SCNM1 (sodium channel modifier 1)

Gene: SCNM1 (sodium channel modifier 1) Canis lupus familiaris

Analyze

Symbol:

SCNM1

Name:

sodium channel modifier 1

RGD ID:

12239732

Description:

ENCODES a protein that exhibits enzyme binding (inferred); metal ion binding (inferred); INVOLVED IN alternative mRNA splicing, via spliceosome (ortholog); RNA splicing (ortholog); ASSOCIATED WITH Dravet syndrome (ortholog); gastrointestinal stromal tumor (ortholog); genetic disease (ortholog); FOUND IN nuclear speck (inferred); nucleoplasm (inferred); nucleus (inferred)

Type:

protein-coding

RefSeq Status:

MODEL

RGD Orthologs

Human

Mouse

Alliance Genes

More Info

more info ...

Latest Assembly:

CanFam3.1 - Dog CanFam3.1 Assembly

Position:

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	17	60,231,034 - 60,233,349 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	17	60,231,104 - 60,233,337 (+)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	17	59,674,590 - 59,676,909 (+)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	17	61,247,120 - 61,249,439 (+)	NCBI		ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	17	61,247,195 - 61,249,427 (+)	Ensembl		ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	17	60,075,855 - 60,078,174 (+)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	17	60,161,177 - 60,163,496 (+)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	17	60,888,949 - 60,891,269 (+)	NCBI		UU_Cfam_GSD_1.0

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

Dravet syndrome (ISO)

gastrointestinal stromal tumor (ISO)

genetic disease (ISO)

immunodeficiency 42 (ISO)

MHC class II deficiency (ISO)

Orofaciodigital Syndrome XIX (ISO)

parathyroid carcinoma (ISO)

severe congenital neutropenia 3 (ISO)

severe congenital neutropenia 5 (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

alternative mRNA splicing, via spliceosome (ISO)

mRNA processing (IEA)

RNA splicing (IEA,ISO)

Cellular Component

nuclear speck (IEA)

nucleoplasm (IEA)

nucleus (IEA)

spliceosomal complex (IEA)

Molecular Function

enzyme binding (IEA)

metal ion binding (IEA)

protein binding (ISO)

References

Additional References at PubMed

PMID:30032202

Genomics

Comparative Map Data

SCNM1
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	17	60,231,034 - 60,233,349 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	17	60,231,104 - 60,233,337 (+)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	17	59,674,590 - 59,676,909 (+)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	17	61,247,120 - 61,249,439 (+)	NCBI		ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	17	61,247,195 - 61,249,427 (+)	Ensembl		ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	17	60,075,855 - 60,078,174 (+)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	17	60,161,177 - 60,163,496 (+)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	17	60,888,949 - 60,891,269 (+)	NCBI		UU_Cfam_GSD_1.0

SCNM1
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	1	151,166,144 - 151,170,296 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	1	151,156,664 - 151,170,296 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	1	151,138,620 - 151,142,772 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Cytogenetic Map	1	q21.3	NCBI
HuRef	1	122,516,524 - 122,520,863 (+)	NCBI		HuRef
CHM1_1	1	152,533,825 - 152,538,100 (+)	NCBI		CHM1_1
T2T-CHM13v2.0	1	150,289,872 - 150,294,025 (+)	NCBI		T2T-CHM13v2.0

Scnm1
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	3	95,037,030 - 95,041,285 (-)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	3	95,036,847 - 95,041,322 (-)	Ensembl		GRCm39 Ensembl
GRCm38	3	95,129,719 - 95,134,050 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	3	95,129,536 - 95,134,011 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	3	94,933,641 - 94,937,934 (-)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	3	95,215,123 - 95,219,392 (-)	NCBI		MGSCv36	mm8
Celera	3	96,560,854 - 96,565,147 (-)	NCBI		Celera
Cytogenetic Map	3	F2.1	NCBI
cM Map	3	40.74	NCBI

Variants

Variants in SCNM1
9 total Variants

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	reproductive system	respiratory system	adipose tissue
High
Medium	4		16		6		6	2	12	8	10	6
Low	1	5	6	6		6		4
Below cutoff

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	XM_003432252	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_005630791	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_038423173	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_038423174	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_038499662	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_038499663	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_038562221	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_038562222	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_038626328	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_038626329	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AAEX04000017	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JAAHUQ010000209	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JAAQRD010000035	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JAAUVH010000359	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	REHQ01000017	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

RefSeq Acc Id:

ENSCAFT00000019855 ⟹ ENSCAFP00000018416

Type:

