Snrpd3 (small nuclear ribonucleoprotein D3 polypeptide) - Rat Genome Database

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Gene: Snrpd3 (small nuclear ribonucleoprotein D3 polypeptide) Rattus norvegicus
Analyze
Symbol: Snrpd3
Name: small nuclear ribonucleoprotein D3 polypeptide
RGD ID: 1597573
Description: Enables U1 snRNP binding activity. Predicted to be involved in spliceosomal snRNP assembly. Predicted to act upstream of or within protein methylation. Located in nucleus. Part of U1 snRNP. Human ortholog(s) of this gene implicated in systemic lupus erythematosus. Orthologous to human SNRPD3 (small nuclear ribonucleoprotein D3 polypeptide); PARTICIPATES IN spliceosome pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; bisphenol A; flutamide.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC687711; similar to small nuclear ribonucleoprotein D3; small nuclear ribonucleoprotein D3; small nuclear ribonucleoprotein Sm D3
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.22013,130,112 - 13,145,947 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2013,130,119 - 13,145,978 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx2013,836,690 - 13,852,053 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.02013,197,636 - 13,212,999 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.02013,670,141 - 13,685,504 (-)NCBIRnor_WKY
Rnor_6.02014,080,562 - 14,095,644 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2014,080,565 - 14,095,181 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02016,265,897 - 16,280,500 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera2014,615,859 - 14,631,320 (-)NCBICelera
Cytogenetic Map20p12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
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. Identification of genes associated with local aggressiveness and metastatic behavior in soft tissue tumors. Cunha IW, etal., Transl Oncol. 2010 Feb;3(1):23-32.
3. 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.
4. Effect of dsDNA binding to SmD-derived peptides on clinical accuracy in the diagnosis of systemic lupus erythematosus. Mahler M, etal., Arthritis Res Ther. 2007;9(4):R68.
5. Separation of nuclear protein complexes by blue native polyacrylamide gel electrophoresis. Novakova Z, etal., Electrophoresis. 2006 Apr;27(7):1277-87.
6. GOA pipeline RGD automated data pipeline
7. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
8. Comprehensive gene review and curation RGD comprehensive gene curation
9. 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:11574479   PMID:11991638   PMID:15146077   PMID:15369763   PMID:17709427   PMID:18082603   PMID:18495660   PMID:18984161   PMID:19470752   PMID:21113136   PMID:21516107   PMID:22681889  
PMID:23376485   PMID:24625528   PMID:25555158   PMID:25931508   PMID:26912367   PMID:28076346   PMID:28781166   PMID:31505169  


