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Gene: Snrpd2 (small nuclear ribonucleoprotein D2 polypeptide) Rattus norvegicus

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Symbol:

Snrpd2 (Ensembl: Snrpd2l)

Name:

small nuclear ribonucleoprotein D2 polypeptide (Ensembl:small nuclear ribonucleoprotein D2-like)

RGD ID:

1593018

Description:

Enables U1 snRNP binding activity. Predicted to be involved in spliceosomal snRNP assembly. Part of U1 snRNP. Human ortholog(s) of this gene implicated in systemic lupus erythematosus. Orthologous to human SNRPD2 (small nuclear ribonucleoprotein D2 polypeptide); PARTICIPATES IN spliceosome pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; bisphenol A; cadmium dichloride.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Previously known as:

LOC680309; similar to small nuclear ribonucleoprotein D2; small nuclear ribonucleoprotein D2; small nuclear ribonucleoprotein Sm D2

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):	SNRPD2 (small nuclear ribonucleoprotein D2 polypeptide)	HGNC	EggNOG, Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, Panther, PhylomeDB, Treefam
Mus musculus (house mouse):	Snrpd2 (small nuclear ribonucleoprotein D2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chinchilla lanigera (long-tailed chinchilla):	Snrpd2 (small nuclear ribonucleoprotein D2 polypeptide)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	SNRPD2 (small nuclear ribonucleoprotein D2 polypeptide)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	SNRPD2 (small nuclear ribonucleoprotein D2 polypeptide)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Snrpd2 (small nuclear ribonucleoprotein D2 polypeptide)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	SNRPD2 (small nuclear ribonucleoprotein D2 polypeptide)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	SNRPD2 (small nuclear ribonucleoprotein D2 polypeptide)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Snrpd2 (small nuclear ribonucleoprotein D2 polypeptide)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Rattus rattus (black rat):	Snrpd2 (small nuclear ribonucleoprotein D2 polypeptide)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Other homologs ²
Homo sapiens (human):	RPL23A (ribosomal protein L23a)	HGNC	OMA
Alliance orthologs ³
Homo sapiens (human):	SNRPD2 (small nuclear ribonucleoprotein D2 polypeptide)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB)
Homo sapiens (human):	SNRPD2 (small nuclear ribonucleoprotein D2 polypeptide)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Mus musculus (house mouse):	Snrpd2 (small nuclear ribonucleoprotein D2)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Mus musculus (house mouse):	Snrpd2 (small nuclear ribonucleoprotein D2)	Alliance	DIOPT (Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB)
Danio rerio (zebrafish):	snrpd2 (small nuclear ribonucleoprotein D2 polypeptide)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Danio rerio (zebrafish):	snrpd2 (small nuclear ribonucleoprotein D2 polypeptide)	Alliance	DIOPT (Hieranoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB)
Drosophila melanogaster (fruit fly):	SmD2	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Drosophila melanogaster (fruit fly):	SmD2	Alliance	DIOPT (Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Saccharomyces cerevisiae (baker's yeast):	SMD2	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Saccharomyces cerevisiae (baker's yeast):	SMD2	Alliance	DIOPT (Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|SonicParanoid)
Caenorhabditis elegans (roundworm):	snr-4	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Caenorhabditis elegans (roundworm):	snr-4	Alliance	DIOPT (Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Xenopus tropicalis (tropical clawed frog):	snrpd2	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|SonicParanoid)
Xenopus tropicalis (tropical clawed frog):	snrpd2	Alliance	DIOPT (Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB)

Related Pseudogenes:

