Ss18l1 (SS18L1 subunit of BAF chromatin remodeling complex) - Rat Genome Database

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Gene: Ss18l1 (SS18L1 subunit of BAF chromatin remodeling complex) Rattus norvegicus
Analyze
Symbol: Ss18l1
Name: SS18L1 subunit of BAF chromatin remodeling complex
RGD ID: 621847
Description: Predicted to enable transcription coactivator activity. Involved in positive regulation of DNA-templated transcription and regulation of dendrite development. Located in nuclear body. Orthologous to human SS18L1 (SS18L1 subunit of BAF chromatin remodeling complex); INTERACTS WITH 17alpha-ethynylestradiol; acetamide; all-trans-retinoic acid.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: calcium-responsive transactivator; calcium-responsive transcription coactivator; CREST; Loc192352; SS18-like protein 1; SS18L1, nBAF chromatin remodeling complex subunit; synovial sarcoma translocation gene on chromosome 18-like 1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr83187,521,616 - 187,542,873 (+)NCBIGRCr8
mRatBN7.23167,143,730 - 167,165,253 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl3167,143,994 - 167,165,253 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx3171,521,081 - 171,542,462 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.03180,480,164 - 180,501,545 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.03177,143,667 - 177,166,213 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.03175,426,754 - 175,445,222 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl3175,426,752 - 175,445,222 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.03181,673,460 - 181,691,928 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.43169,107,519 - 169,125,910 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.13169,013,554 - 169,031,946 (+)NCBI
Celera3165,417,607 - 165,435,886 (-)NCBICelera
Cytogenetic Map3q43NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Dendrite development regulated by CREST, a calcium-regulated transcriptional activator. Aizawa H, etal., Science 2004 Jan 9;303(5655):197-202.
2. 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.
3. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
4. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
5. A multifunctional domain of the calcium-responsive transactivator (CREST) that inhibits dendritic growth in cultured neurons. Pradhan A and Liu Y, J Biol Chem. 2005 Jul 1;280(26):24738-43. Epub 2005 May 2.
6. The calcium-responsive transactivator recruits CREB binding protein to nuclear bodies. Pradhan A and Liu Y, Neurosci Lett. 2004 Nov 11;370(2-3):191-5.
7. A calcium-dependent switch in a CREST-BRG1 complex regulates activity-dependent gene expression. Qiu Z and Ghosh A, Neuron. 2008 Dec 10;60(5):775-87. doi: 10.1016/j.neuron.2008.09.040.
8. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
9. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
10. Information Derived from GenBank Report RGD, Sept. 2003
Additional References at PubMed
PMID:18283110   PMID:18316482   PMID:18331714   PMID:22164254   PMID:23160962   PMID:23785148   PMID:24891606   PMID:30228227   PMID:33398438  


