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Gene: Lysmd3 (LysM domain containing 3) Rattus norvegicus

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Symbol:

Lysmd3

Name:

LysM domain containing 3

RGD ID:

1308805

Description:

Predicted to enable peptidoglycan binding activity. Predicted to be involved in Golgi organization. Predicted to be located in Golgi membrane and plasma membrane. Predicted to be active in Golgi apparatus. Orthologous to human LYSMD3 (LysM domain containing 3); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; bisphenol A; chlorpyrifos.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Previously known as:

LOC315923; lysM and putative peptidoglycan-binding domain-containing protein 3; LysM, putative peptidoglycan-binding, domain containing 3; MGC109090; RGD1308805; similar to cDNA sequence BC003322

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):	LYSMD3 (LysM domain containing 3)	HGNC	EggNOG, Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, Panther, PhylomeDB, Treefam
Mus musculus (house mouse):	Lysmd3 (LysM, putative peptidoglycan-binding, domain containing 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chinchilla lanigera (long-tailed chinchilla):	Lysmd3 (LysM domain containing 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	LYSMD3 (LysM domain containing 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	LYSMD3 (LysM domain containing 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Lysmd3 (LysM domain containing 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	LYSMD3 (LysM domain containing 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	LYSMD3 (LysM domain containing 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Lysmd3 (LysM domain containing 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Rattus rattus (black rat):	Lysmd3 (LysM domain containing 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Mus musculus (house mouse):	Lysmd3 (LysM, putative peptidoglycan-binding, domain containing 3)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Homo sapiens (human):	LYSMD3 (LysM domain containing 3)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Danio rerio (zebrafish):	lysmd3 (LysM, putative peptidoglycan-binding, domain containing 3)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Drosophila melanogaster (fruit fly):	CG17985	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OrthoFinder\|OrthoInspector)
Drosophila melanogaster (fruit fly):	CG17985	Alliance	DIOPT (Ensembl Compara\|InParanoid\|OrthoFinder\|OrthoInspector\|PhylomeDB)
Caenorhabditis elegans (roundworm):	lmd-1	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|OrthoFinder\|OrthoInspector\|PANTHER)
Caenorhabditis elegans (roundworm):	lmd-1	Alliance	DIOPT (Ensembl Compara\|OrthoFinder\|OrthoInspector\|PANTHER)
Xenopus tropicalis (tropical clawed frog):	lysmd3	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)

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	2	13,669,465 - 13,675,622 (+)	NCBI	GRCr8	GRCr8		GRCr8
GRCr8 Ensembl	2	13,669,429 - 13,678,643 (+)	Ensembl				GRCr8
mRatBN7.2	2	11,933,787 - 11,939,944 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	2	11,933,768 - 11,942,961 (+)	Ensembl				mRatBN7.2
UTH_Rnor_SHR_Utx	2	19,047,553 - 19,053,709 (+)	NCBI	UTH_Rnor_SHR_Utx	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	2	17,147,073 - 17,153,229 (+)	NCBI	UTH_Rnor_SHRSP_BbbUtx_1.0	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	2	11,801,598 - 11,807,755 (+)	NCBI	UTH_Rnor_WKY_Bbb_1.0	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	2	9,526,213 - 9,532,370 (+)	NCBI	Rnor_6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	2	9,526,209 - 9,534,362 (+)	Ensembl			rn6	Rnor6.0
Rnor_5.0	2	9,406,235 - 9,412,392 (+)	NCBI	Rnor_5.0	Rnor_5.0	rn5
RGSC_v3.4	2	9,751,947 - 9,758,104 (+)	NCBI	RGSC_v3.4	RGSC_v3.4	rn4
Celera	2	8,293,736 - 8,299,893 (+)	NCBI		Celera
RGSC_v3.1	2	9,675,798 - 9,681,951 (+)	NCBI
Cytogenetic Map	2	q11	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

nicotine dependence (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

(S)-nicotine (ISO)

1,2-dimethylhydrazine (ISO)

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

2-palmitoylglycerol (ISO)

3,4-methylenedioxymethamphetamine (ISO)

4,4'-sulfonyldiphenol (ISO)

aflatoxin B1 (ISO)

arsenite(3-) (ISO)

benzo[a]pyrene (ISO)

bisphenol A (EXP,ISO)

bisphenol F (ISO)

butanal (ISO)

cadmium atom (ISO)

cadmium dichloride (ISO)

caffeine (ISO)

carbon nanotube (ISO)

