Rnu1-39 (RNA, U1 small nuclear 39) - Rat Genome Database

Send us a Message
Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Search RGD Grant Resources Citing RGD About Us Contact Us
Genes Variants Community Projects QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Synteny Browser (VCMap) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) AllianceMine GViewer (Genome Viewer)
Aging & Age-Related Disease Behavioral & Substance Use Disorder Cancer & Neoplastic Disease Cardiovascular Disease Coronavirus Disease Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease
Find Models Genetic Models Autism Models Rat PhenoMiner (Quantitative Phenotypes) Chinchilla PhenoMiner Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive
Pathways
Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Presentations Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
Advanced Search (OLGA)
Gene: Rnu1-39 (RNA, U1 small nuclear 39) Rattus norvegicus
Analyze
Symbol: Rnu1-39
Name: RNA, U1 small nuclear 39
RGD ID: 41018009
Description: Orthologous to human RNU1-44P (RNA, U1 small nuclear 44, pseudogene).
Type: snrna
RefSeq Status: MODEL
Previously known as: LOC120102012; U1; U1 spliceosomal RNA
RGD Orthologs
Human
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr83156,711,060 - 156,711,225 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl3156,711,060 - 156,711,225 (+)EnsemblGRCr8
mRatBN7.23136,257,921 - 136,258,086 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl3136,257,921 - 136,258,086 (+)EnsemblmRatBN7.2
Rnor_6.0 Ensembl3143,142,565 - 143,142,745 (+)NCBIrn6Rnor6.0
Cytogenetic Map3q41NCBI
JBrowse:




References

Genomics

Comparative Map Data
Rnu1-39
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr83156,711,060 - 156,711,225 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl3156,711,060 - 156,711,225 (+)EnsemblGRCr8
mRatBN7.23136,257,921 - 136,258,086 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl3136,257,921 - 136,258,086 (+)EnsemblmRatBN7.2
Rnor_6.0 Ensembl3143,142,565 - 143,142,745 (+)NCBIrn6Rnor6.0
Cytogenetic Map3q41NCBI
RNU1-100P
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh383142,420,205 - 142,420,369 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl3142,420,205 - 142,420,369 (-)Ensemblhg38GRCh38
GRCh373142,139,047 - 142,139,211 (-)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map3q23NCBI
CHM1_13142,102,067 - 142,102,231 (-)NCBICHM1_1
T2T-CHM13v2.03145,167,487 - 145,167,651 (-)NCBIT2T-CHM13v2.0

