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Gene: Ly9 (lymphocyte antigen 9) Rattus norvegicus

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Symbol:

Ly9

Name:

lymphocyte antigen 9

RGD ID:

1308341

Description:

Predicted to be involved in T-helper 17 cell lineage commitment and positive regulation of interleukin-17 production. Predicted to be located in cell surface and plasma membrane. Predicted to be active in external side of plasma membrane. Orthologous to human LY9 (lymphocyte antigen 9); INTERACTS WITH 1-naphthyl isothiocyanate; acetamide; alpha-Zearalanol.

Type:

protein-coding

RefSeq Status:

VALIDATED

Previously known as:

LOC289227; T-lymphocyte surface antigen Ly-9

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):	LY9 (lymphocyte antigen 9)	HGNC	Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, Panther
Mus musculus (house mouse):	Ly9 (lymphocyte antigen 9)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	LY9 (lymphocyte antigen 9)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	LY9 (lymphocyte antigen 9)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	LY9 (lymphocyte antigen 9)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	LY9 (lymphocyte antigen 9)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Rattus rattus (black rat):	Ly9 (lymphocyte antigen 9)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Homo sapiens (human):	LY9 (lymphocyte antigen 9)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Homo sapiens (human):	LY9 (lymphocyte antigen 9)	Alliance	DIOPT (HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Mus musculus (house mouse):	Ly9 (lymphocyte antigen 9)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Mus musculus (house mouse):	Ly9 (lymphocyte antigen 9)	Alliance	DIOPT (Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Xenopus tropicalis (tropical clawed frog):	LOC116406749	Alliance	DIOPT (Ensembl Compara\|OrthoInspector\|PANTHER\|PhylomeDB)
Xenopus tropicalis (tropical clawed frog):	ly9	Alliance	DIOPT (Ensembl Compara\|OrthoInspector\|PANTHER\|PhylomeDB)

Latest Assembly:

GRCr8 - GRCr8 Assembly

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	13	86,610,762 - 86,633,314 (-)	NCBI	GRCr8	GRCr8		GRCr8
GRCr8 Ensembl	13	86,611,784 - 86,657,293 (-)	Ensembl				GRCr8
mRatBN7.2	13	84,079,345 - 84,100,783 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	13	84,079,458 - 84,100,823 (-)	Ensembl				mRatBN7.2
UTH_Rnor_SHR_Utx	13	86,587,072 - 86,606,550 (-)	NCBI	UTH_Rnor_SHR_Utx	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	13	87,984,908 - 88,004,379 (-)	NCBI	UTH_Rnor_SHRSP_BbbUtx_1.0	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	13	85,184,633 - 85,203,854 (-)	NCBI	UTH_Rnor_WKY_Bbb_1.0	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	13	90,002,779 - 90,022,346 (-)	NCBI	Rnor_6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	13	90,002,783 - 90,022,269 (-)	Ensembl			rn6	Rnor6.0
Rnor_5.0	13	94,624,495 - 94,644,219 (-)	NCBI	Rnor_5.0	Rnor_5.0	rn5
RGSC_v3.4	13	87,581,203 - 87,600,810 (-)	NCBI	RGSC_v3.4	RGSC_v3.4	rn4
Celera	13	83,711,096 - 83,730,526 (-)	NCBI		Celera
RGSC_v3.1	13	87,769,871 - 87,789,694 (-)	NCBI
Cytogenetic Map	13	q24	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

multisystem inflammatory syndrome in children (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

1,2-dimethylhydrazine (ISO)

1-naphthyl isothiocyanate (EXP)

17beta-estradiol (ISO)

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

4,4'-sulfonyldiphenol (ISO)

acetamide (EXP)

acetylsalicylic acid (ISO)

alpha-Zearalanol (EXP)

amphetamine (EXP)

antirheumatic drug (ISO)

arsane (ISO)

arsenic atom (ISO)

avobenzone (ISO)

benzo[a]pyrene (ISO)

bis(2-ethylhexyl) phthalate (ISO)

bisphenol A (EXP,ISO)

buta-1,3-diene (ISO)

Butylbenzyl phthalate (ISO)

cadmium atom (ISO)

cadmium dichloride (ISO)

carbon nanotube (ISO)

CGP 52608 (ISO)

copper atom (EXP)

copper(0) (EXP)

DDT (EXP)

Dibutyl phosphate (ISO)

dimethylarsinic acid (ISO)

diquat (ISO)

hydrogen peroxide (ISO)

ibuprofen (ISO)

indole-3-methanol (EXP)

lipopolysaccharide (ISO)

methylarsonic acid (ISO)

N-acetyl-L-cysteine (EXP)

N-ethyl-N-nitrosourea (ISO)

N-nitrosodiethylamine (EXP)

nickel atom (ISO)

ozone (ISO)

perfluorooctanoic acid (ISO)

S-(1,2-dichlorovinyl)-L-cysteine (ISO)

silicon dioxide (ISO)

silver atom (ISO)

silver(0) (ISO)

sodium arsenate (ISO)

sodium arsenite (ISO)

testosterone (ISO)

Theaflavin 3,3'-digallate (ISO)

triphenyl phosphate (ISO)

urethane (ISO)

vinclozolin (EXP)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

adaptive immune response (IEA)

immune response (IBA)

immune system process (IEA)

innate immune response (IEA)

positive regulation of interleukin-17 production (IEA,ISO)

T cell activation (IBA)

T-helper 17 cell lineage commitment (IEA,ISO)

Cellular Component

cell surface (ISO)

external side of plasma membrane (IBA)

membrane (IEA)

plasma membrane (IEA,ISO)

Molecular Function

protein binding (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 GOA human gene data--August 2006	GOA data from the GO Consortium
3.	Rat ISS GO annotations from MGI mouse gene data--August 2006	MGD data from the GO Consortium
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

Additional References at PubMed

PMID:1506686	PMID:22184727

Genomics

Comparative Map Data

Ly9
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	13	86,610,762 - 86,633,314 (-)	NCBI	GRCr8	GRCr8		GRCr8
GRCr8 Ensembl	13	86,611,784 - 86,657,293 (-)	Ensembl				GRCr8
mRatBN7.2	13	84,079,345 - 84,100,783 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	13	84,079,458 - 84,100,823 (-)	Ensembl				mRatBN7.2
UTH_Rnor_SHR_Utx	13	86,587,072 - 86,606,550 (-)	NCBI	UTH_Rnor_SHR_Utx	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	13	87,984,908 - 88,004,379 (-)	NCBI	UTH_Rnor_SHRSP_BbbUtx_1.0	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	13	85,184,633 - 85,203,854 (-)	NCBI	UTH_Rnor_WKY_Bbb_1.0	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	13	90,002,779 - 90,022,346 (-)	NCBI	Rnor_6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	13	90,002,783 - 90,022,269 (-)	Ensembl			rn6	Rnor6.0
Rnor_5.0	13	94,624,495 - 94,644,219 (-)	NCBI	Rnor_5.0	Rnor_5.0	rn5
RGSC_v3.4	13	87,581,203 - 87,600,810 (-)	NCBI	RGSC_v3.4	RGSC_v3.4	rn4
Celera	13	83,711,096 - 83,730,526 (-)	NCBI		Celera
RGSC_v3.1	13	87,769,871 - 87,789,694 (-)	NCBI
Cytogenetic Map	13	q24	NCBI

LY9
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	1	160,796,174 - 160,828,255 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	1	160,796,074 - 160,828,483 (+)	Ensembl			hg38	GRCh38
GRCh37	1	160,765,964 - 160,798,045 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	1	159,032,552 - 159,064,669 (+)	NCBI	Build 36	Build 36	hg18	NCBI36
Build 34	1	157,579,000 - 157,611,116	NCBI
Celera	1	133,834,603 - 133,866,716 (+)	NCBI		Celera
Cytogenetic Map	1	q23.3	NCBI
HuRef	1	132,122,027 - 132,154,181 (+)	NCBI		HuRef
CHM1_1	1	162,161,240 - 162,193,425 (+)	NCBI		CHM1_1
T2T-CHM13v2.0	1	159,933,205 - 159,965,298 (+)	NCBI		T2T-CHM13v2.0