CGP 52608 (ISO)

chlorpyrifos (EXP)

copper atom (ISO)

copper(0) (ISO)

cyclosporin A (ISO)

DDE (ISO)

dibenz[a,h]anthracene (ISO)

dibutyl phthalate (EXP,ISO)

dicrotophos (ISO)

dimethyl sulfoxide (ISO)

diuron (ISO)

ethyl methanesulfonate (ISO)

fluoranthene (ISO)

folic acid (ISO)

FR900359 (ISO)

fulvestrant (ISO)

gentamycin (EXP)

hydrogen peroxide (ISO)

methyl methanesulfonate (ISO)

methylmercury chloride (ISO)

nicotine (ISO)

ozone (ISO)

pentanal (ISO)

perfluorooctane-1-sulfonic acid (ISO)

phenobarbital (ISO)

propiconazole (ISO)

silicon dioxide (ISO)

silver atom (ISO)

silver(0) (ISO)

Soman (EXP)

sunitinib (ISO)

tetrachloromethane (EXP,ISO)

thioacetamide (EXP)

trichloroethene (EXP)

tungsten (ISO)

valproic acid (ISO)

vinclozolin (EXP)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

Golgi organization (IBA,IEA,ISO,ISS)

Cellular Component

Golgi apparatus (IBA,IEA,ISO,ISS)

Golgi membrane (IEA,ISO)

plasma membrane (IEA,ISO,ISS)

Molecular Function

peptidoglycan binding (IEA,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.	Data Import for Chemical-Gene Interactions	RGD automated import pipeline for gene-chemical interactions

Additional References at PubMed

PMID:12477932	PMID:15489334	PMID:29851555

Genomics

Comparative Map Data

Lysmd3
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	2	13,669,465 - 13,675,622 (+)	NCBI	GRCr8	GRCr8		GRCr8
GRCr8 Ensembl	2	13,669,429 - 13,678,643 (+)	Ensembl				GRCr8
mRatBN7.2	2	11,933,787 - 11,939,944 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	2	11,933,768 - 11,942,961 (+)	Ensembl				mRatBN7.2
UTH_Rnor_SHR_Utx	2	19,047,553 - 19,053,709 (+)	NCBI	UTH_Rnor_SHR_Utx	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	2	17,147,073 - 17,153,229 (+)	NCBI	UTH_Rnor_SHRSP_BbbUtx_1.0	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	2	11,801,598 - 11,807,755 (+)	NCBI	UTH_Rnor_WKY_Bbb_1.0	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	2	9,526,213 - 9,532,370 (+)	NCBI	Rnor_6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	2	9,526,209 - 9,534,362 (+)	Ensembl			rn6	Rnor6.0
Rnor_5.0	2	9,406,235 - 9,412,392 (+)	NCBI	Rnor_5.0	Rnor_5.0	rn5
RGSC_v3.4	2	9,751,947 - 9,758,104 (+)	NCBI	RGSC_v3.4	RGSC_v3.4	rn4
Celera	2	8,293,736 - 8,299,893 (+)	NCBI		Celera
RGSC_v3.1	2	9,675,798 - 9,681,951 (+)	NCBI
Cytogenetic Map	2	q11	NCBI

LYSMD3
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	5	90,515,626 - 90,529,584 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	5	90,515,611 - 90,529,596 (-)	Ensembl			hg38	GRCh38
GRCh37	5	89,811,443 - 89,825,401 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	5	89,847,200 - 89,861,157 (-)	NCBI	Build 36	Build 36	hg18	NCBI36
Celera	5	85,713,583 - 85,727,549 (-)	NCBI		Celera
Cytogenetic Map	5	q14.3	NCBI
HuRef	5	85,022,118 - 85,036,084 (-)	NCBI		HuRef
CHM1_1	5	89,244,124 - 89,258,073 (-)	NCBI		CHM1_1
T2T-CHM13v2.0	5	91,002,230 - 91,016,199 (-)	NCBI		T2T-CHM13v2.0

Lysmd3
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	13	81,805,782 - 81,820,990 (+)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	13	81,805,782 - 81,820,990 (+)	Ensembl		GRCm39 Ensembl		GRCm39
GRCm38	13	81,657,658 - 81,672,871 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	13	81,657,663 - 81,672,871 (+)	Ensembl			mm10	GRCm38
MGSCv37	13	81,796,805 - 81,810,891 (+)	NCBI	MGSCv37	MGSCv37	mm9	NCBIm37
MGSCv36	13	82,135,143 - 82,149,229 (+)	NCBI		MGSCv36	mm8
Celera	13	83,918,533 - 83,932,619 (+)	NCBI		Celera
Cytogenetic Map	13	C3	NCBI
cM Map	13	43.64	NCBI

