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 cytosol; intercellular bridge; and nucleoplasm. Predicted to be part of U12-type spliceosomal complex. Orthologous to human SNRNP25 (small nuclear ribonucleoprotein U11/U12 subunit 25); INTERACTS WITH (+)-schisandrin B; 2,3,7,8-tetrachlorodibenzodioxine; 3-chloropropane-1,2-diol.
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
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21015,420,482 - 15,423,806 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1015,420,486 - 15,423,804 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1020,166,502 - 20,169,820 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.01019,655,395 - 19,658,713 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.01015,148,276 - 15,151,593 (-)NCBIRnor_WKY
Rnor_6.01015,685,999 - 15,689,338 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1015,686,008 - 15,689,325 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01015,581,143 - 15,584,474 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41015,667,569 - 15,671,373 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11015,668,617 - 15,672,420 (-)NCBI
Celera1015,087,966 - 15,091,305 (-)NCBICelera
Cytogenetic Map10q12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


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
mRatBN7.21015,420,482 - 15,423,806 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1015,420,486 - 15,423,804 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1020,166,502 - 20,169,820 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.01019,655,395 - 19,658,713 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.01015,148,276 - 15,151,593 (-)NCBIRnor_WKY
Rnor_6.01015,685,999 - 15,689,338 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1015,686,008 - 15,689,325 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01015,581,143 - 15,584,474 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41015,667,569 - 15,671,373 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11015,668,617 - 15,672,420 (-)NCBI
Celera1015,087,966 - 15,091,305 (-)NCBICelera
Cytogenetic Map10q12NCBI
SNRNP25
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381653,828 - 57,669 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl1653,828 - 57,669 (+)EnsemblGRCh38hg38GRCh38
GRCh3716103,828 - 107,669 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361643,017 - 47,444 (+)NCBINCBI36Build 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 Ensembl
GRCm381132,205,415 - 32,208,996 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1132,205,415 - 32,208,984 (+)EnsemblGRCm38mm10GRCm38
MGSCv371132,105,415 - 32,108,996 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361132,105,415 - 32,108,984 (+)NCBIMGSCv36mm8
Celera1134,622,491 - 34,626,091 (+)NCBICelera
Cytogenetic Map11A4NCBI
Snrnp25
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495544217,098,487 - 17,101,497 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495544217,098,487 - 17,101,497 (-)NCBIChiLan1.0ChiLan1.0
SNRNP25
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11643,986 - 48,429 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1643,986 - 48,418 (+)Ensemblpanpan1.1panPan2
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 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha641,677,090 - 41,679,884 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0640,757,101 - 40,759,895 (-)NCBIROS_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_1.0
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
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 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
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_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_004624913934,950 - 937,782 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Snrnp25
14 total Variants
miRNA Target Status

