Scarna6 (small Cajal body-specific RNA 6) - Rat Genome Database

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Gene: Scarna6 (small Cajal body-specific RNA 6) Mus musculus
Analyze
Symbol: Scarna6
Name: small Cajal body-specific RNA 6
RGD ID: 2303932
MGI Page MGI
Description: INTERACTS WITH bisphenol A; choline; paracetamol
Type: ncrna (Ensembl: scaRNA)
RefSeq Status: PROVISIONAL
Previously known as: MBI-4; MBI-46
RGD Orthologs
Human
Rat
Dog
Alliance Genes
More Info more info ...
Latest Assembly: GRCm39 - Mouse Genome Assembly GRCm39
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39187,712,293 - 87,712,540 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl187,712,278 - 87,712,542 (+)EnsemblGRCm39 Ensembl
GRCm38187,784,571 - 87,784,818 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl187,784,556 - 87,784,820 (+)EnsemblGRCm38mm10GRCm38
MGSCv37189,681,146 - 89,681,393 (+)NCBIGRCm37MGSCv37mm9NCBIm37
Celera190,742,502 - 90,742,749 (+)NCBICelera
Cytogenetic Map1DNCBI
cM Map144.44NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


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

Biological Process

Cellular Component

Molecular Function

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:11387227   PMID:11424213  


Genomics

Comparative Map Data
Scarna6
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39187,712,293 - 87,712,540 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl187,712,278 - 87,712,542 (+)EnsemblGRCm39 Ensembl
GRCm38187,784,571 - 87,784,818 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl187,784,556 - 87,784,820 (+)EnsemblGRCm38mm10GRCm38
MGSCv37189,681,146 - 89,681,393 (+)NCBIGRCm37MGSCv37mm9NCBIm37
Celera190,742,502 - 90,742,749 (+)NCBICelera
Cytogenetic Map1DNCBI
cM Map144.44NCBI
SCARNA6
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382233,288,676 - 233,288,941 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl2233,288,676 - 233,288,940 (+)EnsemblGRCh38hg38GRCh38
GRCh372234,197,322 - 234,197,587 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 362233,862,061 - 233,862,326 (+)NCBINCBI36Build 36hg18NCBI36
Celera2227,918,838 - 227,919,103 (+)NCBICelera
Cytogenetic Map2q37.1NCBI
HuRef2225,998,093 - 225,998,358 (+)NCBIHuRef
CHM1_12234,203,403 - 234,203,668 (+)NCBICHM1_1
T2T-CHM13v2.02233,776,759 - 233,777,024 (+)NCBIT2T-CHM13v2.0
Scarna6
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8995,898,409 - 95,898,671 (+)NCBIGRCr8
mRatBN7.2988,450,584 - 88,450,846 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl988,450,584 - 88,450,846 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.0 Ensembl994,908,287 - 94,908,549 (+)NCBIRnor6.0rn6Rnor6.0
Cytogenetic Map9q35NCBI
LOC119866042
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Dog10K_Boxer_Tasha2545,289,042 - 45,289,266 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02545,053,575 - 45,053,799 (+)NCBIROS_Cfam_1.0
UMICH_Zoey_3.12544,977,956 - 44,978,180 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02544,823,930 - 44,824,154 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02544,979,154 - 44,979,378 (+)NCBIUU_Cfam_GSD_1.0

