Snhg11 (small nucleolar RNA host gene 11) - Rat Genome Database

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Gene: Snhg11 (small nucleolar RNA host gene 11) Rattus norvegicus
Analyze
Symbol: Snhg11
Name: small nucleolar RNA host gene 11
RGD ID: 1563912
Description: Orthologous to human SNHG11 (small nucleolar RNA host gene 11); INTERACTS WITH 17alpha-ethynylestradiol; 17beta-estradiol; 2,2',4,4'-Tetrabromodiphenyl ether.
Type: ncrna (Ensembl: protein-coding)
RefSeq Status: VALIDATED
Previously known as: hypothetical LOC362256; LOC362256; MGC105739; RGD1563912; small nucleolar RNA host gene 11 (non-protein coding)
RGD Orthologs
Human
Mouse
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr83167,451,272 - 167,456,945 (+)NCBIGRCr8
mRatBN7.23147,031,367 - 147,037,043 (+)NCBImRatBN7.2mRatBN7.2
UTH_Rnor_SHR_Utx3150,863,894 - 150,869,552 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.03159,363,183 - 159,368,841 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.03157,097,817 - 157,103,492 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.03154,862,717 - 154,870,691 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl3154,863,072 - 154,869,460 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.03160,735,811 - 160,743,513 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.43149,094,213 - 149,102,475 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera3145,732,450 - 145,738,729 (+)NCBICelera
Cytogenetic Map3q42NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:12477932   PMID:15632090  


Genomics

Comparative Map Data
Snhg11
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr83167,451,272 - 167,456,945 (+)NCBIGRCr8
mRatBN7.23147,031,367 - 147,037,043 (+)NCBImRatBN7.2mRatBN7.2
UTH_Rnor_SHR_Utx3150,863,894 - 150,869,552 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.03159,363,183 - 159,368,841 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.03157,097,817 - 157,103,492 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.03154,862,717 - 154,870,691 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl3154,863,072 - 154,869,460 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.03160,735,811 - 160,743,513 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.43149,094,213 - 149,102,475 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera3145,732,450 - 145,738,729 (+)NCBICelera
Cytogenetic Map3q42NCBI
SNHG11
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382038,446,654 - 38,450,921 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl2038,446,343 - 38,450,940 (+)EnsemblGRCh38hg38GRCh38
GRCh372037,075,297 - 37,079,564 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 362036,508,711 - 36,512,978 (+)NCBINCBI36Build 36hg18NCBI36
Celera2033,784,102 - 33,788,368 (+)NCBICelera
Cytogenetic Map20q11.23NCBI
HuRef2033,810,350 - 33,814,618 (+)NCBIHuRef
CHM1_12036,979,038 - 36,983,306 (+)NCBICHM1_1
T2T-CHM13v2.02040,174,250 - 40,178,518 (+)NCBIT2T-CHM13v2.0
Snhg11
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm392158,217,633 - 158,228,394 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl2158,217,558 - 158,228,071 (+)EnsemblGRCm39 Ensembl
GRCm382158,375,713 - 158,386,474 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl2158,375,638 - 158,386,145 (+)EnsemblGRCm38mm10GRCm38
GRCm38.p6 Ensembl2158,375,638 - 158,386,151 (+)EnsemblGRCm38mm10GRCm38
MGSCv372158,201,374 - 158,211,881 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv362158,067,123 - 158,073,031 (+)NCBIMGSCv36mm8
Celera2164,312,074 - 164,322,582 (+)NCBICelera
Cytogenetic Map2H1NCBI
cM Map278.72NCBI