Genomics

Comparative Map Data
Snrpd3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.22013,130,112 - 13,145,947 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2013,130,119 - 13,145,978 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx2013,836,690 - 13,852,053 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.02013,197,636 - 13,212,999 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.02013,670,141 - 13,685,504 (-)NCBIRnor_WKY
Rnor_6.02014,080,562 - 14,095,644 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2014,080,565 - 14,095,181 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02016,265,897 - 16,280,500 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera2014,615,859 - 14,631,320 (-)NCBICelera
Cytogenetic Map20p12NCBI
SNRPD3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382224,555,650 - 24,574,971 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl2224,555,958 - 24,582,052 (+)EnsemblGRCh38hg38GRCh38
GRCh372224,951,618 - 24,970,939 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 362223,281,618 - 23,298,509 (+)NCBINCBI36Build 36hg18NCBI36
Build 342223,276,171 - 23,293,063NCBI
Celera228,751,341 - 8,768,251 (+)NCBICelera
Cytogenetic Map22q11.23NCBI
HuRef227,901,312 - 7,920,624 (+)NCBIHuRef
CHM1_12224,910,367 - 24,929,747 (+)NCBICHM1_1
T2T-CHM13v2.02225,017,257 - 25,036,577 (+)NCBIT2T-CHM13v2.0
Snrpd3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391075,353,876 - 75,371,274 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1075,353,385 - 75,373,215 (+)EnsemblGRCm39 Ensembl
GRCm381075,518,042 - 75,535,440 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1075,517,551 - 75,537,381 (+)EnsemblGRCm38mm10GRCm38
MGSCv371074,980,787 - 74,998,185 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361074,961,758 - 74,979,156 (+)NCBIMGSCv36mm8
Celera1076,562,802 - 76,580,214 (+)NCBICelera
Cytogenetic Map10C1NCBI
Snrpd3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554558,021,946 - 8,046,439 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554558,021,946 - 8,045,325 (+)NCBIChiLan1.0ChiLan1.0
SNRPD3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12222,227,328 - 22,255,511 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2222,227,328 - 22,246,676 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0225,361,886 - 5,378,465 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
SNRPD3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12628,247,878 - 28,263,519 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2627,322,650 - 27,338,477 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02629,651,819 - 29,667,871 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2629,652,275 - 29,667,868 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12627,735,763 - 27,751,600 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02627,352,755 - 27,368,580 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02628,342,420 - 28,358,470 (+)NCBIUU_Cfam_GSD_1.0
Snrpd3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118142,009,519 - 142,025,363 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936619728,114 - 745,551 (+)EnsemblSpeTri2.0
SpeTri2.0NW_004936619728,759 - 744,367 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SNRPD3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.11449,585,177 - 49,598,015 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21453,027,337 - 53,039,880 (+)NCBISscrofa10.2Sscrofa10.2susScr3
SNRPD3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1197,560,946 - 7,577,338 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl197,417,483 - 7,577,914 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660854,743,649 - 4,779,869 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Snrpd3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247479,962,467 - 9,987,511 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247479,973,949 - 9,987,520 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Snrpd3
34 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:117
Count of miRNA genes:100
Interacting mature miRNAs:106
Transcripts:ENSRNOT00000075517
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1354642Despr15Despair related QTL 150.0027locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)20124159021Rat
1600382Edcs3Endometrial carcinoma susceptibility QTL33.50.003uterus morphology trait (VT:0001120)percentage of study population developing endometrioid carcinoma during a period of time (CMO:0001759)20125159026Rat
2317851Alcrsp22Alcohol response QTL 223.20.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20127339237Rat
1641893Alcrsp7Alcohol response QTL 7response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20127339237Rat
8694189Bw153Body weight QTL 1533.130.001body mass (VT:0001259)body weight gain (CMO:0000420)20129191651Rat
9590275Scort15Serum corticosterone level QTL 153.480.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20129191651Rat
7411650Foco23Food consumption QTL 2320.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20129191651Rat
9590109Sffal8Serum free fatty acids level QTL 85.320.01blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)20129191651Rat
9589155Insul32Insulin level QTL 326.380.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)20129191651Rat
6893685Bw111Body weight QTL 1112.70.004body mass (VT:0001259)body weight (CMO:0000012)20132578807Rat
7411668Foco32Food consumption QTL 3280.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20136600972Rat
9590252Scort12Serum corticosterone level QTL 1220.460.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20136600972Rat
2305926Iddm37Insulin dependent diabetes mellitus QTL 376blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)20152784246527842Rat
1641915Colcr9Colorectal carcinoma resistance QTL 92.970.0024intestine integrity trait (VT:0010554)benign colorectal tumor number (CMO:0001795)20153065546530655Rat
1598816Memor12Memory QTL 122.4exploratory behavior trait (VT:0010471)average horizontal distance between subject and target during voluntary locomotion in an experimental apparatus (CMO:0002674)20260683647606836Rat
2317057Aia27Adjuvant induced arthritis QTL 272.83joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)20289259726381954Rat
61432Cia1Collagen induced arthritis QTL 1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)20362165614101050Rat
4889857Pur27Proteinuria QTL 2712.20.001urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)20460660717617956Rat
1558640Prcs2Prostate cancer susceptibility QTL 23.3prostate integrity trait (VT:0010571)percentage of study population developing ventral prostate tumorous lesions during a period of time (CMO:0000943)20460660717617956Rat
70154Insul2Insulin level QTL 23.75blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)20669170617489458Rat
1581577Pur15Proteinuria QTL 154.380.0002urine total protein amount (VT:0000032)urine protein excretion rate (CMO:0000759)20804241017617956Rat
4889870Pur30Proteinuria QTL 30190.005urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)20804241029322208Rat
631265Iresp1Immunoglobin response QTL18.3blood anti-double stranded DNA antibody amount (VT:0004762)serum anti-DNA antibody level (CMO:0001533)20903971913461775Rat
7411652Foco24Food consumption QTL 240.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)201175751554435887Rat
9590092Insglur9Insulin/glucose ratio QTL 918.380.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)201175751554435887Rat


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 3 35 42 33 18 33 1 4 66 32 40 11 1
Low 8 15 8 1 8 7 7 8 3 1 7
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000075517   ⟹   ENSRNOP00000065967
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2013,130,119 - 13,145,978 (-)Ensembl
Rnor_6.0 Ensembl2014,080,565 - 14,095,181 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000093513
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl2014,094,025 - 14,095,176 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000093533
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl2014,080,565 - 14,081,188 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000103973   ⟹   ENSRNOP00000077874
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2013,130,119 - 13,135,796 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000106631   ⟹   ENSRNOP00000094933
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2013,132,567 - 13,145,978 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000109722   ⟹   ENSRNOP00000088111
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2013,132,041 - 13,145,978 (-)Ensembl
RefSeq Acc Id: XM_003751948   ⟹   XP_003751996
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22013,130,112 - 13,145,507 (-)NCBI
Rnor_6.02014,080,563 - 14,095,218 (-)NCBI
Rnor_5.02016,265,897 - 16,280,500 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017601884   ⟹   XP_017457373
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22013,130,112 - 13,145,947 (-)NCBI
Rnor_6.02014,080,562 - 14,095,644 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001386467 (Get FASTA)   NCBI Sequence Viewer  
  XP_003751996 (Get FASTA)   NCBI Sequence Viewer  
  XP_017457373 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL97215 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: XP_003751996   ⟸   XM_003751948
- UniProtKB: M0R907 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017457373   ⟸   XM_017601884
- UniProtKB: M0R907 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000065967   ⟸   ENSRNOT00000075517
RefSeq Acc Id: ENSRNOP00000088111   ⟸   ENSRNOT00000109722
RefSeq Acc Id: ENSRNOP00000094933   ⟸   ENSRNOT00000106631
RefSeq Acc Id: ENSRNOP00000077874   ⟸   ENSRNOT00000103973
Protein Domains
Sm

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-M0R907-F1-model_v2 AlphaFold M0R907 1-126 view protein structure

Transcriptome

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

Promoters
RGD ID:13701542
Promoter ID:EPDNEW_R12065
Type:multiple initiation site
Name:Snrpd3_1
Description:small nuclear ribonucleoprotein D3 polypeptide
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.02014,095,203 - 14,095,263EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1597573 AgrOrtholog
BioCyc Gene G2FUF-4141 BioCyc
Ensembl Genes ENSRNOG00000050410 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000065967 ENTREZGENE
  ENSRNOP00000065967.1 UniProtKB/TrEMBL
  ENSRNOP00000077874.1 UniProtKB/TrEMBL
  ENSRNOP00000088111.1 UniProtKB/TrEMBL
  ENSRNOP00000094933.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000075517 ENTREZGENE
  ENSRNOT00000075517.4 UniProtKB/TrEMBL
  ENSRNOT00000103973.1 UniProtKB/TrEMBL
  ENSRNOT00000106631.1 UniProtKB/TrEMBL
  ENSRNOT00000109722.1 UniProtKB/TrEMBL
InterPro LSm4/Sm_D1/D3 UniProtKB/TrEMBL
  LSM_dom UniProtKB/TrEMBL
  Ribonucl_LSM UniProtKB/TrEMBL
  SmD3 UniProtKB/TrEMBL
KEGG Report rno:687711 UniProtKB/TrEMBL
NCBI Gene 687711 ENTREZGENE
PANTHER PTHR23338 UniProtKB/TrEMBL
Pfam LSM UniProtKB/TrEMBL
PhenoGen Snrpd3 PhenoGen
SMART SM00651 UniProtKB/TrEMBL
Superfamily-SCOP Sm_like_riboprot UniProtKB/TrEMBL
UniProt A0A8I5ZKE3_RAT UniProtKB/TrEMBL
  A0A8I6AI37_RAT UniProtKB/TrEMBL
  A0A8I6AKJ4_RAT UniProtKB/TrEMBL
  M0R907 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-09-26 Snrpd3  small nuclear ribonucleoprotein D3 polypeptide  Snrpd3  small nuclear ribonucleoprotein D3  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2013-08-16 Snrpd3  small nuclear ribonucleoprotein D3  LOC687711  similar to small nuclear ribonucleoprotein D3  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-11-20 LOC687711  similar to small nuclear ribonucleoprotein D3      Symbol and Name status set to provisional 70820 PROVISIONAL