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Gene: Lmcd1 (LIM and cysteine-rich domains 1) Rattus norvegicus

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Symbol:

Lmcd1

Name:

LIM and cysteine-rich domains 1

RGD ID:

1308963

Description:

Predicted to enable transcription corepressor activity. Predicted to be involved in positive regulation of calcineurin-NFAT signaling cascade and regulation of cardiac muscle hypertrophy. Predicted to act upstream of or within negative regulation of transcription by RNA polymerase II. Predicted to be located in cytoplasm. Predicted to be active in nucleus. Orthologous to human LMCD1 (LIM and cysteine rich domains 1); INTERACTS WITH 1-naphthyl isothiocyanate; 2,3,7,8-tetrachlorodibenzodioxine; 3,3',4,4',5-pentachlorobiphenyl.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Previously known as:

dyxin; LIM and cysteine-rich domains protein 1; LIMD1; LOC362411

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):	LMCD1 (LIM and cysteine rich domains 1)	HGNC	EggNOG, Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, Panther, PhylomeDB, Treefam
Mus musculus (house mouse):	Lmcd1 (LIM and cysteine-rich domains 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chinchilla lanigera (long-tailed chinchilla):	Lmcd1 (LIM and cysteine rich domains 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	LMCD1 (LIM and cysteine rich domains 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	LMCD1 (LIM and cysteine rich domains 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Lmcd1 (LIM and cysteine rich domains 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	LMCD1 (LIM and cysteine rich domains 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	LMCD1 (LIM and cysteine rich domains 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Lmcd1 (LIM and cysteine rich domains 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Rattus rattus (black rat):	Lmcd1 (LIM and cysteine rich domains 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Homo sapiens (human):	LMCD1 (LIM and cysteine rich domains 1)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Mus musculus (house mouse):	Lmcd1 (LIM and cysteine-rich domains 1)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Danio rerio (zebrafish):	lmcd1 (LIM and cysteine-rich domains 1)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Drosophila melanogaster (fruit fly):	Tes	Alliance	DIOPT (Ensembl Compara\|InParanoid\|PANTHER\|PhylomeDB\|SonicParanoid)
Drosophila melanogaster (fruit fly):	Tes	Alliance	DIOPT (Ensembl Compara\|InParanoid\|PANTHER\|SonicParanoid)
Caenorhabditis elegans (roundworm):	tes-1	Alliance	DIOPT (Ensembl Compara\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Caenorhabditis elegans (roundworm):	tes-1	Alliance	DIOPT (Ensembl Compara\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|SonicParanoid)
Xenopus tropicalis (tropical clawed frog):	lmcd1	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Xenopus tropicalis (tropical clawed frog):	lmcd1	Alliance	DIOPT (Ensembl Compara\|OMA\|OrthoFinder\|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	4	146,948,993 - 147,007,878 (+)	NCBI	GRCr8	GRCr8		GRCr8
GRCr8 Ensembl	4	146,948,958 - 147,007,875 (+)	Ensembl				GRCr8
mRatBN7.2	4	145,393,153 - 145,452,049 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	4	145,393,145 - 145,452,046 (+)	Ensembl				mRatBN7.2
UTH_Rnor_SHR_Utx	4	150,785,843 - 150,844,729 (+)	NCBI	UTH_Rnor_SHR_Utx	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	4	146,566,657 - 146,625,523 (+)	NCBI	UTH_Rnor_SHRSP_BbbUtx_1.0	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	4	145,187,941 - 145,246,815 (+)	NCBI	UTH_Rnor_WKY_Bbb_1.0	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	4	144,192,989 - 144,252,554 (+)	NCBI	Rnor_6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	4	144,192,989 - 144,252,551 (+)	Ensembl			rn6	Rnor6.0
Rnor_5.0	4	207,494,655 - 207,554,220 (+)	NCBI	Rnor_5.0	Rnor_5.0	rn5
RGSC_v3.4	4	148,071,431 - 148,130,313 (+)	NCBI	RGSC_v3.4	RGSC_v3.4	rn4
Celera	4	133,994,893 - 134,022,583 (+)	NCBI		Celera
RGSC_v3.1	4	148,316,271 - 148,375,153 (+)	NCBI
Cytogenetic Map	4	q41	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

coronary stenosis (ISO)

mitral valve insufficiency (ISO)

mitral valve prolapse (ISO)

tetralogy of Fallot (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

(2,4,5-trichlorophenoxy)acetic acid (ISO)