Variants

.
Variants in Scarna6
9 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:97
Count of miRNA genes:95
Interacting mature miRNAs:96
Transcripts:ENSMUST00000158656
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 (GRCm39)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
13824984Twq5_mtestis weight QTL 5 (mouse)13069992184732197Mouse
11039528Ccc3_mcolitis susceptibility in the Collaborative Cross 3 (mouse)13680142195051546Mouse
1357753Kidq2_mkidney weight QTL 2 (mouse)Not determined134760138150193871Mouse
1357488Splq3_mspleen weight QTL 3 (mouse)Not determined134760138150193871Mouse
1558860W10q7_mweight 10 weeks QTL 7 (mouse)Not determined134760138150193871Mouse
1357721Sle17_msystematic lupus erythematosus susceptibility 17 (mouse)Not determined139132808126445310Mouse
1301722Cia9_mcollagen induced arthritis QTL 9 (mouse)Not determined145783900189303617Mouse
4142291Aec2_mautoimmune exocrinopathy 2 (mouse)Not determined52457737182250592Mouse
1357741Nidd5k_mNidd5 on KK-A<y> (mouse)Not determined15597494889975057Mouse
4142467Wbcq1_mwhite blood cell quantitative locus 1 (mouse)Not determined15626621490266360Mouse
1357505Vtbt1_mvertebral trabecular bone trait 1 (mouse)Not determined15626621490266360Mouse
1558717Ses1a_msalmonella enteritidis susceptibility 1a (mouse)Not determined15672692290727077Mouse
1301933Insq6_minsulin QTL 6 (mouse)Not determined15672692290727077Mouse
14746998Mancz1_mmandible centroid size 1 (mouse)15794135191941351Mouse
14747009Manh49_mmandible shape 49 (mouse)15794135191941351Mouse
1300746Skl1_mskeletal size (tail length) 1 (mouse)Not determined15799197791992080Mouse
1357679Egrm1_mearly growth rate, maternal effect 1 (mouse)Not determined15799197791992080Mouse
1301162Skull1_mskull morphology 1 (mouse)Not determined15799197791992080Mouse
1301667Lxw5_mlupus BXSB x NZW 5 (mouse)Not determined15854919192549443Mouse
1301444Alcw5_malcohol withdrawal 5 (mouse)Not determined15854919192549443Mouse
1301748Abbp1_mA/J and C57BL/6 blood pressure 1 (mouse)Not determined162946755120529678Mouse
10412185Hcs9_mhepatocarcinogenesis susceptibility 9 (mouse)Not determined163854690189303617Mouse
1300841Ssial1_msusceptibility to sialadenitis 1 (mouse)Not determined163920002153557562Mouse
1302119Cia15_mcollagen induced arthritis 15 (mouse)Not determined16588900688496101Mouse
27095918Ulnl1_mulna length 1, 5 week (mouse)167339159129727737Mouse
1302146Cocrb1_mcocaine related behavior 1 (mouse)Not determined170133533104139557Mouse
1300976Bmd19_mbone mineral density 19 (mouse)Not determined173266214108838414Mouse
4142394Mssq1_mmandible size and shape QTL 1 (mouse)Not determined73615692107615830Mouse
1301304Hrq3_mheart rate quantitative locus 3 (mouse)Not determined173615692107615830Mouse
1300989Lrdg1_mlight induced retinal degeneration 1 (mouse)Not determined173755175147125370Mouse
4141914Gcsfis_mG-CSF induced splenomegaly (mouse)Not determined74516235148715579Mouse
1357847Jckm2_mjuvenile cystic kidney modifier 2 (mouse)Not determined174991977133290937Mouse
1300821Lore1_mloss of righting induced by ethanol 1 (mouse)Not determined17554919192941077Mouse
27095931Pglq1_mpelvic girdle length QTL 1, 5 week (mouse)175976637128527737Mouse
27095928Pglq6_mpelvic girdle length QTL 6, 10 week (mouse)175976637148775742Mouse
26884448Sklq1_mskull length QTL 1, 5 week (mouse)175976637181327565Mouse
1558928Mord2_mmodifier of retinal degeneration 2 (mouse)Not determined177123115110536075Mouse
14697706Stsl3a_mSalmonella typhimurium susceptibility locus 3a (mouse)17747663795827725Mouse
14696691Malq1_mmean attack latency QTL 1 (mouse)17797663787927722Mouse
14696693Avd2q1_mattack value day 2 QTL 1 (mouse)17897771790927722Mouse
4141725Wbcq4_mwhite blood cell quantitative locus 4 (mouse)Not determined179858683113858791Mouse
12050069Nabq1_mnasal bone morphology QTL 1 (mouse)179858683113858791Mouse
13452395Leusq2_mleucocytosis susceptibility QTL 2 (mouse)180245593126386517Mouse
14696692Tavq1_mtotal attack value QTL 1 (mouse)18197771588427722Mouse
1301350Nidd4k_mNidd4 on KK-A (mouse)Not determined782291982147125370Mouse
1357439Popoa_mpremature ovulation and primary oocyte arrest (mouse)Not determined182643189135615379Mouse
10412238Alpq5_malcohol preference QTL 5 (mouse)Not determined182832635116832635Mouse
12791004Aath7_maortic arch atherosclerosis 7 (mouse)182832635116832635Mouse
25394564Skmw49_mskeletal muscle weight 49, TA (mouse)18342011988552630Mouse
11667074Led2_mlate embryonic death 2 (mouse)185696027117195081Mouse
12790991Aath1_maortic arch atherosclerosis 1 (mouse)186483929120483929Mouse


Expression


Sequence


Reference Sequences
RefSeq Acc Id: ENSMUST00000158656
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl187,712,278 - 87,712,542 (+)Ensembl
GRCm38.p6 Ensembl187,784,556 - 87,784,820 (+)Ensembl
RefSeq Acc Id: NR_028519
RefSeq Status: PROVISIONAL
Type: NON-CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39187,712,293 - 87,712,540 (+)NCBI
GRCm38187,784,571 - 87,784,818 (+)ENTREZGENE
MGSCv37189,681,146 - 89,681,393 (+)RGD
Celera190,742,502 - 90,742,749 (+)RGD
cM Map1 ENTREZGENE
Sequence:
Promoters
RGD ID:6874388
Promoter ID:EPDNEW_M645
Type:single initiation site
Name:Scarna6_1
Description:Mus musculus small Cajal body-specific RNA 6 , guide RNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38187,784,557 - 87,784,617EPDNEW

Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSMUSG00000089281 Ensembl, ENTREZGENE
Ensembl Transcript ENSMUST00000158656 ENTREZGENE
MGD MGI:3819487 ENTREZGENE
NCBI Gene 100217415 ENTREZGENE
PhenoGen Scarna6 PhenoGen
RNAcentral URS000075DE2F RNACentral