Smcr8 (SMCR8-C9orf72 complex subunit)

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Gene: Smcr8 (SMCR8-C9orf72 complex subunit) Rattus norvegicus

Analyze

Symbol:

Smcr8

Name:

SMCR8-C9orf72 complex subunit

RGD ID:

1564621

Description:

Predicted to enable protein kinase binding activity and protein kinase inhibitor activity. Predicted to contribute to guanyl-nucleotide exchange factor activity. Predicted to be involved in several processes, including negative regulation of macromolecule metabolic process; regulation of TOR signaling; and regulation of macroautophagy. Predicted to be located in several cellular components, including nucleoplasm; postsynapse; and presynapse. Predicted to be part of Atg1/ULK1 kinase complex; chromatin; and guanyl-nucleotide exchange factor complex. Orthologous to human SMCR8 (SMCR8-C9orf72 complex subunit); INTERACTS WITH 17alpha-ethynylestradiol; 2,3,7,8-tetrachlorodibenzodioxine; acetamide.

Type:

protein-coding

RefSeq Status:

INFERRED

Previously known as:

guanine nucleotide exchange protein SMCR8; LOC497918; RGD1564621; similar to Smcr8 protein; Smith-Magenis syndrome chromosome region, candidate 8; Smith-Magenis syndrome chromosome region, candidate 8 homolog; Smith-Magenis syndrome chromosome region, candidate 8 homolog (human)

RGD Orthologs

Human

Mouse

Chinchilla

Bonobo

Dog

Squirrel

Pig

Green Monkey

Naked Mole-Rat

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):	SMCR8 (SMCR8-C9orf72 complex subunit)	HGNC	EggNOG, Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, Panther, PhylomeDB, Treefam
Mus musculus (house mouse):	Smcr8 (Smith-Magenis syndrome chromosome region, candidate 8 homolog (human))	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chinchilla lanigera (long-tailed chinchilla):	Smcr8 (SMCR8-C9orf72 complex subunit)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	SMCR8 (SMCR8-C9orf72 complex subunit)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	SMCR8 (SMCR8-C9orf72 complex subunit)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Smcr8 (SMCR8-C9orf72 complex subunit)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	SMCR8 (SMCR8-C9orf72 complex subunit)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	SMCR8 (SMCR8-C9orf72 complex subunit)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Smcr8 (SMCR8-C9orf72 complex subunit)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Homo sapiens (human):	SMCR8 (SMCR8-C9orf72 complex subunit)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Mus musculus (house mouse):	Smcr8 (Smith-Magenis syndrome chromosome region, candidate 8 homolog (human))	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Danio rerio (zebrafish):	smcr8a (Smith-Magenis syndrome chromosome region, candidate 8a)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Caenorhabditis elegans (roundworm):	smcr-8	Alliance	DIOPT (Ensembl Compara\|OrthoFinder\|OrthoInspector\|PANTHER)
Xenopus tropicalis (tropical clawed frog):	smcr8	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)

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
mRatBN7.2	10	45,457,962 - 45,465,101 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	10	45,457,605 - 45,468,876 (+)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	10	50,159,207 - 50,166,360 (+)	NCBI	Rnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0	10	49,649,603 - 49,656,756 (+)	NCBI	Rnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0	10	45,153,192 - 45,160,345 (+)	NCBI	Rnor_WKY
Rnor_6.0	10	47,019,326 - 47,026,465 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	10	47,018,974 - 47,026,465 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	10	46,791,502 - 46,798,641 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	10	46,924,224 - 46,931,363 (+)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
Celera	10	44,712,528 - 44,719,666 (+)	NCBI		Celera
Cytogenetic Map	10	q22	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

autistic disorder (ISO)

common variable immunodeficiency 2 (ISO)

genetic disease (ISO)

Joubert syndrome (ISO)

Neurodevelopmental Disorders (ISO)

Potocki-Lupski syndrome (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

1,2-dichloroethane (ISO)

1,2-dimethylhydrazine (ISO)

17alpha-ethynylestradiol (EXP)

2,2',4,4'-Tetrabromodiphenyl ether (ISO)

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

3-isobutyl-1-methyl-7H-xanthine (ISO)