1,2-dimethylhydrazine (ISO)

1-naphthyl isothiocyanate (EXP)

17alpha-ethynylestradiol (ISO)

17beta-estradiol (ISO)

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

2,4,6-tribromophenol (ISO)

3,3',4,4',5-pentachlorobiphenyl (EXP)

3,3',5-triiodo-L-thyronine (ISO)

3-phenylprop-2-enal (ISO)

4,4'-sulfonyldiphenol (ISO)

6-propyl-2-thiouracil (EXP)

actinomycin D (ISO)

aflatoxin B1 (EXP,ISO)

all-trans-retinoic acid (ISO)

allyl alcohol (EXP)

Allylamine (EXP)

atrazine (ISO)

benzo[a]pyrene (ISO)

benzo[a]pyrene diol epoxide I (ISO)

beta-naphthoflavone (ISO)

bis(2-ethylhexyl) phthalate (ISO)

bisphenol A (EXP,ISO)

bisphenol AF (ISO)

Bisphenol B (ISO)

bisphenol F (ISO)

cadmium atom (ISO)

cadmium dichloride (EXP,ISO)

calcitriol (ISO)

cantharidin (ISO)

carbamazepine (ISO)

carbofuran (EXP)

carbon nanotube (ISO)

chloroacetaldehyde (ISO)

chloroform (EXP)

cidofovir anhydrous (ISO)

ciglitazone (ISO)

cisplatin (EXP,ISO)

clobetasol (ISO)

cobalt dichloride (EXP)

copper atom (ISO)

copper(0) (ISO)

copper(II) sulfate (ISO)

coumestrol (ISO)

cyclophosphamide (EXP)

cyclosporin A (EXP,ISO)

cytarabine (ISO)

dexamethasone (ISO)

dioxygen (EXP,ISO)

disulfiram (ISO)

diuron (EXP)

doxorubicin (EXP)

endosulfan (EXP)

ethanol (ISO)

fenamic acid (EXP)

fenofibrate (EXP)

fluoranthene (ISO)

folic acid (ISO)

furan (EXP)

gentamycin (EXP)

ifosfamide (ISO)

isoprenaline (EXP)

ivermectin (ISO)

ketamine (EXP)

menadione (ISO)

metaproterenol (EXP)

metformin (EXP)

mifepristone (ISO)

mitoxantrone (EXP)

mono(2-ethylhexyl) phthalate (ISO)

nitrofen (EXP)

nitrofurantoin (EXP)

Nutlin-3 (ISO)

okadaic acid (ISO)

orciprenaline (EXP)

ozone (ISO)

paracetamol (EXP,ISO)

phenobarbital (ISO)

phenylbutazone (EXP)

phenylephrine (EXP)

potassium chromate (ISO)

potassium dichromate (ISO)

progesterone (ISO)

quercetin (ISO)

raloxifene (ISO)

resveratrol (ISO)

S-nitrosoglutathione (ISO)

silver atom (ISO)

silver(0) (ISO)

sodium arsenite (ISO)

succimer (ISO)

sunitinib (ISO)

tamoxifen (ISO)

temozolomide (ISO)

tetrachloromethane (EXP,ISO)

thioacetamide (EXP)

thiram (ISO)

titanium dioxide (ISO)

triadimefon (ISO)

triamterene (EXP)

trichloroethene (EXP)

triclosan (ISO)

troglitazone (EXP)

valproic acid (ISO)

vinclozolin (EXP)

vorinostat (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

negative regulation of transcription by RNA polymerase II (IEA,ISO)

positive regulation of calcineurin-NFAT signaling cascade (IEA,ISO)

regulation of cardiac muscle hypertrophy (IEA,ISO)

