Smarce1-ps6 (SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily e, member 1, pseudogene 6) - Rat Genome Database

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Gene: Smarce1-ps6 (SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily e, member 1, pseudogene 6) Rattus norvegicus
Analyze
Symbol: Smarce1-ps6 (Ensembl: AC123471.1)
Name: SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily e, member 1, pseudogene 6 (Ensembl:SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily e, member 1)
RGD ID: 9145556
Description:
Type: pseudo (Ensembl: protein-coding)
RefSeq Status: MODEL
Previously known as: LOC100359956; LOC103694314; SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily e, member 1; SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1-like
Related Functional Gene: Smarce1  
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81943,032,748 - 43,036,887 (-)NCBIGRCr8
mRatBN7.21926,128,292 - 26,131,416 (-)NCBImRatBN7.2mRatBN7.2
Rnor_6.01929,798,912 - 29,803,955 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1929,800,855 - 29,802,083 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01940,711,187 - 40,712,507 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41927,925,485 - 27,926,754 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1925,652,275 - 25,655,426 (-)NCBICelera
Cytogenetic Map19q11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.

Genomics

Variants

.
Variants in Smarce1-ps6
48 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:15
Count of miRNA genes:15
Interacting mature miRNAs:15
Transcripts:ENSRNOT00000024755
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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
10054132Srcrt9Stress Responsive Cort QTL 92.870.0017blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)19127355345Rat
631678Cm9Cardiac mass QTL 94.270.0001aorta mass (VT:0002845)aorta weight (CMO:0000076)19128982497Rat
631681Cm12Cardiac mass QTL 123.330.00053heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)19128982497Rat
1549847Bss8Bone structure and strength QTL 84lumbar vertebra strength trait (VT:0010574)vertebra ultimate force (CMO:0001678)19131963836Rat
9590298Uminl5Urine mineral level QTL 53.590.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)19136824771Rat
8552935Pigfal10Plasma insulin-like growth factor 1 level QTL 105.7blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)19136824771Rat
9590250Scort11Serum corticosterone level QTL 1123.450.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)19136824771Rat
9590090Insglur8Insulin/glucose ratio QTL 810.810.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)19136824771Rat
9589102Slep13Serum leptin concentration QTL 134.630.001blood leptin amount (VT:0005667)plasma leptin level (CMO:0000781)1956937445569374Rat
8694186Bw152Body weight QTL 1523.340.001body mass (VT:0001259)body weight gain (CMO:0000420)1956937445569374Rat
7247442Uae39Urinary albumin excretion QTL 39urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)19218792746708701Rat
724566Uae12Urinary albumin excretion QTL 125urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19218792756457239Rat
61447Tcas1Tongue tumor susceptibility QTL 16.08tongue integrity trait (VT:0010553)squamous cell carcinoma of the tongue maximum tumor diameter (CMO:0001875)19231612147316121Rat
2317848Alcrsp21Alcohol response QTL 211.8999999761581420.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)19320477748204777Rat
1331737Uae29Urinary albumin excretion QTL 295.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19409615555283277Rat
724518Uae19Urinary albumin excretion QTL 195.5urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)19745724942983518Rat
724565Tcas5Tongue tumor susceptibility QTL 510.04tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)19997775339654489Rat
61423Cia14Collagen induced arthritis QTL 143joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)191082797043544039Rat
61407Scl12Serum cholesterol level QTL 120.001blood HDL cholesterol amount (VT:0000184)serum high density lipoprotein cholesterol level (CMO:0000361)191392640130303727Rat
1558656Prcs1Prostate cancer susceptibility QTL 15prostate integrity trait (VT:0010571)percentage of study population developing ventral prostate tumorous lesions during a period of time (CMO:0000943)191511459834521833Rat
7411549Bw130Body weight QTL 13050.001body mass (VT:0001259)body weight gain (CMO:0000420)191545586057337602Rat
1331788Rf45Renal function QTL 452.818kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)191560502346559041Rat
1578764Stresp19Stress response QTL 193.60.001blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)191563020157337602Rat
2298478Eau8Experimental allergic uveoretinitis QTL 80.0163uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)191715443357337602Rat
61350Bp32Blood pressure QTL 320.012arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)192048357557337602Rat
61328Eae8Experimental allergic encephalomyelitis QTL 84nervous system integrity trait (VT:0010566)percentage of study population developing experimental autoimmune encephalomyelitis during a period of time (CMO:0001047)192481604133061905Rat
1549835Tcas7Tongue tumor susceptibility QTL 70.001tongue integrity trait (VT:0010553)squamous cell carcinoma of the head and neck tumor number (CMO:0001876)192481797839654489Rat


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
Low 3 6 10 19 5 5 10 3 9 10 5
Below cutoff 11 21 15 15 3 6 18 18 18 1 3

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000024755   ⟹   ENSRNOP00000075478
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1929,800,855 - 29,802,083 (-)Ensembl
RefSeq Acc Id: XM_008772543   ⟹   XP_008770765
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01929,800,227 - 29,803,955 (-)NCBI
RefSeq Acc Id: XM_008774219   ⟹   XP_008772441
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera1925,651,698 - 25,655,426 (-)NCBI
Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-A0A0G2KAP8-F1-model_v2 AlphaFold A0A0G2KAP8 1-374 view protein structure

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-5983 BioCyc
Ensembl Genes ENSRNOG00000018377 Ensembl
NCBI Gene LOC103694314 ENTREZGENE
PhenoGen Smarce1-ps6 PhenoGen
RatGTEx ENSRNOG00000018377 RatGTEx


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2022-06-10 Smarce1-ps6  SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily e, member 1, pseudogene 6  LOC103694314  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1-like  Symbol and Name Changed 1299863 APPROVED
2015-07-29 LOC103694314  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1-like  LOC100359956  SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily e, member 1  Data merged from RGD:2323089 737654 PROVISIONAL
2014-08-25 LOC103694314  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2010-05-06 LOC100359956  SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily e, member 1      Symbol and Name status set to provisional 70820 PROVISIONAL