4,4'-sulfonyldiphenol (ISO)

acetamide (EXP)

acrylamide (ISO)

aflatoxin B1 (ISO)

all-trans-retinoic acid (ISO)

antirheumatic drug (ISO)

arsane (ISO)

arsenic atom (ISO)

benzo[a]pyrene (ISO)

bisphenol A (EXP)

bisphenol F (ISO)

cadmium atom (ISO)

caffeine (ISO)

cyclosporin A (ISO)

dexamethasone (ISO)

dicrotophos (ISO)

dorsomorphin (ISO)

doxorubicin (ISO)

ethyl methanesulfonate (ISO)

formaldehyde (ISO)

gentamycin (EXP)

indometacin (ISO)

lead diacetate (ISO)

methotrexate (ISO)

methyl methanesulfonate (ISO)

methylmercury chloride (ISO)

methylparaben (ISO)

paracetamol (ISO)

SB 431542 (ISO)

sunitinib (ISO)

tungsten (ISO)

urethane (ISO)

valproic acid (ISO)

zinc protoporphyrin (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

negative regulation of autophagosome assembly (ISO)

negative regulation of gene expression (ISO)

negative regulation of macroautophagy (ISO)

negative regulation of protein kinase activity (ISO)

positive regulation of autophagosome maturation (ISO)

positive regulation of GTPase activity (ISO)

positive regulation of TOR signaling (ISO)

regulation of autophagy (ISO)

regulation of TORC1 signaling (ISO)

Cellular Component

Atg1/ULK1 kinase complex (ISO)

chromatin (ISO)

cytoplasm (ISO)

guanyl-nucleotide exchange factor complex (IBA,ISO)

nucleoplasm (IEA,ISO)

postsynapse (ISO)

presynapse (ISO)

Molecular Function

GTPase activator activity (IEA)

guanyl-nucleotide exchange factor activity (ISO)

protein binding (ISO)

protein kinase binding (ISO)

protein kinase inhibitor activity (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.	Data Import for Chemical-Gene Interactions	RGD automated import pipeline for gene-chemical interactions

Additional References at PubMed

PMID:27103069	PMID:27193190	PMID:27559131	PMID:27617292	PMID:28195531

Genomics

Comparative Map Data

Smcr8
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	10	45,457,962 - 45,465,101 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	10	45,457,605 - 45,468,876 (+)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	10	50,159,207 - 50,166,360 (+)	NCBI	Rnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0	10	49,649,603 - 49,656,756 (+)	NCBI	Rnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0	10	45,153,192 - 45,160,345 (+)	NCBI	Rnor_WKY
Rnor_6.0	10	47,019,326 - 47,026,465 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	10	47,018,974 - 47,026,465 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	10	46,791,502 - 46,798,641 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	10	46,924,224 - 46,931,363 (+)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
Celera	10	44,712,528 - 44,719,666 (+)	NCBI		Celera
Cytogenetic Map	10	q22	NCBI

SMCR8
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	17	18,315,293 - 18,328,056 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p13 Ensembl	17	18,315,293 - 18,328,056 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	17	18,218,607 - 18,231,370 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	17	18,159,319 - 18,172,095 (+)	NCBI	NCBI36	Build 36	hg18	NCBI36
Build 34	17	18,159,440 - 18,167,109	NCBI
Celera	17	19,159,665 - 19,172,441 (+)	NCBI		Celera
Cytogenetic Map	17	p11.2	NCBI
HuRef	17	17,972,126 - 17,984,902 (+)	NCBI		HuRef
CHM1_1	17	18,227,353 - 18,240,129 (+)	NCBI		CHM1_1
T2T-CHM13v2.0	17	18,262,099 - 18,274,862 (+)	NCBI		T2T-CHM13v2.0

Smcr8
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	11	60,668,351 - 60,679,113 (+)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	11	60,668,350 - 60,679,113 (+)	Ensembl		GRCm39 Ensembl
GRCm38	11	60,777,525 - 60,788,287 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	11	60,777,524 - 60,788,287 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	11	60,591,027 - 60,601,789 (+)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	11	60,593,737 - 60,597,262 (+)	NCBI		MGSCv36	mm8
MGSCv36	11	61,208,627 - 61,212,152 (+)	NCBI		MGSCv36	mm8
Cytogenetic Map	11	B2	NCBI

Smcr8
(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_004955478	11,002,174 - 11,015,123 (-)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955478	11,002,174 - 11,015,123 (-)	NCBI	ChiLan1.0	ChiLan1.0

SMCR8
(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	17	57,651,042 - 57,663,823 (-)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	17	32,858,205 - 32,871,132 (+)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	17	37,884,037 - 37,897,031 (-)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	17	37,884,037 - 37,896,972 (-)	Ensembl	panpan1.1		panPan2