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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
634329Pia15Pristane induced arthritis QTL 153.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)10124158324Rat
2293680Bss40Bone structure and strength QTL 405.660.0001femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)10135225947Rat
634327Hc4Hypercalciuria QTL 42.4urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)10138328221Rat
7411611Foco17Food consumption QTL 1718.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)10142315980Rat
70223Bp57Blood pressure QTL 575arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)10180676123Rat
10401803Kidm50Kidney mass QTL 50kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)1041834445418344Rat
631554Bp133Blood pressure QTL 1330.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1074336463851208Rat
1576304Schws7Schwannoma susceptibility QTL 70.0115nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)10476552719816042Rat
631828Alc5Alcohol consumption QTL 52.4consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)10514402717245662Rat
737820Alc9Alcohol consumption QTL 92.2consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)10514402719233348Rat
2313064Bmd71Bone mineral density QTL 710.90.0001tibia mineral mass (VT:1000283)cortical volumetric bone mineral density (CMO:0001730)10538701450387014Rat
2313066Bss63Bone structure and strength QTL 631.40.0001tibia strength trait (VT:1000284)bone polar moment of inertia (CMO:0001558)10538701450387014Rat
2313081Bss64Bone structure and strength QTL 641.30.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)10538701450387014Rat
2313095Bss62Bone structure and strength QTL 621.50.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)10538701450387014Rat
2313104Bss61Bone structure and strength QTL 610.90.0001tibia area (VT:1000281)tibia midshaft cross-sectional area (CMO:0001717)10538701450387014Rat
2298544Neuinf9Neuroinflammation QTL 94.6nervous system integrity trait (VT:0010566)spinal cord complement component 1, q subcomponent, B chain mRNA level (CMO:0002126)10580199062146030Rat
631660Hcar1Hepatocarcinoma resistance QTL 13.40.0001liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)10615418215990232Rat
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)10615418273453136Rat
61427Cia16Collagen induced arthritis QTL 163.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)10635789696121100Rat
1578761Stresp21Stress response QTL 213.3thymus mass (VT:0004954)thymus wet weight (CMO:0000855)10637574651375746Rat
2303118Mamtr7Mammary tumor resistance QTL 70.003mammary gland integrity trait (VT:0010552)mammary tumor growth rate (CMO:0000344)109658275104670812Rat
9590310Scort19Serum corticosterone level QTL 196.30.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)101147401056474010Rat
9590268Scort13Serum corticosterone level QTL 133.260.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)101147401056474010Rat
9589136Insul27Insulin level QTL 2710.460.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)101147401056474010Rat
2301967Cm73Cardiac mass QTL 734.55heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)101448701189062041Rat
631268Cia21Collagen induced arthritis QTL 213.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1014487011104060283Rat
2316949Gluco60Glucose level QTL 603.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1014487011107057807Rat
1354587Kidm21Kidney mass QTL 213.3kidney mass (VT:0002707)right kidney wet weight (CMO:0000082)101502851360430477Rat
631564Apr3Acute phase response QTL 33.9blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)101527595560275955Rat

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
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 57 41 19 41 8 11 74 35 41 11 8
Low 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000027989   ⟹   ENSRNOP00000027989
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1015,420,486 - 15,423,804 (-)Ensembl
Rnor_6.0 Ensembl1015,686,008 - 15,689,325 (-)Ensembl
RefSeq Acc Id: XM_006246078   ⟹   XP_006246140
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
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_006246079   ⟹   XP_006246141
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21015,420,482 - 15,423,806 (-)NCBI
Rnor_6.01015,686,000 - 15,689,338 (-)NCBI
Rnor_5.01015,581,143 - 15,584,474 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008767620   ⟹   XP_008765842
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
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
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21015,420,485 - 15,423,806 (-)NCBI
RefSeq Acc Id: XR_005490074
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21015,420,485 - 15,423,790 (-)NCBI
Reference Sequences
RefSeq Acc Id: XP_006246141   ⟸   XM_006246079
- Peptide Label: isoform X4
- UniProtKB: D3ZE11 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006246140   ⟸   XM_006246078
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_008765842   ⟸   XM_008767620
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000027989   ⟸   ENSRNOT00000027989
RefSeq Acc Id: XP_038943051   ⟸   XM_039087123
- Peptide Label: isoform X3
Protein Domains
Ubiquitin_4

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, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000027989 ENTREZGENE
  ENSRNOP00000027989.5 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000027989 ENTREZGENE
  ENSRNOT00000027989.8 UniProtKB/TrEMBL
InterPro SNRNP25 UniProtKB/TrEMBL
  SNRNP25_ubiquitin UniProtKB/TrEMBL
  Ubiquitin-rel_dom UniProtKB/TrEMBL
NCBI Gene 287170 ENTREZGENE
PANTHER PTHR14942 UniProtKB/TrEMBL
Pfam Ubiquitin_4 UniProtKB/TrEMBL
PhenoGen Snrnp25 PhenoGen
Superfamily-SCOP SSF54236 UniProtKB/TrEMBL
UniProt 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