Cellular Component

cytoplasm (IEA)

nucleus (IBA,IEA,ISO)

Molecular Function

metal ion binding (IEA)

protein binding (ISO)

transcription corepressor activity (IBA,IEA,ISO)

zinc ion binding (IEA)

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.	Myristoylation of LMCD1 Leads to Its Species-Specific Derepression of E2F1 and NFATc1 in the Modulation of CDC6 and IL-33 Expression During Development of Vascular Lesions.	Govatati S, etal., Arterioscler Thromb Vasc Biol. 2020 May;40(5):1256-1274. doi: 10.1161/ATVBAHA.120.314147. Epub 2020 Mar 12.
3.	Rat ISS GO annotations from MGI mouse gene data--August 2006	MGD data from the GO Consortium
4.	GOA pipeline	RGD automated data pipeline
5.	ClinVar Automated Import and Annotation Pipeline	RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
6.	Data Import for Chemical-Gene Interactions	RGD automated import pipeline for gene-chemical interactions

Additional References at PubMed

PMID:12477932	PMID:16199866	PMID:20026769	PMID:20175653	PMID:20551380

Genomics

Comparative Map Data

Lmcd1
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	4	146,948,993 - 147,007,878 (+)	NCBI	GRCr8	GRCr8		GRCr8
GRCr8 Ensembl	4	146,948,958 - 147,007,875 (+)	Ensembl				GRCr8
mRatBN7.2	4	145,393,153 - 145,452,049 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	4	145,393,145 - 145,452,046 (+)	Ensembl				mRatBN7.2
UTH_Rnor_SHR_Utx	4	150,785,843 - 150,844,729 (+)	NCBI	UTH_Rnor_SHR_Utx	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	4	146,566,657 - 146,625,523 (+)	NCBI	UTH_Rnor_SHRSP_BbbUtx_1.0	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	4	145,187,941 - 145,246,815 (+)	NCBI	UTH_Rnor_WKY_Bbb_1.0	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	4	144,192,989 - 144,252,554 (+)	NCBI	Rnor_6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	4	144,192,989 - 144,252,551 (+)	Ensembl			rn6	Rnor6.0
Rnor_5.0	4	207,494,655 - 207,554,220 (+)	NCBI	Rnor_5.0	Rnor_5.0	rn5
RGSC_v3.4	4	148,071,431 - 148,130,313 (+)	NCBI	RGSC_v3.4	RGSC_v3.4	rn4
Celera	4	133,994,893 - 134,022,583 (+)	NCBI		Celera
RGSC_v3.1	4	148,316,271 - 148,375,153 (+)	NCBI
Cytogenetic Map	4	q41	NCBI

LMCD1
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	3	8,501,823 - 8,574,668 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	3	8,501,587 - 8,574,668 (+)	Ensembl			hg38	GRCh38
GRCh37	3	8,543,509 - 8,616,354 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	3	8,518,511 - 8,584,806 (+)	NCBI	Build 36	Build 36	hg18	NCBI36
Build 34	3	8,518,510 - 8,584,805	NCBI
Celera	3	8,480,112 - 8,546,564 (+)	NCBI		Celera
Cytogenetic Map	3	p25.3	NCBI
HuRef	3	8,478,394 - 8,544,846 (+)	NCBI		HuRef
CHM1_1	3	8,493,836 - 8,560,461 (+)	NCBI		CHM1_1
T2T-CHM13v2.0	3	8,492,967 - 8,566,009 (+)	NCBI		T2T-CHM13v2.0

