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Gene: Snrpc (small nuclear ribonucleoprotein polypeptide C) Rattus norvegicus

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Symbol:

Snrpc

Name:

small nuclear ribonucleoprotein polypeptide C

RGD ID:

1306065

Description:

Enables U1 snRNP binding activity. Predicted to be involved in mRNA 5'-splice site recognition and spliceosomal snRNP assembly. Part of U1 snRNP. Human ortholog(s) of this gene implicated in connective tissue disease; mixed connective tissue disease; and systemic lupus erythematosus. Orthologous to human SNRPC (small nuclear ribonucleoprotein polypeptide C); PARTICIPATES IN spliceosome pathway; INTERACTS WITH 17beta-estradiol; 4,4'-sulfonyldiphenol; bisphenol A.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Previously known as:

LOC361808; Snrp1c; U1 small nuclear ribonucleoprotein 1C; U1 small nuclear ribonucleoprotein C; U1 snRNP C; U1-C; U1C

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):	SNRPC (small nuclear ribonucleoprotein polypeptide C)	HGNC	EggNOG, Ensembl, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, Treefam
Mus musculus (house mouse):	Snrpc (U1 small nuclear ribonucleoprotein C)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chinchilla lanigera (long-tailed chinchilla):	Snrpc (small nuclear ribonucleoprotein polypeptide C)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	SNRPC (small nuclear ribonucleoprotein polypeptide C)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	SNRPC (small nuclear ribonucleoprotein polypeptide C)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Snrpc (small nuclear ribonucleoprotein polypeptide C)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	SNRPC (small nuclear ribonucleoprotein polypeptide C)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	SNRPC (small nuclear ribonucleoprotein polypeptide C)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Snrpc (small nuclear ribonucleoprotein polypeptide C)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Rattus rattus (black rat):	Snrpc (small nuclear ribonucleoprotein polypeptide C)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Other homologs ²
Homo sapiens (human):	RPLP1 (ribosomal protein lateral stalk subunit P1)	HGNC	OMA
Alliance orthologs ³
Homo sapiens (human):	SNRPC (small nuclear ribonucleoprotein polypeptide C)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Mus musculus (house mouse):	Snrpc (U1 small nuclear ribonucleoprotein C)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Danio rerio (zebrafish):	snrpc (small nuclear ribonucleoprotein polypeptide C)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|SonicParanoid)
Danio rerio (zebrafish):	snrpc (small nuclear ribonucleoprotein polypeptide C)	Alliance	DIOPT (Ensembl Compara\|OMA\|OrthoFinder\|PANTHER\|PhylomeDB\|SonicParanoid)
Caenorhabditis elegans (roundworm):	F08B4.7	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|SonicParanoid)
Caenorhabditis elegans (roundworm):	F08B4.7	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Saccharomyces cerevisiae (baker's yeast):	YHC1	Alliance	DIOPT (OrthoFinder\|OrthoInspector\|PANTHER\|SonicParanoid)
Drosophila melanogaster (fruit fly):	snRNP-U1-C	Alliance	DIOPT (Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|SonicParanoid)
Drosophila melanogaster (fruit fly):	snRNP-U1-C	Alliance	DIOPT (Hieranoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Xenopus tropicalis (tropical clawed frog):	snrpc	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Xenopus tropicalis (tropical clawed frog):	snrpc	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|PANTHER\|PhylomeDB\|SonicParanoid)

Related Pseudogenes:

Snrpc-ps1 Snrpc-ps3

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	20	5,890,229 - 5,908,410 (+)	NCBI	GRCr8	GRCr8		GRCr8
GRCr8 Ensembl	20	5,890,229 - 5,908,410 (+)	Ensembl				GRCr8
mRatBN7.2	20	5,888,453 - 5,906,638 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	20	5,888,453 - 5,906,638 (+)	Ensembl				mRatBN7.2
mRatBN7.2 Ensembl	10	14,191,662 - 14,192,401 (-)	Ensembl				mRatBN7.2
UTH_Rnor_SHR_Utx	20	6,601,046 - 6,619,227 (+)	NCBI	UTH_Rnor_SHR_Utx	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	20	5,962,844 - 5,981,025 (+)	NCBI	UTH_Rnor_SHRSP_BbbUtx_1.0	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	20	6,442,643 - 6,460,788 (+)	NCBI	UTH_Rnor_WKY_Bbb_1.0	UTH_Rnor_WKY_Bbb_1.0
Dahl_SR_JrHsd	20	6,240,852 - 6,259,098 (+)	NCBI		Dahl_SR_JrHsd
Lyon_Normotensive	20	7,236,809 - 7,255,055 (+)	NCBI		Lyon_Normotensive
Lyon_Hypertensive	20	7,239,776 - 7,258,022 (+)	NCBI		Lyon_Hypertensive
F344_StmMcwi	20	6,256,447 - 6,274,215 (+)	NCBI		F344_StmMcwi
Rnor_6.0	20	7,409,401 - 7,427,581 (+)	NCBI	Rnor_6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	20	7,409,401 - 7,427,581 (+)	Ensembl			rn6	Rnor6.0
Rnor_5.0	20	9,611,426 - 9,629,606 (+)	NCBI	Rnor_5.0	Rnor_5.0	rn5
RGSC_v3.4	20	6,045,678 - 6,063,842 (+)	NCBI	RGSC_v3.4	RGSC_v3.4	rn4
Celera	20	7,449,532 - 7,467,493 (+)	NCBI		Celera
RGSC_v3.1	20	6,053,401 - 6,064,069 (+)	NCBI
Cytogenetic Map	20	p12	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

connective tissue disease (ISO)

mixed connective tissue disease (ISO)

systemic lupus erythematosus (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

1,2-dichloroethane (ISO)

1,2-dimethylhydrazine (ISO)

17alpha-ethynylestradiol (ISO)

17beta-estradiol (EXP)

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

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

2-palmitoylglycerol (ISO)

4,4'-sulfonyldiphenol (EXP,ISO)

acrolein (ISO)

aflatoxin B1 (ISO)

alpha-pinene (ISO)

arsenite(3-) (ISO)

beta-lapachone (ISO)

bis(2-chloroethyl) sulfide (ISO)

bis(2-ethylhexyl) phthalate (ISO)

bisphenol A (EXP,ISO)

bisphenol F (EXP)

cadmium dichloride (ISO)

caffeine (ISO)

CGP 52608 (ISO)

chlorpyrifos (ISO)

cisplatin (ISO)

clofibrate (ISO)

copper atom (ISO)

copper(0) (ISO)

dibutyl phthalate (ISO)

enzyme inhibitor (ISO)

fipronil (EXP)

flutamide (EXP)

folic acid (ISO)

FR900359 (ISO)

gentamycin (EXP)

indole-3-methanol (EXP)

ivermectin (ISO)

lead(0) (ISO)

N-methyl-N-nitrosourea (ISO)

nefazodone (EXP)

ochratoxin A (EXP)

ozone (ISO)

paracetamol (ISO)

perfluorooctanoic acid (ISO)

sodium arsenite (ISO)

temozolomide (ISO)

thioacetamide (EXP)

titanium dioxide (ISO)

tungsten (ISO)

valproic acid (EXP)

Yessotoxin (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

biological_process (ND)

mRNA 5'-splice site recognition (IBA,IEA)

mRNA splicing, via spliceosome (IEA,ISO)

spliceosomal snRNP assembly (IEA,ISO)

Cellular Component

Cajal body (ISO)

commitment complex (IEA)

nucleoplasm (ISO)

nucleus (IEA)

ribonucleoprotein complex (IEA)

U1 snRNP (IBA,IDA,IEA,ISO,ISS)

U2-type prespliceosome (IEA)

Molecular Function

metal ion binding (IEA)

mRNA binding (IEA)

nucleic acid binding (IEA)

pre-mRNA 5'-splice site binding (IBA,IEA)

protein binding (ISO)

protein homodimerization activity (ISO)

RNA binding (IEA)

single-stranded RNA binding (ISO)

U1 snRNA binding (IEA,ISO)

U1 snRNP binding (IDA)

zinc ion binding (IEA,ISO)

Molecular Pathway Annotations Click to see Annotation Detail View

spliceosome pathway (IEA,ISO)