Snrpd2l

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	1	87,926,030 - 87,929,259 (+)	NCBI	GRCr8	GRCr8		GRCr8
GRCr8 Ensembl	1	87,926,048 - 87,933,339 (+)	Ensembl				GRCr8
GRCr8 Ensembl	20	27,796,409 - 27,796,949 (-)	Ensembl				GRCr8
mRatBN7.2	1	78,798,377 - 78,801,227 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	20	27,253,424 - 27,253,780 (-)	Ensembl				mRatBN7.2
mRatBN7.2 Ensembl	1	78,798,377 - 78,803,351 (+)	Ensembl				mRatBN7.2
UTH_Rnor_SHR_Utx	1	84,187,409 - 84,190,259 (+)	NCBI	UTH_Rnor_SHR_Utx	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	1	92,745,052 - 92,747,904 (+)	NCBI	UTH_Rnor_SHRSP_BbbUtx_1.0	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	1	85,942,511 - 85,945,361 (+)	NCBI	UTH_Rnor_WKY_Bbb_1.0	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	1	80,057,140 - 80,059,990 (+)	NCBI	Rnor_6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	1	80,056,755 - 80,059,996 (+)	Ensembl			rn6	Rnor6.0
Rnor_5.0	1	81,324,033 - 81,326,883 (+)	NCBI	Rnor_5.0	Rnor_5.0	rn5
RGSC_v3.4	1	78,509,142 - 78,511,992 (+)	NCBI	RGSC_v3.4	RGSC_v3.4	rn4
Celera	1	73,264,040 - 73,266,890 (+)	NCBI		Celera
Cytogenetic Map	1	q21	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

systemic lupus erythematosus (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

(-)-alpha-phellandrene (ISO)

(1->4)-beta-D-glucan (ISO)

1,2-dimethylhydrazine (ISO)

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

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

4,4'-sulfonyldiphenol (ISO)

acrolein (ISO)

actinomycin D (ISO)

alpha-phellandrene (ISO)

alpha-pinene (ISO)

Aroclor 1254 (ISO)

arsenite(3-) (ISO)

beauvericin (ISO)

benzatropine (ISO)

benzo[a]pyrene (ISO)

bis(2-ethylhexyl) phthalate (ISO)

bisphenol A (EXP,ISO)

bisphenol F (ISO)

cadmium dichloride (EXP,ISO)

chloropicrin (ISO)

chromium(6+) (ISO)

clobetasol (ISO)

clozapine (ISO)

copper atom (ISO)

copper(0) (ISO)

copper(II) sulfate (ISO)

dibutyl phthalate (ISO)

dihydroartemisinin (ISO)

enniatin (ISO)

enzyme inhibitor (ISO)

epoxiconazole (ISO)

flutamide (EXP)

folic acid (ISO)

FR900359 (ISO)

glafenine (EXP)

haloperidol (ISO)

hinokiflavone (ISO)

hydralazine (ISO)

ivermectin (ISO)

methyl methanesulfonate (ISO)

methylparaben (ISO)

N-methyl-4-phenylpyridinium (ISO)

nitrates (ISO)

Nutlin-3 (ISO)

oxaliplatin (EXP)

ozone (EXP,ISO)

perfluorooctane-1-sulfonic acid (ISO)

perfluorooctanoic acid (ISO)

resveratrol (ISO)

sodium arsenite (ISO)

thiram (ISO)

titanium dioxide (ISO)

toluene (EXP)

topotecan (EXP)

trimellitic anhydride (ISO)

triphenyl phosphate (ISO)

tungsten (ISO)

valproic acid (ISO)

vinclozolin (EXP)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

biological_process (ND)

mRNA processing (IEA)

mRNA splicing, via spliceosome (IEA,ISO)

RNA splicing (IEA)

spliceosomal snRNP assembly (IBA,ISO)

Cellular Component

catalytic step 2 spliceosome (IBA,ISO)

cytosol (IEA,ISO)

methylosome (ISO)

nucleus (IEA,ISO)

pICln-Sm protein complex (IBA,ISO)

post-mRNA release spliceosomal complex (ISO)

post-spliceosomal complex (ISO)

precatalytic spliceosome (IBA,ISO)

ribonucleoprotein complex (IEA)

small nuclear ribonucleoprotein complex (IEA)

SMN-Sm protein complex (ISO)

spliceosomal complex (IEA,ISO)

spliceosomal snRNP complex (IEA)