CODING

Position:

Dog Assembly	Chr	Position (strand)	Source
CanFam3.1 Ensembl	17	60,231,104 - 60,233,337 (+)	Ensembl

RefSeq Acc Id:

ENSCAFT00845038816 ⟹ ENSCAFP00845030398

Type:

CODING

Position:

Dog Assembly	Chr	Position (strand)	Source
ROS_Cfam_1.0 Ensembl	17	61,247,195 - 61,249,427 (+)	Ensembl

RefSeq Acc Id:

XM_003432252 ⟹ XP_003432300

Type:

CODING

Position:

Dog Assembly	Chr	Position (strand)	Source
CanFam3.1	17	60,231,034 - 60,233,349 (+)	NCBI
Dog10K_Boxer_Tasha	17	59,674,592 - 59,676,909 (+)	NCBI

Sequence:

show sequence

GAGCGCTGTGCATCTAGGGAAGTAAGGAGGCCAACCGGAAAGAAACCCGACGGGAGAAGACGCC
TTACTCTCGCTACGGTGGCCTGAGAGGAGTGGCCGAGGCGGCTCGGGAGAATTGTTCGCTTCTG
GAGCTCAGTCGTAATGTCTTTCAAGAGGGAAGGGGATGATTCGAGTCAACTCAATGTGCTCAAA
AAACGGAGAGTCGGGGACCTGCTGGCCAGTTATATCCCAGAGGATGAAGCGCTCATGCTACGGG
ATGGACGCTTCGCTTGTGCTATCTGTCCCCACCGACCTGTACTGGACACCCTGGCCATGCTGAC
TGCCCACCGTGCAGGCAAGAAACATCTGTCCAGCCTGCAGCTTTTCTATGGCAAGAAGCAGCCA
GTAAAGGGAATGGAGCAGAATCCAAGACAGCAGAATGAATTGAGGCAGTCAGAGATCAAGGCTG
AGGCTCCTCTGTTAACGCAGACCCGACTTACCACCCAGAGTGCTCTGCACAGAGCTCCTCACTA
TAACAGTTGCTGCCGCAGGAAGCACAGACCAGAAACCCCTCGTCCCTCTGTCTCCCATCCCCCT
TTACCACCCCCAGAGGTTGAGCCTGAGAGTGGGAAGATCACTAAGGAACCCATGCCTGGAGCTG
GCCCACAGGCCAAGGAGTCAGCAACTGTCTCATCCCCTGTGCCCATGAGCCCCACGAGGAAACG
AGCCCTGGATCATTACCTCACCCTTCGAAGCTCTGGATGGATCCCAGATGGACAAGGTCGATGG
GTAAAAGATGAGAATGTTGAGTTTGACTCTGATGAAGAGGAACCTCCTGACCTTTCCTTAGACT
GATACCCTCTTTTCCCCCTCAGTTCACAAATAAATTTCAGCAGGCTCCAGGAGTCTAACTTTC

hide sequence

RefSeq Acc Id:

XM_005630791 ⟹ XP_005630848

Type:

CODING

Position:

Dog Assembly	Chr	Position (strand)	Source
CanFam3.1	17	60,231,034 - 60,233,349 (+)	NCBI
Dog10K_Boxer_Tasha	17	59,674,590 - 59,676,909 (+)	NCBI

Sequence:

show sequence

GAGCGCTGTGCATCTAGGGAAGTAAGGAGGCCAACCGGAAAGAAACCCGACGGGAGAAGACGCC
TTACTCTCGCTACGGTGGCCTGAGAGGAGTGGCCGAGGCGGCTCGGGAGAATTGTTCGCTTCTG
GAGCTCAGTCGTAATGTCTTTCAAGAGGGAAGGGGATGATTCGAGTCAACTCAATGTGCTCAAA
AAACGGAGAGTCGGGGACCTGCTGGCCAGTTATATCCCAGAGGATGAAGCGCTCATGCTACGGG
ATGGACGCTTCGCTTGTGCTATCTGTCCCCACCGACCTGTACTGGACACCCTGGCCATGCTGAC
TGCCCACCGTGCAGGCCTGCAGCTTTTCTATGGCAAGAAGCAGCCAGTAAAGGGAATGGAGCAG
AATCCAAGACAGCAGAATGAATTGAGGCAGTCAGAGATCAAGGCTGAGGCTCCTCTGTTAACGC
AGACCCGACTTACCACCCAGAGTGCTCTGCACAGAGCTCCTCACTATAACAGTTGCTGCCGCAG
GAAGCACAGACCAGAAACCCCTCGTCCCTCTGTCTCCCATCCCCCTTTACCACCCCCAGAGGTT
GAGCCTGAGAGTGGGAAGATCACTAAGGAACCCATGCCTGGAGCTGGCCCACAGGCCAAGGAGT
CAGCAACTGTCTCATCCCCTGTGCCCATGAGCCCCACGAGGAAACGAGCCCTGGATCATTACCT
CACCCTTCGAAGCTCTGGATGGATCCCAGATGGACAAGGTCGATGGGTAAAAGATGAGAATGTT
GAGTTTGACTCTGATGAAGAGGAACCTCCTGACCTTTCCTTAGACTGATACCCTCTTTTCCCCC
TCAGTTCACAAATAAATTTCAGCAGGCTCCAGGAGTCTAACTTTC