Variants

.
Variants in Rnu1-39
1 total Variants

QTLs in Region (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2312673Scl63Serum cholesterol level QTL 630.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)398535255168026850Rat
1578653Vnigr3Vascular neointimal growth QTL 33.1artery morphology trait (VT:0002191)artery neointimal hyperplastic lesion area (CMO:0001414)3130656562169034231Rat
1598877Bp285Blood pressure QTL 2851.50.03arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3120538241165538241Rat
2302373Gluco39Glucose level QTL 395.01blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)398535386161695835Rat
70216Cm14Cardiac mass QTL 142.1heart mass (VT:0007028)heart wet weight (CMO:0000069)331172320163586636Rat
2292591Esta4Estrogen-induced thymic atrophy QTL 4thymus mass (VT:0004954)thymus wet weight (CMO:0000855)347233211147415807Rat
1581568Rf53Renal function QTL 53urine total protein amount (VT:0000032)urine protein excretion rate to body weight ratio (CMO:0001099)356395968161299569Rat
1578754Stresp16Stress response QTL 1640.001blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)3112681431157681431Rat
1300173Rf11Renal function QTL 113.38renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)3121056165145956249Rat
9589106Insul23Insulin level QTL 2313.860.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)3131635904169034231Rat
8694437Bw167Body weight QTL 16722.460.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)391797474136797474Rat
10755461Coatc16Coat color QTL 16coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)3122438700167438700Rat
8662816Vetf4Vascular elastic tissue fragility QTL 44renal artery integrity trait (VT:0010642)number of ruptures of the internal elastic lamina of the renal arteries (CMO:0002563)359242096157323038Rat
1559282Emca5Estrogen-induced mammary cancer QTL 53.9mammary gland integrity trait (VT:0010552)percentage of study population developing mammary tumors during a period of time (CMO:0000948)343827364169034231Rat
1354611Despr2Despair related QTL 23.030.0028locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)397084464142084464Rat
2303620Vencon4Ventilatory control QTL 43.9respiration trait (VT:0001943)tidal volume (CMO:0000222)3127162703168026850Rat
631841Niddm39Non-insulin dependent diabetes mellitus QTL 393.36blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)394856903159898684Rat
1576306Schws3Schwannoma susceptibility QTL 30.001nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)3118839124163839124Rat
619618Rf3Renal disease susceptibility QTL 36.50.001urine albumin amount (VT:0002871)urine albumin excretion rate to body weight ratio (CMO:0001270)3107693393152693393Rat
1300159Kidm4Kidney mass QTL 43.83kidney mass (VT:0002707)right kidney wet weight to body weight ratio (CMO:0001953)3121056165157309487Rat
631673Iddm13Insulin dependent diabetes mellitus QTL 131.30.663blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)3130193298161695983Rat
2312659Slep7Serum leptin concentration QTL 70.001blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)398535255168026850Rat
2301971Cm71Cardiac mass QTL 714.63heart left ventricle mass (VT:0007031)heart left ventricle weight (CMO:0000776)341874578155617519Rat
2301970Bw81Body weight QTL 815.19body mass (VT:0001259)body weight (CMO:0000012)341874578155617519Rat
1581546Pur13Proteinuria QTL 132.930.0335urine total protein amount (VT:0000032)urine protein excretion rate (CMO:0000759)378196190146592722Rat
1578656Vnigr2Vascular neointimal growth QTL 24.2artery morphology trait (VT:0002191)lesioned artery residual lumen area (CMO:0001417)3130656562169034231Rat
631541Bp81Blood pressure QTL 814arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3124122556169034231Rat
2312670Bw94Body weight QTL 940.01inguinal fat pad mass (VT:0010424)inguinal fat pad weight to body weight ratio (CMO:0001253)398535255168026850Rat
2293087Iddm27Insulin dependent diabetes mellitus QTL 272.68blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)397551417147415807Rat
724532Cm17Cardiac mass QTL 172heart mass (VT:0007028)calculated heart weight (CMO:0000073)395735366140735366Rat


Expression

RNA-SEQ Expression

mesenchyme
renal system
7 7

Sequence

Nucleotide Sequences
RefSeq Transcripts XR_005503055 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide JAXUCZ010000003 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Ensembl Acc Id: ENSRNOT00000086334
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl3156,711,060 - 156,711,225 (+)Ensembl
mRatBN7.2 Ensembl3136,257,921 - 136,258,086 (+)Ensembl
RefSeq Acc Id: XR_005503055
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83156,711,060 - 156,711,225 (+)NCBI
mRatBN7.23136,257,921 - 136,258,086 (+)NCBI
Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:41018009 AgrOrtholog
BioCyc Gene G2FUF-47488 BioCyc
Ensembl Genes ENSRNOG00000056116 Ensembl, ENTREZGENE
Ensembl Transcript ENSRNOT00000086334 ENTREZGENE
NCBI Gene LOC120102012 ENTREZGENE
PhenoGen Rnu1-39 PhenoGen
RatGTEx ENSRNOG00000056116 RatGTEx
RNAcentral URS000066964C RNACentral


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2022-06-02 Rnu1-39  RNA, U1 small nuclear 39  U1  U1 spliceosomal RNA  Data merged from RGD:15009987 737654 PROVISIONAL
2022-04-01 Rnu1-39  RNA, U1 small nuclear 39  LOC120102012  U1 spliceosomal RNA  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2021-01-27 LOC120102012  U1 spliceosomal RNA      Symbol and Name status set to provisional 70820 PROVISIONAL
2019-11-08 U1  U1 spliceosomal RNA      Symbol and Name status set to provisional 45752 PROVISIONAL