References

References - curated

#	Reference Title	Reference Citation
1.	The U2 small nuclear ribonucleoprotein particle as an autoantigen. Analysis with sera from patients with overlap syndromes.	Craft J, etal., J Clin Invest. 1988 Jun;81(6):1716-24.
2.	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.
3.	Rat ISS GO annotations from GOA human gene data--August 2006	GOA data from the GO Consortium
4.	Immunological analysis of pulmonary hypertension in connective tissue diseases.	Nishimaki T, etal., J Rheumatol. 1999 Nov;26(11):2357-62.
5.	Separation of nuclear protein complexes by blue native polyacrylamide gel electrophoresis.	Novakova Z, etal., Electrophoresis. 2006 Apr;27(7):1277-87.
6.	KEGG Annotation Import Pipeline	Pipeline to import KEGG annotations from KEGG into RGD
7.	GOA pipeline	RGD automated data pipeline
8.	Data Import for Chemical-Gene Interactions	RGD automated import pipeline for gene-chemical interactions
9.	Comprehensive gene review and curation	RGD comprehensive gene curation
10.	Distinctive immune response patterns of human and murine autoimmune sera to U1 small nuclear ribonucleoprotein C protein.	Satoh M, etal., J Clin Invest. 1996 Jun 1;97(11):2619-26.
11.	Structural analyses of the pre-mRNA splicing machinery.	Zhang L, etal., Protein Sci. 2013 Jun;22(6):677-92. doi: 10.1002/pro.2266. Epub 2013 May 8.

Additional References at PubMed

PMID:1826349	PMID:8532530	PMID:8798632	PMID:8972845	PMID:10068039	PMID:15312772	PMID:15525645	PMID:21113136	PMID:22681889

Genomics

Comparative Map Data

Snrpc
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	20	5,890,229 - 5,908,410 (+)	NCBI	GRCr8	GRCr8		GRCr8
GRCr8 Ensembl	20	5,890,229 - 5,908,410 (+)	Ensembl				GRCr8
mRatBN7.2	20	5,888,453 - 5,906,638 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	20	5,888,453 - 5,906,638 (+)	Ensembl				mRatBN7.2
mRatBN7.2 Ensembl	10	14,191,662 - 14,192,401 (-)	Ensembl				mRatBN7.2
UTH_Rnor_SHR_Utx	20	6,601,046 - 6,619,227 (+)	NCBI	UTH_Rnor_SHR_Utx	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	20	5,962,844 - 5,981,025 (+)	NCBI	UTH_Rnor_SHRSP_BbbUtx_1.0	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	20	6,442,643 - 6,460,788 (+)	NCBI	UTH_Rnor_WKY_Bbb_1.0	UTH_Rnor_WKY_Bbb_1.0
Dahl_SR_JrHsd	20	6,240,852 - 6,259,098 (+)	NCBI		Dahl_SR_JrHsd
Lyon_Normotensive	20	7,236,809 - 7,255,055 (+)	NCBI		Lyon_Normotensive
Lyon_Hypertensive	20	7,239,776 - 7,258,022 (+)	NCBI		Lyon_Hypertensive
F344_StmMcwi	20	6,256,447 - 6,274,215 (+)	NCBI		F344_StmMcwi
Rnor_6.0	20	7,409,401 - 7,427,581 (+)	NCBI	Rnor_6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	20	7,409,401 - 7,427,581 (+)	Ensembl			rn6	Rnor6.0
Rnor_5.0	20	9,611,426 - 9,629,606 (+)	NCBI	Rnor_5.0	Rnor_5.0	rn5
RGSC_v3.4	20	6,045,678 - 6,063,842 (+)	NCBI	RGSC_v3.4	RGSC_v3.4	rn4
Celera	20	7,449,532 - 7,467,493 (+)	NCBI		Celera
RGSC_v3.1	20	6,053,401 - 6,064,069 (+)	NCBI
Cytogenetic Map	20	p12	NCBI

