Snord54 (small nucleolar RNA, C/D box 54) - Rat Genome Database

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Gene: Snord54 (small nucleolar RNA, C/D box 54) Rattus norvegicus
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Symbol: Snord54
Name: small nucleolar RNA, C/D box 54
RGD ID: 41164745
Description: INTERACTS WITH (-)-epigallocatechin 3-gallate (ortholog); cisplatin (ortholog); potassium chromate (ortholog)
Type: snorna
RefSeq Status: MODEL
Previously known as: Gm24016; LOC120103360; predicted gene, 24016; small nucleolar RNA U54
RGD Orthologs
Human
Mouse
Dog
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8521,617,537 - 21,617,604 (-)NCBIGRCr8
mRatBN7.2516,819,945 - 16,820,012 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl516,819,945 - 16,820,012 (-)EnsemblmRatBN7.2 Ensembl
Rnor_6.0 Ensembl516,706,684 - 16,706,751 (-)NCBIRnor6.0rn6Rnor6.0
Cytogenetic Map5q12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


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

Genomics

Comparative Map Data
Snord54
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8521,617,537 - 21,617,604 (-)NCBIGRCr8
mRatBN7.2516,819,945 - 16,820,012 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl516,819,945 - 16,820,012 (-)EnsemblmRatBN7.2 Ensembl
Rnor_6.0 Ensembl516,706,684 - 16,706,751 (-)NCBIRnor6.0rn6Rnor6.0
Cytogenetic Map5q12NCBI
SNORD54
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38856,073,839 - 56,073,901 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl856,073,835 - 56,073,901 (-)EnsemblGRCh38hg38GRCh38
GRCh37856,986,398 - 56,986,460 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36857,148,952 - 57,149,014 (-)NCBINCBI36Build 36hg18NCBI36
Build 34857,148,951 - 57,149,014NCBI
Celera852,978,235 - 52,978,297 (-)NCBICelera
Cytogenetic Map8q12.1NCBI
HuRef852,453,885 - 52,453,947 (-)NCBIHuRef
CHM1_1857,037,839 - 57,037,901 (-)NCBICHM1_1
T2T-CHM13v2.0856,450,841 - 56,450,903 (-)NCBIT2T-CHM13v2.0
Gm24016
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3943,835,079 - 3,835,146 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl43,835,079 - 3,835,146 (-)EnsemblGRCm39 Ensembl
GRCm3843,835,079 - 3,835,146 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl43,835,079 - 3,835,146 (-)EnsemblGRCm38mm10GRCm38
Cytogenetic Map4A1NCBI
LOC119866815
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Dog10K_Boxer_Tasha297,801,791 - 7,801,857 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0297,563,372 - 7,563,438 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl297,563,372 - 7,563,438 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1297,576,758 - 7,576,824 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0297,709,624 - 7,709,690 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0297,986,489 - 7,986,555 (-)NCBIUU_Cfam_GSD_1.0


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1331756Rf34Renal function QTL 344.16275kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)5190450412Rat
70212Niddm25Non-insulin dependent diabetes mellitus QTL 253.54blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)51131345958Rat
1331771Rf35Renal function QTL 354.36965kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)572947086724018Rat
2312562Pur18Proteinuria QTL 182.60.001urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)5213896532656739Rat
1576314Eutr1Estrogen induced uterine response QTL 1uterus integrity trait (VT:0010575)pyometritis severity score (CMO:0002009)52138965166875058Rat
8662454Vetf3Vascular elastic tissue fragility QTL 327.4artery integrity trait (VT:0010639)number of ruptures of the internal elastic lamina of the abdominal aorta and iliac arteries (CMO:0002562)5228222669540447Rat
2313085Bss59Bone structure and strength QTL 592.90.0001long bone metaphysis morphology trait (VT:0000133)tibia midshaft total cross-sectional area (CMO:0001715)5384401826141981Rat
1300117Hrtrt8Heart rate QTL 83.49heart pumping trait (VT:2000009)heart rate (CMO:0000002)5384401847869213Rat
61462Niddm10Non-insulin dependent diabetes mellitus QTL 103.90.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)5511215947171491Rat
631827Alc4Alcohol consumption QTL 43.5consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)5818750118616199Rat
2293666Bmd38Bone mineral density QTL 384.4femur size trait (VT:1000369)femoral neck cortical cross-sectional area (CMO:0001702)5894822853948228Rat
7394712Emca13Estrogen-induced mammary cancer QTL 13mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)5982326699753708Rat
1641903Alcrsp3Alcohol response QTL 3response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)51268928557689285Rat
634305Mamtr1Mammary tumor resistance QTL 10.0001mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)512789751113558310Rat


Expression


Sequence

Nucleotide Sequences
RefSeq Transcripts XR_005505413 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide JAXUCZ010000005 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000085342
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl516,819,945 - 16,820,012 (-)Ensembl
RefSeq Acc Id: XR_005505413
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8521,617,537 - 21,617,604 (-)NCBI
mRatBN7.2516,819,945 - 16,820,012 (-)NCBI
Transcriptome

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


Additional Information

Database Acc Id Source(s)
BioCyc Gene G2FUF-42118 BioCyc
Ensembl Genes ENSRNOG00000059478 Ensembl, ENTREZGENE
Ensembl Transcript ENSRNOT00000085342 ENTREZGENE
NCBI Gene LOC120103360 ENTREZGENE
PhenoGen Snord54 PhenoGen
RatGTEx ENSRNOG00000059478 RatGTEx


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2022-06-02 Snord54  small nucleolar RNA, C/D box 54  Gm24016  predicted gene, 24016  Data merged from RGD:15012590 737654 PROVISIONAL
2021-12-23 Snord54  small nucleolar RNA, C/D box 54  LOC120103360  small nucleolar RNA U54  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2021-01-27 LOC120103360  small nucleolar RNA U54      Symbol and Name status set to provisional 70820 PROVISIONAL
2019-11-08 Gm24016  predicted gene, 24016      Symbol and Name status set to provisional 45752 PROVISIONAL