Snrnp25 (small nuclear ribonucleoprotein U11/U12 subunit 25) - Rat Genome Database

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Gene: Snrnp25 (small nuclear ribonucleoprotein U11/U12 subunit 25) Rattus norvegicus
Analyze
Symbol: Snrnp25
Name: small nuclear ribonucleoprotein U11/U12 subunit 25
RGD ID: 1310922
Description: Predicted to be involved in mRNA splicing, via spliceosome. Predicted to be located in nucleus. Predicted to be part of U12-type spliceosomal complex. Orthologous to human SNRNP25 (small nuclear ribonucleoprotein U11/U12 subunit 25); INTERACTS WITH (+)-schisandrin B; 17beta-estradiol; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC287170; minus -99 protein; RGD1310922; similar to chromosome 16 open reading frame 33; small nuclear ribonucleoprotein 25 (U11/U12); U11/U12 small nuclear ribonucleoprotein 25 kDa protein
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81015,924,932 - 15,928,279 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1015,924,940 - 15,928,252 (-)EnsemblGRCr8
mRatBN7.21015,420,482 - 15,423,806 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1015,420,486 - 15,423,804 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1020,166,502 - 20,169,820 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01019,655,395 - 19,658,713 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01015,148,276 - 15,151,593 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01015,685,999 - 15,689,338 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1015,686,008 - 15,689,325 (-)Ensemblrn6Rnor6.0
Rnor_5.01015,581,143 - 15,584,474 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41015,667,569 - 15,671,373 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1015,087,966 - 15,091,305 (-)NCBICelera
RGSC_v3.11015,668,617 - 15,672,420 (-)NCBI
Cytogenetic Map10q12NCBI
JBrowse:




Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:15146077   PMID:18559850  


Genomics

Comparative Map Data
Snrnp25
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81015,924,932 - 15,928,279 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1015,924,940 - 15,928,252 (-)EnsemblGRCr8
mRatBN7.21015,420,482 - 15,423,806 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1015,420,486 - 15,423,804 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1020,166,502 - 20,169,820 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01019,655,395 - 19,658,713 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01015,148,276 - 15,151,593 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01015,685,999 - 15,689,338 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1015,686,008 - 15,689,325 (-)Ensemblrn6Rnor6.0
Rnor_5.01015,581,143 - 15,584,474 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41015,667,569 - 15,671,373 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1015,087,966 - 15,091,305 (-)NCBICelera
RGSC_v3.11015,668,617 - 15,672,420 (-)NCBI
Cytogenetic Map10q12NCBI
SNRNP25
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381653,828 - 57,669 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1653,828 - 57,669 (+)Ensemblhg38GRCh38
GRCh3716103,828 - 107,669 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361643,017 - 47,444 (+)NCBIBuild 36Build 36hg18NCBI36
Build 341643,016 - 47,443NCBI
Celera16305,723 - 309,564 (+)NCBICelera
Cytogenetic Map16p13.3NCBI
HuRef1622,220 - 26,061 (+)NCBIHuRef
CHM1_116103,765 - 107,606 (+)NCBICHM1_1
T2T-CHM13v2.01647,364 - 51,206 (+)NCBIT2T-CHM13v2.0
Snrnp25
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391132,155,415 - 32,158,996 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1132,155,415 - 32,158,984 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm381132,205,415 - 32,208,996 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1132,205,415 - 32,208,984 (+)Ensemblmm10GRCm38
MGSCv371132,105,415 - 32,108,996 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv361132,105,415 - 32,108,984 (+)NCBIMGSCv36mm8
Celera1134,622,491 - 34,626,091 (+)NCBICelera
Cytogenetic Map11A4NCBI
cM Map1118.82NCBI
Snrnp25
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495544217,098,487 - 17,101,497 (-)Ensembl
ChiLan1.0NW_00495544217,098,487 - 17,101,497 (-)NCBIChiLan1.0ChiLan1.0
SNRNP25
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v218269,139 - 272,655 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1164,061,138 - 4,064,755 (+)NCBINHGRI_mPanPan1
PanPan1.11643,986 - 48,429 (+)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1643,986 - 48,418 (+)EnsemblpanPan2panpan1.1
SNRNP25
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1640,414,073 - 40,416,985 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl640,414,370 - 40,416,873 (-)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha641,677,090 - 41,679,884 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0640,757,101 - 40,759,895 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl640,757,398 - 40,759,901 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1640,444,657 - 40,447,447 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0640,405,584 - 40,408,374 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0640,884,769 - 40,887,563 (-)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Snrnp25
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024409344112,712,563 - 112,715,425 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936501805,861 - 813,367 (-)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_004936501810,423 - 813,273 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SNRNP25
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl341,568,041 - 41,571,642 (-)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1341,568,030 - 41,571,728 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2340,865,594 - 40,869,005 (+)NCBISscrofa10.2Sscrofa10.2susScr3
SNRNP25
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.159,643 - 14,514 (+)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366606831,210,403 - 31,215,573 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Snrnp25
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_004624913934,846 - 937,790 (+)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_004624913934,950 - 937,782 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
Snrnp25
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v193,675,131 - 3,678,437 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Snrnp25
29 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:58
Count of miRNA genes:52
Interacting mature miRNAs:57
Transcripts:ENSRNOT00000027989
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.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2313095Bss62Bone structure and strength QTL 621.50.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)10589381150893811Rat
631660Hcar1Hepatocarcinoma resistance QTL 13.40.0001liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)10666111835509383Rat
631564Apr3Acute phase response QTL 33.9blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)101577675460776754Rat
8662860Vetf10Vascular elastic tissue fragility QTL 10artery integrity trait (VT:0010639)number of ruptures of the internal elastic lamina of the abdominal aorta and iliac arteries (CMO:0002562)10666092373950353Rat
2313066Bss63Bone structure and strength QTL 631.40.0001tibia strength trait (VT:1000284)bone polar moment of inertia (CMO:0001558)10589381150893811Rat
631554Bp133Blood pressure QTL 1330.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)10125055464349221Rat
2313064Bmd71Bone mineral density QTL 710.90.0001tibia mineral mass (VT:1000283)compact volumetric bone mineral density (CMO:0001730)10589381150893811Rat
2301967Cm73Cardiac mass QTL 734.55heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)101499153586964295Rat
631268Cia21Collagen induced arthritis QTL 213.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1014991535107713808Rat
70223Bp57Blood pressure QTL 575arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)101465354159653541Rat
1354587Kidm21Kidney mass QTL 213.3kidney mass (VT:0002707)right kidney wet weight (CMO:0000082)101553301273695498Rat
1578761Stresp21Stress response QTL 213.3thymus mass (VT:0004954)thymus wet weight (CMO:0000855)10687714251877142Rat
2293680Bss40Bone structure and strength QTL 405.660.0001femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)10135730538Rat
7387235Uae41Urinary albumin excretion QTL 415.260.1874urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)10130004247Rat
2313104Bss61Bone structure and strength QTL 610.90.0001tibia area (VT:1000281)tibia midshaft cross-sectional area (CMO:0001717)10589381150893811Rat
61427Cia16Collagen induced arthritis QTL 163.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)10686461896620484Rat
10401803Kidm50Kidney mass QTL 50kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)1092219745922197Rat
2316949Gluco60Glucose level QTL 603.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1014991535107556066Rat
737820Alc9Alcohol consumption QTL 92.2consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)101576223019737486Rat
2317754Glom25Glomerulus QTL 253.5urine protein amount (VT:0005160)urine protein level (CMO:0000591)10210370847103708Rat
2313081Bss64Bone structure and strength QTL 641.30.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)10589381150893811Rat
631828Alc5Alcohol consumption QTL 52.4consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)10117749933Rat
634327Hc4Hypercalciuria QTL 42.4urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)10138832698Rat

Markers in Region
3300001G02Rik  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21015,422,672 - 15,423,679 (+)MAPPERmRatBN7.2
Rnor_6.01015,688,194 - 15,689,200NCBIRnor6.0
Rnor_5.01015,583,337 - 15,584,343UniSTSRnor5.0
RGSC_v3.41015,669,760 - 15,670,766UniSTSRGSC3.4
Celera1015,090,161 - 15,091,167UniSTS
Cytogenetic Map10q12UniSTS


