenopus tropicalis (tropical clawed frog):	plxnd1	Alliance	DIOPT (Ensembl Compara\|OMA\|OrthoFinder\|PANTHER\|PhylomeDB)

Latest Assembly:

mRatBN7.2 - mRatBN7.2 Assembly

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	4	150,675,377 - 150,715,706 (-)	NCBI		GRCr8
mRatBN7.2	4	149,002,786 - 149,043,097 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	4	149,002,784 - 149,043,244 (-)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	4	155,231,230 - 155,271,066 (-)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	4	151,015,255 - 151,055,089 (-)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	4	149,638,154 - 149,677,989 (-)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	4	147,854,309 - 147,894,170 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	4	147,854,309 - 147,893,992 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	4	211,138,020 - 211,177,844 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	4	152,080,259 - 152,119,942 (-)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	4	152,325,102 - 152,373,872 (-)	NCBI
Celera	4	137,892,445 - 137,932,104 (-)	NCBI		Celera
Cytogenetic Map	4	q42	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

alkaptonuria (ISO)

Congenital Heart Defects, Multiple Types, 9 (ISO)

diastolic heart failure (ISO)

DiGeorge syndrome (ISS)

immunodeficiency 21 (ISO)

Kleine-Levin syndrome (ISO)

Moebius syndrome (ISO)

Primary Lymphedema with Myelodysplasia (ISO)

transient cerebral ischemia (IMP)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

(1->4)-beta-D-glucan (ISO)

1,2-dimethylhydrazine (ISO)

17beta-estradiol (ISO)

2,3,7,8-tetrachlorodibenzodioxine (EXP)

3,4-methylenedioxymethamphetamine (ISO)

3-Nitrobenzanthrone (ISO)

4,4'-sulfonyldiphenol (ISO)

4-hydroxyphenyl retinamide (ISO)

6-propyl-2-thiouracil (EXP)

acrylamide (EXP,ISO)

aflatoxin B1 (ISO)

Aflatoxin B2 alpha (ISO)

aldrin (ISO)

all-trans-retinoic acid (ISO)

arsenite(3-) (ISO)

aspartame (ISO)

atrazine (EXP)

benzo[a]pyrene (ISO)

benzo[e]pyrene (ISO)

bisphenol A (EXP,ISO)

bisphenol F (ISO)

buta-1,3-diene (ISO)

caffeine (ISO)

carbamazepine (ISO)

carbon nanotube (ISO)

CGP 52608 (ISO)

chloroprene (ISO)

cisplatin (ISO)

clobetasol (ISO)

cobalt dichloride (ISO)

coumestrol (ISO)

DDD (ISO)

DDE (ISO)

DDT (ISO)

dexamethasone (ISO)

dextran sulfate (ISO)

Dibutyl phosphate (ISO)

dicrotophos (ISO)

dieldrin (ISO)

diquat (ISO)

dorsomorphin (ISO)

doxorubicin (ISO)

endosulfan (EXP)

endrin (ISO)

ethanol (ISO)

gamma-hexachlorocyclohexane (ISO)

gentamycin (EXP)

glycidol (EXP)

isoprenaline (ISO)

lead(0) (ISO)

lipopolysaccharide (ISO)

methapyrilene (ISO)

methoxychlor (EXP)

monosodium L-glutamate (ISO)

N-methyl-4-phenylpyridinium (ISO)

ozone (EXP)

paracetamol (EXP)

perfluorohexanesulfonic acid (ISO)

perfluorononanoic acid (ISO)

perfluorooctane-1-sulfonic acid (ISO)

perfluorooctanoic acid (ISO)

pinostrobin (ISO)

raloxifene (ISO)