Lmcd1
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	6	112,250,747 - 112,307,384 (+)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	6	112,250,719 - 112,307,386 (+)	Ensembl		GRCm39 Ensembl		GRCm39
GRCm38	6	112,273,758 - 112,330,423 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	6	112,273,758 - 112,330,425 (+)	Ensembl			mm10	GRCm38
MGSCv37	6	112,223,752 - 112,280,417 (+)	NCBI	MGSCv37	MGSCv37	mm9	NCBIm37
MGSCv36	6	112,239,591 - 112,296,202 (+)	NCBI		MGSCv36	mm8
Celera	6	114,110,587 - 114,167,245 (+)	NCBI		Celera
Cytogenetic Map	6	E3	NCBI
cM Map	6	52.14	NCBI

Lmcd1
(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_004955561	151,308 - 214,476 (+)	Ensembl
ChiLan1.0	NW_004955561	151,315 - 213,904 (+)	NCBI	ChiLan1.0	ChiLan1.0

LMCD1
(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	8,507,235 - 8,573,884 (+)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	3	8,511,847 - 8,585,307 (+)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	3	8,448,143 - 8,521,214 (+)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	3	8,692,557 - 8,765,522 (+)	NCBI	PanPan1.1	PanPan1.1	panPan2

LMCD1
(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	9,524,393 - 9,582,939 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	20	9,524,413 - 9,583,529 (-)	Ensembl			canFam3	CanFam3.1
Dog10K_Boxer_Tasha	20	9,557,871 - 9,616,422 (-)	NCBI	Dog10K_Boxer_Tasha	Dog10K_Boxer_Tasha
ROS_Cfam_1.0	20	9,555,858 - 9,614,448 (-)	NCBI	ROS_Cfam_1.0	ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	20	9,555,878 - 9,614,921 (-)	Ensembl				ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	20	9,276,475 - 9,335,001 (-)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	20	9,622,849 - 9,681,370 (-)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	20	9,595,563 - 9,654,153 (-)	NCBI	UU_Cfam_GSD_1.0	UU_Cfam_GSD_1.0

Lmcd1
(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	14,431,414 - 14,489,110 (+)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936602	4,420,597 - 4,478,384 (-)	Ensembl		SpeTri2.0 Ensembl
SpeTri2.0	NW_004936602	4,420,600 - 4,478,384 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

LMCD1
(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	64,933,700 - 64,994,228 (+)	Ensembl			susScr11	Sscrofa11.1
Sscrofa11.1	13	64,933,692 - 64,994,204 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	13	72,215,911 - 72,275,069 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

LMCD1
(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	44,531,441 - 44,598,612 (+)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
Vero_WHO_p1.0	NW_023666041	121,964,274 - 122,035,271 (-)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Lmcd1
(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_004624731	3,158,561 - 3,218,658 (+)	Ensembl		HetGla_female_1.0 Ensembl	hetGla2	HetGla_female_1.0 Ensembl
HetGla 1.0	NW_004624731	3,158,682 - 3,218,253 (+)	NCBI	HetGla 1.0	HetGla 1.0	hetGla2

Lmcd1
(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	6	34,184,905 - 34,243,858 (-)	NCBI		Rrattus_CSIRO_v1

Variants

Variants in Lmcd1
357 total Variants

miRNA Target Status (No longer updated)