Ly9
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	1	171,416,172 - 171,434,917 (-)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	1	171,416,192 - 171,434,978 (-)	Ensembl		GRCm39 Ensembl		GRCm39
GRCm38	1	171,588,613 - 171,607,410 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	1	171,588,624 - 171,607,410 (-)	Ensembl			mm10	GRCm38
MGSCv37	1	173,518,744 - 173,537,491 (-)	NCBI	MGSCv37	MGSCv37	mm9	NCBIm37
MGSCv36	1	173,425,307 - 173,443,949 (-)	NCBI		MGSCv36	mm8
Celera	1	174,446,275 - 174,464,989 (-)	NCBI		Celera
Cytogenetic Map	1	H3	NCBI
cM Map	1	79.54	NCBI

LY9
(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	1	89,019,244 - 89,054,064 (-)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	1	88,759,668 - 88,794,378 (-)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	1	136,151,608 - 136,185,365 (+)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	1	140,075,646 - 140,107,790 (+)	NCBI	PanPan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	1	140,075,646 - 140,107,784 (+)	Ensembl			panPan2	panpan1.1

LY9
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	38	21,522,898 - 21,554,652 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	38	21,523,637 - 21,554,579 (-)	Ensembl			canFam3	CanFam3.1
Dog10K_Boxer_Tasha	38	21,595,867 - 21,627,680 (-)	NCBI	Dog10K_Boxer_Tasha	Dog10K_Boxer_Tasha
ROS_Cfam_1.0	38	21,640,415 - 21,671,866 (-)	NCBI	ROS_Cfam_1.0	ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	38	21,640,585 - 21,671,783 (-)	Ensembl				ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	38	21,527,340 - 21,559,137 (-)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	38	21,941,122 - 21,972,926 (-)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	38	22,351,067 - 22,382,513 (-)	NCBI	UU_Cfam_GSD_1.0	UU_Cfam_GSD_1.0

LY9
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	4	89,701,359 - 89,729,855 (-)	Ensembl			susScr11	Sscrofa11.1
Sscrofa11.1	4	89,701,806 - 89,728,848 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	4	97,518,786 - 97,545,794 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

LY9
(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	20	3,140,059 - 3,145,818 (-)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
Vero_WHO_p1.0	NW_023666038	2,180,473 - 2,209,597 (-)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Ly9
(Rattus rattus - black rat)

Black Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Black Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Rrattus_CSIRO_v1	10	50,759,699 - 50,778,878 (-)	NCBI		Rrattus_CSIRO_v1

Variants

Variants in Ly9
217 total Variants

miRNA Target Status (No longer updated)

Predicted Target Of

	Summary Value
Count of predictions:	148
Count of miRNA genes:	120
Interacting mature miRNAs:	125
Transcripts:	ENSRNOT00000035498
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 (GRCr8)