Expression

RNA-SEQ Expression

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


Ensembl Acc Id: ENSRNOT00000027989   ⟹   ENSRNOP00000027989
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1015,924,940 - 15,928,252 (-)Ensembl
mRatBN7.2 Ensembl1015,420,486 - 15,423,804 (-)Ensembl
Rnor_6.0 Ensembl1015,686,008 - 15,689,325 (-)Ensembl
RefSeq Acc Id: NM_001398566   ⟹   NP_001385495
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81015,924,932 - 15,928,252 (-)NCBI
mRatBN7.21015,420,482 - 15,423,802 (-)NCBI
RefSeq Acc Id: XM_006246078   ⟹   XP_006246140
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81015,924,935 - 15,928,256 (-)NCBI
mRatBN7.21015,420,485 - 15,423,805 (-)NCBI
Rnor_6.01015,685,999 - 15,689,316 (-)NCBI
Rnor_5.01015,581,143 - 15,584,474 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008767620   ⟹   XP_008765842
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81015,926,420 - 15,928,257 (-)NCBI
mRatBN7.21015,422,022 - 15,423,806 (-)NCBI
Rnor_6.01015,687,537 - 15,689,316 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039087123   ⟹   XP_038943051
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81015,924,935 - 15,928,279 (-)NCBI
mRatBN7.21015,420,485 - 15,423,806 (-)NCBI
RefSeq Acc Id: XM_063268571   ⟹   XP_063124641
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81015,924,935 - 15,928,279 (-)NCBI
RefSeq Acc Id: XP_006246140   ⟸   XM_006246078
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_008765842   ⟸   XM_008767620
- Peptide Label: isoform X1
- Sequence:
Ensembl Acc Id: ENSRNOP00000027989   ⟸   ENSRNOT00000027989
RefSeq Acc Id: XP_038943051   ⟸   XM_039087123
- Peptide Label: isoform X4
RefSeq Acc Id: NP_001385495   ⟸   NM_001398566
- UniProtKB: D3ZE11 (UniProtKB/TrEMBL),   A6HDB5 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063124641   ⟸   XM_063268571
- Peptide Label: isoform X3
Protein Domains
SNRNP25 ubiquitin-like

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZE11-F1-model_v2 AlphaFold D3ZE11 1-123 view protein structure

Transcriptome

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

Promoters
RGD ID:13697095
Promoter ID:EPDNEW_R7605
Type:multiple initiation site
Name:Snrnp25_1
Description:small nuclear ribonucleoprotein U11/U12 subunit 25
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_6.01015,689,312 - 15,689,372EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1310922 AgrOrtholog
BioCyc Gene G2FUF-25696 BioCyc
Ensembl Genes ENSRNOG00000020626 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000027989.9 UniProtKB/TrEMBL
Gene3D-CATH Phosphatidylinositol 3-kinase Catalytic Subunit, Chain A, domain 1 UniProtKB/TrEMBL
InterPro SNRNP25 UniProtKB/TrEMBL
  SNRNP25_ubiquitin UniProtKB/TrEMBL
  Ubiquitin-rel_dom UniProtKB/TrEMBL
NCBI Gene 287170 ENTREZGENE
PANTHER PTHR14942 UniProtKB/TrEMBL
  U11/U12 SMALL NUCLEAR RIBONUCLEOPROTEIN 25 KDA PROTEIN UniProtKB/TrEMBL
Pfam Ubiquitin_4 UniProtKB/TrEMBL
PhenoGen Snrnp25 PhenoGen
RatGTEx ENSRNOG00000020626 RatGTEx
Superfamily-SCOP SSF54236 UniProtKB/TrEMBL
UniProt A6HDB5 ENTREZGENE, UniProtKB/TrEMBL
  D3ZE11 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-03-16 Snrnp25  small nuclear ribonucleoprotein U11/U12 subunit 25  Snrnp25  small nuclear ribonucleoprotein 25 (U11/U12)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2010-04-23 Snrnp25  small nuclear ribonucleoprotein 25 (U11/U12)  RGD1310922  similar to chromosome 16 open reading frame 33; minus -99 protein  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 RGD1310922  similar to chromosome 16 open reading frame 33; minus -99 protein   RGD1310922_predicted  similar to chromosome 16 open reading frame 33; minus -99 protein (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-20 RGD1310922_predicted  similar to chromosome 16 open reading frame 33; minus -99 protein (predicted)  LOC287170_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC287170_predicted  similar to chromosome 16 open reading frame 33; minus -99 protein (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL