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Gene: Scnm1 (sodium channel modifier 1) Rattus norvegicus

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Symbol:

Scnm1

Name:

sodium channel modifier 1

RGD ID:

1308968

Description:

Predicted to enable enzyme binding activity. Predicted to be involved in RNA splicing. Predicted to be located in nuclear speck. Predicted to be part of spliceosomal complex. Predicted to be active in nucleus. Human ortholog(s) of this gene implicated in orofaciodigital syndrome XIX. Orthologous to human SCNM1 (sodium channel modifier 1); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,4-dinitrotoluene; 2,6-dinitrotoluene.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Previously known as:

LOC310662

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):	SCNM1 (sodium channel modifier 1)	HGNC	EggNOG, Ensembl, HomoloGene, Inparanoid, OMA, OrthoDB, OrthoMCL, Panther, Treefam
Chinchilla lanigera (long-tailed chinchilla):	Scnm1 (sodium channel modifier 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	SCNM1 (sodium channel modifier 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Scnm1 (sodium channel modifier 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	SCNM1 (sodium channel modifier 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	SCNM1 (sodium channel modifier 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Other homologs ²
Homo sapiens (human):	SCNM1 (sodium channel modifier 1)	HGNC	Ensembl, HomoloGene, Inparanoid, NCBI, OrthoDB, Panther, Treefam
Homo sapiens (human):	DEFA5 (defensin alpha 5)	HGNC	OMA
Homo sapiens (human):	DEFA4 (defensin alpha 4)	HGNC	OMA
Alliance orthologs ³
Homo sapiens (human):	SCNM1 (sodium channel modifier 1)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Homo sapiens (human):	SCNM1 (sodium channel modifier 1)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Mus musculus (house mouse):	Scnm1 (sodium channel modifier 1)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Danio rerio (zebrafish):	scnm1 (sodium channel modifier 1)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Xenopus tropicalis (tropical clawed frog):	scnm1	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	185,389,892 - 185,394,126 (-)	NCBI	GRCr8	GRCr8		GRCr8
GRCr8 Ensembl	2	185,389,892 - 185,394,214 (-)	Ensembl				GRCr8
mRatBN7.2	2	182,700,883 - 182,705,119 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	2	182,700,348 - 182,704,835 (-)	Ensembl				mRatBN7.2
UTH_Rnor_SHR_Utx	2	190,365,582 - 190,369,512 (-)	NCBI	UTH_Rnor_SHR_Utx	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	2	188,161,826 - 188,165,756 (-)	NCBI	UTH_Rnor_SHRSP_BbbUtx_1.0	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	2	182,998,066 - 183,001,996 (-)	NCBI	UTH_Rnor_WKY_Bbb_1.0	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	2	196,300,239 - 196,304,419 (-)	NCBI	Rnor_6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	2	196,300,239 - 196,304,169 (-)	Ensembl			rn6	Rnor6.0
Rnor_5.0	2	215,794,553 - 215,798,889 (-)	NCBI	Rnor_5.0	Rnor_5.0	rn5
RGSC_v3.4	2	190,035,097 - 190,039,027 (-)	NCBI	RGSC_v3.4	RGSC_v3.4	rn4
Celera	2	175,237,678 - 175,241,608 (-)	NCBI		Celera
RGSC_v3.1	2	189,996,175 - 189,999,993 (-)	NCBI
Cytogenetic Map	2	q34	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Annotation Click to see Annotation Detail View

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

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

2,4-dinitrotoluene (EXP)

2,6-dinitrotoluene (EXP)

bisphenol A (EXP)

dibutyl phthalate (EXP)

thioacetamide (EXP)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

mRNA processing (IEA)

pointed-end actin filament capping (IEA)

RNA splicing (IBA,IEA)

Cellular Component

nuclear speck (IEA)

nucleoplasm (IEA)

nucleus (IBA)

spliceosomal complex (IEA,ISO)

U12-type catalytic step 2 spliceosome (IEA,ISO)

U12-type precatalytic spliceosome (IEA,ISO)

U12-type spliceosomal complex (IEA,ISO)

Molecular Function

enzyme binding (IEA,ISO)

metal ion binding (IEA)

protein binding (ISO)

tropomyosin binding (IEA)

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.	ClinVar Automated Import and Annotation Pipeline	RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
3.	Data Import for Chemical-Gene Interactions	RGD automated import pipeline for gene-chemical interactions

