Smarca5 (SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 5) - Rat Genome Database

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Gene: Smarca5 (SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 5) Rattus norvegicus
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Symbol: Smarca5
Name: SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 5
RGD ID: 1308832
Description: Predicted to enable several functions, including ATP binding activity; ATP hydrolysis activity; and histone octamer slider activity. Predicted to contribute to histone binding activity. Predicted to be involved in several processes, including chromatin remodeling; positive regulation of histone modification; and regulation of nucleobase-containing compound metabolic process. Predicted to act upstream of or within cellular response to leukemia inhibitory factor; chromatin remodeling; and positive regulation of DNA-templated transcription. Predicted to be located in chromosome; cytosol; and nuclear lumen. Predicted to be part of nucleus. Predicted to be active in nucleus and site of double-strand break. Predicted to colocalize with nuclear replication fork. Orthologous to human SMARCA5 (SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 5); PARTICIPATES IN ISWI family mediated chromatin remodeling pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,6-dinitrotoluene; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC307766; SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21927,271,918 - 27,304,594 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1927,271,148 - 27,304,594 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1934,130,292 - 34,162,927 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.01934,784,348 - 34,816,983 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.01937,004,248 - 37,036,904 (+)NCBIRnor_WKY
Rnor_6.01930,936,703 - 30,969,454 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1930,936,703 - 30,969,454 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01941,840,174 - 41,873,900 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41929,122,301 - 29,155,293 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11929,126,640 - 29,160,112 (+)NCBI
Celera1926,788,347 - 26,821,018 (+)NCBICelera
Cytogenetic Map19q11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

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

Molecular Pathway Annotations     Click to see Annotation Detail View
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.
2. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
3. ATP-dependent chromatin remodeling: genetics, genomics and mechanisms. Hargreaves DC and Crabtree GR, Cell Res. 2011 Mar;21(3):396-420. doi: 10.1038/cr.2011.32. Epub 2011 Mar 1.
4. GOA pipeline RGD automated data pipeline
5. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
6. Comprehensive gene review and curation RGD comprehensive gene curation
Additional References at PubMed
PMID:9836642   PMID:11532953   PMID:11980720   PMID:12477932   PMID:12972596   PMID:15543136   PMID:16085498   PMID:16880268   PMID:20439489   PMID:20850016   PMID:22154806  


Genomics

Comparative Map Data
Smarca5
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21927,271,918 - 27,304,594 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1927,271,148 - 27,304,594 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1934,130,292 - 34,162,927 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.01934,784,348 - 34,816,983 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.01937,004,248 - 37,036,904 (+)NCBIRnor_WKY
Rnor_6.01930,936,703 - 30,969,454 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1930,936,703 - 30,969,454 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01941,840,174 - 41,873,900 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41929,122,301 - 29,155,293 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11929,126,640 - 29,160,112 (+)NCBI
Celera1926,788,347 - 26,821,018 (+)NCBICelera
Cytogenetic Map19q11NCBI
SMARCA5
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh384143,513,702 - 143,557,486 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl4143,513,702 - 143,557,486 (+)EnsemblGRCh38hg38GRCh38
GRCh374144,434,855 - 144,478,639 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 364144,654,066 - 144,694,017 (+)NCBINCBI36Build 36hg18NCBI36
Build 344144,792,220 - 144,832,171NCBI
Celera4141,764,634 - 141,804,574 (+)NCBICelera
Cytogenetic Map4q31.21NCBI
HuRef4140,164,707 - 140,208,721 (+)NCBIHuRef
CHM1_14144,411,831 - 144,455,839 (+)NCBICHM1_1
T2T-CHM13v2.04146,830,915 - 146,874,681 (+)NCBIT2T-CHM13v2.0
Smarca5
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39881,426,572 - 81,466,088 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl881,425,136 - 81,466,126 (-)EnsemblGRCm39 Ensembl
GRCm38880,699,943 - 80,739,459 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl880,698,507 - 80,739,497 (-)EnsemblGRCm38mm10GRCm38
MGSCv37883,223,842 - 83,263,358 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36883,595,689 - 83,635,205 (-)NCBIMGSCv36mm8
Celera884,973,840 - 85,010,486 (-)NCBICelera
Cytogenetic Map8C2NCBI
Smarca5
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495547112,203,318 - 12,237,333 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495547112,206,462 - 12,240,219 (-)NCBIChiLan1.0ChiLan1.0
SMARCA5
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.14147,174,145 - 147,214,809 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl4147,174,060 - 147,214,809 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v04135,874,888 - 135,917,096 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
SMARCA5
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11542,731,147 - 42,771,577 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1542,731,426 - 42,770,624 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1543,114,109 - 43,154,330 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01543,391,125 - 43,431,354 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1543,391,132 - 43,431,358 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11542,668,391 - 42,708,501 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01542,752,138 - 42,792,336 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01543,023,307 - 43,063,521 (+)NCBIUU_Cfam_GSD_1.0
Smarca5
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440530147,420,476 - 47,452,913 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365354,856,672 - 4,890,225 (-)EnsemblSpeTri2.0
SpeTri2.0NW_0049365354,857,816 - 4,890,266 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SMARCA5
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl884,184,576 - 84,224,871 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1884,184,572 - 84,224,943 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2889,339,602 - 89,379,481 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SMARCA5
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1790,366,359 - 90,406,707 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl790,370,305 - 90,410,137 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366603769,966,455 - 70,007,230 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Smarca5
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248483,569,744 - 3,611,104 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Smarca5
87 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:690
Count of miRNA genes:280
Interacting mature miRNAs:342
Transcripts:ENSRNOT00000024568
Prediction methods:Microtar, Miranda
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 3 38 54 38 19 38 8 8 74 35 41 11 8
Low 5 3 3 3 3
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000024568   ⟹   ENSRNOP00000024568
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1927,274,260 - 27,304,594 (+)Ensembl
Rnor_6.0 Ensembl1930,936,703 - 30,969,454 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000095459   ⟹   ENSRNOP00000080637
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1927,271,148 - 27,304,594 (+)Ensembl
RefSeq Acc Id: NM_001107419   ⟹   NP_001100889
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21927,271,918 - 27,304,594 (+)NCBI
Rnor_6.01930,936,703 - 30,969,454 (+)NCBI
Rnor_5.01941,840,174 - 41,873,900 (+)NCBI
RGSC_v3.41929,122,301 - 29,155,293 (+)RGD
Celera1926,788,347 - 26,821,018 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001100889 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAI66868 (Get FASTA)   NCBI Sequence Viewer  
  EDL92299 (Get FASTA)   NCBI Sequence Viewer  
  EDL92300 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001100889   ⟸   NM_001107419
- UniProtKB: F1LNL2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000024568   ⟸   ENSRNOT00000024568
RefSeq Acc Id: ENSRNOP00000080637   ⟸   ENSRNOT00000095459
Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-F1LNL2-F1-model_v2 AlphaFold F1LNL2 1-995 view protein structure