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
1298066	Bp159	Blood pressure QTL 159		0.004	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	13	48639634	93639634	Rat
10755495	Bp387	Blood pressure QTL 387	3.78		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	13	37216241	90057603	Rat
1354655	Bp241	Blood pressure QTL 241	3.9		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	13	38975045	103588154	Rat
8655951	Rf63	Renal function QTL 63	12.2		blood urea nitrogen amount (VT:0005265)	plasma urea nitrogen level (CMO:0000586)	13	71610804	109350286	Rat
4889606	Gluco63	Glucose level QTL 63	2.86	0.003	blood glucose amount (VT:0000188)	blood glucose level area under curve (AUC) (CMO:0000350)	13	83286150	109350286	Rat
8655945	Rf61	Renal function QTL 61	3.6		blood creatinine amount (VT:0005328)	creatinine clearance (CMO:0000765)	13	71610804	89333251	Rat
71119	Thym2	Thymus enlargement QTL 2	3.8		thymus mass (VT:0004954)	thymus weight to body weight ratio (CMO:0000612)	13	48749814	87285480	Rat
1331783	Bp221	Blood pressure QTL 221	3.72886		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	13	71610804	89333251	Rat
8655959	Pur32	Proteinuria QTL 32	8.4		urine total protein amount (VT:0000032)	urine total protein excretion rate (CMO:0000756)	13	72984506	99745408	Rat
1300166	Kidm6	Kidney mass QTL 6	3.93		kidney mass (VT:0002707)	single kidney wet weight to body weight ratio (CMO:0000622)	13	71610804	89333251	Rat
2293687	Bss26	Bone structure and strength QTL 26	4.6	0.0001	femur morphology trait (VT:0000559)	femur cross-sectional area (CMO:0001661)	13	67635937	109350286	Rat
619615	Bp80	Blood pressure QTL 80		0.0354	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	13	7421791	87286911	Rat
1581573	Uae36	Urinary albumin excretion QTL 36			urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	13	6002008	88706694	Rat
724564	Uae11	Urinary albumin excretion QTL 11	5.7		urine albumin amount (VT:0002871)	urine albumin level (CMO:0000130)	13	47354258	94285672	Rat
738027	Lnnr6	Liver neoplastic nodule remodeling QTL 6	3.3		liver integrity trait (VT:0010547)	liver remodeling tumorous lesion number (CMO:0001461)	13	65613454	109350286	Rat
7207885	Glom27	Glomerulus QTL 27	3.9		kidney glomerulus integrity trait (VT:0010546)	kidney crescentic glomeruli count to kidney normal glomeruli count ratio (CMO:0002139)	13	21120177	109350286	Rat
7387280	Uae43	Urinary albumin excretion QTL 43	5.69	0.4174	urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	13	68983334	109350286	Rat
738026	Lnnr5	Liver neoplastic nodule remodeling QTL 5	3.29		liver integrity trait (VT:0010547)	liver remodeling tumorous lesion number (CMO:0001461)	13	62424592	88113509	Rat
2293702	Bss34	Bone structure and strength QTL 34	4.61	0.0001	femur strength trait (VT:0010010)	femur midshaft polar moment of inertia (CMO:0001669)	13	67635937	109350286	Rat
1576318	Schws5	Schwannoma susceptibility QTL 5		0.0351	nervous system integrity trait (VT:0010566)	post-insult time to trigeminal nerve neurilemmoma formation (CMO:0002019)	13	64497900	109350286	Rat
1354621	Rf47	Renal function QTL 47	3.7		kidney renin amount (VT:0010559)	kidney renin level (CMO:0002166)	13	11081740	103588154	Rat
1581554	Pur11	Proteinuria QTL 11			urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	13	6002008	88706694	Rat
12879475	Bp400	Blood pressure QTL 400			arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	13	64375743	109350286	Rat
1354666	Bp244	Blood pressure QTL 244	4.9		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	13	1	103588154	Rat
2293341	Glom15	Glomerulus QTL 15	9.1		kidney glomerulus integrity trait (VT:0010546)	kidney sclerotic glomeruli count to total glomeruli count ratio (CMO:0001269)	13	67635937	109350286	Rat

Markers in Region

G42060

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	13	84,099,761 - 84,099,910 (+)	MAPPER	mRatBN7.2
Rnor_6.0	13	90,021,262 - 90,021,410	NCBI	Rnor6.0
Rnor_5.0	13	94,643,553 - 94,643,701	UniSTS	Rnor5.0
RGSC_v3.4	13	87,599,682 - 87,599,830	UniSTS	RGSC3.4
Celera	13	83,729,573 - 83,729,721	UniSTS
Cytogenetic Map	13	q24	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	musculoskeletal system	nervous system	renal system	reproductive system	respiratory system	sensory system	visual system
16	10	52	110	81	80	49	92	49	6	314	175	11	85	66	78	31	12	12

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001191673	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_008769732	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_063272129	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	CH473985	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JAXUCZ010000013	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Ensembl Acc Id:

ENSRNOT00000035498 ⟹ ENSRNOP00000036230

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8 Ensembl	13	86,615,234 - 86,633,190 (-)	Ensembl
mRatBN7.2 Ensembl	13	84,082,824 - 84,100,823 (-)	Ensembl
Rnor_6.0 Ensembl	13	90,002,783 - 90,022,269 (-)	Ensembl

Ensembl Acc Id:

ENSRNOT00000096361 ⟹ ENSRNOP00000087223

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8 Ensembl	13	86,611,784 - 86,633,190 (-)	Ensembl
mRatBN7.2 Ensembl	13	84,079,458 - 84,100,823 (-)	Ensembl