Genomics

Comparative Map Data
Ss18l1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr83187,521,616 - 187,542,873 (+)NCBIGRCr8
mRatBN7.23167,143,730 - 167,165,253 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl3167,143,994 - 167,165,253 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx3171,521,081 - 171,542,462 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.03180,480,164 - 180,501,545 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.03177,143,667 - 177,166,213 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.03175,426,754 - 175,445,222 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl3175,426,752 - 175,445,222 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.03181,673,460 - 181,691,928 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.43169,107,519 - 169,125,910 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.13169,013,554 - 169,031,946 (+)NCBI
Celera3165,417,607 - 165,435,886 (-)NCBICelera
Cytogenetic Map3q43NCBI
SS18L1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382062,143,769 - 62,182,514 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl2062,143,769 - 62,182,514 (+)EnsemblGRCh38hg38GRCh38
GRCh372060,718,825 - 60,757,570 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 362060,152,217 - 60,190,961 (+)NCBINCBI36Build 36hg18NCBI36
Build 342060,152,216 - 60,190,961NCBI
Celera2057,453,993 - 57,492,739 (+)NCBICelera
Cytogenetic Map20q13.33NCBI
HuRef2057,510,764 - 57,534,867 (+)NCBIHuRef
CHM1_12060,619,891 - 60,658,521 (+)NCBICHM1_1
T2T-CHM13v2.02063,934,636 - 63,973,390 (+)NCBIT2T-CHM13v2.0
Ss18l1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm392179,684,276 - 179,711,994 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl2179,684,302 - 179,711,994 (+)EnsemblGRCm39 Ensembl
GRCm382180,042,483 - 180,070,201 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl2180,042,509 - 180,070,201 (+)EnsemblGRCm38mm10GRCm38
MGSCv372179,777,188 - 179,804,906 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv362179,971,917 - 179,999,609 (+)NCBIMGSCv36mm8
Celera2184,127,089 - 184,152,510 (+)NCBICelera
Cytogenetic Map2H4NCBI
cM Map2102.56NCBI
Ss18l1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555281,849,462 - 1,870,872 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049555281,849,457 - 1,881,138 (-)NCBIChiLan1.0ChiLan1.0
SS18L1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v22167,925,093 - 67,965,090 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan12067,918,149 - 67,958,211 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v02058,509,322 - 58,549,380 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.12059,830,156 - 59,869,529 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2059,843,921 - 59,869,504 (+)Ensemblpanpan1.1panPan2
SS18L1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12446,195,278 - 46,214,613 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2446,194,852 - 46,212,543 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2445,425,261 - 45,451,749 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02447,044,716 - 47,071,192 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2447,044,703 - 47,071,191 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12446,146,313 - 46,172,804 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02446,269,259 - 46,295,904 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02447,023,526 - 47,050,136 (+)NCBIUU_Cfam_GSD_1.0
Ss18l1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024408640194,363,365 - 194,385,660 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365149,821,319 - 9,839,475 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365149,820,449 - 9,839,341 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SS18L1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1761,571,614 - 61,598,099 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11761,571,619 - 61,598,104 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21769,093,385 - 69,106,704 (+)NCBISscrofa10.2Sscrofa10.2susScr3
SS18L1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.122,058,073 - 2,094,048 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl22,065,042 - 2,094,018 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366605050,005,178 - 50,044,001 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Ss18l1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462474128,017,400 - 28,049,456 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462474128,017,400 - 28,064,617 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Ss18l1
88 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:30
Count of miRNA genes:26
Interacting mature miRNAs:29
Transcripts:ENSRNOT00000011306
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
9589106Insul23Insulin level QTL 2313.860.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)3131635904169034231Rat
10755461Coatc16Coat color QTL 16coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)3122438700167438700Rat
2312673Scl63Serum cholesterol level QTL 630.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)398535255168026850Rat
1559282Emca5Estrogen-induced mammary cancer QTL 53.9mammary gland integrity trait (VT:0010552)percentage of study population developing mammary tumors during a period of time (CMO:0000948)343827364169034231Rat
1578653Vnigr3Vascular neointimal growth QTL 33.1artery morphology trait (VT:0002191)artery neointimal hyperplastic lesion area (CMO:0001414)3130656562169034231Rat
1298068Bp167Blood pressure QTL 1670.004arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3141074471169034231Rat
2303620Vencon4Ventilatory control QTL 43.9respiration trait (VT:0001943)tidal volume (CMO:0000222)3127162703168026850Rat
2298477Eau4Experimental allergic uveoretinitis QTL 40.0011uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)3137398739169034231Rat
2312659Slep7Serum leptin concentration QTL 70.001blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)398535255168026850Rat
1578666Vnigr1Vascular neointimal growth QTL 14.6artery morphology trait (VT:0002191)artery lumen area (CMO:0001409)3149040888168026850Rat
1300161Rf10Renal function QTL 103.57renal blood flow trait (VT:2000006)absolute change in renal vascular resistance (CMO:0001900)3161192952169034231Rat
8552791Vie2Viral induced encephalitis QTL 24.1brain integrity trait (VT:0010579)encephalitis incidence/prevalence measurement (CMO:0002361)3145956084169034231Rat
1578656Vnigr2Vascular neointimal growth QTL 24.2artery morphology trait (VT:0002191)lesioned artery residual lumen area (CMO:0001417)3130656562169034231Rat
2317883Alcrsp26Alcohol response QTL 261.80.63response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)3145526770169034231Rat
8552952Pigfal13Plasma insulin-like growth factor 1 level QTL 13blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)3138799500169034231Rat
631541Bp81Blood pressure QTL 814arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3124122556169034231Rat
2312670Bw94Body weight QTL 940.01inguinal fat pad mass (VT:0010424)inguinal fat pad weight to body weight ratio (CMO:0001253)398535255168026850Rat