SMCR8
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ROS_Cfam_1.0	5	41,356,732 - 41,369,920 (-)	NCBI		ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	5	41,361,422 - 41,369,287 (-)	Ensembl		ROS_Cfam_1.0 Ensembl

Smcr8
(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_024405602	61,018,506 - 61,028,302 (-)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936741	1,838,834 - 1,844,459 (+)	Ensembl	SpeTri2.0
SpeTri2.0	NW_004936741	1,838,974 - 1,848,742 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

SMCR8
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	12	60,435,273 - 60,443,520 (-)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	12	60,435,276 - 60,443,525 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1

SMCR8
(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	16	17,358,952 - 17,367,323 (+)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	16	17,359,577 - 17,366,851 (+)	Ensembl	ChlSab1.1	ChlSab1.1 Ensembl	chlSab2
Vero_WHO_p1.0	NW_023666059	3,537,962 - 3,546,697 (-)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Smcr8
(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_004624849	3,149,121 - 3,159,273 (-)	Ensembl	HetGla_female_1.0	HetGla_female_1.0 Ensembl	hetGla2
HetGla 1.0	NW_004624849	3,147,251 - 3,159,358 (-)	NCBI	HetGla_female_1.0	HetGla 1.0	hetGla2

Variants

Variants in Smcr8
10 total Variants

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	205
Count of miRNA genes:	146
Interacting mature miRNAs:	161
Transcripts:	ENSRNOT00000006984
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
70223	Bp57	Blood pressure QTL 57	5		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	10	1	80676123	Rat
631554	Bp133	Blood pressure QTL 133		0.005	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	10	743364	63851208	Rat
2313064	Bmd71	Bone mineral density QTL 71	0.9	0.0001	tibia mineral mass (VT:1000283)	compact volumetric bone mineral density (CMO:0001730)	10	5387014	50387014	Rat
2313066	Bss63	Bone structure and strength QTL 63	1.4	0.0001	tibia strength trait (VT:1000284)	bone polar moment of inertia (CMO:0001558)	10	5387014	50387014	Rat
2313081	Bss64	Bone structure and strength QTL 64	1.3	0.0001	tibia strength trait (VT:1000284)	tibia total energy absorbed before break (CMO:0001736)	10	5387014	50387014	Rat
2313095	Bss62	Bone structure and strength QTL 62	1.5	0.0001	tibia size trait (VT:0100001)	tibia midshaft cross-sectional area (CMO:0001717)	10	5387014	50387014	Rat
2313104	Bss61	Bone structure and strength QTL 61	0.9	0.0001	tibia area (VT:1000281)	tibia midshaft cross-sectional area (CMO:0001717)	10	5387014	50387014	Rat
2298544	Neuinf9	Neuroinflammation QTL 9	4.6		nervous system integrity trait (VT:0010566)	spinal cord complement component 1, q subcomponent, B chain mRNA level (CMO:0002126)	10	5801990	62146030	Rat
8662860	Vetf10	Vascular elastic tissue fragility QTL 10			artery integrity trait (VT:0010639)	number of ruptures of the internal elastic lamina of the abdominal aorta and iliac arteries (CMO:0002562)	10	6154182	73453136	Rat
61427	Cia16	Collagen induced arthritis QTL 16	3.2		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	10	6357896	96121100	Rat
1578761	Stresp21	Stress response QTL 21	3.3		thymus mass (VT:0004954)	thymus wet weight (CMO:0000855)	10	6375746	51375746	Rat
2303118	Mamtr7	Mammary tumor resistance QTL 7		0.003	mammary gland integrity trait (VT:0010552)	mammary tumor growth rate (CMO:0000344)	10	9658275	104670812	Rat
9590310	Scort19	Serum corticosterone level QTL 19	6.3	0.001	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	10	11474010	56474010	Rat
9590268	Scort13	Serum corticosterone level QTL 13	3.26	0.001	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	10	11474010	56474010	Rat
9589136	Insul27	Insulin level QTL 27	10.46	0.001	blood insulin amount (VT:0001560)	plasma insulin level (CMO:0000342)	10	11474010	56474010	Rat