Variants

.
Variants in Snhg11
48 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:432
Count of miRNA genes:229
Interacting mature miRNAs:273
Transcripts:ENSRNOT00000055200
Prediction methods:Microtar, Miranda
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
70216Cm14Cardiac mass QTL 142.1heart mass (VT:0007028)heart wet weight (CMO:0000069)331172320163586636Rat
2301970Bw81Body weight QTL 815.19body mass (VT:0001259)body weight (CMO:0000012)341874578155617519Rat
2301971Cm71Cardiac mass QTL 714.63heart left ventricle mass (VT:0007031)heart left ventricle weight (CMO:0000776)341874578155617519Rat
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
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
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
631841Niddm39Non-insulin dependent diabetes mellitus QTL 393.36blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)394856903159898684Rat
2293087Iddm27Insulin dependent diabetes mellitus QTL 272.68blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)397551417147415807Rat
2312659Slep7Serum leptin concentration QTL 70.001blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)398535255168026850Rat
2312670Bw94Body weight QTL 940.01inguinal fat pad mass (VT:0010424)inguinal fat pad weight to body weight ratio (CMO:0001253)398535255168026850Rat
2312673Scl63Serum cholesterol level QTL 630.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)398535255168026850Rat
2302373Gluco39Glucose level QTL 395.01blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)398535386161695835Rat
619618Rf3Renal disease susceptibility QTL 36.50.001urine albumin amount (VT:0002871)urine albumin excretion rate to body weight ratio (CMO:0001270)3107693393152693393Rat
1578754Stresp16Stress response QTL 1640.001blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)3112681431157681431Rat
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
1598877Bp285Blood pressure QTL 2851.50.03arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3120538241165538241Rat
1300159Kidm4Kidney mass QTL 43.83kidney mass (VT:0002707)right kidney wet weight to body weight ratio (CMO:0001953)3121056165157309487Rat
10755461Coatc16Coat color QTL 16coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)3122438700167438700Rat
631541Bp81Blood pressure QTL 814arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3124122556169034231Rat
2303620Vencon4Ventilatory control QTL 43.9respiration trait (VT:0001943)tidal volume (CMO:0000222)3127162703168026850Rat
631673Iddm13Insulin dependent diabetes mellitus QTL 131.30.663blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)3130193298161695983Rat
1578656Vnigr2Vascular neointimal growth QTL 24.2artery morphology trait (VT:0002191)lesioned artery residual lumen area (CMO:0001417)3130656562169034231Rat
1578653Vnigr3Vascular neointimal growth QTL 33.1artery morphology trait (VT:0002191)artery neointimal hyperplastic lesion area (CMO:0001414)3130656562169034231Rat
9589106Insul23Insulin level QTL 2313.860.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)3131635904169034231Rat
2298477Eau4Experimental allergic uveoretinitis QTL 40.0011uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)3137398739169034231Rat
8552952Pigfal13Plasma insulin-like growth factor 1 level QTL 13blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)3138799500169034231Rat
1298068Bp167Blood pressure QTL 1670.004arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3141074471169034231Rat
1331726Bp208Blood pressure QTL 2083.129arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)3141339013162184794Rat
61335Bp20Blood pressure QTL 203arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3141339236155617360Rat
2317883Alcrsp26Alcohol response QTL 261.80.63response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)3145526770169034231Rat
12879871Am7Aortic mass QTL 70.001aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)3145925360166177555Rat
12879872Cm97Cardiac mass QTL 970.001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)3145925360166177555Rat
12879873Cm96Cardiac mass QTL 960.001heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)3145925360166177555Rat
12879874Cm98Cardiac mass QTL 980.005heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)3145925360166177555Rat
12879875Kidm64Kidney mass QTL 640.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)3145925360166177555Rat
12879876Bw182Body weight QTL 1820.003body mass (VT:0001259)body weight (CMO:0000012)3145925360166177555Rat
2301411Bp320Blood pressure QTL 3200.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)3145925360166177555Rat
1300113Bp176Blood pressure QTL 1763.9arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)3145956084157309487Rat
1598854Memor10Memory QTL 102exploratory behavior trait (VT:0010471)average horizontal distance between subject and target during voluntary locomotion in an experimental apparatus (CMO:0002674)3145956084161299569Rat
8552791Vie2Viral induced encephalitis QTL 24.1brain integrity trait (VT:0010579)encephalitis incidence/prevalence measurement (CMO:0002361)3145956084169034231Rat

Markers in Region
RH143181  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.23147,034,341 - 147,034,494 (+)MAPPERmRatBN7.2
Rnor_6.03154,866,005 - 154,866,157NCBIRnor6.0
Rnor_5.03160,740,311 - 160,740,463UniSTSRnor5.0
RGSC_v3.43149,097,698 - 149,097,850UniSTSRGSC3.4
Celera3145,735,263 - 145,735,415UniSTS
RH 3.4 Map31357.1UniSTS
Cytogenetic Map3q42UniSTS


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 9 4 4 60 12 11 4
Low 3 4 20 9 8 9 14 23 27 7
Below cutoff 26 25 25 8 25 8 9 3 8

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000055200   ⟹   ENSRNOP00000052073
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl3154,863,072 - 154,869,460 (+)Ensembl
RefSeq Acc Id: NR_172014
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83167,451,272 - 167,456,945 (+)NCBI
mRatBN7.23147,031,367 - 147,037,043 (+)NCBI
Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q52KR9-F1-model_v2 AlphaFold Q52KR9 1-86 view protein structure

Transcriptome

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

Promoters
RGD ID:13692621
Promoter ID:EPDNEW_R3145
Type:multiple initiation site
Name:Snhg11_1
Description:small nucleolar RNA host gene 11
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_6.03154,863,004 - 154,863,064EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1563912 AgrOrtholog
BioCyc Gene G2FUF-47022 BioCyc
Ensembl Genes ENSRNOG00000036802 Ensembl
IMAGE_CLONE IMAGE:7314456 IMAGE-MGC_LOAD
KEGG Report rno:362256 UniProtKB/TrEMBL
MGC_CLONE MGC:105739 IMAGE-MGC_LOAD
NCBI Gene 362256 ENTREZGENE
PhenoGen Snhg11 PhenoGen
RatGTEx ENSRNOG00000036802 RatGTEx
RNAcentral URS00021EDA6C RNACentral
UniProt Q52KR9_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-02-25 Snhg11  small nucleolar RNA host gene 11  Snhg11  small nucleolar RNA host gene 11 (non-protein coding)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2012-02-02 Snhg11  small nucleolar RNA host gene 11 (non-protein coding)  Snhg11  small nucleolar RNA host gene 11  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2010-09-14 Snhg11  small nucleolar RNA host gene 11  RGD1563912  RGD1563912  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 RGD1563912  RGD1563912   RGD1563912_predicted  RGD1563912 (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-07 RGD1563912_predicted  RGD1563912 (predicted)  LOC362256  hypothetical LOC362256  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC362256  hypothetical LOC362256      Symbol and Name status set to provisional 70820 PROVISIONAL