Additional References at PubMed

PMID:12920299	PMID:17656373	PMID:23382074

Genomics

Comparative Map Data

Scnm1
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	2	185,389,892 - 185,394,126 (-)	NCBI	GRCr8	GRCr8		GRCr8
GRCr8 Ensembl	2	185,389,892 - 185,394,214 (-)	Ensembl				GRCr8
mRatBN7.2	2	182,700,883 - 182,705,119 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	2	182,700,348 - 182,704,835 (-)	Ensembl				mRatBN7.2
UTH_Rnor_SHR_Utx	2	190,365,582 - 190,369,512 (-)	NCBI	UTH_Rnor_SHR_Utx	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	2	188,161,826 - 188,165,756 (-)	NCBI	UTH_Rnor_SHRSP_BbbUtx_1.0	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	2	182,998,066 - 183,001,996 (-)	NCBI	UTH_Rnor_WKY_Bbb_1.0	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	2	196,300,239 - 196,304,419 (-)	NCBI	Rnor_6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	2	196,300,239 - 196,304,169 (-)	Ensembl			rn6	Rnor6.0
Rnor_5.0	2	215,794,553 - 215,798,889 (-)	NCBI	Rnor_5.0	Rnor_5.0	rn5
RGSC_v3.4	2	190,035,097 - 190,039,027 (-)	NCBI	RGSC_v3.4	RGSC_v3.4	rn4
Celera	2	175,237,678 - 175,241,608 (-)	NCBI		Celera
RGSC_v3.1	2	189,996,175 - 189,999,993 (-)	NCBI
Cytogenetic Map	2	q34	NCBI

SCNM1
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	1	151,156,649 - 151,170,296 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	1	151,156,664 - 151,170,296 (+)	Ensembl			hg38	GRCh38
GRCh37	1	151,129,125 - 151,142,772 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	1	149,405,141 - 149,408,238 (+)	NCBI	Build 36	Build 36	hg18	NCBI36
Build 34	1	147,951,589 - 147,954,687	NCBI
Celera	1	124,253,808 - 124,256,905 (+)	NCBI		Celera
Cytogenetic Map	1	q21.3	NCBI
HuRef	1	122,507,131 - 122,520,863 (+)	NCBI		HuRef
CHM1_1	1	152,524,432 - 152,538,100 (+)	NCBI		CHM1_1
T2T-CHM13v2.0	1	150,280,351 - 150,294,025 (+)	NCBI		T2T-CHM13v2.0

Scnm1
(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_004955588	526,986 - 529,774 (+)	Ensembl
ChiLan1.0	NW_004955588	526,986 - 529,774 (+)	NCBI	ChiLan1.0	ChiLan1.0

SCNM1
(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	98,664,426 - 98,667,557 (-)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	1	98,415,625 - 98,418,727 (-)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	1	126,515,210 - 126,518,313 (+)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	1	130,163,855 - 130,166,728 (+)	NCBI	PanPan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	1	130,163,855 - 130,166,728 (+)	Ensembl			panPan2	panpan1.1

Scnm1
(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_024405058	22,340,523 - 22,344,289 (+)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936580	1,370,944 - 1,374,831 (+)	Ensembl		SpeTri2.0 Ensembl
SpeTri2.0	NW_004936580	1,370,944 - 1,374,671 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

SCNM1
(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	98,079,851 - 98,082,351 (-)	Ensembl			susScr11	Sscrofa11.1
Sscrofa11.1	4	98,079,844 - 98,082,374 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	4	107,332,633 - 107,335,163 (-)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

SCNM1
(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	12,519,187 - 12,523,890 (-)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	20	12,520,394 - 12,523,790 (-)	Ensembl		ChlSab1.1 Ensembl	chlSab2	Vervet-AGM
Vero_WHO_p1.0	NW_023666038	12,097,704 - 12,102,222 (-)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Variants

Variants in Scnm1
60 total Variants

miRNA Target Status (No longer updated)