Predicted Target Of

	Summary Value
Count of predictions:	47
Count of miRNA genes:	39
Interacting mature miRNAs:	45
Transcripts:	ENSRNOT00000007523
Prediction methods:	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
1582232	Gluco25	Glucose level QTL 25	3.6	0.0023	blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	4	86583980	149763391	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	146370897	184426481	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	107346299	152346299	Rat
724558	Plsm2	Polydactyly-luxate syndrome (PLS) morphotypes QTL 2		0.0003	hindlimb integrity trait (VT:0010563)	hind foot phalanges count (CMO:0001949)	4	134095016	179095016	Rat
1300116	Hrtrt5	Heart rate QTL 5	3.76		heart pumping trait (VT:2000009)	heart rate (CMO:0000002)	4	117737142	152833657	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	146370897	184426481	Rat
1358364	Sradr4	Stress Responsive Adrenal Weight QTL 4	4.92		adrenal gland mass (VT:0010420)	both adrenal glands wet weight (CMO:0000164)	4	131384565	176384565	Rat
10755501	Bp390	Blood pressure QTL 390	2.5		arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	4	27730518	170099664	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	112427331	157427331	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	112427331	157427331	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	123870974	168870974	Rat
1331802	Srn5	Serum renin concentration QTL 5	3.045		renin activity (VT:0005581)	plasma renin activity level (CMO:0000116)	4	117559384	162559384	Rat
1331738	Bp209	Blood pressure QTL 209	2.979		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	4	140059299	181024663	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	146370897	184426481	Rat
1298524	Oia8	Oil induced arthritis QTL 8			joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	4	140059299	184426481	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	60916264	184426481	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	111383604	156383604	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	94638356	168870820	Rat
737821	Hcar9	Hepatocarcinoma resistance QTL 9	3.7		liver integrity trait (VT:0010547)	volume of individual liver tumorous lesion (CMO:0001078)	4	106848959	168870974	Rat
731165	Uae21	Urinary albumin excretion QTL 21	2.4	0.0001	urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	4	108206096	153206096	Rat
7411558	Bw133	Body weight QTL 133	13.84	0.001	body mass (VT:0001259)	body weight gain (CMO:0000420)	4	127263297	172263297	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	126334185	171334185	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	146370897	184426481	Rat
631511	Pia7	Pristane induced arthritis QTL 7	4.3		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	4	123870974	168870974	Rat
1549832	Bss3	Bone structure and strength QTL 3	11		femur morphology trait (VT:0000559)	femur midshaft cortical cross-sectional area (CMO:0001663)	4	111383604	156383604	Rat
1354612	Foco1	Food consumption QTL 1	8.87		eating behavior trait (VT:0001431)	food intake rate (CMO:0000427)	4	45429897	149763204	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	82944895	154403548	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	124700988	169700988	Rat
2303168	Bp330	Blood pressure QTL 330	4.25	0.017	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	4	5889999	148002343	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	60916264	174095838	Rat
1576316	Ept5	Estrogen-induced pituitary tumorigenesis QTL 5	3.8		pituitary gland mass (VT:0010496)	pituitary gland wet weight (CMO:0000853)	4	100752691	179366077	Rat
1581566	Eae21	Experimental allergic encephalomyelitis QTL 21	6.2		body mass (VT:0001259)	maximum body weight loss to initial body weight ratio (CMO:0001400)	4	137447185	182447185	Rat
1576305	Emca6	Estrogen-induced mammary cancer QTL 6	5.8		mammary gland integrity trait (VT:0010552)	mammary tumor number (CMO:0000343)	4	45429709	157555683	Rat
1578674	Bmd12	Bone mineral density QTL 12	3.8		femur mineral mass (VT:0010011)	compact volumetric bone mineral density (CMO:0001730)	4	137430611	182430611	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	60916264	184426481	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	86709649	168870974	Rat
61422	Cia13	Collagen induced arthritis QTL 13	4.5		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	4	134199006	168870974	Rat
1354660	Salc1	Saline consumption QTL 1	11.26		drinking behavior trait (VT:0001422)	saline drink intake rate (CMO:0001627)	4	45429897	149763204	Rat
737978	Pia23	Pristane induced arthritis QTL 23	5.3		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	4	123870974	168870974	Rat
61362	Oia2	Oil induced arthritis QTL 2		0.001	joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	4	140059299	184426481	Rat
631674	Iddm14	Insulin dependent diabetes mellitus QTL 14			blood glucose amount (VT:0000188)	plasma glucose level (CMO:0000042)	4	65495851	159259805	Rat
2293840	Kiddil9	Kidney dilation QTL 9	2.9		kidney pelvis morphology trait (VT:0004194)	hydronephrosis severity score (CMO:0001208)	4	113634167	149763391	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	116184844	161184844	Rat
70201	Gcr1	Gastric cancer resistance QTL 1	2.7		stomach morphology trait (VT:0000470)	stomach tumor susceptibility score (CMO:0002043)	4	103834277	148834277	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	57613339	151163960	Rat
12798527	Anxrr58	Anxiety related response QTL 58	4.11	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	121020385	148834277	Rat
2316958	Gluco58	Glucose level QTL 58	10		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	4	12212457	182430611	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	146370897	184426481	Rat