2301967	Cm73	Cardiac mass QTL 73	4.55		heart left ventricle mass (VT:0007031)	heart left ventricle weight to body weight ratio (CMO:0000530)	10	14487011	89062041	Rat
631268	Cia21	Collagen induced arthritis QTL 21	3.1		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	10	14487011	104060283	Rat
2316949	Gluco60	Glucose level QTL 60	3.7		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	10	14487011	107057807	Rat
1354587	Kidm21	Kidney mass QTL 21	3.3		kidney mass (VT:0002707)	right kidney wet weight (CMO:0000082)	10	15028513	60430477	Rat
631564	Apr3	Acute phase response QTL 3	3.9		blood interleukin-6 amount (VT:0008595)	plasma interleukin-6 level (CMO:0001927)	10	15275955	60275955	Rat
6893350	Bw99	Body weight QTL 99	0.87	0.16	body mass (VT:0001259)	body weight (CMO:0000012)	1	15906665	60906665	Rat
6893352	Bw100	Body weight QTL 100	0.33	0.6	body mass (VT:0001259)	body weight (CMO:0000012)	1	15906665	60906665	Rat
631532	Cm50	Cardiac mass QTL 50	6.6		heart mass (VT:0007028)	calculated heart weight (CMO:0000073)	10	17907113	51786432	Rat
1598852	Anxrr19	Anxiety related response QTL 19	5.07		body movement coordination trait (VT:0005424)	number of rearing movements in an experimental apparatus (CMO:0001752)	10	18167841	63167841	Rat
2313055	Bw96	Body weight QTL 96	3.6	0.0001	body mass (VT:0001259)	body weight (CMO:0000012)	10	19606483	64606483	Rat
2313087	Bmd80	Bone mineral density QTL 80	3.2	0.0001	tibia mineral mass (VT:1000283)	total volumetric bone mineral density (CMO:0001728)	10	19606483	64606483	Rat
1554317	Bmd4	Bone mineral density QTL 4	9.4	0.0001	lumbar vertebra mineral mass (VT:0010511)	volumetric bone mineral density (CMO:0001553)	10	19816042	99406971	Rat
1581497	Esta1	Estrogen-induced thymic atrophy QTL 1			thymus mass (VT:0004954)	thymus wet weight (CMO:0000855)	10	21329805	61345413	Rat
724556	Pur2	Proteinuria QTL 2	5.5		urine protein amount (VT:0005160)	urine protein level (CMO:0000591)	10	22427500	90627625	Rat
61354	Pia10	Pristane induced arthritis QTL 10		0.01	joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	10	23444813	104060283	Rat
631267	Cia20	Collagen induced arthritis QTL 20	3.2		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	10	23444813	104060283	Rat
61325	Aia5	Adjuvant induced arthritis QTL 5		0.01	joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	10	23444813	104060283	Rat
70224	Eae3	Experimental allergic encephalomyelitis QTL 3	4.1		nervous system integrity trait (VT:0010566)	experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)	10	26521957	61345413	Rat
1298069	Bp168	Blood pressure QTL 168	5.5		blood pressure trait (VT:0000183)	systolic blood pressure (CMO:0000004)	10	26521957	98003205	Rat
631542	Bp82	Blood pressure QTL 82	6.8		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	10	26521957	98952741	Rat
2300171	Bmd58	Bone mineral density QTL 58	4.9	0.0001	lumbar vertebra mineral mass (VT:0010511)	volumetric bone mineral density (CMO:0001553)	10	26944628	71944628	Rat
10402859	Bp381	Blood pressure QTL 381		0.002	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	10	27606468	72606468	Rat
2292441	Bp308	Blood pressure QTL 308			arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	10	27606468	72606468	Rat
724527	Bp148	Blood pressure QTL 148		0.0001	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	10	28453136	73453136	Rat
1600371	Mcs21	Mammary carcinoma susceptibility QTL 21	3		mammary gland integrity trait (VT:0010552)	mammary tumor growth rate (CMO:0000344)	10	28875650	52200160	Rat
1331762	Rf40	Renal function QTL 40	3.873		kidney blood vessel physiology trait (VT:0100012)	absolute change in renal vascular resistance (CMO:0001900)	10	29299504	64155584	Rat
1331791	Cm31	Cardiac mass QTL 31	3.84606		heart mass (VT:0007028)	heart wet weight (CMO:0000069)	10	29299504	107211142	Rat
631557	Bp136	Blood pressure QTL 136		0.003	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	10	30632053	75632053	Rat