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 49 113 91 90 59 25 59 6 218 97 93 45 60 31

Sequence


Ensembl Acc Id: ENSRNOT00000085718   ⟹   ENSRNOP00000072296
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl3167,143,994 - 167,162,111 (+)Ensembl
Rnor_6.0 Ensembl3175,426,752 - 175,445,222 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000111398   ⟹   ENSRNOP00000080662
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl3167,143,996 - 167,165,253 (+)Ensembl
RefSeq Acc Id: NM_138918   ⟹   NP_620273
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83187,521,616 - 187,542,873 (+)NCBI
mRatBN7.23167,143,996 - 167,165,253 (+)NCBI
Rnor_6.03175,426,754 - 175,445,222 (+)NCBI
Rnor_5.03181,673,460 - 181,691,928 (-)NCBI
RGSC_v3.43169,107,519 - 169,125,910 (+)RGD
Celera3165,417,607 - 165,435,886 (-)RGD
Sequence:
RefSeq Acc Id: XM_039104228   ⟹   XP_038960156
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83187,522,077 - 187,542,873 (+)NCBI
mRatBN7.23167,144,112 - 167,161,219 (+)NCBI
Protein Sequences
Protein RefSeqs NP_620273 (Get FASTA)   NCBI Sequence Viewer  
  XP_038960156 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAK53461 (Get FASTA)   NCBI Sequence Viewer  
  EDL88832 (Get FASTA)   NCBI Sequence Viewer  
  EDL88833 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000072296.2
  ENSRNOP00000080662.1
GenBank Protein Q91XJ0 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_620273   ⟸   NM_138918
- UniProtKB: Q91XJ0 (UniProtKB/Swiss-Prot),   A0A8I5ZQS4 (UniProtKB/TrEMBL),   A6KMC5 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000072296   ⟸   ENSRNOT00000085718
RefSeq Acc Id: XP_038960156   ⟸   XM_039104228
- Peptide Label: isoform X1
Ensembl Acc Id: ENSRNOP00000080662   ⟸   ENSRNOT00000111398
Protein Domains
SS18 N-terminal

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q91XJ0-F1-model_v2 AlphaFold Q91XJ0 1-401 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)
AGR Gene RGD:621847 AgrOrtholog
BioCyc Gene G2FUF-46372 BioCyc
Ensembl Genes ENSRNOG00000060010 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000085718.2 UniProtKB/TrEMBL
  ENSRNOT00000111398.1 UniProtKB/TrEMBL
InterPro SS18 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SS18_fam UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:192352 UniProtKB/Swiss-Prot
NCBI Gene 192352 ENTREZGENE
PANTHER CALCIUM-RESPONSIVE TRANSACTIVATOR UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR23107 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam SSXT UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Ss18l1 PhenoGen
RatGTEx ENSRNOG00000060010 RatGTEx
UniProt A0A8I5ZQS4 ENTREZGENE, UniProtKB/TrEMBL
  A0A8L2R5F4_RAT UniProtKB/TrEMBL
  A6KMC4_RAT UniProtKB/TrEMBL
  A6KMC5 ENTREZGENE, UniProtKB/TrEMBL
  CREST_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2019-04-02 Ss18l1  SS18L1 subunit of BAF chromatin remodeling complex  Ss18l1  SS18L1, nBAF chromatin remodeling complex subunit  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2016-05-04 Ss18l1  SS18L1, nBAF chromatin remodeling complex subunit  Ss18l1  synovial sarcoma translocation gene on chromosome 18-like 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2004-09-10 Ss18l1  synovial sarcoma translocation gene on chromosome 18-like 1  Loc192352  calcium-responsive transcription coactivator  Symbol and Name updated 1299863 APPROVED
2002-08-07 Loc192352  calcium-responsive transcription coactivator      Symbol and Name status set to provisional 70820 PROVISIONAL