Markers in Region

D4Got119

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	4	145,399,780 - 145,399,931 (+)	MAPPER	mRatBN7.2
Rnor_6.0	4	144,199,794 - 144,199,944	NCBI	Rnor6.0
Rnor_5.0	4	207,501,460 - 207,501,610	UniSTS	Rnor5.0
RGSC_v3.4	4	148,078,059 - 148,078,209	UniSTS	RGSC3.4
RGSC_v3.4	4	148,078,058 - 148,078,209	RGD	RGSC3.4
Celera	4	133,970,335 - 133,970,487	UniSTS
RGSC_v3.1	4	148,322,900 - 148,323,050	RGD
RH 3.4 Map	4	928.8	UniSTS
RH 3.4 Map	4	928.8	RGD
RH 2.0 Map	4	886.6	RGD
Cytogenetic Map	4	q42	UniSTS

AW455500

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	4	145,451,850 - 145,451,963 (+)	MAPPER	mRatBN7.2
Rnor_6.0	4	144,252,356 - 144,252,468	NCBI	Rnor6.0
Rnor_5.0	4	207,554,022 - 207,554,134	UniSTS	Rnor5.0
RGSC_v3.4	4	148,130,115 - 148,130,227	UniSTS	RGSC3.4
Celera	4	134,022,385 - 134,022,497	UniSTS
Cytogenetic Map	4	q42	UniSTS

AI071230

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	4	145,451,780 - 145,451,975 (+)	MAPPER	mRatBN7.2
Rnor_6.0	4	144,252,286 - 144,252,480	NCBI	Rnor6.0
Rnor_5.0	4	207,553,952 - 207,554,146	UniSTS	Rnor5.0
RGSC_v3.4	4	148,130,045 - 148,130,239	UniSTS	RGSC3.4
Celera	4	134,022,315 - 134,022,509	UniSTS
RH 3.4 Map	4	927.6	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	musculoskeletal system	nervous system	renal system	reproductive system	respiratory system	sensory system	visual system
16	12	67	162	91	90	59	45	59	6	309	145	11	134	81	92	31	16	16

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001008562	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	BC079071	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473957	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JAXUCZ010000004	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Ensembl Acc Id:

ENSRNOT00000007523 ⟹ ENSRNOP00000007523

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8 Ensembl	4	146,948,958 - 147,007,875 (+)	Ensembl
mRatBN7.2 Ensembl	4	145,393,145 - 145,452,042 (+)	Ensembl
Rnor_6.0 Ensembl	4	144,192,989 - 144,252,551 (+)	Ensembl

Ensembl Acc Id:

ENSRNOT00000117173 ⟹ ENSRNOP00000090319

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	4	145,423,707 - 145,452,046 (+)	Ensembl

RefSeq Acc Id:

NM_001008562 ⟹ NP_001008562

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	4	146,948,993 - 147,007,878 (+)	NCBI
mRatBN7.2	4	145,393,153 - 145,452,049 (+)	NCBI
Rnor_6.0	4	144,192,989 - 144,252,554 (+)	NCBI
Rnor_5.0	4	207,494,655 - 207,554,220 (+)	NCBI
RGSC_v3.4	4	148,071,431 - 148,130,313 (+)	RGD
Celera	4	133,994,893 - 134,022,583 (+)	RGD