Predicted Target Of

	Summary Value
Count of predictions:	44
Count of miRNA genes:	40
Interacting mature miRNAs:	42
Transcripts:	ENSRNOT00000028639
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
1358356	Srcrt1	Stress Responsive Cort QTL1	3.66		blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	2	163997722	225110681	Rat
1578648	Bss11	Bone structure and strength QTL 11	4.7		femur morphology trait (VT:0000559)	femoral neck cortical cross-sectional area (CMO:0001702)	2	169358774	214358774	Rat
1331734	Bp204	Blood pressure QTL 204	3.61192		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	2	170656145	239614549	Rat
631566	Bp90	Blood pressure QTL 90		0.0001	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	149957381	221199885	Rat
1298074	Bp164	Blood pressure QTL 164		0.003	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	44537979	205135428	Rat
1354648	Bp239	Blood pressure QTL 239		0.001	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	67845370	229470703	Rat
1354649	Kidm17	Kidney mass QTL 17	2.9		kidney mass (VT:0002707)	calculated kidney weight (CMO:0000160)	2	83465462	229820014	Rat
10755499	Bp389	Blood pressure QTL 389	2.61		arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	2	20695736	231474293	Rat
1298076	Bp166	Blood pressure QTL 166		0.0009	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	138595962	205135428	Rat
1581576	Pur7	Proteinuria QTL 7		0.0001	urine total protein amount (VT:0000032)	urine total protein excretion rate (CMO:0000756)	2	80396178	220931218	Rat
152025245	Scl81	Serum cholesterol level QTL 81	3.49		blood cholesterol amount (VT:0000180)		2	124537199	209621565	Rat
1581578	Cm49	Cardiac mass QTL 49	4.9	0.01	heart left ventricle mass (VT:0007031)	heart left ventricle weight to body weight ratio (CMO:0000530)	2	145807215	220931416	Rat
631198	Cm22	Cardiac mass QTL 22	4.3	0.0008	heart left ventricle mass (VT:0007031)	heart left ventricle weight to body weight ratio (CMO:0000530)	2	78269809	208420281	Rat
1554319	Bmd2	Bone mineral density QTL 2	13.4	0.0001	lumbar vertebra area (VT:0010570)	lumbar vertebra cross-sectional area (CMO:0001689)	2	122597372	215234002	Rat
12879836	Kidm61	Kidney mass QTL 61		0.001	kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	2	154723085	199723085	Rat
1581569	Uae32	Urinary albumin excretion QTL 32		0.0001	urine protein amount (VT:0005160)	urine albumin excretion rate (CMO:0000757)	2	80396178	220931218	Rat
10043136	Iddm54	Insulin dependent diabetes mellitus QTL 54	3.4	0.0001	blood glucose amount (VT:0000188)	age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)	2	145807215	190807215	Rat
12879837	Am2	Aortic mass QTL 2		0.001	aorta mass (VT:0002845)	aorta weight to aorta length to body weight ratio (CMO:0002722)	2	154723085	199723085	Rat
10043139	Iddm55	Insulin dependent diabetes mellitus QTL 55	3.1	0.0001	blood glucose amount (VT:0000188)	age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)	2	150313808	195313808	Rat
12879838	Cm86	Cardiac mass QTL 86		0.002	heart left ventricle mass (VT:0007031)	heart left ventricle weight to body weight ratio (CMO:0000530)	2	154723085	199723085	Rat
1302793	Bw16	Body weight QTL 16	5	0.0001	body mass (VT:0001259)	body weight (CMO:0000012)	2	159440891	205135267	Rat
12879839	Cm85	Cardiac mass QTL 85		0.001	heart mass (VT:0007028)	heart wet weight to body weight ratio (CMO:0002408)	2	154723085	199723085	Rat
1549833	Bp257	Blood pressure QTL 257		0.003	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	2	170652929	215652929	Rat
1358900	Bw48	Body weight QTL 48	4.88		body mass (VT:0001259)	body weight (CMO:0000012)	2	159440891	220931218	Rat
4889834	Pur24	Proteinuria QTL 24	5.8	0.014	urine total protein amount (VT:0000032)	urine total protein excretion rate (CMO:0000756)	2	171994826	205135428	Rat
1359030	Bp277	Blood pressure QTL 277			arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	2	143565208	188565208	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
12879840	Bw179	Body weight QTL 179		0.005	body mass (VT:0001259)	body weight (CMO:0000012)	2	154723085	199723085	Rat
1581502	Esta3	Estrogen-induced thymic atrophy QTL 3			thymus mass (VT:0004954)	thymus wet weight (CMO:0000855)	2	139067258	192287892	Rat
9589044	Scfw1	Subcutaneous fat weight QTL 1	5.8	0.001	subcutaneous adipose mass (VT:1000472)	abdominal subcutaneous fat pad weight (CMO:0002069)	2	184856304	229856304	Rat
8694435	Bw166	Body weight QTL 166	14.08	0.001	retroperitoneal fat pad mass (VT:0010430)	retroperitoneal fat pad weight to body weight ratio (CMO:0000635)	2	184856304	229856304	Rat
1359032	Hrtrt18	Heart rate QTL 18			heart pumping trait (VT:2000009)	heart rate (CMO:0000002)	2	159440760	195313808	Rat
2301966	Bp322	Blood pressure QTL 322	3.58		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	144882354	205135428	Rat
1298080	Bp163	Blood pressure QTL 163		0.02	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	67845182	205135428	Rat