SNRPC
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	6	34,757,505 - 34,773,857 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	6	34,757,454 - 34,773,857 (+)	Ensembl			hg38	GRCh38
GRCh37	6	34,725,282 - 34,741,634 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	6	34,833,293 - 34,849,549 (+)	NCBI	Build 36	Build 36	hg18	NCBI36
Build 34	6	34,833,289 - 34,849,549	NCBI
Celera	6	36,279,328 - 36,296,094 (+)	NCBI		Celera
Cytogenetic Map	6	p21.31	NCBI
HuRef	6	34,447,196 - 34,464,127 (+)	NCBI		HuRef
CHM1_1	6	34,726,959 - 34,743,758 (+)	NCBI		CHM1_1
T2T-CHM13v2.0	6	34,580,289 - 34,596,650 (+)	NCBI		T2T-CHM13v2.0

Snrpc
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	17	28,059,002 - 28,070,942 (+)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	17	28,057,124 - 28,070,942 (+)	Ensembl		GRCm39 Ensembl		GRCm39
GRCm38	17	27,840,028 - 27,851,968 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	17	27,838,150 - 27,851,968 (+)	Ensembl			mm10	GRCm38
MGSCv37	17	27,977,032 - 27,988,913 (+)	NCBI	MGSCv37	MGSCv37	mm9	NCBIm37
MGSCv36	17	27,567,676 - 27,579,557 (+)	NCBI		MGSCv36	mm8
Celera	17	28,392,632 - 28,404,747 (+)	NCBI		Celera
Cytogenetic Map	17	A3.3	NCBI
cM Map	17	14.59	NCBI

Snrpc
(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_004955437	2,813,296 - 2,831,036 (+)	Ensembl
ChiLan1.0 Ensembl	NW_004955453	8,264,516 - 8,265,255 (+)	Ensembl
ChiLan1.0	NW_004955437	2,770,251 - 2,830,871 (+)	NCBI	ChiLan1.0	ChiLan1.0

SNRPC
(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	5	49,229,100 - 49,246,221 (+)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	6	45,096,458 - 45,113,595 (+)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	6	34,324,127 - 34,340,526 (+)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	6	35,421,467 - 35,437,622 (+)	NCBI	PanPan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	6	35,421,467 - 35,437,622 (+)	Ensembl			panPan2	panpan1.1

SNRPC
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	12	3,996,483 - 4,010,904 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	12	3,996,520 - 4,010,889 (+)	Ensembl			canFam3	CanFam3.1
Dog10K_Boxer_Tasha	12	4,011,962 - 4,026,257 (+)	NCBI	Dog10K_Boxer_Tasha	Dog10K_Boxer_Tasha
ROS_Cfam_1.0	12	4,332,597 - 4,346,900 (+)	NCBI	ROS_Cfam_1.0	ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	12	4,332,683 - 4,352,401 (+)	Ensembl				ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	12	3,994,020 - 4,008,494 (+)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	12	4,075,193 - 4,089,433 (+)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	12	4,173,683 - 4,188,080 (+)	NCBI	UU_Cfam_GSD_1.0	UU_Cfam_GSD_1.0

Snrpc
(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_024404946	39,570,835 - 39,588,900 (+)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936476	24,368,521 - 24,389,596 (-)	Ensembl		SpeTri2.0 Ensembl
SpeTri2.0	NW_004936476	24,371,268 - 24,389,355 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

SNRPC
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	7	30,708,332 - 30,724,045 (+)	Ensembl			susScr11	Sscrofa11.1
Sscrofa11.1	7	30,708,243 - 30,723,480 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	7	35,451,476 - 35,466,721 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

SNRPC
(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	17	37,332,697 - 37,348,968 (-)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	17	37,332,687 - 37,349,133 (-)	Ensembl		ChlSab1.1 Ensembl	chlSab2	Vervet-AGM
Vero_WHO_p1.0	NW_023666044	34,682,069 - 34,698,671 (+)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Snrpc
(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_004624754	22,553,491 - 22,567,529 (-)	Ensembl		HetGla_female_1.0 Ensembl	hetGla2	HetGla_female_1.0 Ensembl
HetGla 1.0	NW_004624754	22,553,485 - 22,567,601 (-)	NCBI	HetGla 1.0	HetGla 1.0	hetGla2

Snrpc
(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	18	6,004,676 - 6,016,262 (-)	NCBI		Rrattus_CSIRO_v1

Variants

Variants in Snrpc
125 total Variants

miRNA Target Status (No longer updated)

Predicted Target Of

	Summary Value
Count of predictions:	19
Count of miRNA genes:	19
Interacting mature miRNAs:	19
Transcripts:	ENSRNOT00000000586
Prediction methods:	Miranda, Rnahybrid
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
4889610	Pancm3	Pancreatic morphology QTL 3	3.75	0.001	pancreas mass (VT:0010144)	pancreas wet weight (CMO:0000626)	20	4189476	49189476	Rat
61474	Eae1	Experimental allergic encephalomyelitis QTL 1	3		nervous system integrity trait (VT:0010566)	experimental autoimmune encephalomyelitis severity score (CMO:0001419)	20	1	6693431	Rat
2317057	Aia27	Adjuvant induced arthritis QTL 27	2.83		joint integrity trait (VT:0010548)	right rear ankle joint diameter (CMO:0002150)	20	1	26925056	Rat
1641915	Colcr9	Colorectal carcinoma resistance QTL 9	2.97	0.0024	intestine integrity trait (VT:0010554)	benign colorectal tumor number (CMO:0001795)	20	1	33724594	Rat
7387283	Uae44	Urinary albumin excretion QTL 44		0.1712	urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	20	1	26128279	Rat
7411668	Foco32	Food consumption QTL 32	8	0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	20	1	36600300	Rat
2305926	Iddm37	Insulin dependent diabetes mellitus QTL 37	6		blood glucose amount (VT:0000188)	plasma glucose level (CMO:0000042)	20	1533083	46533083	Rat
1354642	Despr15	Despair related QTL 15		0.0027	locomotor behavior trait (VT:0001392)	amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)	20	1	24164241	Rat
1558640	Prcs2	Prostate cancer susceptibility QTL 2	3.3		prostate integrity trait (VT:0010571)	percentage of study population developing ventral prostate tumorous lesions during a period of time (CMO:0000943)	20	1	34066551	Rat
1331772	Cdexp2	CD45RC expression in CD8 T cells QTL 2	5.7		CD8-positive T cell quantity (VT:0008077)	blood CD45RC(high) CD8 T cell count to CD45RC(low) CD8 T cell count ratio (CMO:0001990)	20	3626323	10078622	Rat
8694189	Bw153	Body weight QTL 153	3.13	0.001	body mass (VT:0001259)	body weight gain (CMO:0000420)	20	1	29193376	Rat
70154	Insul2	Insulin level QTL 2	3.75		blood insulin amount (VT:0001560)	plasma insulin level (CMO:0000342)	20	1	6693431	Rat
4889857	Pur27	Proteinuria QTL 27	12.2	0.001	urine total protein amount (VT:0000032)	urine total protein excretion rate (CMO:0000756)	20	1	27341128	Rat
1300152	Bp195	Blood pressure QTL 195	3.46		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	20	3626323	9244918	Rat
9590109	Sffal8	Serum free fatty acids level QTL 8	5.32	0.01	blood free fatty acid amount (VT:0001553)	plasma free fatty acids level (CMO:0000546)	20	1	29193376	Rat
9589155	Insul32	Insulin level QTL 32	6.38	0.001	blood insulin amount (VT:0001560)	plasma insulin level (CMO:0000342)	20	1	29193376	Rat
9590275	Scort15	Serum corticosterone level QTL 15	3.48	0.001	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	20	1	29193376	Rat
7411650	Foco23	Food consumption QTL 23	20.7	0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	20	1	29193376	Rat
61432	Cia1	Collagen induced arthritis QTL 1			joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	20	1	14100378	Rat
2317851	Alcrsp22	Alcohol response QTL 22	3.2	0.05	response to alcohol trait (VT:0010489)	duration of loss of righting reflex (CMO:0002289)	20	1	27341128	Rat
1641893	Alcrsp7	Alcohol response QTL 7			response to alcohol trait (VT:0010489)	duration of loss of righting reflex (CMO:0002289)	20	1	27341128	Rat
6893685	Bw111	Body weight QTL 111	2.7	0.004	body mass (VT:0001259)	body weight (CMO:0000012)	20	1	32578510	Rat
9590252	Scort12	Serum corticosterone level QTL 12	20.46	0.001	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	20	1	36600300	Rat