hide sequence

RefSeq Acc Id:

XM_038423173 ⟹ XP_038279101

Type:

CODING

Position:

Dog Assembly	Chr	Position (strand)	Source
ROS_Cfam_1.0	17	61,247,122 - 61,249,439 (+)	NCBI

RefSeq Acc Id:

XM_038423174 ⟹ XP_038279102

Type:

CODING

Position:

Dog Assembly	Chr	Position (strand)	Source
ROS_Cfam_1.0	17	61,247,120 - 61,249,439 (+)	NCBI

RefSeq Acc Id:

XM_038499662 ⟹ XP_038355590

Type:

CODING

Position:

Dog Assembly	Chr	Position (strand)	Source
UMICH_Zoey_3.1	17	60,075,857 - 60,078,174 (+)	NCBI

RefSeq Acc Id:

XM_038499663 ⟹ XP_038355591

Type:

CODING

Position:

Dog Assembly	Chr	Position (strand)	Source
UMICH_Zoey_3.1	17	60,075,855 - 60,078,174 (+)	NCBI

RefSeq Acc Id:

XM_038562221 ⟹ XP_038418149

Type:

CODING

Position:

Dog Assembly	Chr	Position (strand)	Source
UU_Cfam_GSD_1.0	17	60,888,951 - 60,891,269 (+)	NCBI

RefSeq Acc Id:

XM_038562222 ⟹ XP_038418150

Type:

CODING

Position:

Dog Assembly	Chr	Position (strand)	Source
UU_Cfam_GSD_1.0	17	60,888,949 - 60,891,269 (+)	NCBI

RefSeq Acc Id:

XM_038626328 ⟹ XP_038482256

Type:

CODING

Position:

Dog Assembly	Chr	Position (strand)	Source
UNSW_CanFamBas_1.0	17	60,161,179 - 60,163,496 (+)	NCBI

RefSeq Acc Id:

XM_038626329 ⟹ XP_038482257

Type:

CODING

Position:

Dog Assembly	Chr	Position (strand)	Source
UNSW_CanFamBas_1.0	17	60,161,177 - 60,163,496 (+)	NCBI

Protein Sequences


Protein RefSeqs	XP_003432300	(Get FASTA)	NCBI Sequence Viewer
	XP_005630848	(Get FASTA)	NCBI Sequence Viewer
	XP_038279101	(Get FASTA)	NCBI Sequence Viewer
	XP_038279102	(Get FASTA)	NCBI Sequence Viewer
	XP_038355590	(Get FASTA)	NCBI Sequence Viewer
	XP_038355591	(Get FASTA)	NCBI Sequence Viewer
	XP_038418149	(Get FASTA)	NCBI Sequence Viewer
	XP_038418150	(Get FASTA)	NCBI Sequence Viewer
	XP_038482256	(Get FASTA)	NCBI Sequence Viewer
	XP_038482257	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSCAFP00000018416.3
	ENSCAFP00030012783.1
	ENSCAFP00040020543.1
	ENSCAFP00845030398
	ENSCAFP00845030398.1

RefSeq Acc Id:	XP_003432300 ⟸ XM_003432252
- Peptide Label:	isoform X1
- UniProtKB:	A0A8C0KL78 (UniProtKB/TrEMBL), A0A8C0SF58 (UniProtKB/TrEMBL), A0A8I3PPR7 (UniProtKB/TrEMBL)
- Sequence:	show sequence MSFKREGDDSSQLNVLKKRRVGDLLASYIPEDEALMLRDGRFACAICPHRPVLDTLAMLTAHRA GKKHLSSLQLFYGKKQPVKGMEQNPRQQNELRQSEIKAEAPLLTQTRLTTQSALHRAPHYNSCC RRKHRPETPRPSVSHPPLPPPEVEPESGKITKEPMPGAGPQAKESATVSSPVPMSPTRKRALDH YLTLRSSGWIPDGQGRWVKDENVEFDSDEEEPPDLSLD hide sequence

