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
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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: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81943,032,748 - 43,036,887 (-)NCBIGRCr8GRCr8GRCr8
mRatBN7.21926,128,292 - 26,131,416 (-)NCBImRatBN7.2mRatBN7.2
Rnor_6.01929,798,912 - 29,803,955 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1929,800,855 - 29,802,083 (-)Ensemblrn6Rnor6.0
Rnor_5.01940,711,187 - 40,712,507 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41927,925,485 - 27,926,754 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1925,652,275 - 25,655,426 (-)NCBICelera
Cytogenetic Map19q11NCBI
JBrowse:




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
46 total Variants
miRNA Target Status (No longer updated)

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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
61447Tcas1Tongue tumor susceptibility QTL 16.08tongue integrity trait (VT:0010553)squamous cell carcinoma of the tongue maximum tumor diameter (CMO:0001875)191922068964220689Rat
9590298Uminl5Urine mineral level QTL 53.590.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)19799775052997750Rat
1331737Uae29Urinary albumin excretion QTL 295.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)193628974246245Rat
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)194172060949971820Rat
1578764Stresp19Stress response QTL 193.60.001blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)193253961574246245Rat
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)193128753251431640Rat
9590090Insglur8Insulin/glucose ratio QTL 810.810.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)19799775052997750Rat
1331788Rf45Renal function QTL 452.818kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)193177788874246245Rat
1554318Bmd5Bone mineral density QTL 512.10.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)192318858668188586Rat
1549835Tcas7Tongue tumor susceptibility QTL 70.001tongue integrity trait (VT:0010553)squamous cell carcinoma of the head and neck tumor number (CMO:0001876)194172254674246245Rat
724566Uae12Urinary albumin excretion QTL 125urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19219431774246245Rat
1354633Bw28Body weight QTL 286.04body mass (VT:0001259)body weight (CMO:0000012)194072709254856850Rat
61407Scl12Serum cholesterol level QTL 120.001blood HDL cholesterol amount (VT:0000184)serum high density lipoprotein cholesterol level (CMO:0000361)193009938347207961Rat
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)19799775052997750Rat
631840Niddm38Non-insulin dependent diabetes mellitus QTL 383.86blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)191032907674246245Rat
1358200Insglur2Insulin/glucose ratio QTL 24.1blood glucose amount (VT:0000188)serum glucose level (CMO:0000543)19574806450748064Rat
7411549Bw130Body weight QTL 13050.001body mass (VT:0001259)body weight gain (CMO:0000420)193236531174246245Rat
724518Uae19Urinary albumin excretion QTL 195.5urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)192409397369093973Rat
61423Cia14Collagen induced arthritis QTL 143joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)191083361874246245Rat
2303628Vencon9Ventilatory control QTL 90.005respiration trait (VT:0001943)minute ventilation (CMO:0000132)192318858668188586Rat
9590250Scort11Serum corticosterone level QTL 1123.450.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)19799775052997750Rat
2317848Alcrsp21Alcohol response QTL 211.8999999761581420.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)192010930665109306Rat
1354607Gmadr1Adrenal mass QTL 15.83adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)194072709254856850Rat
7247442Uae39Urinary albumin excretion QTL 39urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)19219431774246245Rat
1354600Salc2Saline consumption QTL 29.910.001drinking behavior trait (VT:0001422)saline drink intake rate (CMO:0001627)194072709254856850Rat


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
9 11 23 65 61 60 29 25 29 6 146 71 45 29 45 31

Sequence


Ensembl 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