Markers in Region

RH128028

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Cytogenetic Map	20	p12	UniSTS
Cytogenetic Map	10	q12	UniSTS

BE108400

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	20	5,905,452 - 5,905,628 (+)	MAPPER	mRatBN7.2
Rnor_6.0	20	7,426,396 - 7,426,571	NCBI	Rnor6.0
Rnor_5.0	20	9,628,421 - 9,628,596	UniSTS	Rnor5.0
RGSC_v3.4	20	6,062,657 - 6,062,832	UniSTS	RGSC3.4
Celera	20	7,466,308 - 7,466,483	UniSTS
RH 3.4 Map	20	58.9	UniSTS
Cytogenetic Map	20	p12	UniSTS

BM386877

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	20	5,890,192 - 5,890,366 (+)	MAPPER	mRatBN7.2
Rnor_6.0	20	7,411,140 - 7,411,313	NCBI	Rnor6.0
Rnor_5.0	20	9,613,165 - 9,613,338	UniSTS	Rnor5.0
RGSC_v3.4	20	6,047,402 - 6,047,575	UniSTS	RGSC3.4
Celera	20	7,451,272 - 7,451,445	UniSTS
RH 3.4 Map	20	72.9	UniSTS
Cytogenetic Map	20	p12	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	165	91	90	59	92	59	6	356	192	11	144	81	92	31	17	17

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001271040	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039098816	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_063279217	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_063279218	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_063279219	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	CH473988	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ209526	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JAXUCZ010000020	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Ensembl Acc Id:

ENSRNOT00000000586 ⟹ ENSRNOP00000000586

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8 Ensembl	20	5,890,229 - 5,908,406 (+)	Ensembl
mRatBN7.2 Ensembl	20	5,888,453 - 5,906,638 (+)	Ensembl
Rnor_6.0 Ensembl	20	7,409,401 - 7,427,581 (+)	Ensembl

Ensembl Acc Id:

ENSRNOT00000105887 ⟹ ENSRNOP00000094321

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	20	5,896,484 - 5,906,638 (+)	Ensembl

Ensembl Acc Id:

ENSRNOT00000115940 ⟹ ENSRNOP00000080304

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8 Ensembl	20	5,897,982 - 5,908,410 (+)	Ensembl
mRatBN7.2 Ensembl	20	5,896,210 - 5,906,638 (+)	Ensembl

RefSeq Acc Id:

NM_001271040 ⟹ NP_001257969

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	20	5,890,229 - 5,908,410 (+)	NCBI
mRatBN7.2	20	5,888,453 - 5,906,638 (+)	NCBI
Dahl_SR_JrHsd	20	6,240,852 - 6,259,098 (+)	NCBI
Lyon_Normotensive	20	7,236,809 - 7,255,055 (+)	NCBI
Lyon_Hypertensive	20	7,239,776 - 7,258,022 (+)	NCBI
F344_StmMcwi	20	6,256,447 - 6,274,215 (+)	NCBI
Rnor_6.0	20	7,409,401 - 7,427,581 (+)	NCBI
Rnor_5.0	20	9,611,426 - 9,629,606 (+)	NCBI
Celera	20	7,449,532 - 7,467,493 (+)	NCBI

Sequence:

show sequence

ATTACCCTTGAGTTTGCTTCAGACCATCACACAACTGGAAGATGTTTTGCACACTCCTGTGCCT
GGGAACTTTCATCTCTCTTGCTTACATTTCATTCAAGAGTGCTGTGTGCACCGGAGCACGCTTG
TGAAGCCGGCATCTGGGAGACAAAGCACAGAGATCACAGAGAACTAAGTAACGCACTTCCGAGA
GGGAATAACCAATCACGAGTAAGTGAGCGCGGGTTGAACCTCCGAGGCACCCATAGCCCACTTC
CTGGCCGTCCTCAGTAAAGACCGGAAGCAGAAGTCCTATTCTTCGCGTTTGCATCCCTGCGTCG
GCGCAGCCTGTGTGCGTCAGTTCCTGGCGGCGGGGACCGGGATAGCCAACGGCCTGTGGAGCAA
CATGCCCAAGTTTTATTGTGACTACTGTGATACGTATCTTACCCACGATTCTCCGTCTGTGAGG
AAGACACACTGCAGTGGTCGGAAACACAAAGAGAATGTGAAAGACTATTACCAGAAATGGATGG
AAGAACAGGCCCAGAGCCTGATTGACAAAACAACGGCTGCATTTCAACAAGGAAAGATCCCTCC
AGCTCCGTTCTCTGCTCCTCCGCCTGCAGGGGCCATGATCCCGCCTCCCCCCAGTCTCCCGGGT
CCTCCTCGGCCTGGCATGATGCCTGCACCCCACATGGGAGGCCCTCCCATGATGCCAATGATGG
GCCCCCCTCCTCCTGGGATGATGCCTGTGGGACCAGCTCCTGGGATGAGACCACCCATGGGAGG
CCATATGCCCATGATGCCCGGGCCTCCAATGATGAGACCTCCCGCCCGCCCTATGATGGTGCCC
ACACGGCCTGGCATGACCCGGCCAGACAGATAAGAGCAGAAGCGCTCTTTATCCTTTTGTATTT
CTTGTTGTTTCGCCAGGAGATCTTGGTGCTGACCCTGAGTGTTTCCTAGGTGCATGATGAGGAA
CTTCCCTTCCTAACAGAGAGAACGCTTCTGGAGGGAGAAGTGGTACAAAAAAGTGCGGTTTTCA
CTTACATTGTGAAATGTGAAAATAAAGTCGTCAGCTCTTTTAGTTAAA

hide sequence

RefSeq Acc Id:

XM_039098816 ⟹ XP_038954744

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	20	5,897,824 - 5,908,410 (+)	NCBI
mRatBN7.2	20	5,896,105 - 5,906,638 (+)	NCBI

RefSeq Acc Id:

XM_063279217 ⟹ XP_063135287

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	20	5,898,201 - 5,908,410 (+)	NCBI

RefSeq Acc Id:

XM_063279218 ⟹ XP_063135288

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	20	5,898,242 - 5,908,410 (+)	NCBI

RefSeq Acc Id:

XM_063279219 ⟹ XP_063135289

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	20	5,898,076 - 5,908,410 (+)	NCBI

Protein Sequences


Protein RefSeqs	NP_001257969	(Get FASTA)	NCBI Sequence Viewer
	XP_038954744	(Get FASTA)	NCBI Sequence Viewer
	XP_063135287	(Get FASTA)	NCBI Sequence Viewer
	XP_063135288	(Get FASTA)	NCBI Sequence Viewer
	XP_063135289	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	D3ZCL3	(Get FASTA)	NCBI Sequence Viewer
	EDL96903	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSRNOP00000000586
	ENSRNOP00000000586.6

RefSeq Acc Id:	NP_001257969 ⟸ NM_001271040
- UniProtKB:	D3ZCL3 (UniProtKB/Swiss-Prot), A0A8I6A3U2 (UniProtKB/TrEMBL), A6HD02 (UniProtKB/TrEMBL)
- Sequence:	show sequence MPKFYCDYCDTYLTHDSPSVRKTHCSGRKHKENVKDYYQKWMEEQAQSLIDKTTAAFQQGKIPP APFSAPPPAGAMIPPPPSLPGPPRPGMMPAPHMGGPPMMPMMGPPPPGMMPVGPAPGMRPPMGG HMPMMPGPPMMRPPARPMMVPTRPGMTRPDR hide sequence

Ensembl Acc Id:

ENSRNOP00000000586 ⟸ ENSRNOT00000000586

RefSeq Acc Id:	XP_038954744 ⟸ XM_039098816
- Peptide Label:	isoform X2

Ensembl Acc Id:

ENSRNOP00000080304 ⟸ ENSRNOT00000115940

Ensembl Acc Id:

ENSRNOP00000094321 ⟸ ENSRNOT00000105887

RefSeq Acc Id:	XP_063135289 ⟸ XM_063279219
- Peptide Label:	isoform X2

RefSeq Acc Id:	XP_063135287 ⟸ XM_063279217
- Peptide Label:	isoform X1
- UniProtKB:	A0A8I6AJC1 (UniProtKB/TrEMBL), A0A8I6A3U2 (UniProtKB/TrEMBL), A6HD02 (UniProtKB/TrEMBL)

RefSeq Acc Id:	XP_063135288 ⟸ XM_063279218
- Peptide Label:	isoform X2

Protein Domains

Matrin-type

Protein Structures

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-D3ZCL3-F1-model_v2	AlphaFold	D3ZCL3	1-159	view protein structure

Transcriptome

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

Promoters

RGD ID:

13701451

Promoter ID:

EPDNEW_R11975

Type:

initiation region

Name:

Snrpc_2

Description:

small nuclear ribonucleoprotein polypeptide C

SO ACC ID:

SO:0000170

Source:

EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)

Alternative Promoters:

null; see alsoEPDNEW_R11976

Experiment Methods:

Single-end sequencing.

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0	20	7,409,405 - 7,409,465	EPDNEW

RGD ID:

13701452

Promoter ID:

EPDNEW_R11976

Type:

initiation region

Name:

Snrpc_1

Description:

small nuclear ribonucleoprotein polypeptide C

SO ACC ID:

SO:0000170

Source:

EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)

Alternative Promoters:

null; see alsoEPDNEW_R11975

Experiment Methods:

Single-end sequencing.

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0	20	7,416,980 - 7,417,040	EPDNEW

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:1306065	AgrOrtholog
BioCyc Gene	G2FUF-4456	BioCyc
Ensembl Genes	ENSRNOG00000000493	Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
	ENSRNOG00000017586	Ensembl
Ensembl Transcript	ENSRNOT00000000586	ENTREZGENE
	ENSRNOT00000000586.8	UniProtKB/Swiss-Prot
Gene3D-CATH	Classic Zinc Finger	UniProtKB/Swiss-Prot
InterPro	Matrin/U1-C_Znf_C2H2	UniProtKB/Swiss-Prot
	Matrin/U1-like-C_Znf_C2H2	UniProtKB/Swiss-Prot
	U1-CZ_Znf_C2H2	UniProtKB/Swiss-Prot
	U1_snRNP-C	UniProtKB/Swiss-Prot
	Znf_C2H2_sf	UniProtKB/Swiss-Prot
KEGG Report	rno:361808	UniProtKB/Swiss-Prot
NCBI Gene	361808	ENTREZGENE
PANTHER	PTHR31148	UniProtKB/Swiss-Prot
	U1 SMALL NUCLEAR RIBONUCLEOPROTEIN C	UniProtKB/Swiss-Prot
Pfam	zf-U1	UniProtKB/Swiss-Prot
PhenoGen	Snrpc	PhenoGen
PIRSF	U1_snRNP-C	UniProtKB/Swiss-Prot
PROSITE	ZF_MATRIN	UniProtKB/Swiss-Prot
RatGTEx	ENSRNOG00000000493	RatGTEx
	ENSRNOG00000017586	RatGTEx
SMART	ZnF_U1	UniProtKB/Swiss-Prot
Superfamily-SCOP	SSF57667	UniProtKB/Swiss-Prot
UniProt	A0A8I6A3U2	ENTREZGENE
	A0A8I6AJC1	ENTREZGENE, UniProtKB/TrEMBL
	A0A8I6G6E8_RAT	UniProtKB/TrEMBL
	A6HD02	ENTREZGENE, UniProtKB/TrEMBL
	D3ZCL3	ENTREZGENE, UniProtKB/Swiss-Prot

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2008-09-18	Snrpc	small nuclear ribonucleoprotein polypeptide C	Snrpc	U1 small nuclear ribonucleoprotein C	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2008-03-07	Snrpc	U1 small nuclear ribonucleoprotein C	Snrp1c_predicted	U1 small nuclear ribonucleoprotein 1C (predicted)	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2005-01-12	Snrp1c_predicted	U1 small nuclear ribonucleoprotein 1C (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)

RGD Manual Annotations

Imported Annotations - KEGG (archival)

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RGD Manual Annotations

Imported Annotations - KEGG (archival)