1576311	Pia26	Pristane induced arthritis QTL 26			joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	10	31224026	75632053	Rat
1578779	Tcas10	Tongue tumor susceptibility QTL 10	3.12		tongue integrity trait (VT:0010553)	number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)	10	31297439	76297439	Rat
1576319	Cia29	Collagen induced arthritis QTL 29			joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	10	33973921	78973921	Rat
61332	Eau3	Experimental allergic uveoretinitis QTL 3		0.004	uvea integrity trait (VT:0010551)	experimental autoimmune uveitis score (CMO:0001504)	10	34490559	45579777	Rat
1354614	Hpcl1	Hepatic cholesterol level QTL 1	3.3		liver cholesterol amount (VT:0010498)	liver cholesterol level (CMO:0001597)	10	35392267	51793994	Rat
1358897	Stresp6	Stress response QTL 6	4.17	0.022	blood norepinephrine amount (VT:0005663)	plasma norepinephrine level (CMO:0001010)	10	35392267	64155584	Rat
61441	Btemp1	Thermal response to stress QTL 1	4		body temperature trait (VT:0005535)	core body temperature (CMO:0001036)	10	35392457	63642539	Rat
2317042	Aia20	Adjuvant induced arthritis QTL 20	3.38		joint integrity trait (VT:0010548)	right rear ankle joint diameter (CMO:0002150)	10	37565079	82565079	Rat
2317043	Aia7	Adjuvant induced arthritis QTL 7	3.82		joint integrity trait (VT:0010548)	left rear ankle joint diameter (CMO:0002149)	10	37565079	82565079	Rat
1576308	Schws1	Schwannoma susceptibility QTL 1		0.0041	nervous system integrity trait (VT:0010566)	percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)	10	40035094	102359817	Rat
631269	Cia22	Collagen induced arthritis QTL 22	8.9		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	10	40035094	104060283	Rat
631270	Cia23	Collagen induced arthritis QTL 23	3.9		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	10	40035094	104060283	Rat
631552	Vetf2	Vascular elastic tissue fragility QTL 2	4.5	0.0002	aorta elastic tissue integrity trait (VT:0010556)	artery internal elastic lamina non-tumorous lesion count (CMO:0001913)	10	41142633	86142633	Rat
61463	Bp12	Blood pressure QTL 12	6.3	0.0001	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	10	41333258	86333258	Rat
8552805	Bw145	Body weight QTL 145	2.2		body mass (VT:0001259)	change in body weight to body weight ratio (CMO:0002216)	10	41944526	78307017	Rat
1298078	Stresp5	Stress response QTL 5	2.99	0.00025	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	10	42045676	104670812	Rat
70188	BpQTLcluster1	Blood pressure QTL cluster 1	4.864		arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	1	42323132	87323132	Rat
70188	BpQTLcluster1	Blood pressure QTL cluster 1	4.864		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	42323132	87323132	Rat
70188	BpQTLcluster1	Blood pressure QTL cluster 1	4.864		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	1	42323132	87323132	Rat
70188	BpQTLcluster1	Blood pressure QTL cluster 1	4.864		arterial blood pressure trait (VT:2000000)	pulse pressure (CMO:0000292)	1	42323132	87323132	Rat
70198	BpQTLcluster9	Blood pressure QTL cluster 9	2.94		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	10	42323132	87323132	Rat
6893342	Cm78	Cardiac mass QTL 78	0.1	0.88	heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	10	42876766	79813922	Rat
9589030	Epfw9	Epididymal fat weight QTL 9	19.24	0.001	epididymal fat pad mass (VT:0010421)	epididymal fat pad weight to body weight ratio (CMO:0000658)	10	44441699	89441699	Rat
7411614	Foco18	Food consumption QTL 18		0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	10	44441699	89441699	Rat
8694173	Bw149	Body weight QTL 149	4.38	0.001	body mass (VT:0001259)	body weight gain (CMO:0000420)	10	44441699	89441699	Rat
2300218	Hpcl2	Hepatic cholesterol level QTL 2			liver cholesterol amount (VT:0010498)	liver cholesterol level (CMO:0001597)	10	45029650	95600334	Rat

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	1	5	28	12	19	12	1	1	74	35	34	11	1
Low	2	37	29	29		29	7	10			7		7
Below cutoff		1

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001191919	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	JACYVU010000220	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000006984 ⟹ ENSRNOP00000006984

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	10	45,457,605 - 45,468,876 (+)	Ensembl
Rnor_6.0 Ensembl	10	47,019,326 - 47,026,465 (+)	Ensembl

RefSeq Acc Id:

ENSRNOT00000079375 ⟹ ENSRNOP00000069945

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	10	47,018,974 - 47,026,319 (+)	Ensembl

RefSeq Acc Id:

NM_001191919 ⟹ NP_001178848

RefSeq Status:

INFERRED

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	10	45,457,962 - 45,465,101 (+)	NCBI
Rnor_6.0	10	47,019,326 - 47,026,465 (+)	NCBI
Rnor_5.0	10	46,791,502 - 46,798,641 (+)	NCBI
Celera	10	44,712,528 - 44,719,666 (+)	NCBI

Sequence:

show sequence

CCCGGAAGTACAAAGAAGGCCGCAAGAACTTCGCTTTCTCATCCAGAGGCCTGACTTCCCTGCC
GAGTAACCCTGCATTATTTCCCATTTCCTCTCAATGTGCTCTCCATATTTCAGGAAATATGATC
AGCGCCCCTGATGTGGTGGCCTTTACCAAGGAAGACGAATACGAGGAAGAACCTTACAATGAAC
CCGCTTTGCCTGAAGAATACTCAGTTCCTCTCTTTCCTTATGCCAGCCAGGGCGCTAACCCCTG
GTCTAAACTGTCTGGGGCCAAGTTCTCCAGGGACTTTATCCTTATTTCAGAGTTCTCTGAGCAG
GTGGGACCACAGCCCTTGCTAACCATCCCCAATGACACCAAAGTTTTTGGCACTTTTGATCTCA
ATTACTTCTCCTTGCGGATCATGTCAGTGGATTATCAGGCCTCTTTCGTAGGGCATCCTCCTGG
TTCTGCCTACCCCAAGTTGAACTTTGTGGAGGACTCTAAAGTGGTACTTGGAGACTCTAAGGAA
GGGGCATTTGCATATGTGCACCACCTTACCTTGTATGACCTGGAGGCCAGGGGCTTCGTGCGGC
CCTTTTGTATGGCTTATATCTCTGCAGACCAGCATAAAATCATGCAGCAATTCCAAGAGCTCTC
AGCCGAATTTTCCAAAGCATCTGAGTGCTTGAAGACGGGTAACAGGAAGGCATTCGCTGGGGAA
CTTGAAAAAAAGCTGAAAGACTTGGATTACACGAGGACAGTGCTACACACAGAAACCGAGATCC
AGAAGAAAGCCAATGACAAGGGTTTTTATTCTTCTCAGGCAATTGAGAAAGCCAATGAACTGGC
CAATGTGGAGAAGTCCATCATTGAACATCAAGATTTGCTGAGGCAGATCCGCTCATACCCTCGT
CAGAAGATGAAGAAGCCTGATTTGCATCCAGGTGATACAGAGCATACCCAGGATCAGGCTGACC
AGGTATGCCCTACCTCTAATCCTGAGGAGTCAGCTAATGCAGACCTTTATACCTGCAGGCCGGC
TTACACCCCCAAACTCATCAAAGCAAAGTCCACCAAGTGTTTTGACAAGAAGTTGAAGACCTTG
GAGGAACTCTGTGACACTGAGTATTTCACTGAGACCCTGGCCCAGCTTAGCCACATTGAACACA
TGTTCAGAGGGGACCTGTGCTACCTCCTGACCAGTCAGATTGACAGAGCACTTCGAAAACAACA
GCCCATAACAAATTTCCTCTTTGAAGATTTTGTAGAGGTTGATGACAGGATGGAGAAGCAAGAG
AATGTGCCCTCTCAACCCAGTCACGGCAGGCTGCCTTCCAAGCCTGTAGAAGAATGCCCCATTC
CTAAAGTGTTAATTAGTGTTGGCTCTTACAAGTCCAGTGTGGAGTCTGTATTGATCAAGATGGA
GCAGGAACTTGGAGACGAAGAATACAAGGAAGTAGAGGCAACAGAGTCAAGCAGTTTTGACCCC
CAAGAAAACCTGGACTACATGGGTATGGATATGAAAGGGAGCATCAGTAGTGGGGAAAGCATTG
AGGTTCTGGGCACTGAGAAGTCAGCTTCTGTGTTGTCGAAATCTGACAGCCAGGCTAGCCTCAC
CGTGCCATTGAGCCCCCATGTAGTCCGTAGCAAAGCGGTCAGCCACAGGACAATCAGTGAGGAC
AGCATTGAAGTCTTAAGCACCTGCCCTTCTGAGGCCCTCATTCCTGATGACTTTAAGGCCAGCT
ACCCAAGTGCCATTAATGAAGAAGAAGCCTATGCAGACAATGAGGGGGCCATCCATTTCCAGGC
AAGTGCCAGCTCACCAGAACTAGATGAGACTCAGGAGGGCAACTTAGAAAATATCCCATCCCAA
ATAGACTCCAGCTGCTGTATTGGAAAGGAGAGTGAAGGTCAGTTGGTGCCTCTCCCCACCCCAG
CTTACACCCTTTCTGATGAGGATGGTGTGGTGAGCATTCCCCCACAGCGCTACATACAGAAGGA
CCAGGGGCTCCACATGGACTTCGGGATGGAGAACACTGACCCTTCTCCCCGAGACAACAGTTGT
GAAATGTTCCCAGCTTATGATCTGGATCCAAGCTGCCTTCTGGCTAGCCGAGATATTAGTAAGA
TGAGCCTGGATAACTACTCGGATAGCACTAGCTACATGGGCAGTGTGGCCTCTACCAGCTCGGA
CAGAATCCCCTCTGCTCCTCCTGCTGGCCTATCCTCTGAGAGGCACAAAAAGAGAGCTGGCCAG
AATGCCTTAAAATTCATCCGCCAGTACCCTTTTGCCCACCCAGCCATCTACTCCCTGCTCAGTG
GGAGGACACTTGTGGTCCTGGGCGAAGATGAAACCATAGTCAGGAAGCTGGTAACTGCACTGTC
CATCTTCGTTCCCAACTATGGCTGCTATGCCAAGCCCGTGAAGCACTGGATTTCCTCCCCTTTG
CATATTATGGATTTTCAGAAGTGGAAGCTTATTGGCCTACAAAGAGTGGCCTCTCCTGCCAATG
TGGGTACCCTTCATACCCTGAGCCGTTACAGCCGCTATACAAGCATCCTGGACCTGGACAGCAA
GACTCTACGTTGTCCCCTGTACAGGGGTACACTGGTACCCCGCCTGGCTGACCACCGCACTCAG
ATCAAGCGGGGCAGCACATACTACCTTCATGTCCAGAGCATGCTCACCCAGCTCTGCTCCAAGG
CATTCCTCTATACCTTTTGCCACCACTTGCATTTGCCTGCTCACAGTGAGGAGACACAAGAAGC
AGTGGCCAGCAGACAAACCAGCTTCCTAAAGCTAAACCTGGGACTAGTGAATGAGGACATCAGA
GTGGTACAGTACCTGGCCGAGCTGTTGAAATTGCACTATATGCAGGAGTCACCTGGGACCACCC
ACCCACTGCTCAGGTTTGACTATGTCCCCAGCTTTTTATACAAAATCTAAGGGTTCCAGCCACT
ATGACCAAGACCTGTGACTCAGGGTATGGGGAGGGAAATGGGTTGCTGTGACTAAATGGTTGCC
TGAGCTGGAGTGTTGAGCCTTCTGCTGTCAGCGGGAAGGGAACAGGTGGCAGTTCCAGTTCCAA
CACAGCCCAGGGCAGTGTGTGAAGGGCTGAGTAGAGGTGGCACCCAGCCCTCCAGAGGTAGCTG
GAAGAACAGGAGCAGCTGCTCTTCGTTTGTTAGGGAAGTAGCTCCCAAATAAGGGGGTGTCCTT
AATTTTCCAAGGAGCAGCAGTGTGAGCAGAAGAGAAAGCTCCAGACACTGGGACTGGAAAAGAT
GAGGCTAAGT