Ensembl Acc Id:

ENSRNOT00000100394 ⟹ ENSRNOP00000088162

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8 Ensembl	13	86,611,784 - 86,633,164 (-)	Ensembl
mRatBN7.2 Ensembl	13	84,079,458 - 84,100,757 (-)	Ensembl

Ensembl Acc Id:

ENSRNOT00000103580 ⟹ ENSRNOP00000092458

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8 Ensembl	13	86,611,784 - 86,633,190 (-)	Ensembl
mRatBN7.2 Ensembl	13	84,079,458 - 84,100,823 (-)	Ensembl

Ensembl Acc Id:

ENSRNOT00000113721 ⟹ ENSRNOP00000081109

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8 Ensembl	13	86,611,784 - 86,657,293 (-)	Ensembl
mRatBN7.2 Ensembl	13	84,079,458 - 84,100,823 (-)	Ensembl

Ensembl Acc Id:

ENSRNOT00000165565 ⟹ ENSRNOP00000103047

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8 Ensembl	13	86,612,692 - 86,633,190 (-)	Ensembl

RefSeq Acc Id:

NM_001191673 ⟹ NP_001178602

RefSeq Status:

VALIDATED

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	13	86,611,755 - 86,633,190 (-)	NCBI
mRatBN7.2	13	84,079,345 - 84,100,783 (-)	NCBI
Rnor_6.0	13	90,002,783 - 90,022,269 (-)	NCBI
Rnor_5.0	13	94,624,495 - 94,644,219 (-)	NCBI
Celera	13	83,711,096 - 83,730,526 (-)	NCBI

Sequence:

show sequence

ATGGCGGATCTAAAAAGATATTGGTGTGAACGGGCTCTAGATGCATTCTCTGAAAAAACAAGAA
AGAGTCAGCAGCAGATATTTTCTCCCATTCTTTGGATCCCTCTCCTCTTCCTACTCATGGGGCT
AGGAGCCTCTGGGAAGGAAACACCCCCAAGAGTGATATCAGGGATCCTAGGGGGTTCTGTGACT
TTCCCCCTAAATATCTCAATAAATGCAGAAATTGAGCTCATCACCTGGACTTACCTCTCAAAGA
CTCTTGTTTTAGCCATCACCAGCAGATCTGGTATAACGATTCTGCTCAAAGAATACAGTGGCCG
ACTCAACATCAGCCAAGATGGCTACTCCTTGTGCATGAGTAACCTAACCAAGAGTGATTCAGGA
TCCTACCAGGCTCAAATAATCCAAAAGAATGTTGACCACACCGTGAGGAACGAGTTCATACTGC
ACATCTATGAGCAGCTACAGGAGCCTCAAGTCACCGTGAAATCTATGACCTCATCTGAGAATGA
TTCCTGCACTGTCACCCTAATCTGCACTGTAAATGGGTCAAAGGATGGTGTCCAGTACAGCTGG
ATCCAAAAGGACACCCATAATAAGACATCCCATGAAAGTCACATCCTCAGGGTTTCCCCAAGTG
CCTGTGACCCGGACCTACCGTATACCTGCACAGCTCGCAATCCAGTCAGCCAAAACAGCTCCCA
ACCTGTCCGCGTCCGGCAGTTCTGTACAGGAACCTCCAGAAAAAAAACAACTGGGAAGACTGTG
ATAGGAATCCTGGGAGAGCCAGTGACCCTGTCCTTGGAATTCCCGGCCAGTGAGGAAACAAAGA
ATGTTGTCTGGGTATTTAACACATCGGTTATCAGCCAAGAACCGAAAGGAGCAGCAACAGTGGA
TCCTCACCGCCATAAGTCCAAAAGTTCTGAAGAAAGGAGGTTGAGGATCTCTGACCAGGACAGC
TCCCTGAAGATCAGCCAGCTGAAGATGGAGGACACAGGCCCCTACCATGCCTATGTGTGCTCAG
AGACCTCCAGAGGCCCCAGTGTGAGACACTTCACCCTGCTCGTCTACCAGAGACTGAAGAAGCC
CAACGTCACCCAGAGTCCTGTGCACATGACGAATGGCATCTGCGAGGTTGTCCTGACCTGCTCA
GTGGAAGGTGGTGAAAAAGACGTGAGGTACACGTGGATGCCTCTGCAAAAGGAAACTGTCATGT
CCCAAGGGAAGTCGCACCTCAACGTCTCCTGGAAGATTGGTGAACGCCTGCCCAACTTCACATG
CACAACCCATAACCCTGTCAGCAACAGCTCCCGCCAGTTGTCTTCTGGGAGCCTCTGTTCAGGC
CCAGAGAGAAACAAAAGGCTTTGGATCCTGCTCCTCCTGGGTTTGTTCTTGGGGATGCTCATTG
GCGGTTGCTTCATTTTGAAGAAAAGGAAACTGTGTTCATCTTTGGCCATCAGGAACAGCCAAGC
CAAGGTCCCAGCTGAAATACCAGAAACCCCAGCTGGCCACATAGGATTTTCCGTGCTCTCCCAA
CAGTATGAGAAATTAGATATGCCTGCTAAGACTATCAGACATCACTCTACATCCACCTCAGATA
CCAGCTCTGAGAGCAGCGCAACAACAGAAGAGGATGATGAAAAGACCAGAATGCATAGCACTGT
TAACGGTAGAAGTCAGGTGTACGACTTATTCACTCAAGAGGACATTGCACATGACTTGGCCTCT
GAGGGGCAAGCAGAATATGAAGCAGTTAGTCCAGATGATAAAGTGGCTAAGTCTATGGATGAAG
AAGACACAGCATACACACAAGAGTCCCTGATTGTGCAGGGAGAGAACCCACTTCCTCAGAAGAA
AGAAGGCTCAAATACAATCTACTGCTCTTTACAGAAACATAAAACGATGGTGCAGACACCACAG
CAAGATACTGAGTCTCCTGAAACCCCTACCTATGAAAATTTCACCTGA