Lysmd3
(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_004955418	21,103,679 - 21,116,005 (+)	Ensembl
ChiLan1.0	NW_004955418	21,103,679 - 21,116,005 (+)	NCBI	ChiLan1.0	ChiLan1.0

LYSMD3
(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	4	24,861,662 - 24,876,737 (+)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	5	23,013,382 - 23,032,126 (+)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	5	24,839,015 - 24,854,449 (+)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	5	24,974,666 - 24,988,674 (+)	NCBI	PanPan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	5	24,974,684 - 24,988,674 (+)	Ensembl			panPan2	panpan1.1

LYSMD3
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	3	18,412,824 - 18,425,832 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	3	18,412,829 - 18,422,454 (+)	Ensembl			canFam3	CanFam3.1
Dog10K_Boxer_Tasha	3	19,780,296 - 19,793,017 (+)	NCBI	Dog10K_Boxer_Tasha	Dog10K_Boxer_Tasha
ROS_Cfam_1.0	3	18,319,106 - 18,331,831 (+)	NCBI	ROS_Cfam_1.0	ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	3	18,319,221 - 18,332,542 (+)	Ensembl				ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	3	18,292,758 - 18,305,479 (+)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	3	18,258,057 - 18,270,773 (+)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	3	18,546,862 - 18,559,580 (+)	NCBI	UU_Cfam_GSD_1.0	UU_Cfam_GSD_1.0

Lysmd3
(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_024407213	174,000,095 - 174,012,343 (+)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936469	8,612,690 - 8,625,652 (-)	Ensembl		SpeTri2.0 Ensembl
SpeTri2.0	NW_004936469	8,612,758 - 8,625,566 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

LYSMD3
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	2	97,689,376 - 97,703,745 (-)	Ensembl			susScr11	Sscrofa11.1
Sscrofa11.1	2	97,688,763 - 97,703,918 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	2	100,768,843 - 100,781,843 (-)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

LYSMD3
(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	4	84,460,745 - 84,475,669 (-)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	4	84,460,821 - 84,475,196 (-)	Ensembl		ChlSab1.1 Ensembl	chlSab2	Vervet-AGM
Vero_WHO_p1.0	NW_023666049	33,520,700 - 33,534,643 (-)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Lysmd3
(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_004624743	9,766,160 - 9,778,628 (-)	Ensembl		HetGla_female_1.0 Ensembl	hetGla2	HetGla_female_1.0 Ensembl
HetGla 1.0	NW_004624743	9,766,680 - 9,778,696 (-)	NCBI	HetGla 1.0	HetGla 1.0	hetGla2

Lysmd3
(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	3	214,709,734 - 214,715,896 (-)	NCBI		Rrattus_CSIRO_v1

Variants

Variants in Lysmd3
34 total Variants

miRNA Target Status (No longer updated)

Predicted Target Of

	Summary Value
Count of predictions:	63
Count of miRNA genes:	61
Interacting mature miRNAs:	63
Transcripts:	ENSRNOT00000021818
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 (GRCr8)

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
1578664	Bmd9	Bone mineral QTL density 9	5		femur mineral mass (VT:0010011)	total volumetric bone mineral density (CMO:0001728)	2	5736325	50736325	Rat
738010	Lnnr3	Liver neoplastic nodule remodeling QTL 3	2.94		liver integrity trait (VT:0010547)	liver remodeling tumorous lesion number (CMO:0001461)	2	1	42977529	Rat
9590080	Insglur4	Insulin/glucose ratio QTL 4	28.7	0.001	blood insulin amount (VT:0001560)	calculated plasma insulin level (CMO:0002170)	2	6152767	51152767	Rat
10755430	Coatc6	Coat color QTL 6		0.02576	coat/hair pigmentation trait (VT:0010463)	pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)	2	13325041	58325041	Rat
1600379	Mcs18	Mammary carcinoma susceptibility QTL 18	2.6		mammary gland integrity trait (VT:0010552)	mammary tumor number (CMO:0000343)	2	9623581	44538110	Rat
1331760	Bp206	Blood pressure QTL 206	3.62454		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	2	4265106	205135428	Rat
731166	Mamtr2	Mammary tumor resistance QTL 2		0.0001	mammary gland integrity trait (VT:0010552)	mammary tumor number (CMO:0000343)	2	9623581	54623581	Rat
61368	Mcs1	Mammary carcinoma susceptibility QTL 1	4.4		mammary gland integrity trait (VT:0010552)	mammary tumor number (CMO:0000343)	2	9623581	25054526	Rat
61355	Bp36	Blood pressure QTL 36	2.9		blood pressure trait (VT:0000183)	systolic blood pressure (CMO:0000004)	2	7605533	104774005	Rat

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	12	67	165	91	90	59	92	59	6	355	192	11	144	80	92	31	17	17

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001009698	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AC099304	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BC088262	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473955	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ225025	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ225894	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ227395	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ227953	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ233176	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ234752	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JAXUCZ010000002	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Ensembl Acc Id:

ENSRNOT00000021818 ⟹ ENSRNOP00000021818

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8 Ensembl	2	13,669,429 - 13,678,643 (+)	Ensembl
mRatBN7.2 Ensembl	2	11,933,768 - 11,942,961 (+)	Ensembl
Rnor_6.0 Ensembl	2	9,526,209 - 9,534,362 (+)	Ensembl

RefSeq Acc Id:

NM_001009698 ⟹ NP_001009698

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	2	13,669,465 - 13,675,622 (+)	NCBI
mRatBN7.2	2	11,933,787 - 11,939,944 (+)	NCBI
Rnor_6.0	2	9,526,213 - 9,532,370 (+)	NCBI
Rnor_5.0	2	9,406,235 - 9,412,392 (+)	NCBI
RGSC_v3.4	2	9,751,947 - 9,758,104 (+)	RGD
Celera	2	8,293,736 - 8,299,893 (+)	RGD

Sequence:

show sequence

GGCGGCGGCTGTCGGTGCGGAAGGCGGGGACGGCGGCGACAGCGGCGAAGGCGGCGACAGTGGC
AGAAGCGGACCCAGACATCCGAGGACCGGGAGTCGGTCATGAACTTCCCCGGGGCCGCGGCTGT
GGTGGCGTACATAACCGTGTCGCCGCGCCCCTGCTAGAAGACAGATATAACATCATGGCAGGAA
GGAATCAGAACCGGACTGCTTCCCTCGCAGGAATTCAGGCCAGTGGCCATGTGCACACCTTTGG
GAATTGTACAGACAATGACATGTTGGAAGAAGATGCTGAAGTCTACGAACTTCGGTCCAGGGGA
AAGGAGAAGGTTCGGAGAAGCACATCGAGAGACAGACTTGATGACATCGTTATATTAACGAAAG
ATATACAGGAAGGAGATACTCTGAACGCAGTAGCCCTTCAGTACTGTTGTACGGTAGCAGATAT
CAAAAGAGTTAACAATCTCATCAGTGATCAAGACTTTTTTGCGCTTAGGTCTATCAAAATACCA
GTTAAAAGGTTTAGTTCTTTGACTGAAACTCTTCATCCTCTGAAAGGAAGACAAGTTTTGCATC
CTCCACCTGTTCCGTATTTCCAAGAGCAAGACACTGTGCCAGCTAACGACTCTCCTTCTTCCAG
CGAGTCAGCCGGCAGTTTCCTGAAAGAGGTGGATCGCGACATAGAGCAAATAGTCAAGTGTACA
GACACCAAGAAGGAGAACCTGAATGAAGTAGTGTCCGCCTTAACAGCACAACAGGTCCGATTTG
AGCCTGATAACAAAAGCGTTCACCGAAAGGATCCATATTACGGCGCAGACTGGGGGATGGGTTG
GTGGACAGCTGTCGTGATAATGTTGATAGTGGGCATAATAACCCCAGTGTTTTATTTGCTGTAT
TATGAGATTTTAGCTAAAGTGGATGTTAGCCACCATTCCACAGTGGACTCTTCGCACTTACATC
CAGGACTCACACCTCCATCACACCACAGAGAGATGGGAAATGCAATTGGTCCAACAAAAGGAAT
ACCTGTTGGCCAACAGGATGACCACAGACTCTATAGGCAAGACCCTCAGGCACGCGACTGATGC
TCCACACAAAATGTAACGGTGAGGGGTTGGGGATTTAGCTCAGTGGTAGAGCACTTCGGTCCCC
AGCTCCGAAGAAAAAAAAAAAAAAAAAAAAAAAA