Transcriptome

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

Promoters
RGD ID:13701047
Promoter ID:EPDNEW_R11570
Type:multiple initiation site
Name:Smarca5_1
Description:SWI/SNF related, matrix associated, actin dependent regulatorof chromatin, subfamily a, member 5
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01930,936,636 - 30,936,696EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1308832 AgrOrtholog
BioCyc Gene G2FUF-5972 BioCyc
Ensembl Genes ENSRNOG00000018149 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000024568.6 UniProtKB/TrEMBL
  ENSRNOP00000080637 ENTREZGENE
  ENSRNOP00000080637.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000024568.6 UniProtKB/TrEMBL
  ENSRNOT00000095459 ENTREZGENE
  ENSRNOT00000095459.1 UniProtKB/TrEMBL
Gene3D-CATH 1.10.1040.30 UniProtKB/TrEMBL
  3.40.50.10810 UniProtKB/TrEMBL
  3.40.50.300 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:9023518 IMAGE-MGC_LOAD
InterPro ATPase_nucl-remodel_HAND-dom UniProtKB/TrEMBL
  DEAD-like_helicase UniProtKB/TrEMBL
  Helicase_C UniProtKB/TrEMBL
  Homeodomain-like UniProtKB/TrEMBL
  ISWI_HAND-dom_sf UniProtKB/TrEMBL
  P-loop_NTPase UniProtKB/TrEMBL
  SANT_DNA-bd UniProtKB/TrEMBL
  SANT_eukarya UniProtKB/TrEMBL
  SLIDE UniProtKB/TrEMBL
  SNF2-like_sf UniProtKB/TrEMBL
  SNF2_N UniProtKB/TrEMBL
KEGG Report rno:307766 UniProtKB/TrEMBL
MGC_CLONE MGC:188785 IMAGE-MGC_LOAD
NCBI Gene 307766 ENTREZGENE
Pfam HAND UniProtKB/TrEMBL
  Helicase_C UniProtKB/TrEMBL
  SLIDE UniProtKB/TrEMBL
  SNF2_N UniProtKB/TrEMBL
PhenoGen Smarca5 PhenoGen
PROSITE HELICASE_ATP_BIND_1 UniProtKB/TrEMBL
  HELICASE_CTER UniProtKB/TrEMBL
  SANT UniProtKB/TrEMBL
SMART DEXDc UniProtKB/TrEMBL
  HELICc UniProtKB/TrEMBL
  SANT UniProtKB/TrEMBL
Superfamily-SCOP Homeodomain_like UniProtKB/TrEMBL
  Nucl_remodel_ATPase_ISWI_HAND UniProtKB/TrEMBL
  SSF52540 UniProtKB/TrEMBL
UniProt A0A8I5ZQQ5_RAT UniProtKB/TrEMBL
  B2RYQ9_RAT UniProtKB/TrEMBL
  F1LNL2 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Smarca5  SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 5   Smarca5_predicted  SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 5 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Smarca5_predicted  SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 5 (predicted)      Symbol and Name status set to approved 70820 APPROVED