1357991	Ael2	Aortic elastin QTL 2	4.2	0.000071	aorta elastin amount (VT:0003905)	aortic elastin	2	169227906	214227906	Rat
8662832	Vetf7	Vascular elastic tissue fragility QTL 7	3.5		aorta elastin amount (VT:0003905)	aorta wall extracellular elastin dry weight to aorta wall dry weight ratio (CMO:0002002)	2	83400752	223709938	Rat
1298085	Bp165	Blood pressure QTL 165		0.0006	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	44537979	205135428	Rat
8694194	Abfw1	Abdominal fat weight QTL 1	11.7	0.001	visceral adipose mass (VT:0010063)	abdominal fat pad weight to body weight ratio (CMO:0000095)	2	184856304	229856304	Rat
1578671	Bmd10	Bone mineral density QTL 10	5.4		femur mineral mass (VT:0010011)	compact volumetric bone mineral density (CMO:0001730)	2	175931416	220931416	Rat
1641891	Alcrsp17	Alcohol response QTL 17			response to alcohol trait (VT:0010489)	duration of loss of righting reflex (CMO:0002289)	2	151869660	251712708	Rat
724534	Uae6	Urinary albumin excretion QTL 6	10		urine albumin amount (VT:0002871)	urine albumin level (CMO:0000130)	2	80396034	220931416	Rat
61374	Edpm2	Estrogen-dependent pituitary mass QTL 2	4.42	0.86	pituitary gland mass (VT:0010496)	pituitary gland wet weight (CMO:0000853)	2	78269809	205135428	Rat
2300189	Bmd48	Bone mineral density QTL 48	5.8	0.0001	femur mineral mass (VT:0010011)	volumetric bone mineral density (CMO:0001553)	2	182024327	227024327	Rat
8662843	Vetf9	Vascular elastic tissue fragility QTL 9	2.05		thoracic aorta molecular composition trait (VT:0010568)	aorta wall extracellular elastin dry weight to aorta wall extracellular collagen weight ratio (CMO:0002003)	2	159440760	228950743	Rat
2301408	Kidm36	Kidney mass QTL 36		0.002	kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	2	184482291	229482291	Rat
1331794	Bp202	Blood pressure QTL 202	3.66819		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	143344967	251712708	Rat
71113	Cari2	Carrageenan-induced inflammation QTL 2	2.7	0.009	hypodermis integrity trait (VT:0010550)	inflammatory exudate volume (CMO:0001429)	2	143746578	205135428	Rat
1331805	Cm29	Cardiac mass QTL 29	3.50746		heart mass (VT:0007028)	heart wet weight (CMO:0000069)	2	143344967	251712708	Rat
634308	Sach6	Saccharin preference QTL 6	4.9		taste sensitivity trait (VT:0001986)	saccharin intake volume to total fluid intake volume ratio (CMO:0001601)	2	114384617	215381366	Rat
1598805	Memor8	Memory QTL 8	3		exploratory behavior trait (VT:0010471)	average horizontal distance between subject and target during voluntary locomotion in an experimental apparatus (CMO:0002674)	2	150096616	195096616	Rat
1358917	Cm42	Cardiac mass QTL 42	2.82		heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	2	27148328	206613235	Rat
724568	Uae13	Urinary albumin excretion QTL 13	4.4		urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	2	145306936	212705578	Rat
1358913	Cm41	Cardiac mass QTL 41	2.73		heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	2	27148328	206613235	Rat
1300165	Rf9	Renal function QTL 9	3.28		kidney glomerulus integrity trait (VT:0010546)	index of glomerular damage (CMO:0001135)	2	113746222	205135428	Rat
61401	Niddm2	Non-insulin dependent diabetes mellitus QTL 2	4.54		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	2	147287892	192287892	Rat
631507	Bp105	Blood pressure QTL 105		0.001	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	2	114384617	215381366	Rat
1641925	Alcrsp2	Alcohol response QTL 2			response to alcohol trait (VT:0010489)	duration of loss of righting reflex (CMO:0002289)	2	151869660	223841096	Rat
1354609	Niddm62	Non-insulin dependent diabetes mellitus QTL 62	4.72	0.000006	insulin secretion trait (VT:0003564)	plasma insulin level (CMO:0000342)	2	117415288	205135428	Rat
1598833	Bp295	Blood pressure QTL 295	3.5		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	150096616	195096616	Rat
61417	Cia10	Collagen induced arthritis QTL 10	3.4		joint integrity trait (VT:0010548)	experimental arthritis severity measurement (CMO:0001459)	2	182635347	227635347	Rat
1354622	Kidm16	Kidney mass QTL 16	3		kidney mass (VT:0002707)	left kidney wet weight (CMO:0000083)	2	83465462	225110681	Rat
631266	Bp132	Blood pressure QTL 132		0.0005	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	47856345	205135428	Rat
631522	Bp74	Blood pressure QTL 74		0.05	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	175008837	220008837	Rat
8694383	Bw158	Body weight QTL 158	7.69	0.001	body lean mass (VT:0010483)	lean tissue morphological measurement (CMO:0002184)	2	184856304	229856304	Rat
7488927	Bp365	Blood pressure QTL 365		0.008	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	2	165453811	210453811	Rat
7488925	Bp364	Blood pressure QTL 364		0.001	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	2	163253030	208253030	Rat
2306901	Bp337	Blood pressure QTL 337		0.01	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	166372086	229820014	Rat
1354605	Rf48	Renal function QTL 48	2.9		blood creatinine amount (VT:0005328)	plasma creatinine level (CMO:0000537)	2	76328396	209350714	Rat