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Protein Sequences


Protein RefSeqs	NP_001009698	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAH88262	(Get FASTA)	NCBI Sequence Viewer
	EDM09947	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSRNOP00000021818
	ENSRNOP00000021818.4
GenBank Protein	Q5M836	(Get FASTA)	NCBI Sequence Viewer

RefSeq Acc Id:

NP_001009698 ⟸ NM_001009698

- UniProtKB:

Q5M836 (UniProtKB/Swiss-Prot), A6I4I9 (UniProtKB/TrEMBL)

- Sequence:

show sequence

MAGRNQNRTASLAGIQASGHVHTFGNCTDNDMLEEDAEVYELRSRGKEKVRRSTSRDRLDDIVI
LTKDIQEGDTLNAVALQYCCTVADIKRVNNLISDQDFFALRSIKIPVKRFSSLTETLHPLKGRQ
VLHPPPVPYFQEQDTVPANDSPSSSESAGSFLKEVDRDIEQIVKCTDTKKENLNEVVSALTAQQ
VRFEPDNKSVHRKDPYYGADWGMGWWTAVVIMLIVGIITPVFYLLYYEILAKVDVSHHSTVDSS
HLHPGLTPPSHHREMGNAIGPTKGIPVGQQDDHRLYRQDPQARD

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Ensembl Acc Id:

ENSRNOP00000021818 ⟸ ENSRNOT00000021818

Protein Domains

LysM

Protein Structures

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-Q5M836-F1-model_v2	AlphaFold	Q5M836	1-300	view protein structure

Transcriptome

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

Promoters

RGD ID:

13691044

Promoter ID:

EPDNEW_R1569

Type:

initiation region

Name:

Lysmd3_1

Description:

LysM 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	2	9,526,250 - 9,526,310	EPDNEW

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:1308805	AgrOrtholog
BioCyc Gene	G2FUF-55015	BioCyc
Ensembl Genes	ENSRNOG00000016298	Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript	ENSRNOT00000021818	ENTREZGENE
	ENSRNOT00000021818.8	UniProtKB/Swiss-Prot
Gene3D-CATH	3.10.350.10	UniProtKB/Swiss-Prot
IMAGE_CLONE	IMAGE:7376577	IMAGE-MGC_LOAD
InterPro	LYSM1-4	UniProtKB/Swiss-Prot
	LysM_dom	UniProtKB/Swiss-Prot
	LysM_dom_sf	UniProtKB/Swiss-Prot
KEGG Report	rno:315923	UniProtKB/Swiss-Prot
MGC_CLONE	MGC:109090	IMAGE-MGC_LOAD
NCBI Gene	315923	ENTREZGENE
PANTHER	AND PUTATIVE PEPTIDOGLYCAN-BINDING DOMAIN-CONTAINING PROTEIN 3-RELATED	UniProtKB/Swiss-Prot
	PTHR20932	UniProtKB/Swiss-Prot
Pfam	LysM	UniProtKB/Swiss-Prot
PhenoGen	Lysmd3	PhenoGen
PROSITE	LYSM	UniProtKB/Swiss-Prot
RatGTEx	ENSRNOG00000016298	RatGTEx
SMART	LysM	UniProtKB/Swiss-Prot
UniProt	A6I4I9	ENTREZGENE, UniProtKB/TrEMBL
	LYSM3_RAT	UniProtKB/Swiss-Prot, ENTREZGENE

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2016-02-10	Lysmd3	LysM domain containing 3	Lysmd3	LysM, putative peptidoglycan-binding, domain containing 3	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2006-03-30	Lysmd3	LysM, putative peptidoglycan-binding, domain containing 3	RGD1308805	similar to cDNA sequence BC003322	Symbol and Name updated	1299863	APPROVED
2005-12-06	RGD1308805	similar to cDNA sequence BC003322	RGD1308805_predicted	similar to cDNA sequence BC003322 (predicted)	Symbol and Name updated	1559027	APPROVED
2005-01-20	RGD1308805_predicted	similar to cDNA sequence BC003322 (predicted)	LOC315923_predicted		Symbol and Name status set to approved	1331353	APPROVED
2005-01-12	LOC315923_predicted	similar to cDNA sequence BC003322 (predicted)			Symbol and Name status set to provisional	70820	PROVISIONAL

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