U1 snRNP (IBA,IDA,ISO)

U11/U12 snRNP (ISO)

U12-type catalytic step 2 spliceosome (ISO)

U12-type precatalytic spliceosome (ISO)

U12-type spliceosomal complex (IEA,ISO)

U2 snRNP (IBA)

U2-type catalytic step 1 spliceosome (ISO)

U2-type catalytic step 2 spliceosome (ISO)

U2-type precatalytic spliceosome (ISO)

U2-type spliceosomal complex (ISO)

U4 snRNP (ISO)

U4/U6 x U5 tri-snRNP complex (IBA,ISO)

U5 snRNP (IBA)

Molecular Function

protein binding (ISO)

RNA binding (IEA)

U1 snRNP binding (IDA)

Molecular Pathway Annotations Click to see Annotation Detail View

spliceosome pathway (IEA,ISO)

References

References - curated

#	Reference Title	Reference Citation
1.	Proteomic analysis of in vivo-assembled pre-mRNA splicing complexes expands the catalog of participating factors.	Chen YI, etal., Nucleic Acids Res. 2007;35(12):3928-44. Epub 2007 May 30.
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.	Anti-sm autoantibodies in systemic lupus target highly basic surface structures of complexed spliceosomal autoantigens.	McClain MT, etal., J Immunol. 2002 Feb 15;168(4):2054-62.
4.	Separation of nuclear protein complexes by blue native polyacrylamide gel electrophoresis.	Novakova Z, etal., Electrophoresis. 2006 Apr;27(7):1277-87.
5.	KEGG Annotation Import Pipeline	Pipeline to import KEGG annotations from KEGG into RGD
6.	Data Import for Chemical-Gene Interactions	RGD automated import pipeline for gene-chemical interactions
7.	Comprehensive gene review and curation	RGD comprehensive gene curation
8.	The spliceosome: design principles of a dynamic RNP machine.	Wahl MC, etal., Cell. 2009 Feb 20;136(4):701-18. doi: 10.1016/j.cell.2009.02.009.

Additional References at PubMed

PMID:11991638	PMID:12477932	PMID:15146077	PMID:18984161	PMID:20458337	PMID:21113136	PMID:21516107	PMID:22658674	PMID:23376485	PMID:25555158	PMID:26912367	PMID:28076346
PMID:28781166	PMID:31505169

Genomics

Comparative Map Data

Snrpd2
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	1	87,926,030 - 87,929,259 (+)	NCBI	GRCr8	GRCr8		GRCr8
GRCr8 Ensembl	1	87,926,048 - 87,933,339 (+)	Ensembl				GRCr8
GRCr8 Ensembl	20	27,796,409 - 27,796,949 (-)	Ensembl				GRCr8
mRatBN7.2	1	78,798,377 - 78,801,227 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	20	27,253,424 - 27,253,780 (-)	Ensembl				mRatBN7.2
mRatBN7.2 Ensembl	1	78,798,377 - 78,803,351 (+)	Ensembl				mRatBN7.2
UTH_Rnor_SHR_Utx	1	84,187,409 - 84,190,259 (+)	NCBI	UTH_Rnor_SHR_Utx	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	1	92,745,052 - 92,747,904 (+)	NCBI	UTH_Rnor_SHRSP_BbbUtx_1.0	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	1	85,942,511 - 85,945,361 (+)	NCBI	UTH_Rnor_WKY_Bbb_1.0	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	1	80,057,140 - 80,059,990 (+)	NCBI	Rnor_6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	1	80,056,755 - 80,059,996 (+)	Ensembl			rn6	Rnor6.0
Rnor_5.0	1	81,324,033 - 81,326,883 (+)	NCBI	Rnor_5.0	Rnor_5.0	rn5
RGSC_v3.4	1	78,509,142 - 78,511,992 (+)	NCBI	RGSC_v3.4	RGSC_v3.4	rn4
Celera	1	73,264,040 - 73,266,890 (+)	NCBI		Celera
Cytogenetic Map	1	q21	NCBI

