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: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr83167,451,272 - 167,456,945 (+)NCBIGRCr8GRCr8GRCr8
mRatBN7.23147,031,367 - 147,037,043 (+)NCBImRatBN7.2mRatBN7.2
UTH_Rnor_SHR_Utx3150,863,894 - 150,869,552 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.03159,363,183 - 159,368,841 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.03157,097,817 - 157,103,492 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.03154,862,717 - 154,870,691 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl3154,863,072 - 154,869,460 (+)Ensemblrn6Rnor6.0
Rnor_5.03160,735,811 - 160,743,513 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.43149,094,213 - 149,102,475 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera3145,732,450 - 145,738,729 (+)NCBICelera
Cytogenetic Map3q42NCBI
JBrowse:




Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,1-dichloroethene  (ISO)
1,2-dimethylhydrazine  (ISO)
1-benzofuran  (ISO)
17alpha-ethynylestradiol  (EXP)
17beta-estradiol  (EXP)
2,2',4,4'-Tetrabromodiphenyl ether  (EXP)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4-dibromophenyl 2,4,5-tribromophenyl ether  (ISO)
4,4'-sulfonyldiphenol  (ISO)
4-hydroxyphenyl retinamide  (ISO)
all-trans-retinoic acid  (ISO)
alpha-Zearalanol  (EXP)
aristolochic acid A  (ISO)
atrazine  (ISO)
benzo[a]pyrene  (ISO)
benzo[b]fluoranthene  (ISO)
Benzo[ghi]perylene  (ISO)
Benzo[k]fluoranthene  (ISO)
beta-lapachone  (ISO)
bis(2-ethylhexyl) phthalate  (EXP,ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
buta-1,3-diene  (ISO)
Butylbenzyl phthalate  (EXP)
cadmium dichloride  (EXP,ISO)
carbon nanotube  (ISO)
chloroprene  (EXP)
copper(II) sulfate  (ISO)
Cuprizon  (EXP)
DDT  (ISO)
dibutyl phthalate  (EXP)
diethyl phthalate  (EXP)
diisobutyl phthalate  (EXP)
diisononyl phthalate  (EXP)
dioxygen  (ISO)
diuron  (EXP)
fenvalerate  (EXP)
folic acid  (ISO)
gentamycin  (EXP)
graphene oxide  (ISO)
methyl methanesulfonate  (ISO)
N-nitrosodiethylamine  (ISO)
naphthalene-1,5-diamine  (ISO)
nitrofen  (EXP)
ozone  (ISO)
paracetamol  (ISO)
paraquat  (EXP)
pentachlorophenol  (ISO)
perfluorooctane-1-sulfonic acid  (ISO)
perfluorooctanoic acid  (EXP)
phenobarbital  (ISO)
pirinixic acid  (ISO)
quercetin  (ISO)
sodium arsenate  (ISO)
sodium arsenite  (ISO)
sulforaphane  (ISO)
temozolomide  (ISO)
tetrachloromethane  (ISO)
tetraphene  (ISO)
troglitazone  (ISO)
tunicamycin  (ISO)
valproic acid  (ISO)
vinclozolin  (EXP)

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 (+)NCBIGRCr8GRCr8GRCr8
mRatBN7.23147,031,367 - 147,037,043 (+)NCBImRatBN7.2mRatBN7.2
UTH_Rnor_SHR_Utx3150,863,894 - 150,869,552 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.03159,363,183 - 159,368,841 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.03157,097,817 - 157,103,492 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.03154,862,717 - 154,870,691 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl3154,863,072 - 154,869,460 (+)Ensemblrn6Rnor6.0
Rnor_5.03160,735,811 - 160,743,513 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.43149,094,213 - 149,102,475 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
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 - 38,450,943 (+)Ensemblhg38GRCh38
GRCh372037,075,297 - 37,079,564 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 362036,508,711 - 36,512,978 (+)NCBIBuild 36Build 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 EnsemblGRCm39
GRCm382158,375,713 - 158,386,474 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl2158,375,638 - 158,386,145 (+)Ensemblmm10GRCm38
GRCm38.p6 Ensembl2158,375,638 - 158,386,151 (+)Ensemblmm10GRCm38
MGSCv372158,201,374 - 158,211,881 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv362158,067,123 - 158,073,031 (+)NCBIMGSCv36mm8
Celera2164,312,074 - 164,322,582 (+)NCBICelera
Cytogenetic Map2H1NCBI
cM Map278.72NCBI

Variants

.
Variants in Snhg11
33 total Variants
miRNA Target Status (No longer updated)