Markers in Region

BE097455

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	2	182,705,276 - 182,705,443 (+)	MAPPER	mRatBN7.2
Rnor_6.0	2	196,304,633 - 196,304,799	NCBI	Rnor6.0
Rnor_5.0	2	215,799,179 - 215,799,345	UniSTS	Rnor5.0
RGSC_v3.4	2	190,039,491 - 190,039,657	UniSTS	RGSC3.4
Celera	2	175,242,072 - 175,242,238	UniSTS
RH 3.4 Map	2	1195.01	UniSTS
Cytogenetic Map	2	q34	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	164	91	90	59	91	59	6	355	191	11	143	81	92	31	17	17

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001107696	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_006232882	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_006232883	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AC117098	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH474015	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ232097	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ232474	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JAXUCZ010000002	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Ensembl Acc Id:

ENSRNOT00000028639 ⟹ ENSRNOP00000028639

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8 Ensembl	2	185,389,892 - 185,394,214 (-)	Ensembl
mRatBN7.2 Ensembl	2	182,700,348 - 182,704,790 (-)	Ensembl
Rnor_6.0 Ensembl	2	196,300,239 - 196,304,169 (-)	Ensembl

Ensembl Acc Id:

ENSRNOT00000116995 ⟹ ENSRNOP00000084017

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8 Ensembl	2	185,390,129 - 185,393,822 (-)	Ensembl
mRatBN7.2 Ensembl	2	182,701,120 - 182,704,813 (-)	Ensembl

Ensembl Acc Id:

ENSRNOT00000117918 ⟹ ENSRNOP00000081974

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	2	182,700,348 - 182,704,835 (-)	Ensembl

RefSeq Acc Id:

NM_001107696 ⟹ NP_001101166

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	2	185,389,892 - 185,393,822 (-)	NCBI
mRatBN7.2	2	182,700,883 - 182,704,813 (-)	NCBI
Rnor_6.0	2	196,300,239 - 196,304,169 (-)	NCBI
Rnor_5.0	2	215,794,553 - 215,798,889 (-)	NCBI
RGSC_v3.4	2	190,035,097 - 190,039,027 (-)	RGD
Celera	2	175,237,678 - 175,241,608 (-)	RGD