SNRPD2
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	19	45,687,454 - 45,692,316 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	19	45,687,460 - 45,692,569 (-)	Ensembl			hg38	GRCh38
GRCh37	19	46,190,712 - 46,195,574 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	19	50,882,558 - 50,887,282 (-)	NCBI	Build 36	Build 36	hg18	NCBI36
Build 34	19	50,882,557 - 50,887,282	NCBI
Celera	19	42,996,835 - 43,001,568 (-)	NCBI		Celera
Cytogenetic Map	19	q13.32	NCBI
HuRef	19	42,619,677 - 42,624,410 (-)	NCBI		HuRef
CHM1_1	19	46,194,181 - 46,198,916 (-)	NCBI		CHM1_1
T2T-CHM13v2.0	19	48,514,991 - 48,519,856 (-)	NCBI		T2T-CHM13v2.0

Snrpd2
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	7	18,883,370 - 18,886,659 (+)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	7	18,883,647 - 18,887,467 (+)	Ensembl		GRCm39 Ensembl		GRCm39
GRCm38	7	19,149,445 - 19,152,734 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	7	19,149,722 - 19,153,542 (+)	Ensembl			mm10	GRCm38
MGSCv37	7	19,735,187 - 19,738,075 (+)	NCBI	MGSCv37	MGSCv37	mm9	NCBIm37
MGSCv36	7	18,308,360 - 18,311,248 (+)	NCBI		MGSCv36	mm8
Celera	7	16,561,189 - 16,564,077 (+)	NCBI		Celera
Cytogenetic Map	7	A3	NCBI
cM Map	7	9.46	NCBI

Snrpd2
(Chinchilla lanigera - long-tailed chinchilla)

Chinchilla Assembly	Chr	Position (strand)	Source	Genome Browsers
Chinchilla Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChiLan1.0 Ensembl	NW_004955561	1,083,057 - 1,083,413 (-)	Ensembl
ChiLan1.0	NW_004955574	157,769 - 164,947 (-)	NCBI	ChiLan1.0	ChiLan1.0

SNRPD2
(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	20	51,849,077 - 51,853,700 (-)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	19	53,720,533 - 53,725,113 (-)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	19	42,692,963 - 42,697,512 (-)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	19	51,230,822 - 51,235,661 (-)	NCBI	PanPan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	19	51,230,822 - 51,235,661 (-)	Ensembl			panPan2	panpan1.1

SNRPD2
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	1	109,891,253 - 109,896,712 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	1	109,891,223 - 109,896,711 (+)	Ensembl			canFam3	CanFam3.1
Dog10K_Boxer_Tasha	1	109,376,402 - 109,381,860 (+)	NCBI	Dog10K_Boxer_Tasha	Dog10K_Boxer_Tasha
ROS_Cfam_1.0	1	110,424,516 - 110,429,978 (+)	NCBI	ROS_Cfam_1.0	ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	13	4,259,831 - 4,260,778 (-)	Ensembl				ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	1	110,100,067 - 110,105,533 (+)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	1	109,734,707 - 109,740,174 (+)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	1	110,603,576 - 110,609,034 (+)	NCBI	UU_Cfam_GSD_1.0	UU_Cfam_GSD_1.0

Snrpd2
(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_024409349	17,717,972 - 17,721,426 (-)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936706	2,065,419 - 2,067,487 (-)	Ensembl		SpeTri2.0 Ensembl
SpeTri2.0	NW_004936706	2,065,315 - 2,068,709 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

SNRPD2
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	6	52,035,134 - 52,042,474 (-)	Ensembl			susScr11	Sscrofa11.1
Sscrofa11.1	6	52,035,900 - 52,042,474 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1