RefSeq Acc Id:

XP_005630848 ⟸ XM_005630791

- Peptide Label:

isoform X2

- Sequence:

show sequence

MSFKREGDDSSQLNVLKKRRVGDLLASYIPEDEALMLRDGRFACAICPHRPVLDTLAMLTAHRA
GLQLFYGKKQPVKGMEQNPRQQNELRQSEIKAEAPLLTQTRLTTQSALHRAPHYNSCCRRKHRP
ETPRPSVSHPPLPPPEVEPESGKITKEPMPGAGPQAKESATVSSPVPMSPTRKRALDHYLTLRS
SGWIPDGQGRWVKDENVEFDSDEEEPPDLSLD

hide sequence

RefSeq Acc Id:

ENSCAFP00000018416 ⟸ ENSCAFT00000019855

RefSeq Acc Id:	XP_038355591 ⟸ XM_038499663
- Peptide Label:	isoform X2

RefSeq Acc Id:	XP_038355590 ⟸ XM_038499662
- Peptide Label:	isoform X1

RefSeq Acc Id:	XP_038482257 ⟸ XM_038626329
- Peptide Label:	isoform X2

RefSeq Acc Id:	XP_038482256 ⟸ XM_038626328
- Peptide Label:	isoform X1

RefSeq Acc Id:	XP_038279102 ⟸ XM_038423174
- Peptide Label:	isoform X2

RefSeq Acc Id:	XP_038279101 ⟸ XM_038423173
- Peptide Label:	isoform X1
- UniProtKB:	A0A8C0KL78 (UniProtKB/TrEMBL), A0A8C0SF58 (UniProtKB/TrEMBL), A0A8I3PPR7 (UniProtKB/TrEMBL)

RefSeq Acc Id:	XP_038418150 ⟸ XM_038562222
- Peptide Label:	isoform X2

RefSeq Acc Id:	XP_038418149 ⟸ XM_038562221
- Peptide Label:	isoform X1
- UniProtKB:	A0A8C0KL78 (UniProtKB/TrEMBL), A0A8C0SF58 (UniProtKB/TrEMBL), A0A8I3PPR7 (UniProtKB/TrEMBL)

RefSeq Acc Id:

ENSCAFP00845030398 ⟸ ENSCAFT00845038816

Protein Domains

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

Promoters

RGD ID:

13686401

Promoter ID:

EPDNEW_C4466

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:

Dog Assembly	Chr	Position (strand)	Source
CanFam3.1	17	60,231,095 - 60,231,155	EPDNEW

Additional Information

External Database Links

Database	Acc Id	Source(s)
Ensembl Genes	ENSCAFG00000012499	Ensembl, UniProtKB/TrEMBL
	ENSCAFG00030007977	UniProtKB/TrEMBL
	ENSCAFG00040012825	UniProtKB/TrEMBL
	ENSCAFG00845022000	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript	ENSCAFT00000019855.5	UniProtKB/TrEMBL
	ENSCAFT00030014655.1	UniProtKB/TrEMBL
	ENSCAFT00040023659.1	UniProtKB/TrEMBL
	ENSCAFT00845038816	ENTREZGENE
	ENSCAFT00845038816.1	UniProtKB/TrEMBL
InterPro	SCNM1	UniProtKB/TrEMBL
	SCNM1_acidic	UniProtKB/TrEMBL
	Znf-SCNM1	UniProtKB/TrEMBL
KEGG Report	cfa:100683396	UniProtKB/TrEMBL
NCBI Gene	SCNM1	ENTREZGENE
PANTHER	PTHR32297	UniProtKB/TrEMBL
	SODIUM CHANNEL MODIFIER 1	UniProtKB/TrEMBL
Pfam	SCNM1_acidic	UniProtKB/TrEMBL
	zf-SCNM1	UniProtKB/TrEMBL
UniProt	A0A8C0KL78	ENTREZGENE
	A0A8C0SF58	ENTREZGENE, UniProtKB/TrEMBL
	A0A8I3PPR7	ENTREZGENE, UniProtKB/TrEMBL
VGNC ID	VGNC:49785	ENTREZGENE

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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