Sequence:

show sequence

TACAGACTCAGAAAGAAACCGGAAGCAGAGAAGGCGATAGTGTACTCTTCCTACGGTGGCCTAA
AGGAGCAGCGAAGTAGGCGTAGAATTTATCATATTCTCATAGTCGCGATGTCTTTTAAGAGGGA
AGGGGACGACTGGAGTCAGCTCAATGTGCTCAAAAAACGAAGAGTTGGAGACTTGCTAGCTAGT
TACATCCCCGAGGATGAGGCGCTGATGCTGCGGGATGGACGCTTTGCTTGTGCCATCTGCCCCC
ATCGACCAGTACTGGACACCCTGGCCATGCTGACAGCTCACCGTGCAGGCAAGAAGCATCTATC
CAGTCTGAAGCTTTTCTATGGAAAAAAGCAGTCAGGCAAGGGAACAGAGCAAAATCCACGACCG
CAGAACGAACTGAAGACAGAAAGCAAAACTGAGGCTCCTTTGCTAACCCAGACTCGAATAATCA
CCCAGAATGCTCTACACAGAGCTCCCCACTATAACAGCTGCTGCCGGAGGAAGCACAGACCAGA
AGCCCCTGCTCCCTCTGTCTCCAGTTCCTCTGTGCCAACTCCAGAGGCCGAACTCCAGAGTGCA
AAGATCAGTAAGGAGCCTGAGCCTAGGCAGAGATCAGACGCCAAAAAGTCACCAGCTCTTTCCA
CCTCTGCACCCATGAGTCCCACAAAACGTCGAGTCTTGAACCACTACCTTACCCTCCGAAGCTC
TGGATGGGTCCCAGATGGACGAGGCCGATGGGTAAAAGATGAAAACGTTGAGTTTGACTCTGAT
GAGGAAGAGCCCCCTGACCTCCCCTTGGACTGATAACCCCTATTTGTTCTACAAATAAACTGCT
GTGGGTCCTGGGAGTGTGCTGACCGCCGAGGCCACTTCCTCCTTCCGTCTTAGGATTTCAAGTC
TGCTCCTCAGGCTGGCCACTCCTTCCCTACAAGGTACATGACTCCCCATACTTCTGGCCCCTCC
CCCACCTTCTCTCAGACTCTTGCCAAGTGTCAGCTGCATCCAGCCCGGTGCCCTATTAATAAGT
CTGTCAGAAAGAGG

hide sequence

RefSeq Acc Id:

XM_006232882 ⟹ XP_006232944

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	2	185,390,085 - 185,394,126 (-)	NCBI
mRatBN7.2	2	182,701,028 - 182,705,119 (-)	NCBI
Rnor_6.0	2	196,300,241 - 196,304,419 (-)	NCBI
Rnor_5.0	2	215,794,553 - 215,798,889 (-)	NCBI

Sequence:

show sequence

TGAAATTCCGGCTCCACGTACAGGATCTTGGGTCTCCAAACACCTGGATCCTTCGAGATGCGAG
GACCTGTGTCCAGAAACGAAGAGTTGGAGACTTGCTAGCTAGTTACATCCCCGAGGATGAGGCG
CTGATGCTGCGGGATGGACGCTTTGCTTGTGCCATCTGCCCCCATCGACCAGTACTGGACACCC
TGGCCATGCTGACAGCTCACCGTGCAGGCAAGAAGCATCTATCCAGTCTGAAGCTTTTCTATGG
AAAAAAGCAGTCAGGCAAGGGAACAGAGCAAAATCCACGACCGCAGAACGAACTGAAGACAGAA
AGCAAAACTGAGGCTCCTTTGCTAACCCAGACTCGAATAATCACCCAGAATGCTCTACACAGAG
CTCCCCACTATAACAGCTGCTGCCGGAGGAAGCACAGACCAGAAGCCCCTGCTCCCTCTGTCTC
CAGTTCCTCTGTGCCAACTCCAGAGGCCGAACTCCAGAGTGCAAAGATCAGTAAGGAGCCTGAG
CCTAGGCAGAGATCAGACGCCAAAAAGTCACCAGCTCTTTCCACCTCTGCACCCATGAGTCCCA
CAAAACGTCGAGTCTTGAACCACTACCTTACCCTCCGAAGCTCTGGATGGGTCCCAGATGGACG
AGGCCGATGGGTAAAAGATGAAAACGTTGAGTTTGACTCTGATGAGGAAGAGCCCCCTGACCTC
CCCTTGGACTGATAACCCCTATTTGTTCTACAAATAAACTGCTGTGGGTCCTGGGAGTGTGCTG
ACCGCCGAGGCCACTTCCTCCTTCCGTCTTAGGATTTCAAGTCTGCTCCTCAGGCTGGCCACTC
CTTCCCTACAAGGTACATGACTCCCCATACTTCTGGCCCCTCCCCCACCTTCTCTCAGACTCTT
GCCAAGTGTCAGCTGCATCCAGCCCGGTGCCCTATTAATAAGTCTGTCAGAAAGA