SNRPD2
(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	6	39,127,974 - 39,134,771 (-)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	6	39,127,877 - 39,134,626 (-)	Ensembl		ChlSab1.1 Ensembl	chlSab2	Vervet-AGM
Vero_WHO_p1.0	NW_023666073	18,755,632 - 18,760,350 (-)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Snrpd2
(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_004624832	7,488,674 - 7,495,306 (+)	Ensembl		HetGla_female_1.0 Ensembl	hetGla2	HetGla_female_1.0 Ensembl
HetGla 1.0	NW_004624832	7,488,259 - 7,495,305 (+)	NCBI	HetGla 1.0	HetGla 1.0	hetGla2

Snrpd2
(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	2	171,469,867 - 171,472,741 (-)	NCBI		Rrattus_CSIRO_v1

Variants

Variants in Snrpd2
13 total Variants

miRNA Target Status (No longer updated)

Predicted Target Of

	Summary Value
Count of predictions:	47
Count of miRNA genes:	46
Interacting mature miRNAs:	47
Transcripts:	ENSRNOT00000021221
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
1578649	Bmd8	Bone mineral density QTL 8	4.9		femur mineral mass (VT:0010011)	trabecular volumetric bone mineral density (CMO:0001729)	1	51940904	101229020	Rat
1582234	Gluco18	Glucose level QTL 18	3.4	0.0003	blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	1	87889942	132889942	Rat
634314	Niddm44	Non-insulin dependent diabetes mellitus QTL 44			blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	1	51941022	208479811	Rat
1358359	Sradr1	Stress Responsive Adrenal Weight QTL 1	4.74		adrenal gland mass (VT:0010420)	both adrenal glands wet weight (CMO:0000164)	1	39728272	132889942	Rat
4889929	Bss87	Bone structure and strength QTL 87	6.7		tibia area (VT:1000281)	tibia-fibula cortical bone endosteal cross-sectional area (CMO:0001722)	1	46302615	91302615	Rat
2313062	Bmd73	Bone mineral density QTL 73	3.9	0.0001	tibia mineral mass (VT:1000283)	compact volumetric bone mineral density (CMO:0001730)	1	46302615	91302615	Rat
1578654	Bss10	Bone structure and strength QTL 10	4		femur morphology trait (VT:0000559)	femoral neck cortical cross-sectional area (CMO:0001702)	1	51940904	168768703	Rat
8552900	Pigfal1	Plasma insulin-like growth factor 1 level QTL 1	7.4		blood insulin-like growth factor amount (VT:0010479)	plasma insulin-like growth factor 1 level (CMO:0001299)	1	43509952	88509952	Rat
2313065	Bss67	Bone structure and strength QTL 67	3.1	0.0001	tibia area (VT:1000281)	tibia total energy absorbed before break (CMO:0001736)	1	46302615	91302615	Rat
1331800	Scl25	Serum cholesterol level QTL 25	3.013		blood cholesterol amount (VT:0000180)	serum total cholesterol level (CMO:0000363)	1	87785026	142582336	Rat
7421628	Bp361	Blood pressure QTL 361		0.001	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	1	83019780	128019780	Rat
631495	Bp96	Blood pressure QTL 96	4.52		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	66404680	111404680	Rat
2313069	Bss68	Bone structure and strength QTL 68	2.9	0.0001	tibia size trait (VT:0100001)	tibia total energy absorbed before break (CMO:0001736)	1	46302615	91302615	Rat
70225	Bp58	Blood pressure QTL 58	3.3		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	34184556	172281316	Rat
2313075	Bss66	Bone structure and strength QTL 66	3.4	0.0001	tibia length (VT:0004357)	tibia length (CMO:0000450)	1	46302615	91302615	Rat
631512	Scl6	Serum cholesterol level QTL 6	9.6		blood cholesterol amount (VT:0000180)	serum total cholesterol level (CMO:0000363)	1	81269860	99645535	Rat
2298545	Neuinf8	Neuroinflammation QTL 8	4.6		nervous system integrity trait (VT:0010566)	spinal cord beta-2 microglobulin mRNA level (CMO:0002125)	1	66009857	160501508	Rat
10059597	Bp377	Blood pressure QTL 377	3.42	0.025	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	34565911	208798288	Rat
2313077	Bss69	Bone structure and strength QTL 69	3.5	0.0001	tibia strength trait (VT:1000284)	bone polar moment of inertia (CMO:0001558)	1	46302615	91302615	Rat
1302788	Scl19	Serum cholesterol QTL 19	4.6	0.001	blood cholesterol amount (VT:0000180)	plasma total cholesterol level (CMO:0000585)	1	66400974	132889942	Rat
1549903	Bp267	Blood pressure QTL 267			arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	84107164	115183752	Rat
2313402	Anxrr24	Anxiety related response QTL 24			aggression-related behavior trait (VT:0015014)	tameness/aggressiveness composite score (CMO:0002136)	1	51511344	153680016	Rat
61342	Bp27	Blood pressure QTL 27	3.4	0.0006	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	65405637	96805205	Rat
4889962	Bss94	Bone structure and strength QTL 94	3.8		tibia area (VT:1000281)	tibia-fibula cortical bone endosteal cross-sectional area (CMO:0001722)	1	51909206	91302615	Rat
1358192	Ept13	Estrogen-induced pituitary tumorigenesis QTL 13	3.4		pituitary gland mass (VT:0010496)	pituitary gland wet weight (CMO:0000853)	1	86622262	131622262	Rat
6903308	Scl36	Serum cholesterol QTL 36	2	0.0125	blood cholesterol amount (VT:0000180)	plasma total cholesterol level (CMO:0000585)	1	58769992	103769992	Rat
2300164	Bmd44	Bone mineral density QTL 44	5.4	0.0001	lumbar vertebra mineral mass (VT:0010511)	volumetric bone mineral density (CMO:0001553)	1	66077886	111077886	Rat
2313092	Bmd72	Bone mineral density QTL 72	2.5	0.0001	tibia mineral mass (VT:1000283)	total volumetric bone mineral density (CMO:0001728)	1	46302615	91302615	Rat
2313097	Bss70	Bone structure and strength QTL 70	3.5	0.0001	tibia strength trait (VT:1000284)	tibia total energy absorbed before break (CMO:0001736)	1	46302615	91302615	Rat
9589820	Insglur3	Insulin/glucose ratio QTL 3	10.75	0.001	blood insulin amount (VT:0001560)	calculated plasma insulin level (CMO:0002170)	1	43509952	88509952	Rat
10054135	Gmadr2	Adrenal mass QTL 2	1.97	0.0129	adrenal gland mass (VT:0010420)	both adrenal glands wet weight (CMO:0000164)	1	86993904	131993904	Rat
152025249	Scl82	Serum cholesterol level QTL 82	4.77		blood cholesterol amount (VT:0000180)		1	52891222	109116986	Rat
7411712	Strs4	Sensitivity to stroke QTL 4	8.7		cerebrum integrity trait (VT:0010549)	percentage of study population developing cerebrovascular lesions during a period of time (CMO:0000932)	1	87558587	132558587	Rat
4889919	Bss86	Bone structure and strength QTL 86	4.1		tibia area (VT:1000281)	tibia midshaft total cross-sectional area (CMO:0001715)	1	46302615	91302615	Rat
8552948	Pigfal11	Plasma insulin-like growth factor 1 level QTL 11	4.7		blood insulin-like growth factor amount (VT:0010479)	plasma insulin-like growth factor 1 level (CMO:0001299)	1	43509952	88509952	Rat

Markers in Region

RH126590

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	6	21,282,218 - 21,282,416 (+)	MAPPER	mRatBN7.2
mRatBN7.2	1	78,799,838 - 78,801,063 (+)	MAPPER	mRatBN7.2
Rnor_6.0	1	80,058,602 - 80,059,826	NCBI	Rnor6.0
Rnor_6.0	6	22,457,430 - 22,457,627	NCBI	Rnor6.0
Rnor_5.0	6	32,343,125 - 32,343,322	UniSTS	Rnor5.0
Rnor_5.0	1	81,325,495 - 81,326,719	UniSTS	Rnor5.0
RGSC_v3.4	1	78,510,604 - 78,511,828	UniSTS	RGSC3.4
RGSC_v3.4	6	21,245,180 - 21,245,377	UniSTS	RGSC3.4
Celera	6	20,839,275 - 20,839,472	UniSTS
Celera	1	73,265,502 - 73,266,726	UniSTS
Cytogenetic Map	6	q13	UniSTS
Cytogenetic Map	1	q21	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_001109399	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_063273625	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AC120692	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BC168781	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473979	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ222619	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ228670	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JAXUCZ010000001	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Ensembl Acc Id:

ENSRNOT00000021221 ⟹ ENSRNOP00000021221

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8 Ensembl	1	87,926,048 - 87,929,408 (+)	Ensembl
mRatBN7.2 Ensembl	1	78,799,579 - 78,801,226 (+)	Ensembl
Rnor_6.0 Ensembl	1	80,056,755 - 80,059,996 (+)	Ensembl

Ensembl Acc Id:

ENSRNOT00000109557 ⟹ ENSRNOP00000081057

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	1	78,798,377 - 78,803,351 (+)	Ensembl

Ensembl Acc Id:

ENSRNOT00000138384 ⟹ ENSRNOP00000101122

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8 Ensembl	1	87,926,048 - 87,933,339 (+)	Ensembl

RefSeq Acc Id:

NM_001109399 ⟹ NP_001102869

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	1	87,926,409 - 87,929,259 (+)	NCBI
mRatBN7.2	1	78,798,377 - 78,801,227 (+)	NCBI
Rnor_6.0	1	80,057,140 - 80,059,990 (+)	NCBI
Rnor_5.0	1	81,324,033 - 81,326,883 (+)	NCBI
RGSC_v3.4	1	78,509,142 - 78,511,992 (+)	RGD
Celera	1	73,264,040 - 73,266,890 (+)	RGD

Sequence:

show sequence

CTTCTCTTGCTGTGCTCCAAAGGCTAAAGCAACGCGCTTGGAGGCGGGAGTGATCTGCTAGCGA
AACCTTCACCATGAGTCTCCTCAATAAACCCAAGAGTGAGATGACCCCAGAGGAGCTGCAGAAG
CGGGAGGAGGAGGAATTCAACACAGGTCCCCTCTCGGTGCTCACACAGTCGGTCAAAAACAACA
CGCAAGTGCTCATTAACTGTCGAAACAACAAGAAGCTCCTGGGCCGGGTGAAGGCCTTTGACAG
GCACTGCAACATGGTGCTGGAAAATGTGAAGGAGATGTGGACTGAGGTCCCCAAGAGCGGCAAG
GGCAAGAAGAAGTCCAAGCCTGTCAACAAGGACCGCTACATCTCCAAGATGTTCCTGCGCGGGG
ACTCAGTCATTGTGGTGCTGCGGAACCCGCTCATCGCTGGCAAGTAAACTAGAGGCCAGCCTCA
GCCCGCTGAGAGCCTGCTCCCTGCCCAGCCAAGTCCCGCAGAGCCCTGCCCAATGAGCTAGAAA
TAAAACCCTGTGCTTTTTGTTTTTTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAA

hide sequence

RefSeq Acc Id:

XM_063273625 ⟹ XP_063129695

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	1	87,926,030 - 87,929,259 (+)	NCBI

Protein Sequences


Protein RefSeqs	NP_001102869	(Get FASTA)	NCBI Sequence Viewer
	XP_063129695	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAI68781	(Get FASTA)	NCBI Sequence Viewer
	EDM08232	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSRNOP00000021221
	ENSRNOP00000021221.4
	ENSRNOP00000065798.1
	ENSRNOP00000101122.1

