Scarna16 (small Cajal body-specific RNA 16) - Rat Genome Database

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Gene: Scarna16 (small Cajal body-specific RNA 16) Rattus norvegicus
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Symbol: Scarna16 (Ensembl: LOC120095426)
Name: small Cajal body-specific RNA 16
RGD ID: 41249041
Description: Orthologous to human SCARNA16 (small Cajal body-specific RNA 16); INTERACTS WITH benzo[a]pyrene (ortholog); cisplatin (ortholog); doxorubicin (ortholog).
Type: ncrna (Ensembl: scaRNA)
RefSeq Status: MODEL
Previously known as: AABR07030841.2; Gm26083; LOC120095426; predicted gene, 26083
RGD Orthologs
Human
Mouse
Dog
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr85147,908,870 - 147,909,057 (-)NCBIGRCr8
mRatBN7.210102,276,365 - 102,276,548 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl10102,276,365 - 102,276,548 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.0 Ensembl10106,022,125 - 106,022,308 (+)NCBIRnor6.0rn6Rnor6.0
Cytogenetic Map10q32.2NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model



  
Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
Scarna16Ratbenzo[a]pyrene affects methylationISOSCARNA16 (Homo sapiens)6480464Benzo(a)pyrene affects the methylation of SCARNA16 promoterCTDPMID:27901495
Scarna16Ratcisplatin increases expressionISOSCARNA16 (Homo sapiens)6480464Cisplatin results in increased expression of SCARNA16 mRNACTDPMID:27392435
Scarna16Ratdoxorubicin increases expressionISOSCARNA16 (Homo sapiens)6480464Doxorubicin results in increased expression of SCARNA16 mRNACTDPMID:29803840
Scarna16Ratpicene increases expressionISOSCARNA16 (Homo sapiens)6480464picene results in increased expression of SCARNA16 mRNACTDPMID:32251684
Scarna16Ratresveratrol multiple interactionsISOSCARNA16 (Homo sapiens)6480464[Plant Extracts co-treated with Resveratrol] results in increased expression of SCARNA16 mRNACTDPMID:23557933



Scarna16
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr85147,908,870 - 147,909,057 (-)NCBIGRCr8
mRatBN7.210102,276,365 - 102,276,548 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl10102,276,365 - 102,276,548 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.0 Ensembl10106,022,125 - 106,022,308 (+)NCBIRnor6.0rn6Rnor6.0
Cytogenetic Map10q32.2NCBI
SCARNA16
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381777,089,307 - 77,089,493 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1777,089,307 - 77,089,493 (+)EnsemblGRCh38hg38GRCh38
GRCh371775,085,389 - 75,085,575 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361772,596,984 - 72,597,170 (+)NCBINCBI36Build 36hg18NCBI36
Celera1771,680,172 - 71,680,358 (+)NCBICelera
Cytogenetic Map17q25.2NCBI
HuRef1770,512,594 - 70,512,780 (+)NCBIHuRef
CHM1_11775,150,303 - 75,150,489 (+)NCBICHM1_1
T2T-CHM13v2.01777,982,158 - 77,982,344 (+)NCBIT2T-CHM13v2.0
Gm25434
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm396139,173,063 - 139,173,229 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl6139,173,063 - 139,173,229 (-)EnsemblGRCm39 Ensembl
GRCm386139,196,065 - 139,196,231 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl6139,196,065 - 139,196,231 (-)EnsemblGRCm38mm10GRCm38
Cytogenetic Map6G1NCBI
LOC119869911
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Dog10K_Boxer_Tasha1110,173,431 - 110,173,612 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01111,254,715 - 111,254,896 (+)NCBIROS_Cfam_1.0
UMICH_Zoey_3.11110,896,360 - 110,896,541 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01110,532,066 - 110,532,247 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01111,401,761 - 111,401,942 (+)NCBIUU_Cfam_GSD_1.0

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Variants in Scarna16
1 total Variants

1 to 10 of 56 rows
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD ID
Symbol
Name
LOD
P Value
Trait
Sub Trait
Chr
Start
Stop
Species
1354641Bvd2Brain ventricular dilatation QTL 26.360.001brain ventricle morphology trait (VT:0000822)hydrocephalus severity score (CMO:0001881)1093223816107057807Rat
61449Ciaa2CIA Autoantibody QTL 27.1blood autoantibody amount (VT:0003725)calculated serum anti-type 2 collagen antibody titer (CMO:0001279)1063221094107211142Rat
61325Aia5Adjuvant induced arthritis QTL 50.01joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023444813104060283Rat
1298078Stresp5Stress response QTL 52.990.00025blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)1042045676104670812Rat
1549831Bss6Bone structure and strength QTL 64lumbar vertebra strength trait (VT:0010574)vertebra ultimate force (CMO:0001678)1057576521102576521Rat
1579915Bp280Blood pressure QTL 2800.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1090404397107211142Rat
2298548Neuinf7Neuroinflammation QTL 73.4nervous system integrity trait (VT:0010566)spinal cord RT1-B protein level (CMO:0002132)1072224939107211142Rat
1302404Cia27Collagen induced arthritis QTL 272.60.0045joint integrity trait (VT:0010548)experimental arthritis severity measurement (CMO:0001459)1076452683107211142Rat
2317754Glom25Glomerulus QTL 253.5urine protein amount (VT:0005160)urine protein level (CMO:0000591)1082685200107211142Rat
70171Cari1Carrageenan-induced inflammation QTL 14.90.0005hypodermis integrity trait (VT:0010550)inflammatory exudate volume (CMO:0001429)1053797385107211142Rat

1 to 10 of 56 rows





RefSeq Transcripts XR_005505360 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide JAXUCZ010000005 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Ensembl Acc Id: ENSRNOT00000081692
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl10102,276,365 - 102,276,548 (+)Ensembl
RefSeq Acc Id: XR_005505360
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr85147,908,870 - 147,909,057 (-)NCBI

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



Database
Acc Id
Source(s)
BioCyc Gene G2FUF-22572 BioCyc
Ensembl Genes ENSRNOG00000061622 Ensembl
NCBI Gene LOC120095426 ENTREZGENE
PhenoGen Scarna16 PhenoGen
RatGTEx ENSRNOG00000061622 RatGTEx
RNAcentral URS0000662A49 RNACentral


Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2023-09-12 Scarna16  small Cajal body-specific RNA 16  LOC120095426  small Cajal body-specific RNA 16  Symbol changed 629549 APPROVED
2022-06-02 LOC120095426  small Cajal body-specific RNA 16  Gm26083  predicted gene, 26083  Data merged from RGD:15014217 737654 PROVISIONAL
2021-01-27 LOC120095426  small Cajal body-specific RNA 16      Symbol and Name status set to provisional 70820 PROVISIONAL
2020-02-07 Gm26083  predicted gene, 26083  AABR07030841.2    Symbol and/or name change 19259462 PROVISIONAL