SB 431542 (ISO)

silver atom (ISO)

silver(0) (ISO)

simvastatin (ISO)

sodium arsenite (ISO)

tetrachloromethane (EXP,ISO)

triptonide (ISO)

troglitazone (ISO)

trovafloxacin (ISO)

tungsten (ISO)

valproic acid (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

angiogenesis (ISO)

aorta development (ISO)

branching involved in blood vessel morphogenesis (ISO)

cardiac septum development (ISO)

coronary vasculature development (ISO)

dichotomous subdivision of terminal units involved in salivary gland branching (ISO)

endothelial cell migration (IBA,ISO)

kidney development (ISO)

negative regulation of cell adhesion (IBA)

negative regulation of neuron apoptotic process (ISO)

outflow tract morphogenesis (ISO)

positive regulation of axonogenesis (IBA)

regulation of angiogenesis (ISO)

regulation of cell migration (IBA,ISO)

regulation of cell shape (IBA)

semaphorin-plexin signaling pathway (ISO)

synapse assembly (ISO)

synaptic target recognition (ISO)

Cellular Component

axon (ISO)

cell body (ISO)

glutamatergic synapse (ISO)

lamellipodium (ISO)

plasma membrane (IBA,ISO)

semaphorin receptor complex (IBA)

Molecular Function

protein binding (ISO)

protein domain specific binding (ISO)

semaphorin receptor activity (IBA,ISO)

References

References - curated

#	Reference Title	Reference Citation
1.	Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium.	Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2.	Rat ISS GO annotations from MGI mouse gene data--August 2006	MGD data from the GO Consortium
3.	GOA pipeline	RGD automated data pipeline
4.	ClinVar Automated Import and Annotation Pipeline	RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
5.	Data Import for Chemical-Gene Interactions	RGD automated import pipeline for gene-chemical interactions
6.	Sema3E/PlexinD1 signaling inhibits postischemic angiogenesis by regulating endothelial DLL4 and filopodia formation in a rat model of ischemic stroke.	Zhou YF, etal., FASEB J. 2019 Apr;33(4):4947-4961. doi: 10.1096/fj.201801706RR. Epub 2019 Jan 17.

Additional References at PubMed

PMID:15239958	PMID:17318185	PMID:17626059	PMID:18992737	PMID:22179111	PMID:23918385	PMID:24841563	PMID:25807483	PMID:26053665	PMID:30007159

Genomics

Comparative Map Data

Plxnd1
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	4	150,675,377 - 150,715,706 (-)	NCBI		GRCr8
mRatBN7.2	4	149,002,786 - 149,043,097 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	4	149,002,784 - 149,043,244 (-)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	4	155,231,230 - 155,271,066 (-)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	4	151,015,255 - 151,055,089 (-)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	4	149,638,154 - 149,677,989 (-)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	4	147,854,309 - 147,894,170 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	4	147,854,309 - 147,893,992 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	4	211,138,020 - 211,177,844 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	4	152,080,259 - 152,119,942 (-)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	4	152,325,102 - 152,373,872 (-)	NCBI
Celera	4	137,892,445 - 137,932,104 (-)	NCBI		Celera
Cytogenetic Map	4	q42	NCBI

PLXND1
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	3	129,555,214 - 129,606,676 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	3	129,555,214 - 129,606,676 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	3	129,274,057 - 129,325,519 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	3	130,756,746 - 130,808,272 (-)	NCBI	NCBI36	Build 36	hg18	NCBI36
Celera	3	127,700,885 - 127,752,418 (-)	NCBI		Celera
Cytogenetic Map	3	q22.1	NCBI
HuRef	3	126,657,250 - 126,708,655 (-)	NCBI		HuRef
CHM1_1	3	129,237,165 - 129,288,702 (-)	NCBI		CHM1_1
T2T-CHM13v2.0	3	132,299,641 - 132,351,112 (-)	NCBI		T2T-CHM13v2.0

Plxnd1
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	6	115,931,772 - 115,972,300 (-)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	6	115,931,772 - 115,971,966 (-)	Ensembl		GRCm39 Ensembl
GRCm38	6	115,954,811 - 115,995,339 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	6	115,954,811 - 115,995,005 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	6	115,904,829 - 115,945,023 (-)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	6	115,921,359 - 115,960,583 (-)	NCBI		MGSCv36	mm8
Celera	6	117,790,105 - 117,830,028 (-)	NCBI		Celera
Cytogenetic Map	6	E3	NCBI
cM Map	6	53.72	NCBI