RefSeq Acc Id:	NP_001102869 ⟸ NM_001109399
- UniProtKB:	B5DES0 (UniProtKB/TrEMBL), M0R8K2 (UniProtKB/TrEMBL)
- Sequence:	show sequence MSLLNKPKSEMTPEELQKREEEEFNTGPLSVLTQSVKNNTQVLINCRNNKKLLGRVKAFDRHCN MVLENVKEMWTEVPKSGKGKKKSKPVNKDRYISKMFLRGDSVIVVLRNPLIAGK hide sequence

Ensembl Acc Id:

ENSRNOP00000021221 ⟸ ENSRNOT00000021221

Ensembl Acc Id:

ENSRNOP00000081057 ⟸ ENSRNOT00000109557

RefSeq Acc Id:	XP_063129695 ⟸ XM_063273625
- Peptide Label:	isoform X1
- UniProtKB:	B5DES0 (UniProtKB/TrEMBL), M0R8K2 (UniProtKB/TrEMBL)

Ensembl Acc Id:

ENSRNOP00000101122 ⟸ ENSRNOT00000138384

Protein Domains

Protein Structures

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-B5DES0-F1-model_v2	AlphaFold	B5DES0	1-118	view protein structure

Transcriptome

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

Promoters

RGD ID:

13689763

Promoter ID:

EPDNEW_R287

Type:

multiple initiation site

Name:

Snrpd2_1

Description:

small nuclear ribonucleoprotein D2 polypeptide

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	1	80,057,140 - 80,057,200	EPDNEW

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:1593018	AgrOrtholog
BioCyc Gene	G2FUF-60528	BioCyc
Ensembl Genes	ENSRNOG00000015844	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
	ENSRNOG00000048758	Ensembl, UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000021221	ENTREZGENE
	ENSRNOT00000021221.6	UniProtKB/TrEMBL
	ENSRNOT00000071064.3	UniProtKB/TrEMBL
	ENSRNOT00000138384.1	UniProtKB/TrEMBL
Gene3D-CATH	2.30.30.100	UniProtKB/TrEMBL
InterPro	IPR047575	UniProtKB/TrEMBL
	LSM_domain	UniProtKB/TrEMBL
	LSM_related_domain	UniProtKB/TrEMBL
	Sm_D2	UniProtKB/TrEMBL
KEGG Report	rno:680309	UniProtKB/TrEMBL
NCBI Gene	680309	ENTREZGENE
PANTHER	PTHR12777	UniProtKB/TrEMBL
Pfam	LSM	UniProtKB/TrEMBL
PhenoGen	Snrpd2	PhenoGen
PROSITE	PS52002	UniProtKB/TrEMBL
RatGTEx	ENSRNOG00000015844	RatGTEx
	ENSRNOG00000048758	RatGTEx
SMART	SM00651	UniProtKB/TrEMBL
Superfamily-SCOP	Sm_like_riboprot	UniProtKB/TrEMBL
UniProt	A0ABK0LAP5_RAT	UniProtKB/TrEMBL
	B5DES0	ENTREZGENE, UniProtKB/TrEMBL
	F7FB70_RAT	UniProtKB/TrEMBL
	M0R8K2	ENTREZGENE, UniProtKB/TrEMBL

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2013-05-24	Snrpd2	small nuclear ribonucleoprotein D2 polypeptide	LOC686737	similar to small nuclear ribonucleoprotein D2	Data merged from RGD:1593724	1643240	APPROVED
2009-10-22	Snrpd2	small nuclear ribonucleoprotein D2 polypeptide	Snrpd2	small nuclear ribonucleoprotein D2	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2008-03-05	Snrpd2	small nuclear ribonucleoprotein D2	LOC680309	similar to small nuclear ribonucleoprotein D2	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2006-11-20	LOC680309	similar to small nuclear ribonucleoprotein D2			Symbol and Name status set to provisional	70820	PROVISIONAL
2006-11-20	LOC686737	similar to small nuclear ribonucleoprotein D2			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)

RGD Manual Annotations

Imported Annotations - KEGG (archival)

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RGD Manual Annotations

Imported Annotations - KEGG (archival)