hide sequence

RefSeq Acc Id:

XM_006232883 ⟹ XP_006232945

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	2	185,390,085 - 185,393,608 (-)	NCBI
mRatBN7.2	2	182,700,991 - 182,704,615 (-)	NCBI
Rnor_6.0	2	196,300,241 - 196,303,980 (-)	NCBI
Rnor_5.0	2	215,794,553 - 215,798,889 (-)	NCBI

Sequence:

show sequence

ACCTTCAGCCGCCCTGTTGCTTTGGTTTGTTGCTTTGGCGACATCTAGGGGAGGGTGTTAGGGG
ACCAGAACTGAGAGAAACGAAGAGTTGGAGACTTGCTAGCTAGTTACATCCCCGAGGATGAGGC
GCTGATGCTGCGGGATGGACGCTTTGCTTGTGCCATCTGCCCCCATCGACCAGTACTGGACACC
CTGGCCATGCTGACAGCTCACCGTGCAGGCAAGAAGCATCTATCCAGTCTGAAGCTTTTCTATG
GAAAAAAGCAGTCAGGCAAGGGAACAGAGCAAAATCCACGACCGCAGAACGAACTGAAGACAGA
AAGCAAAACTGAGGCTCCTTTGCTAACCCAGACTCGAATAATCACCCAGAATGCTCTACACAGA
GCTCCCCACTATAACAGCTGCTGCCGGAGGAAGCACAGACCAGAAGCCCCTGCTCCCTCTGTCT
CCAGTTCCTCTGTGCCAACTCCAGAGGCCGAACTCCAGAGTGCAAAGATCAGTAAGGAGCCTGA
GCCTAGGCAGAGATCAGACGCCAAAAAGTCACCAGCTCTTTCCACCTCTGCACCCATGAGTCCC
ACAAAACGTCGAGTCTTGAACCACTACCTTACCCTCCGAAGCTCTGGATGGGTCCCAGATGGAC
GAGGCCGATGGGTAAAAGATGAAAACGTTGAGTTTGACTCTGATGAGGAAGAGCCCCCTGACCT
CCCCTTGGACTGATAACCCCTATTTGTTCTACAAATAAACTGCTGTGGGTCCTGGGAGTGTGCT
GACCGCCGAGGCCACTTCCTCCTTCCGTCTTAGGATTTCAAGTCTGCTCCTCAGGCTGGCCACT
CCTTCCCTACAAGGTACATGACTCCCCATACTTCTGGCCCCTCCCCCACCTTCTCTCAGACTCT
TGCCAAGTGTCAGCTGCATCCAGCCCGGTGCCCTATTAATAAGTCTGTCAGAAAGA

hide sequence

Protein Sequences


Protein RefSeqs	NP_001101166	(Get FASTA)	NCBI Sequence Viewer
	XP_006232944	(Get FASTA)	NCBI Sequence Viewer
	XP_006232945	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	EDL85751	(Get FASTA)	NCBI Sequence Viewer
	EDL85752	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSRNOP00000028639.6
	ENSRNOP00000081974.2
	ENSRNOP00000084017.1

RefSeq Acc Id:

NP_001101166 ⟸ NM_001107696

- UniProtKB:

D3ZSG1 (UniProtKB/TrEMBL), A6K2U8 (UniProtKB/TrEMBL), A0A8I5ZU22 (UniProtKB/TrEMBL), A6K2U9 (UniProtKB/TrEMBL)