Plxnd1
(Chinchilla lanigera - long-tailed chinchilla)

Chinchilla Assembly	Chr	Position (strand)	Source	Genome Browsers
Chinchilla Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChiLan1.0 Ensembl	NW_004955429	17,746,814 - 17,776,246 (+)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955429	17,746,814 - 17,775,072 (+)	NCBI	ChiLan1.0	ChiLan1.0

PLXND1
(Pan paniscus - bonobo/pygmy chimpanzee)

Bonobo Assembly	Chr	Position (strand)	Source	Genome Browsers
Bonobo Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
NHGRI_mPanPan1-v2	2	127,487,927 - 127,539,403 (-)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	3	127,492,655 - 127,544,093 (-)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	3	126,613,065 - 126,664,643 (-)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	3	133,964,989 - 133,999,268 (-)	NCBI	panpan1.1	PanPan1.1	panPan2

PLXND1
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	20	5,554,814 - 5,610,417 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	20	5,554,708 - 5,610,122 (+)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	20	5,592,327 - 5,647,912 (+)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	20	5,584,594 - 5,640,188 (+)	NCBI		ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	20	5,584,594 - 5,639,876 (+)	Ensembl		ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	20	5,300,473 - 5,356,062 (+)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	20	5,653,488 - 5,707,957 (+)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	20	5,629,100 - 5,684,701 (+)	NCBI		UU_Cfam_GSD_1.0

Plxnd1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HiC_Itri_2	NW_024404942	18,027,468 - 18,061,533 (-)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936602	848,140 - 881,873 (+)	Ensembl	SpeTri2.0	SpeTri2.0 Ensembl
SpeTri2.0	NW_004936602	848,130 - 882,195 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

PLXND1
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	13	68,946,665 - 68,996,618 (-)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	13	68,946,658 - 68,996,625 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	13	76,179,382 - 76,230,177 (-)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

PLXND1
(Chlorocebus sabaeus - green monkey)

Green Monkey Assembly	Chr	Position (strand)	Source	Genome Browsers
Green Monkey Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1	22	51,440,797 - 51,493,370 (+)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	22	51,441,127 - 51,495,118 (+)	Ensembl	ChlSab1.1	ChlSab1.1 Ensembl	chlSab2
Vero_WHO_p1.0	NW_023666041	114,984,196 - 115,036,739 (-)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Plxnd1
(Heterocephalus glaber - naked mole-rat)

Naked Mole-Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Naked Mole-Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HetGla_female_1.0 Ensembl	NW_004624872	543,553 - 571,019 (-)	Ensembl	HetGla_female_1.0	HetGla_female_1.0 Ensembl	hetGla2
HetGla 1.0	NW_004624872	542,776 - 571,019 (-)	NCBI	HetGla_female_1.0	HetGla 1.0	hetGla2

Variants

Variants in Plxnd1
178 total Variants

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	263
Count of miRNA genes:	168
Interacting mature miRNAs:	185
Transcripts:	ENSRNOT00000032158
Prediction methods:	Microtar, Miranda, Rnahybrid
Result types:	miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.

QTLs in Region (mRatBN7.2)