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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
12879876Bw182Body weight QTL 1820.003body mass (VT:0001259)body weight (CMO:0000012)3141555229186555229Rat
2301411Bp320Blood pressure QTL 3200.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)3141555229186555229Rat
1582233Insul10Insulin level QTL 105.40.0015blood insulin amount (VT:0001560)serum insulin level times blood glucose level (CMO:0002040)3133259579178259579Rat
1300113Bp176Blood pressure QTL 1763.9arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)3166376089177728348Rat
12879872Cm97Cardiac mass QTL 970.001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)3141555229186555229Rat
12879873Cm96Cardiac mass QTL 960.001heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)3141555229186555229Rat
1578653Vnigr3Vascular neointimal growth QTL 33.1artery morphology trait (VT:0002191)artery neointimal hyperplastic lesion area (CMO:0001414)3151075912189428310Rat
2302373Gluco39Glucose level QTL 395.01blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)3129154923182114333Rat
12879874Cm98Cardiac mass QTL 980.005heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)3141555229186555229Rat
12879875Kidm64Kidney mass QTL 640.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)3141555229186555229Rat
1298068Bp167Blood pressure QTL 1670.004arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3161492708189428310Rat
70216Cm14Cardiac mass QTL 142.1heart mass (VT:0007028)heart wet weight (CMO:0000069)351581665184004958Rat
2292591Esta4Estrogen-induced thymic atrophy QTL 4thymus mass (VT:0004954)thymus wet weight (CMO:0000855)367641776167835660Rat
8552791Vie2Viral induced encephalitis QTL 24.1brain integrity trait (VT:0010579)encephalitis incidence/prevalence measurement (CMO:0002361)3166376089189428310Rat
61335Bp20Blood pressure QTL 203arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3161799493176036425Rat
1578754Stresp16Stress response QTL 1640.001blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)3133134628178134628Rat
1331726Bp208Blood pressure QTL 2083.129arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)3161799270187311134Rat
1582213Insul6Insulin level QTL 63.70.0009blood insulin amount (VT:0001560)calculated serum insulin level (CMO:0000359)3155759447189428310Rat
1598854Memor10Memory QTL 102exploratory behavior trait (VT:0010471)average horizontal distance between subject and target during voluntary locomotion in an experimental apparatus (CMO:0002674)3166376089189428310Rat
9589106Insul23Insulin level QTL 2313.860.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)3152055202189428310Rat
10755461Coatc16Coat color QTL 16coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)3142898802187898802Rat
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)379649560177741895Rat
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)3145335553189428310Rat
2303620Vencon4Ventilatory control QTL 43.9respiration trait (VT:0001943)tidal volume (CMO:0000222)3125116475170116475Rat
1582256Insul9Insulin level QTL 94.40.0016blood insulin amount (VT:0001560)absolute change in serum insulin level (CMO:0002038)3155759447189428310Rat
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)3139299381184299381Rat
1300159Kidm4Kidney mass QTL 43.83kidney mass (VT:0002707)right kidney wet weight to body weight ratio (CMO:0001953)3141508991177728348Rat
2301971Cm71Cardiac mass QTL 714.63heart left ventricle mass (VT:0007031)heart left ventricle weight (CMO:0000776)3131036586176036586Rat
631673Iddm13Insulin dependent diabetes mellitus QTL 131.30.663blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)3137114333182114333Rat
1582248Insul7Insulin level QTL 73.90.0041blood insulin amount (VT:0001560)calculated serum insulin level (CMO:0000359)3155759447189428310Rat
2301970Bw81Body weight QTL 815.19body mass (VT:0001259)body weight (CMO:0000012)3131036586176036586Rat
1578666Vnigr1Vascular neointimal growth QTL 14.6artery morphology trait (VT:0002191)artery lumen area (CMO:0001409)3151075912189428310Rat
1578656Vnigr2Vascular neointimal growth QTL 24.2artery morphology trait (VT:0002191)lesioned artery residual lumen area (CMO:0001417)3151075912189428310Rat
12879871Am7Aortic mass QTL 70.001aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)3141555229186555229Rat
631541Bp81Blood pressure QTL 814arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3144575244189428310Rat
2293087Iddm27Insulin dependent diabetes mellitus QTL 272.68blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)3160357340167835660Rat

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

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
10 9 41 141 87 86 55 26 55 6 241 88 121 80 92 31 17 17

Sequence


Ensembl 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 Sequences
Ensembl Protein ENSRNOP00000107940.1
Ensembl Acc Id: ENSRNOP00000052073   ⟸   ENSRNOT00000055200

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
  ENSRNOG00000085106 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000143947.1 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7314456 IMAGE-MGC_LOAD
MGC_CLONE MGC:105739 IMAGE-MGC_LOAD
NCBI Gene 362256 ENTREZGENE
PhenoGen Snhg11 PhenoGen
RatGTEx ENSRNOG00000036802 RatGTEx
  ENSRNOG00000085106 RatGTEx
RNAcentral URS00021EDA6C RNACentral
UniProt A0ABK0LBB6_RAT UniProtKB/TrEMBL
  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