Lypd3 (Ly6/Plaur domain containing 3)

Gene: Lypd3 (Ly6/Plaur domain containing 3) Rattus norvegicus

Analyze

Symbol:

Lypd3

Name:

Ly6/Plaur domain containing 3

RGD ID:

69053

Description:

Enables laminin binding activity. Acts upstream of or within cell-matrix adhesion. Located in membrane. Orthologous to human LYPD3 (LY6/PLAUR domain containing 3); INTERACTS WITH 17alpha-ethynylestradiol; 2,3,7,8-tetrachlorodibenzodioxine; 6-propyl-2-thiouracil.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Previously known as:

C4.4a; GPI-anchored metastasis-associated protein C4.4A; GPI-anchored metastasis-associated protein homolog; ly6/PLAUR domain-containing protein 3; metastasis-associated GPI-anchored protein; metastasis-associated molecule

RGD Orthologs

Alliance Genes

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):	LYPD3 (LY6/PLAUR domain containing 3)	HGNC	EggNOG, Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, Panther, PhylomeDB, Treefam
Mus musculus (house mouse):	Lypd3 (Ly6/Plaur domain containing 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chinchilla lanigera (long-tailed chinchilla):	Lypd3 (LY6/PLAUR domain containing 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	LYPD3 (LY6/PLAUR domain containing 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	LYPD3 (LY6/PLAUR domain containing 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Lypd3 (LY6/PLAUR domain containing 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	LYPD3 (LY6/PLAUR domain containing 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	LYPD3 (LY6/PLAUR domain containing 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Lypd3 (LY6/PLAUR domain containing 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Homo sapiens (human):	LYPD3 (LY6/PLAUR domain containing 3)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Mus musculus (house mouse):	Lypd3 (Ly6/Plaur domain containing 3)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)

Is Marker For:

Strains: BDX

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	1	89,354,354 - 89,358,806 (+)	NCBI		GRCr8
mRatBN7.2	1	80,226,449 - 80,230,901 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	1	80,226,449 - 80,230,901 (+)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	1	85,618,908 - 85,623,352 (+)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	1	94,169,886 - 94,174,330 (+)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	1	87,374,657 - 87,379,095 (+)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	1	81,499,856 - 81,504,306 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	1	81,499,821 - 81,504,318 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	1	82,757,258 - 82,761,708 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	1	79,917,952 - 79,922,402 (+)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	1	79,996,062 - 80,000,513 (+)	NCBI
Celera	1	74,678,988 - 74,683,438 (+)	NCBI		Celera
Cytogenetic Map	1	q21	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

genetic disease (ISO)

schizophrenia (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

1,2-dimethylhydrazine (ISO)

17alpha-ethynylestradiol (EXP)

17beta-estradiol (ISO)

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

2-acetamidofluorene (ISO)

6-propyl-2-thiouracil (EXP)

afimoxifene (ISO)

all-trans-retinoic acid (ISO)

amitrole (EXP)

ammonium chloride (EXP)

arsane (ISO)

arsenic atom (ISO)

atrazine (ISO)

benzo[a]pyrene (ISO)

bisphenol A (EXP)

bleomycin A5 (ISO)

bromobenzene (EXP)

calcitriol (ISO)

dimethylarsinic acid (EXP)

dorsomorphin (ISO)

endosulfan (EXP)

entinostat (ISO)

ethylparaben (ISO)

fluorescein 5-isothiocyanate (ISO)

gentamycin (EXP)

ketamine (EXP)

lead diacetate (ISO)

lead(0) (ISO)

leflunomide (ISO)

methimazole (EXP)

methylisothiazolinone (ISO)

panobinostat (ISO)

phenethyl isothiocyanate (EXP)

potassium dichromate (ISO)

propanal (ISO)

propiconazole (EXP)

SB 431542 (ISO)

silicon dioxide (ISO)

sodium arsenate (ISO)

sodium arsenite (ISO)

titanium dioxide (ISO)

trichloroethene (EXP)

urethane (ISO)

valproic acid (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

cell-matrix adhesion (IDA)

negative regulation of smooth muscle cell apoptotic process (ISO)

Cellular Component

membrane (IDA)

plasma membrane (IBA)

side of membrane (IEA)

Molecular Function

laminin binding (IDA)

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.	Electronic Transfer of LocusLink and RefSeq Data	NCBI rat LocusLink and RefSeq merged data July 26, 2002
3.	Ly6 family member C4.4A binds laminins 1 and 5, associates with galectin-3 and supports cell migration.	Paret C, etal., Int J Cancer. 2005 Jul 10;115(5):724-33.
4.	GOA pipeline	RGD automated data pipeline
5.	Data Import for Chemical-Gene Interactions	RGD automated import pipeline for gene-chemical interactions
6.	Cloning and functional characterization of a new phosphatidyl-inositol anchored molecule of a metastasizing rat pancreatic tumor.	Rosel M, etal., Oncogene 1998 Oct 15;17(15):1989-2002.
7.	Tentative Sequence Identification Numbers	Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
8.	Cloning of the human homologue of the metastasis-associated rat C4.4A.	Wurfel J, etal., Gene 2001 Jan 10;262(1-2):35-41.

Additional References at PubMed

PMID:16502470	PMID:21339181	PMID:22431918

Genomics

Comparative Map Data

Lypd3
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	1	89,354,354 - 89,358,806 (+)	NCBI		GRCr8
mRatBN7.2	1	80,226,449 - 80,230,901 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	1	80,226,449 - 80,230,901 (+)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	1	85,618,908 - 85,623,352 (+)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	1	94,169,886 - 94,174,330 (+)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	1	87,374,657 - 87,379,095 (+)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	1	81,499,856 - 81,504,306 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	1	81,499,821 - 81,504,318 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	1	82,757,258 - 82,761,708 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	1	79,917,952 - 79,922,402 (+)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	1	79,996,062 - 80,000,513 (+)	NCBI
Celera	1	74,678,988 - 74,683,438 (+)	NCBI		Celera
Cytogenetic Map	1	q21	NCBI

LYPD3
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	19	43,460,787 - 43,465,608 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	19	43,460,787 - 43,465,608 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	19	43,964,939 - 43,969,760 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	19	48,656,786 - 48,661,671 (-)	NCBI	NCBI36	Build 36	hg18	NCBI36
Build 34	19	48,656,778 - 48,661,648	NCBI
Celera	19	40,765,674 - 40,770,557 (-)	NCBI		Celera
Cytogenetic Map	19	q13.31	NCBI
HuRef	19	40,394,803 - 40,399,686 (-)	NCBI		HuRef
CHM1_1	19	43,966,592 - 43,971,477 (-)	NCBI		CHM1_1
T2T-CHM13v2.0	19	46,281,130 - 46,285,954 (-)	NCBI		T2T-CHM13v2.0

Lypd3
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	7	24,335,995 - 24,340,543 (+)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	7	24,335,975 - 24,340,543 (+)	Ensembl		GRCm39 Ensembl
GRCm38	7	24,636,570 - 24,641,118 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	7	24,636,550 - 24,641,118 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	7	25,421,589 - 25,426,137 (+)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	7	24,345,330 - 24,349,878 (+)	NCBI		MGSCv36	mm8
Celera	7	19,250,477 - 19,255,025 (+)	NCBI		Celera
Cytogenetic Map	7	A3	NCBI
cM Map	7	11.95	NCBI

Lypd3
(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_004955555	1,228,879 - 1,234,097 (-)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955555	1,229,559 - 1,233,932 (-)	NCBI	ChiLan1.0	ChiLan1.0

LYPD3
(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	20	49,618,230 - 49,626,686 (-)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	19	51,487,104 - 51,495,564 (-)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	19	40,400,919 - 40,406,756 (-)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	19	49,010,593 - 49,015,489 (-)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	19	49,011,152 - 49,015,381 (-)	Ensembl	panpan1.1		panPan2

LYPD3
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	1	111,634,910 - 111,639,250 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	1	111,634,978 - 111,638,541 (+)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	1	111,114,615 - 111,118,438 (+)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	1	112,245,066 - 112,248,887 (+)	NCBI		ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	1	112,245,132 - 112,248,897 (+)	Ensembl		ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	1	111,833,190 - 111,837,011 (+)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	1	111,466,962 - 111,470,784 (+)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	1	112,351,223 - 112,355,047 (+)	NCBI		UU_Cfam_GSD_1.0

Lypd3
(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_024409349	16,346,360 - 16,350,420 (-)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936706	693,694 - 697,796 (-)	Ensembl	SpeTri2.0	SpeTri2.0 Ensembl
SpeTri2.0	NW_004936706	693,703 - 697,714 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

LYPD3
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	6	50,341,161 - 50,345,338 (-)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	6	50,341,157 - 50,346,407 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	6	46,262,470 - 46,267,707 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

LYPD3
(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	6	36,976,204 - 36,981,382 (-)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	6	36,976,773 - 36,980,995 (-)	Ensembl	ChlSab1.1	ChlSab1.1 Ensembl	chlSab2
Vero_WHO_p1.0	NW_023666073	16,515,718 - 16,520,610 (-)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Lypd3
(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_004624907	1,022,500 - 1,028,102 (-)	Ensembl	HetGla_female_1.0	HetGla_female_1.0 Ensembl	hetGla2
HetGla 1.0	NW_004624907	1,024,083 - 1,028,179 (-)	NCBI	HetGla_female_1.0	HetGla 1.0	hetGla2

Variants

Variants in Lypd3
22 total Variants

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	259
Count of miRNA genes:	166
Interacting mature miRNAs:	187
Transcripts:	ENSRNOT00000027100
Prediction methods:	Microtar, Miranda, Rnahybrid, Targetscan
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
1554320	Bmd1	Bone mineral density QTL 1	12.2	0.0001	femur mineral mass (VT:0010011)	volumetric bone mineral density (CMO:0001553)	1	509108	86060548	Rat
631688	Hcas2	Hepatocarcinoma susceptibility QTL 2	3	0.0001	liver integrity trait (VT:0010547)	liver tumorous lesion number (CMO:0001068)	1	5925874	115540829	Rat
2313062	Bmd73	Bone mineral density QTL 73	3.9	0.0001	tibia mineral mass (VT:1000283)	compact volumetric bone mineral density (CMO:0001730)	1	11481312	82174945	Rat
2313065	Bss67	Bone structure and strength QTL 67	3.1	0.0001	tibia area (VT:1000281)	tibia total energy absorbed before break (CMO:0001736)	1	11481312	82174945	Rat
2313069	Bss68	Bone structure and strength QTL 68	2.9	0.0001	tibia size trait (VT:0100001)	tibia total energy absorbed before break (CMO:0001736)	1	11481312	82174945	Rat
2313075	Bss66	Bone structure and strength QTL 66	3.4	0.0001	tibia length (VT:0004357)	tibia length (CMO:0000450)	1	11481312	82174945	Rat
2313077	Bss69	Bone structure and strength QTL 69	3.5	0.0001	tibia strength trait (VT:1000284)	bone polar moment of inertia (CMO:0001558)	1	11481312	82174945	Rat
2313092	Bmd72	Bone mineral density QTL 72	2.5	0.0001	tibia mineral mass (VT:1000283)	total volumetric bone mineral density (CMO:0001728)	1	11481312	82174945	Rat
2313097	Bss70	Bone structure and strength QTL 70	3.5	0.0001	tibia strength trait (VT:1000284)	tibia total energy absorbed before break (CMO:0001736)	1	11481312	82174945	Rat
631495	Bp96	Blood pressure QTL 96	4.52		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	22340647	102268831	Rat
1358359	Sradr1	Stress Responsive Adrenal Weight QTL 1	4.74		adrenal gland mass (VT:0010420)	both adrenal glands wet weight (CMO:0000164)	1	30882023	123479925	Rat
70225	Bp58	Blood pressure QTL 58	3.3		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	32356093	162846471	Rat
1300172	Bp172	Blood pressure QTL 172	3.56		arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	1	32737273	90665040	Rat
10059597	Bp377	Blood pressure QTL 377	3.42	0.025	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	32737458	199368955	Rat
2313051	Bss57	Bone structure and strength QTL 57	3.7	0.0001	tibia strength trait (VT:1000284)	bone polar moment of inertia (CMO:0001558)	1	43284731	118944897	Rat
2313059	Bss55	Bone structure and strength QTL 55	3.2	0.0001	tibia size trait (VT:0100001)	tibia midshaft cross-sectional area (CMO:0001717)	1	43284731	118944897	Rat
2313072	Bss53	Bone structure and strength QTL 53	4.3	0.0001	tibia length (VT:0004357)	tibia length (CMO:0000450)	1	43284731	118944897	Rat
2313078	Bss54	Bone structure and strength QTL 54	3.5	0.0001	tibia area (VT:1000281)	tibia midshaft cross-sectional area (CMO:0001717)	1	43284731	118944897	Rat
2313094	Bss58	Bone structure and strength QTL 58	3.7	0.0001	tibia strength trait (VT:1000284)	tibia total energy absorbed before break (CMO:0001736)	1	43284731	118944897	Rat
2313098	Bmd70	Bone mineral density QTL 70	3.6	0.0001	tibia mineral mass (VT:1000283)	compact volumetric bone mineral density (CMO:0001730)	1	43284731	118944897	Rat
2313099	Bss56	Bone structure and strength QTL 56	2.4	0.0001	tibia size trait (VT:0100001)	tibia midshaft endosteal cross-sectional area (CMO:0001716)	1	43284731	118944897	Rat
2302059	Pia36	Pristane induced arthritis QTL 36	3.8	0.001	blood immunoglobulin amount (VT:0002460)	serum immunoglobulin G1 level (CMO:0002115)	1	43333002	88333002	Rat
2313402	Anxrr24	Anxiety related response QTL 24			aggression-related behavior trait (VT:0015014)	tameness/aggressiveness composite score (CMO:0002136)	1	48963584	144267916	Rat
4889962	Bss94	Bone structure and strength QTL 94	3.8		tibia area (VT:1000281)	tibia-fibula cortical bone endosteal cross-sectional area (CMO:0001722)	1	49361465	82174945	Rat
1578649	Bmd8	Bone mineral density QTL 8	4.9		femur mineral mass (VT:0010011)	trabecular volumetric bone mineral density (CMO:0001729)	1	49393172	94393172	Rat
1578654	Bss10	Bone structure and strength QTL 10	4		femur morphology trait (VT:0000559)	femoral neck cortical cross-sectional area (CMO:0001702)	1	49393172	159356837	Rat
634314	Niddm44	Non-insulin dependent diabetes mellitus QTL 44			blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	1	49393289	199050459	Rat
6903308	Scl36	Serum cholesterol QTL 36	2	0.0125	blood cholesterol amount (VT:0000180)	plasma total cholesterol level (CMO:0000585)	1	53863041	90532583	Rat
4889919	Bss86	Bone structure and strength QTL 86	4.1		tibia area (VT:1000281)	tibia midshaft total cross-sectional area (CMO:0001715)	1	53895117	82174945	Rat
4889929	Bss87	Bone structure and strength QTL 87	6.7		tibia area (VT:1000281)	tibia-fibula cortical bone endosteal cross-sectional area (CMO:0001722)	1	53895117	82174945	Rat
61342	Bp27	Blood pressure QTL 27	3.4	0.0006	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	56732668	98773277	Rat
2300164	Bmd44	Bone mineral density QTL 44	5.4	0.0001	lumbar vertebra mineral mass (VT:0010511)	volumetric bone mineral density (CMO:0001553)	1	56949932	101949932	Rat
2298545	Neuinf8	Neuroinflammation QTL 8	4.6		nervous system integrity trait (VT:0010566)	spinal cord beta-2 microglobulin mRNA level (CMO:0002125)	1	57336763	151090257	Rat
1300121	Hrtrt1	Heart rate QTL 1	3.7		heart pumping trait (VT:2000009)	heart rate (CMO:0000002)	1	65789093	115540829	Rat
7421628	Bp361	Blood pressure QTL 361		0.001	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	1	66023617	118608521	Rat
631512	Scl6	Serum cholesterol level QTL 6	9.6		blood cholesterol amount (VT:0000180)	serum total cholesterol level (CMO:0000363)	1	72197680	90508767	Rat
1358192	Ept13	Estrogen-induced pituitary tumorigenesis QTL 13	3.4		pituitary gland mass (VT:0010496)	pituitary gland wet weight (CMO:0000853)	1	77494165	122494165	Rat
10054135	Gmadr2	Adrenal mass QTL 2	1.97	0.0129	adrenal gland mass (VT:0010420)	both adrenal glands wet weight (CMO:0000164)	1	77857876	122857876	Rat
1549903	Bp267	Blood pressure QTL 267			arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	77876254	106047988	Rat
61344	Bp29	Blood pressure QTL 29	7.5		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	78350581	123350581	Rat
7411712	Strs4	Sensitivity to stroke QTL 4	8.7		cerebrum integrity trait (VT:0010549)	percentage of study population developing cerebrovascular lesions during a period of time (CMO:0000932)	1	78430536	123430536	Rat
61433	Cia2	Collagen induced arthritis QTL 2	5		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	1	78430754	91209302	Rat
1582234	Gluco18	Glucose level QTL 18	3.4	0.0003	blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	1	78479925	123479925	Rat

Markers in Region

RH140611

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	1	80,230,619 - 80,230,808 (+)	MAPPER	mRatBN7.2
Rnor_6.0	1	81,504,025 - 81,504,213	NCBI	Rnor6.0
Rnor_5.0	1	82,761,427 - 82,761,615	UniSTS	Rnor5.0
RGSC_v3.4	1	79,922,121 - 79,922,309	UniSTS	RGSC3.4
Celera	1	74,683,157 - 74,683,345	UniSTS
RH 3.4 Map	1	823.2	UniSTS
Cytogenetic Map	1	q21	UniSTS

Related Rat Strains

The following Strains have been annotated to Lypd3

BDX

Expression

RNA-SEQ Expression

High: > 1000 TPM value Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM Below Cutoff: < 0.5 TPM

	alimentary part of gastrointestinal system	circulatory system	endocrine system	exocrine system	hemolymphoid system	hepatobiliary system	integumental system	musculoskeletal system	nervous system	renal system	reproductive system	respiratory system	appendage
High
Medium											5
Low	3	4	30	21	19	21	1	1	59	31	30	11	1
Below cutoff		12	24	17		17	6	7	15	4	3		6

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_021759	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AJ001043	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AM075190	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473979	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JAXUCZ010000001	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

RefSeq Acc Id:

ENSRNOT00000027100 ⟹ ENSRNOP00000027100

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	1	80,226,449 - 80,230,901 (+)	Ensembl
Rnor_6.0 Ensembl	1	81,499,821 - 81,504,318 (+)	Ensembl

RefSeq Acc Id:

NM_021759 ⟹ NP_068527

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	1	89,354,354 - 89,358,806 (+)	NCBI
mRatBN7.2	1	80,226,449 - 80,230,901 (+)	NCBI
Rnor_6.0	1	81,499,856 - 81,504,306 (+)	NCBI
Rnor_5.0	1	82,757,258 - 82,761,708 (+)	NCBI
RGSC_v3.4	1	79,917,952 - 79,922,402 (+)	RGD
Celera	1	74,678,988 - 74,683,438 (+)	RGD

Sequence:

show sequence

CTCATCTAAGGCTCAGGTAAGAGGGCCCGGGTTGGAAGGTGGCACACCCAGGGGGGACTCGGAG
AGAGCAGGACACAGCTATGGATGCTGCCAGGAGAGGAGATACACAGCCAGTGATGTGGACCACC
AGATGGCTGCTGCTGCTACCGCTACTGCTGTGTGAAGGAGCGCAAGCCCTGGAGTGCTACAGCT
GCGTGCAAAAGGCGGATGATGGATGCTCTCCGCACAAGATGAAGACAGTCAAATGTGGTCCCGG
AGTGGACGTCTGTACCGAGGCCGTGGGGGCGGTGGAGAGCATCCACGGGCAATTCTCTGTGGCA
GTGCGGGGCTGCGGTTCCGGAATCCCGGGCAAGAACGACCGCGGACTGGACCTTCACGGGCTCC
TGGCCTTCATTCAGCTACAGCAGTGCACCGAGGACCGATGCAACGCCAAACTCAACCTCACTTT
GCGAGGCCTCAACCCTGCAGGCAATGAGAGTGCGTATGAGCACAACGGCGCAGAGTGCTACAGC
TGTATGGGGCTGAGCCGCGAGAAGTGCCAGGGCGCTATGCCGCCTGTCGTGAATTGCTACAATG
CCAGCGGCCGTGTCTACAAGGGCTGCTTCGATGGTAACGTCACCTTGACCGCAGCCAATGTGAC
CGTGTCCTTACCTGTCCGAGGCTGCGTCCAGGACGAAGCCTGCACCCGGGATGGGGTGACGGGT
CCAGGATTCACACTCAGCGGTTCCTGCTGTCAAGGGCCCCGCTGTAACTCTGACCTTCGCAACA
AGACCTATTTCTCCCCTCGAATCCCACCCCTAGTCCTGCTGCCCCCTCCAACCACCCCAGCCCC
ATCCACTCGGACCCAGAACTCCTCCAGCACAACCTCTACAACAGCTCCAACCACGGCCACCACT
ACCATCAAGCCCACCACAGTCCAAGCCAGTCATACTTCTTCAACCCATGAAACAGAGCACGAGG
TCATACAGGAAGAGGGGTCGCATTTGAGTGGAGGTGCTACGGGCCACCAAGACCGCAGCAATAT
GGGGAAGTTTCCAGAAAAAGGTGGAGCCCAAATCCCATCTAAAGGAGGCTCTGACGCTCTGGGG
TCCTGGTTGTCAGCAATTCTGTTGACTGTGGTTGCTGGCGCGATGCTGTGAACGTCTCCTGTCG
CGGTCCATCTCACCTTGTTTCCCTGGCCCCGTGGTACCAACTCCTTCCATTTCCCACTTGACTG
GACTGGCTCCGCCCCCATCCTCCAGCATCCGCAGTTCCAACTGCACTGGTTTGCAGCTTCGGGA
AACAGTCTACTGTTGTAAATACTCCGCTGGGGTGGCCCTACTTTTTGGATGCGGCCACAGCATT
CCCCCTGACGGTGACCAGGACAGAAGGAAGAGAAATCTACAGGCTGAGAGAGGCCCGGAGAGTC
CACGGCAAACCTCCTCTTCCCGTTTTCCTGACCAGGCTAGAAGATTACCCGGCAGGTGGACAAT
AGATTCATCCTCTGAGCGCTGCGCTTGCCCGGCATCTGTGCAGGAATCTGGTCGCCTGTCTTCC
TTAGGAGACTGTGAACAACTCCACGACAGGGTCTTGCCTCTGGCCTCTCTATGTGTTCTGTCTG
GCACAAGAAAGTGTCAATAAAGATTTAGTTACTTTGT

hide sequence

Protein Sequences


Protein RefSeqs	NP_068527	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	CAA04497	(Get FASTA)	NCBI Sequence Viewer
	CAJ27106	(Get FASTA)	NCBI Sequence Viewer
	EDM08079	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSRNOP00000027100
	ENSRNOP00000027100.1
	ENSRNOP00055046530
	ENSRNOP00060036915
	ENSRNOP00065047873
GenBank Protein	O55162	(Get FASTA)	NCBI Sequence Viewer

RefSeq Acc Id:	NP_068527 ⟸ NM_021759
- Peptide Label:	precursor
- UniProtKB:	O55162 (UniProtKB/Swiss-Prot), A6J905 (UniProtKB/TrEMBL)
- Sequence:	show sequence MDAARRGDTQPVMWTTRWLLLLPLLLCEGAQALECYSCVQKADDGCSPHKMKTVKCGPGVDVCT EAVGAVESIHGQFSVAVRGCGSGIPGKNDRGLDLHGLLAFIQLQQCTEDRCNAKLNLTLRGLNP AGNESAYEHNGAECYSCMGLSREKCQGAMPPVVNCYNASGRVYKGCFDGNVTLTAANVTVSLPV RGCVQDEACTRDGVTGPGFTLSGSCCQGPRCNSDLRNKTYFSPRIPPLVLLPPPTTPAPSTRTQ NSSSTTSTTAPTTATTTIKPTTVQASHTSSTHETEHEVIQEEGSHLSGGATGHQDRSNMGKFPE KGGAQIPSKGGSDALGSWLSAILLTVVAGAML hide sequence