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
1582237	Kidm34	Kidney mass QTL 34	4	0.0001	kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	4	148090542	168069246	Rat
61446	Coreg2	Compensatory renal growth QTL 2	3.5		kidney mass (VT:0002707)	compensatory renal growth score (CMO:0001894)	4	148423102	157580971	Rat
1300116	Hrtrt5	Heart rate QTL 5	3.76		heart pumping trait (VT:2000009)	heart rate (CMO:0000002)	4	116179486	151161268	Rat
6478693	Anxrr32	Anxiety related response QTL 32		0.00092	locomotor behavior trait (VT:0001392)	measurement of voluntary locomotion into, out of or within a discrete space in an experimental apparatus (CMO:0000957)	4	144639524	182687754	Rat
631683	Bp116	Blood pressure QTL 116		0.0001	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	4	124303370	169303370	Rat
61451	Ciaa4	CIA Autoantibody QTL 4	3.1		blood autoantibody amount (VT:0003725)	calculated serum anti-rat type 2 collagen autoantibody titer (CMO:0001281)	4	126395976	167139601	Rat
1331738	Bp209	Blood pressure QTL 209	2.979		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	4	138503169	179293946	Rat
6478700	Anxrr33	Anxiety related response QTL 33		0.00896	locomotor behavior trait (VT:0001392)	amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)	4	144639524	182687754	Rat
1549827	Scl46	Serum cholesterol level QTL 46	3.5		blood cholesterol amount (VT:0000180)	serum total cholesterol level (CMO:0000363)	4	132396220	177396220	Rat
731165	Uae21	Urinary albumin excretion QTL 21	2.4	0.0001	urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	4	106649412	151649412	Rat
737821	Hcar9	Hepatocarcinoma resistance QTL 9	3.7		liver integrity trait (VT:0010547)	volume of individual liver tumorous lesion (CMO:0001078)	4	109866907	167139601	Rat
7411558	Bw133	Body weight QTL 133	13.84	0.001	body mass (VT:0001259)	body weight gain (CMO:0000420)	4	125590636	170590636	Rat
10401796	Kidm48	Kidney mass QTL 48			kidney mass (VT:0002707)	both kidneys wet weight (CMO:0000085)	4	145568712	182687754	Rat
6478718	Anxrr34	Anxiety related response QTL 34		0.00896	locomotor behavior trait (VT:0001392)	amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)	4	144639524	182687754	Rat
1549832	Bss3	Bone structure and strength QTL 3	11		femur morphology trait (VT:0000559)	femur midshaft cortical cross-sectional area (CMO:0001663)	4	109827074	154827074	Rat
70177	Xhs1	X-ray hypersensitivity QTL 1	25.1		intestine integrity trait (VT:0010554)	post-insult time to onset of moribundity (CMO:0001896)	4	82798864	152731274	Rat
2303623	Vencon2	Ventilatory control QTL 2	3.8		respiration trait (VT:0001943)	minute ventilation (CMO:0000132)	4	135204660	180204660	Rat
1578674	Bmd12	Bone mineral density QTL 12	3.8		femur mineral mass (VT:0010011)	compact volumetric bone mineral density (CMO:0001730)	4	135699135	180699135	Rat
737978	Pia23	Pristane induced arthritis QTL 23	5.3		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	4	131730738	167139601	Rat
61362	Oia2	Oil induced arthritis QTL 2		0.001	joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	4	138503169	173369699	Rat
70200	Alc18	Alcohol consumption QTL 18	9.2		drinking behavior trait (VT:0001422)	ethanol intake volume to total fluid intake volume ratio (CMO:0001591)	4	56647873	149491524	Rat
2293659	Bmd35	Bone mineral density QTL 35	4.5	0.0001	femur strength trait (VT:0010010)	femoral neck ultimate force (CMO:0001703)	4	137755016	181392681	Rat
1331759	Hrtrt13	Heart rate QTL 13	3.54628		heart pumping trait (VT:2000009)	heart rate (CMO:0000002)	4	110275411	168266883	Rat
724535	Cm18	Cardiac mass QTL 18	2.6		heart mass (VT:0007028)	calculated heart weight (CMO:0000073)	4	118856416	163856416	Rat
2316958	Gluco58	Glucose level QTL 58	10		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	4	11320076	180699135	Rat
6478754	Anxrr43	Anxiety related response QTL 43		0.14035	locomotor behavior trait (VT:0001392)	distance moved per unit of time into, out of or within a discrete space in an experimental apparatus (CMO:0001493)	4	144639524	182687754	Rat
2302049	Pia32	Pristane induced arthritis QTL 32	5.1	0.001	blood autoantibody amount (VT:0003725)	serum immunoglobulin G-type rheumatoid factor level relative to an arbitrary reference serum (CMO:0002112)	4	105789505	150789505	Rat