hide sequence

Protein Sequences


Protein RefSeqs	NP_001178848	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:

NP_001178848 ⟸ NM_001191919

- UniProtKB:

D3ZJR6 (UniProtKB/TrEMBL)

- Sequence:

show sequence

MISAPDVVAFTKEDEYEEEPYNEPALPEEYSVPLFPYASQGANPWSKLSGAKFSRDFILISEFS
EQVGPQPLLTIPNDTKVFGTFDLNYFSLRIMSVDYQASFVGHPPGSAYPKLNFVEDSKVVLGDS
KEGAFAYVHHLTLYDLEARGFVRPFCMAYISADQHKIMQQFQELSAEFSKASECLKTGNRKAFA
GELEKKLKDLDYTRTVLHTETEIQKKANDKGFYSSQAIEKANELANVEKSIIEHQDLLRQIRSY
PRQKMKKPDLHPGDTEHTQDQADQVCPTSNPEESANADLYTCRPAYTPKLIKAKSTKCFDKKLK
TLEELCDTEYFTETLAQLSHIEHMFRGDLCYLLTSQIDRALRKQQPITNFLFEDFVEVDDRMEK
QENVPSQPSHGRLPSKPVEECPIPKVLISVGSYKSSVESVLIKMEQELGDEEYKEVEATESSSF
DPQENLDYMGMDMKGSISSGESIEVLGTEKSASVLSKSDSQASLTVPLSPHVVRSKAVSHRTIS
EDSIEVLSTCPSEALIPDDFKASYPSAINEEEAYADNEGAIHFQASASSPELDETQEGNLENIP
SQIDSSCCIGKESEGQLVPLPTPAYTLSDEDGVVSIPPQRYIQKDQGLHMDFGMENTDPSPRDN
SCEMFPAYDLDPSCLLASRDISKMSLDNYSDSTSYMGSVASTSSDRIPSAPPAGLSSERHKKRA
GQNALKFIRQYPFAHPAIYSLLSGRTLVVLGEDETIVRKLVTALSIFVPNYGCYAKPVKHWISS
PLHIMDFQKWKLIGLQRVASPANVGTLHTLSRYSRYTSILDLDSKTLRCPLYRGTLVPRLADHR
TQIKRGSTYYLHVQSMLTQLCSKAFLYTFCHHLHLPAHSEETQEAVASRQTSFLKLNLGLVNED
IRVVQYLAELLKLHYMQESPGTTHPLLRFDYVPSFLYKI

hide sequence

RefSeq Acc Id:

ENSRNOP00000069945 ⟸ ENSRNOT00000079375

RefSeq Acc Id:

ENSRNOP00000006984 ⟸ ENSRNOT00000006984

Protein Structures

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-D3ZJR6-F1-model_v2	AlphaFold	D3ZJR6	1-935	view protein structure

Transcriptome

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

Promoters

RGD ID:

13697254

Promoter ID:

EPDNEW_R7777

Type:

multiple initiation site

Name:

Smcr8_1

Description:

Smith-Magenis syndrome chromosome region, candidate 8

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	10	47,018,968 - 47,019,028	EPDNEW

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:1564621	AgrOrtholog
BioCyc Gene	G2FUF-24842	BioCyc
Ensembl Genes	ENSRNOG00000005165	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein	ENSRNOP00000006984	ENTREZGENE
	ENSRNOP00000006984.5	UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000006984	ENTREZGENE
	ENSRNOT00000006984.7	UniProtKB/TrEMBL
InterPro	FLCN/SMCR8_DENN	UniProtKB/TrEMBL
	Folliculin_N	UniProtKB/TrEMBL
KEGG Report	rno:497918	UniProtKB/TrEMBL
NCBI Gene	497918	ENTREZGENE
PANTHER	GUANINE NUCLEOTIDE EXCHANGE PROTEIN SMCR8	UniProtKB/TrEMBL
	SMITH-MAGENIS SYNDROME REGION GENE 8 PROTEIN	UniProtKB/TrEMBL
Pfam	Folliculin	UniProtKB/TrEMBL
PhenoGen	Smcr8	PhenoGen
PROSITE	DENN_FLCN_SMCR8	UniProtKB/TrEMBL
UniProt	D3ZJR6	ENTREZGENE, UniProtKB/TrEMBL

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2019-04-02	Smcr8	SMCR8-C9orf72 complex subunit	Smcr8	Smith-Magenis syndrome chromosome region, candidate 8	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2013-03-01	Smcr8	Smith-Magenis syndrome chromosome region, candidate 8	Smcr8	Smith-Magenis syndrome chromosome region, candidate 8 homolog (human)	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2008-03-06	Smcr8	Smith-Magenis syndrome chromosome region, candidate 8 homolog (human)	RGD1564621_predicted	similar to Smcr8 protein (predicted)	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2006-03-07	RGD1564621_predicted	similar to Smcr8 protein (predicted)	LOC497918	similar to Smcr8 protein	Symbol and Name status set to approved	1299863	APPROVED
2006-02-09	LOC497918	similar to Smcr8 protein			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 - ClinVar