RefSeq Acc Id:

ENSRNOP00000027100 ⟸ ENSRNOT00000027100

Protein Domains

UPAR/Ly6

Protein Structures

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-O55162-F1-model_v2	AlphaFold	O55162	1-352	view protein structure

Transcriptome

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

Promoters

RGD ID:

13689803

Promoter ID:

EPDNEW_R327

Type:

single initiation site

Name:

Lypd3_1

Description:

Ly6/Plaur domain containing 3

SO ACC ID:

SO:0000170

Source:

EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)

Experiment Methods:

Single-end sequencing.

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0	1	81,499,899 - 81,499,959	EPDNEW

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:69053	AgrOrtholog
BioCyc Gene	G2FUF-60434	BioCyc
Ensembl Genes	ENSRNOG00000019999	Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
	ENSRNOG00055032656	UniProtKB/Swiss-Prot
	ENSRNOG00060025764	UniProtKB/Swiss-Prot
	ENSRNOG00065033896	UniProtKB/Swiss-Prot
Ensembl Transcript	ENSRNOT00000027100	ENTREZGENE
	ENSRNOT00000027100.4	UniProtKB/Swiss-Prot
	ENSRNOT00055056424	UniProtKB/Swiss-Prot
	ENSRNOT00060044557	UniProtKB/Swiss-Prot
	ENSRNOT00065058196	UniProtKB/Swiss-Prot
Gene3D-CATH	2.10.60.10	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro	LY6_UPA_recep-like	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Snake_toxin-like_sf	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report	rno:60378	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
NCBI Gene	60378	ENTREZGENE
PANTHER	LY6/PLAUR DOMAIN-CONTAINING PROTEIN 3	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	UROKINASE PLASMINOGEN ACTIVATOR SURFACE RECEPTOR-RELATED	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam	UPAR_LY6	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen	Lypd3	PhenoGen
RatGTEx	ENSRNOG00000019999	RatGTEx
	ENSRNOG00055032656	RatGTEx
	ENSRNOG00060025764	RatGTEx
	ENSRNOG00065033896	RatGTEx
SMART	SM00134	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP	Snake toxin-like	UniProtKB/TrEMBL, UniProtKB/Swiss-Prot
TIGR	TC219083
UniProt	A6J905	ENTREZGENE, UniProtKB/TrEMBL
	LYPD3_RAT	UniProtKB/Swiss-Prot, ENTREZGENE

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2006-03-30	Lypd3	Ly6/Plaur domain containing 3	C4.4a	GPI-anchored metastasis-associated protein homolog	Symbol and Name updated	1299863	APPROVED
2005-01-20	C4.4a	GPI-anchored metastasis-associated protein homolog			Symbol and Name status set to approved	1299863	APPROVED
2002-06-10	C4.4a	GPI-anchored metastasis-associated protein homolog			Name updated	70585	PROVISIONAL

RGD Curation Notes

Note Type	Note	Reference
gene_cellular_localization	phosphatidyl-inositol membrane anchored protein	68667
gene_disease	has a role in metastasis formation and matrix penetration	62416
gene_disease	has a role in metastasis formation and matrix penetration	68667
gene_expression	upregulated during implantation of the blastocyst	62416
gene_expression	upregulated during implantation of the blastocyst	68667
gene_expression	expressed only in adults in gravid uterus and upper gastrointestinal tract basal epithelial layer	62416
gene_expression	expressed only in adults in gravid uterus and upper gastrointestinal tract basal epithelial layer	68667
gene_expression	expressed in placental tissue, skin, esophagus and peripheral blood leukocytes, but not in brain, lung, liver, kidney, stomach, colon and lymphoid organs	62416
gene_other	GPI anchored	62416
gene_other	GPI anchored	68667
gene_process	functions in adhesion to laminin	62416
gene_process	functions in adhesion to laminin	68667
gene_protein	352aa, 36.96 kDa protein

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 - ClinVar