724558	Plsm2	Polydactyly-luxate syndrome (PLS) morphotypes QTL 2		0.0003	hindlimb integrity trait (VT:0010563)	hind foot phalanges count (CMO:0001949)	4	132422778	177422778	Rat
6478763	Anxrr46	Anxiety related response QTL 46		0.07428	locomotor behavior trait (VT:0001392)	amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)	4	110870972	155870972	Rat
6478760	Anxrr45	Anxiety related response QTL 45		0.06717	locomotor behavior trait (VT:0001392)	amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)	4	110870972	155870972	Rat
1331802	Srn5	Serum renin concentration QTL 5	3.045		renin activity (VT:0005581)	plasma renin activity level (CMO:0000116)	4	119428175	157578333	Rat
1298524	Oia8	Oil induced arthritis QTL 8			joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	4	138503169	173369699	Rat
738009	Sach4	Saccharine consumption QTL 4	4.9	0.000016	consumption behavior trait (VT:0002069)	saccharin intake volume to total fluid intake volume ratio (CMO:0001601)	4	59948935	154902892	Rat
7207480	Bss105	Bone structure and strength QTL 105	8.1		femur strength trait (VT:0010010)	femur midshaft polar moment of inertia (CMO:0001669)	4	109827074	154827074	Rat
634335	Anxrr16	Anxiety related response QTL 16	7.22		locomotor behavior trait (VT:0001392)	number of entries into a discrete space in an experimental apparatus (CMO:0000960)	4	93308457	167139447	Rat
6478778	Anxrr51	Anxiety related response QTL 51		0.25384	locomotor behavior trait (VT:0001392)	measurement of voluntary locomotion into, out of or within a discrete space in an experimental apparatus (CMO:0000957)	4	124778595	169778595	Rat
61406	Scwia1	Streptococcal cell wall induced arthritis QTL 1	2.3		joint integrity trait (VT:0010548)	experimental arthritis severity measurement (CMO:0001459)	4	106805662	151805662	Rat
631511	Pia7	Pristane induced arthritis QTL 7	4.3		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	4	131730738	167139601	Rat
634347	Hcar8	Hepatocarcinoma resistance QTL 8	5.8		liver integrity trait (VT:0010547)	liver tumorous lesion area to total liver area ratio (CMO:0001075)	4	123143783	168143783	Rat
738031	Alc14	Alcohol consumption QTL 14	7.6	0.00003	consumption behavior trait (VT:0002069)	ethanol drink intake rate to body weight ratio (CMO:0001616)	4	59948935	154902892	Rat
1576316	Ept5	Estrogen-induced pituitary tumorigenesis QTL 5	3.8		pituitary gland mass (VT:0010496)	pituitary gland wet weight (CMO:0000853)	4	83428419	177635233	Rat
1576305	Emca6	Estrogen-induced mammary cancer QTL 6	5.8		mammary gland integrity trait (VT:0010552)	mammary tumor number (CMO:0000343)	4	44463720	155883716	Rat
738016	Alc16	Alcohol consumption QTL 16	3.6	0.00015	consumption behavior trait (VT:0002069)	ethanol drink intake rate to body weight ratio (CMO:0001616)	4	59948935	154902892	Rat
1358202	Gluco11	Glucose level QTL 11	2.4	0.02	adipocyte glucose uptake trait (VT:0004185)	absolute change in adipocyte glucose uptake (CMO:0000873)	4	85379421	167139601	Rat
61422	Cia13	Collagen induced arthritis QTL 13	4.5		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	4	132642577	167139601	Rat
634342	Cia24	Collagen induced arthritis QTL 24	4.5		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	4	146565735	175236377	Rat
631674	Iddm14	Insulin dependent diabetes mellitus QTL 14			blood glucose amount (VT:0000188)	plasma glucose level (CMO:0000042)	4	64528739	157573521	Rat
12798519	Anxrr54	Anxiety related response QTL 54	2.54	0.05	locomotor behavior trait (VT:0001392)	distance moved per unit of time into, out of or within a discrete space in an experimental apparatus (CMO:0001493)	4	114627026	159627026	Rat
12798523	Anxrr56	Anxiety related response QTL 56	2.83	0.05	locomotor behavior trait (VT:0001392)	amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)	4	85253748	150276390	Rat
6478748	Anxrr42	Anxiety related response QTL 42		0.28008	locomotor behavior trait (VT:0001392)	amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)	4	144639524	182687754	Rat
12798525	Anxrr57	Anxiety related response QTL 57	3.21	0.05	locomotor behavior trait (VT:0001392)	amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)	4	147278504	167139601	Rat