- Sequence:

show sequence

MSFKREGDDWSQLNVLKKRRVGDLLASYIPEDEALMLRDGRFACAICPHRPVLDTLAMLTAHRA
GKKHLSSLKLFYGKKQSGKGTEQNPRPQNELKTESKTEAPLLTQTRIITQNALHRAPHYNSCCR
RKHRPEAPAPSVSSSSVPTPEAELQSAKISKEPEPRQRSDAKKSPALSTSAPMSPTKRRVLNHY
LTLRSSGWVPDGRGRWVKDENVEFDSDEEEPPDLPLD

hide sequence

RefSeq Acc Id:	XP_006232945 ⟸ XM_006232883
- Peptide Label:	isoform X1
- Sequence:	show sequence MLRDGRFACAICPHRPVLDTLAMLTAHRAGKKHLSSLKLFYGKKQSGKGTEQNPRPQNELKTES KTEAPLLTQTRIITQNALHRAPHYNSCCRRKHRPEAPAPSVSSSSVPTPEAELQSAKISKEPEP RQRSDAKKSPALSTSAPMSPTKRRVLNHYLTLRSSGWVPDGRGRWVKDENVEFDSDEEEPPDLP LD hide sequence

RefSeq Acc Id:	XP_006232944 ⟸ XM_006232882
- Peptide Label:	isoform X1
- Sequence:	show sequence MLRDGRFACAICPHRPVLDTLAMLTAHRAGKKHLSSLKLFYGKKQSGKGTEQNPRPQNELKTES KTEAPLLTQTRIITQNALHRAPHYNSCCRRKHRPEAPAPSVSSSSVPTPEAELQSAKISKEPEP RQRSDAKKSPALSTSAPMSPTKRRVLNHYLTLRSSGWVPDGRGRWVKDENVEFDSDEEEPPDLP LD hide sequence

Ensembl Acc Id:

ENSRNOP00000028639 ⟸ ENSRNOT00000028639

Ensembl Acc Id:

ENSRNOP00000081974 ⟸ ENSRNOT00000117918

Ensembl Acc Id:

ENSRNOP00000084017 ⟸ ENSRNOT00000116995

Protein Domains

Sodium channel modifier 1 acidic C-terminal Sodium channel modifier 1 zinc-finger

Protein Structures

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-D3ZSG1-F1-model_v2	AlphaFold	D3ZSG1	1-229	view protein structure

Transcriptome

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

Promoters

RGD ID:

13691540

Promoter ID:

EPDNEW_R2065

Type:

initiation region

Name:

Scnm1_1

Description:

sodium channel modifier 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	2	196,304,131 - 196,304,191	EPDNEW

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:1308968	AgrOrtholog
BioCyc Gene	G2FUF-52113	BioCyc
Ensembl Genes	ENSRNOG00000021088	UniProtKB/TrEMBL
	ENSRNOG00000021092	Ensembl, UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000028639.7	UniProtKB/TrEMBL
	ENSRNOT00000116995.2	UniProtKB/TrEMBL
	ENSRNOT00000117918.2	UniProtKB/TrEMBL
InterPro	SCNM1	UniProtKB/TrEMBL
	SCNM1_acidic	UniProtKB/TrEMBL
	zf-SCNM1	UniProtKB/TrEMBL
KEGG Report	rno:310662	UniProtKB/TrEMBL
NCBI Gene	310662	ENTREZGENE
PANTHER	PTHR32297	UniProtKB/TrEMBL
	SODIUM CHANNEL MODIFIER 1	UniProtKB/TrEMBL
Pfam	SCNM1_acidic	UniProtKB/TrEMBL
	zf-SCNM1	UniProtKB/TrEMBL
PhenoGen	Scnm1	PhenoGen
RatGTEx	ENSRNOG00000021088	RatGTEx
	ENSRNOG00000021092	RatGTEx
UniProt	A0A8I5ZU22	ENTREZGENE, UniProtKB/TrEMBL
	A0A8I5ZYA6_RAT	UniProtKB/TrEMBL
	A6K2U8	ENTREZGENE, UniProtKB/TrEMBL
	A6K2U9	ENTREZGENE, UniProtKB/TrEMBL
	D3ZSG1	ENTREZGENE, UniProtKB/TrEMBL

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2008-04-30	Scnm1	sodium channel modifier 1	Scnm1_predicted	sodium channel modifier 1 (predicted)	'predicted' is removed	2292626	APPROVED
2005-01-12	Scnm1_predicted	sodium channel modifier 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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