hide sequence

RefSeq Acc Id:

XM_063272129 ⟹ XP_063128199

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	13	86,610,762 - 86,633,314 (-)	NCBI

Protein Sequences


Protein RefSeqs	NP_001178602	(Get FASTA)	NCBI Sequence Viewer
	XP_063128199	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	EDL94660	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSRNOP00000036230.6
	ENSRNOP00000081109.2
	ENSRNOP00000087223
	ENSRNOP00000087223.1
	ENSRNOP00000088162.1
	ENSRNOP00000092458
	ENSRNOP00000092458.1
	ENSRNOP00000103047.1

RefSeq Acc Id:

NP_001178602 ⟸ NM_001191673

- UniProtKB:

A0A8I6GJS8 (UniProtKB/TrEMBL), A0A8I5ZS62 (UniProtKB/TrEMBL)

- Sequence:

show sequence

MADLKRYWCERALDAFSEKTRKSQQQIFSPILWIPLLFLLMGLGASGKETPPRVISGILGGSVT
FPLNISINAEIELITWTYLSKTLVLAITSRSGITILLKEYSGRLNISQDGYSLCMSNLTKSDSG
SYQAQIIQKNVDHTVRNEFILHIYEQLQEPQVTVKSMTSSENDSCTVTLICTVNGSKDGVQYSW
IQKDTHNKTSHESHILRVSPSACDPDLPYTCTARNPVSQNSSQPVRVRQFCTGTSRKKTTGKTV
IGILGEPVTLSLEFPASEETKNVVWVFNTSVISQEPKGAATVDPHRHKSKSSEERRLRISDQDS
SLKISQLKMEDTGPYHAYVCSETSRGPSVRHFTLLVYQRLKKPNVTQSPVHMTNGICEVVLTCS
VEGGEKDVRYTWMPLQKETVMSQGKSHLNVSWKIGERLPNFTCTTHNPVSNSSRQLSSGSLCSG
PERNKRLWILLLLGLFLGMLIGGCFILKKRKLCSSLAIRNSQAKVPAEIPETPAGHIGFSVLSQ
QYEKLDMPAKTIRHHSTSTSDTSSESSATTEEDDEKTRMHSTVNGRSQVYDLFTQEDIAHDLAS
EGQAEYEAVSPDDKVAKSMDEEDTAYTQESLIVQGENPLPQKKEGSNTIYCSLQKHKTMVQTPQ
QDTESPETPTYENFT

hide sequence

Ensembl Acc Id:

ENSRNOP00000036230 ⟸ ENSRNOT00000035498

Ensembl Acc Id:

ENSRNOP00000087223 ⟸ ENSRNOT00000096361

Ensembl Acc Id:

ENSRNOP00000088162 ⟸ ENSRNOT00000100394

Ensembl Acc Id:

ENSRNOP00000081109 ⟸ ENSRNOT00000113721

Ensembl Acc Id:

ENSRNOP00000092458 ⟸ ENSRNOT00000103580

RefSeq Acc Id:	XP_063128199 ⟸ XM_063272129
- Peptide Label:	isoform X1
- UniProtKB:	A0A8I6A5H0 (UniProtKB/TrEMBL), A0A8I5ZS62 (UniProtKB/TrEMBL)

Ensembl Acc Id:

ENSRNOP00000103047 ⟸ ENSRNOT00000165565

Protein Domains

Ig-like

Protein Structures

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-D3ZEF7-F1-model_v2	AlphaFold	D3ZEF7	1-655	view protein structure

Transcriptome

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

Promoters

RGD ID:

13699012

Promoter ID:

EPDNEW_R9537

Type:

single initiation site

Name:

Ly9_1

Description:

lymphocyte antigen 9

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	13	90,022,295 - 90,022,355	EPDNEW

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:1308341	AgrOrtholog
BioCyc Gene	G2FUF-17356	BioCyc
Ensembl Genes	ENSRNOG00000025069	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000035498.7	UniProtKB/TrEMBL
	ENSRNOT00000096361	ENTREZGENE
	ENSRNOT00000096361.2	UniProtKB/TrEMBL
	ENSRNOT00000100394.2	UniProtKB/TrEMBL
	ENSRNOT00000103580	ENTREZGENE
	ENSRNOT00000103580.2	UniProtKB/TrEMBL
	ENSRNOT00000113721.2	UniProtKB/TrEMBL
	ENSRNOT00000165565.1	UniProtKB/TrEMBL
Gene3D-CATH	2.60.40.10	UniProtKB/TrEMBL
InterPro	CD2/SLAM_rcpt	UniProtKB/TrEMBL
	Ig-like	UniProtKB/TrEMBL
	Ig-like_dom_sf	UniProtKB/TrEMBL
	Ig-like_fold	UniProtKB/TrEMBL
	Ig_sub	UniProtKB/TrEMBL
	Ig_V-set	UniProtKB/TrEMBL
KEGG Report	rno:289227	UniProtKB/TrEMBL
NCBI Gene	289227	ENTREZGENE
PANTHER	SIGNALING LYMPHOCYTIC ACTIVATION MOLECULE	UniProtKB/TrEMBL
	T-LYMPHOCYTE SURFACE ANTIGEN LY-9	UniProtKB/TrEMBL
Pfam	Ig_2	UniProtKB/TrEMBL
	V-set	UniProtKB/TrEMBL
PhenoGen	Ly9	PhenoGen
PROSITE	IG_LIKE	UniProtKB/TrEMBL
RatGTEx	ENSRNOG00000025069	RatGTEx
SMART	SM00409	UniProtKB/TrEMBL
Superfamily-SCOP	SSF48726	UniProtKB/TrEMBL
UniProt	A0A8I5ZS62	ENTREZGENE, UniProtKB/TrEMBL
	A0A8I6A4J1_RAT	UniProtKB/TrEMBL
	A0A8I6A5H0	ENTREZGENE, UniProtKB/TrEMBL
	A0A8I6GJS8	ENTREZGENE, UniProtKB/TrEMBL
	A0ABK0LC97_RAT	UniProtKB/TrEMBL
	D3ZEF7_RAT	UniProtKB/TrEMBL

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2008-04-30	Ly9	lymphocyte antigen 9	Ly9_predicted	lymphocyte antigen 9 (predicted)	'predicted' is removed	2292626	APPROVED
2005-01-12	Ly9_predicted	lymphocyte antigen 9 (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 - ClinVar