Markers in Region

RH134617

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	4	149,003,145 - 149,003,334 (+)	MAPPER	mRatBN7.2
Rnor_6.0	4	147,854,671 - 147,854,859	NCBI	Rnor6.0
Rnor_5.0	4	211,138,382 - 211,138,570	UniSTS	Rnor5.0
RGSC_v3.4	4	152,080,621 - 152,080,809	UniSTS	RGSC3.4
Celera	4	137,892,807 - 137,892,995	UniSTS
RH 3.4 Map	4	950.71	UniSTS
Cytogenetic Map	4	q42	UniSTS

AA964803

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	4	149,002,814 - 149,003,001 (+)	MAPPER	mRatBN7.2
Rnor_6.0	4	147,854,340 - 147,854,526	NCBI	Rnor6.0
Rnor_5.0	4	211,138,051 - 211,138,237	UniSTS	Rnor5.0
RGSC_v3.4	4	152,080,290 - 152,080,476	UniSTS	RGSC3.4
Celera	4	137,892,476 - 137,892,662	UniSTS
RH 3.4 Map	4	950.8	UniSTS
Cytogenetic Map	4	q42	UniSTS

Expression

RNA-SEQ Expression

Click on a value in the shaded box below the category label to view a detailed expression data table for that system.

Download All Expressed Objects for this Gene

alimentary part of gastrointestinal system	appendage	circulatory system	ectoderm	endocrine system	endoderm	exocrine system	hemolymphoid system	hepatobiliary system	integumental system	mesenchyme	mesoderm	nervous system	renal system	reproductive system	respiratory system
9	11	49	113	91	90	59	25	59	6	218	97	93	45	60	31

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001395052	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XR_005503232	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XR_005503233	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	CH473964	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JAXUCZ010000004	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Ensembl Acc Id:

ENSRNOT00000032158 ⟹ ENSRNOP00000033101

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	4	149,002,784 - 149,043,244 (-)	Ensembl
Rnor_6.0 Ensembl	4	147,854,309 - 147,893,992 (-)	Ensembl

RefSeq Acc Id:

NM_001395052 ⟹ NP_001381981

RefSeq Status:

VALIDATED

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	4	150,675,377 - 150,715,187 (-)	NCBI
mRatBN7.2	4	149,002,786 - 149,042,598 (-)	NCBI

RefSeq Acc Id:

XR_005503232

Type:

NON-CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	4	150,679,474 - 150,715,696 (-)	NCBI
mRatBN7.2	4	149,005,566 - 149,043,091 (-)	NCBI

RefSeq Acc Id:

XR_005503233

Type:

NON-CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	4	150,683,710 - 150,715,706 (-)	NCBI
mRatBN7.2	4	149,011,119 - 149,043,097 (-)	NCBI

Protein Sequences


Protein RefSeqs	NP_001381981	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	EDM02133	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSRNOP00000033101.6

Ensembl Acc Id:

ENSRNOP00000033101 ⟸ ENSRNOT00000032158

RefSeq Acc Id:	NP_001381981 ⟸ NM_001395052
- UniProtKB:	D4AA77 (UniProtKB/TrEMBL)

Protein Domains

Sema

Protein Structures

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-D4AA77-F1-model_v2	AlphaFold	D4AA77	1-1716	view protein structure

Transcriptome

eQTL		View at Phenogen
WGCNA		View at Phenogen
Tissue/Strain Expression		View at Phenogen