Sequence:

show sequence

CTGGAAGCAGGCAAGGGAATCTGAACTTGGCCCATCAGCAGCGCTGTCCATTCTGCGTGCCCTC
TCTCCCCTGCCTGAGAAGCCAGGTGCTAGTTCTGCACCCCCAGGATGGCAAAGGTAGCCAAGGA
CCTCAACCCTCGAGTGCAAAAGATGTCCCTGGGCCAGCAGCAGTCCGCAAGAGGAGTGGCTTGT
CTGCGGTGCAAGGGGATGTGCTCCGGCTTCGAGCCGCATTCATGGAGGAAAATATGCAAGTCTT
GTAAATGCAGCCAGGAGGAGCACTGCCTAAGCTCTGACCTGGAGGATGATCGGAAAATTGGGCG
CCTGCTGATGGACTCCAAGTATGCCACTCTTACTGCCAGGGTGAAAGGTGGAGACGGCATTCGC
ATCTATAAGAGAAACCGCATGATCATGACCAACCCCATTGCCACTGGCAAAGACCCCACCTTTG
ACACTATCACCTATGAGTGGGCTCCCCCAGGAGTCACCCAGAAACTGGGCTTGCAGTACATGGA
GCTCATCCCCAAGGAGAAGCAGCCTGTGACAGGTACTGAGGGTGCCCTCTACCGCCGACGCCAG
CTCATGCACCAGCTCCCAATCTATGATCAGGACCCCTCTCGATGCCGCGGACTTGTGGAGAATG
AGCTGAAAGCTATGGAAGAGTTCGTCAAGCAGTACAAGAGCGAGGCCCTTGGGGTGGGCGAGGT
GGCCCTCCCAGGGCAGGGAGGCTTGCCCAAGGAAGAAAACAAGACACAGGAAAAGCCAGAGGGC
ACAGAGACCACTGCCCCAACCACCAATGGCAGCCTGGGTGATCCATCCAAGGAAGTGGAATATG
TCTGTGAGCTCTGCAAGGGAGTAGCCCCTGCTGACAGCCCTGTGGTCTACGCTGACAGGGCTGG
ATACAGCAAGCAGTGGCACCCCACATGCTTTCTGTGTATCAAGTGCTCAGAGCCACTGGTGGAC
CTCATCTACTTCTGGAAGGATGGTGCACCCTGGTGTGGGCGCCACTACTGCGAGAGCTTGCGGC
CCCGGTGCTCAGGCTGTGACGAGATCATCTTCTCAGAAGACTACCAGCGTGTGGAAGACTTAGC
CTGGCATCGGAAACACTTCATTTGTGAGGGCTGTGAGCAGCTGCTGAGCGGCCGTGCATACATC
ATCACCAAGGGTCAGCTCCTGTGCCCCACTTGCAGCAAGTCCAAACGCTCCTGAAGGGCTGCCC
ACCCACACCCAAAACCAGCAGAGTCAATCAGATTTCACCAGGAGACTGAAGCCATCCTATGGGG
CGGATGCCACAGCCAGCAAGTGATGCATATTCTAGGTCGAGTTGTGGTAGATCTTTGAGGTTCA
GTAGTTTCAAACCCAGAGGTATTCTAAGAAATCTTAGAATGGATTTATTGTTCCTAGCTGCAGC
CAACTAAAGACACACTGGTATCCTACAAGGGAGCTCTAGGAGAAATTTCCCAGAATGCACTTCT
GAGGGATCCAATCAAGTAGATGTAGGTTATGGTTTTTTTTTCTCGTGGACAAGGGATCTCTCCT
GGGGGGAAAGGATGGGATTTCAACTCTCATTTGTTTGCCTCTTTCTCAAGTGGAATCTGAATCT
TCAATAAACAATGTTTTTGGCATGATAAGCATATCAATAAAAGGTTTATGAGTTTCACACATAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA

hide sequence

Protein Sequences


Protein RefSeqs	NP_001008562	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAH79071	(Get FASTA)	NCBI Sequence Viewer
	EDL91494	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSRNOP00000007523
	ENSRNOP00000007523.4

RefSeq Acc Id:

NP_001008562 ⟸ NM_001008562

- UniProtKB:

Q6AYF2 (UniProtKB/TrEMBL), A6IBM6 (UniProtKB/TrEMBL)

- Sequence:

show sequence

MAKVAKDLNPRVQKMSLGQQQSARGVACLRCKGMCSGFEPHSWRKICKSCKCSQEEHCLSSDLE
DDRKIGRLLMDSKYATLTARVKGGDGIRIYKRNRMIMTNPIATGKDPTFDTITYEWAPPGVTQK
LGLQYMELIPKEKQPVTGTEGALYRRRQLMHQLPIYDQDPSRCRGLVENELKAMEEFVKQYKSE
ALGVGEVALPGQGGLPKEENKTQEKPEGTETTAPTTNGSLGDPSKEVEYVCELCKGVAPADSPV
VYADRAGYSKQWHPTCFLCIKCSEPLVDLIYFWKDGAPWCGRHYCESLRPRCSGCDEIIFSEDY
QRVEDLAWHRKHFICEGCEQLLSGRAYIITKGQLLCPTCSKSKRS

hide sequence

Ensembl Acc Id:

ENSRNOP00000007523 ⟸ ENSRNOT00000007523

Ensembl Acc Id:

ENSRNOP00000090319 ⟸ ENSRNOT00000117173

Protein Domains

LIM zinc-binding PET

Protein Structures

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-Q6AYF2-F1-model_v2	AlphaFold	Q6AYF2	1-365	view protein structure

Transcriptome

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

Promoters

RGD ID:

13693286

Promoter ID:

EPDNEW_R3811

Type:

multiple initiation site

Name:

Lmcd1_1

Description:

LIM and cysteine-rich domains 1

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	4	144,192,976 - 144,193,036	EPDNEW

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:1308963	AgrOrtholog
BioCyc Gene	G2FUF-43422	BioCyc
Ensembl Genes	ENSRNOG00000005690	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000007523	ENTREZGENE
	ENSRNOT00000007523.7	UniProtKB/TrEMBL
Gene3D-CATH	Cysteine Rich Protein	UniProtKB/TrEMBL
IMAGE_CLONE	IMAGE:7121826	IMAGE-MGC_LOAD
InterPro	PET_domain	UniProtKB/TrEMBL
	PET_testin	UniProtKB/TrEMBL
	Pk/Esn/Tes	UniProtKB/TrEMBL
	Znf_LIM	UniProtKB/TrEMBL
KEGG Report	rno:494021	UniProtKB/TrEMBL
MGC_CLONE	MGC:94025	IMAGE-MGC_LOAD
NCBI Gene	494021	ENTREZGENE
PANTHER	LIM AND CYSTEINE-RICH DOMAINS PROTEIN 1	UniProtKB/TrEMBL
	LIM DOMAIN-CONTAINING PROTEIN	UniProtKB/TrEMBL
Pfam	LIM	UniProtKB/TrEMBL
	PET	UniProtKB/TrEMBL
PhenoGen	Lmcd1	PhenoGen
PROSITE	LIM_DOMAIN_1	UniProtKB/TrEMBL
	LIM_DOMAIN_2	UniProtKB/TrEMBL
	PET	UniProtKB/TrEMBL
RatGTEx	ENSRNOG00000005690	RatGTEx
SMART	LIM	UniProtKB/TrEMBL
Superfamily-SCOP	Glucocorticoid receptor-like (DNA-binding domain)	UniProtKB/TrEMBL
UniProt	A6IBM6	ENTREZGENE, UniProtKB/TrEMBL
	Q6AYF2	ENTREZGENE, UniProtKB/TrEMBL

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2008-04-30	Lmcd1	LIM and cysteine-rich domains 1	Lmcd1_predicted	LIM and cysteine-rich domains 1 (predicted)	'predicted' is removed	2292626	APPROVED
2005-01-12	Lmcd1_predicted	LIM and cysteine-rich domains 1 (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