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:1310796	AgrOrtholog
BioCyc Gene	G2FUF-43305	BioCyc
Ensembl Genes	ENSRNOG00000025209	Ensembl, UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000032158.7	UniProtKB/TrEMBL
Gene3D-CATH	2.130.10.10	UniProtKB/TrEMBL
	2.60.40.10	UniProtKB/TrEMBL
InterPro	Ig-like_fold	UniProtKB/TrEMBL
	Ig_E-set	UniProtKB/TrEMBL
	IPT_TIG_rcpt	UniProtKB/TrEMBL
	Plexin	UniProtKB/TrEMBL
	Plexin-D1_Sema	UniProtKB/TrEMBL
	Plexin-like_fold	UniProtKB/TrEMBL
	Plexin_cytoplasmic_RasGAP_dom	UniProtKB/TrEMBL
	Plexin_RBD	UniProtKB/TrEMBL
	Plexin_repeat	UniProtKB/TrEMBL
	Rho_GTPase_activation_prot	UniProtKB/TrEMBL
	Semap_dom_sf	UniProtKB/TrEMBL
	Semaphorin/CD100_Ag	UniProtKB/TrEMBL
	TIG1_plexin	UniProtKB/TrEMBL
	WD40/YVTN_repeat-like_dom	UniProtKB/TrEMBL
NCBI Gene	312652	ENTREZGENE
PANTHER	PLEXIN-D1	UniProtKB/TrEMBL
	PTHR22625	UniProtKB/TrEMBL
Pfam	Plexin_cytopl	UniProtKB/TrEMBL
	Plexin_RBD	UniProtKB/TrEMBL
	PSI	UniProtKB/TrEMBL
	Sema	UniProtKB/TrEMBL
	TIG	UniProtKB/TrEMBL
	TIG_plexin	UniProtKB/TrEMBL
PhenoGen	Plxnd1	PhenoGen
PROSITE	SEMA	UniProtKB/TrEMBL
RatGTEx	ENSRNOG00000025209	RatGTEx
SMART	IPT	UniProtKB/TrEMBL
	PSI	UniProtKB/TrEMBL
	Sema	UniProtKB/TrEMBL
Superfamily-SCOP	Ig_E-set	UniProtKB/TrEMBL
	Plexin repeat	UniProtKB/TrEMBL
	Rho_GAP	UniProtKB/TrEMBL
	Sema	UniProtKB/TrEMBL
UniProt	D4AA77	ENTREZGENE, UniProtKB/TrEMBL

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2008-04-30	Plxnd1	plexin D1	Plxnd1_predicted	plexin D1 (predicted)	'predicted' is removed	2292626	APPROVED
2005-01-12	Plxnd1_predicted	plexin D1 (predicted)			Symbol and Name status set to approved	70820	APPROVED

Gene Annotator (Functional Annotation) unavailable	Gene Annotator (Annotation Distribution) unavailable	Variant Visualizer (Genomic Variants) unavailble Variant Visualizer (Genomic Variants) unavailable
Gene Annotator (Functional Annotation)	Gene Annotator (Annotation Distribution)	Variant Visualizer (Genomic Variants)

InterViewer (Protein-Protein Interactions) unavailable	Gviewer (Genome Viewer) unavailable	Variant Visualizer (Damaging Variants) unavailble Variant Visualizer (Damaging Variants) unavailable
InterViewer (Protein-Protein Interactions)	GViewer (Genome Viewer)	Variant Visualizer (Damaging Variants)

Gene Annotator (Annotation Comparison) unavailable	OLGA (Gene List Generator) unavailable
Gene Annotator (Annotation Comparison)	OLGA (Gene List Generator)	Excel (Download)

MOET (Multi-Ontology Enrichement) unavailable	GOLF (Gene-Ortholog Location Finder) unavailable
MOET (Multi-Ontology Enrichement)	GOLF (Gene-Ortholog Location Finder)

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Imported Disease Annotations - CTD

Imported Disease Annotations - MGI

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Imported Disease Annotations - ClinVar

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