Ss18l1 (SS18, nBAF chromatin remodeling complex subunit like 1) - Rat Genome Database

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Gene: Ss18l1 (SS18, nBAF chromatin remodeling complex subunit like 1) Mus musculus
Analyze
Symbol: Ss18l1
Name: SS18, nBAF chromatin remodeling complex subunit like 1
RGD ID: 1332001
MGI Page MGI
Description: Predicted to enable DNA binding activity; DNA-binding transcription factor activity; and transcription coactivator activity. Acts upstream of or within dendrite development and positive regulation of dendrite morphogenesis. Located in condensed chromosome, centromeric region. Part of nBAF complex. Is expressed in brain; primary oocyte; spermatocyte; telencephalon; and testis. Orthologous to human SS18L1 (SS18L1 subunit of BAF chromatin remodeling complex).
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: A230053O16Rik; calcium-responsive transactivator; CRE; CREST; SS18-like protein 1; synovial sarcoma translocation gene on chromosome 18-like 1
RGD Orthologs
Human
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: GRCm39 - Mouse Genome Assembly GRCm39
Position:
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
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

Phenotype Annotations     Click to see Annotation Detail View
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. Electronic Transfer of Homolog Data MGD and Homologene mouse data transfer
3. MGDs mouse GO annotations MGD data from the GO Consortium
4. MGD IEA MGD IEA
5. Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Okazaki Y, etal., Nature. 2002 Dec 5;420(6915):563-73.
6. Mouse MP Annotation Import Pipeline RGD automated import pipeline
7. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
8. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:10349636   PMID:10922068   PMID:11042159   PMID:11076861   PMID:11217851   PMID:12477932   PMID:12520002   PMID:15368895   PMID:15680357   PMID:16141072   PMID:16141073   PMID:16926188  
PMID:16968740   PMID:18180366   PMID:18283110   PMID:18316482   PMID:18331714   PMID:19279220   PMID:19531582   PMID:20059953   PMID:21677750   PMID:21873635   PMID:22164254   PMID:23090997  
PMID:23151479   PMID:23321477   PMID:23759310   PMID:23785148   PMID:24891606   PMID:24952961   PMID:25824710   PMID:26362258   PMID:26655900   PMID:28302748   PMID:28768200   PMID:30228227  
PMID:30272023   PMID:30976389   PMID:30995416   PMID:31485074   PMID:31598710   PMID:32094118   PMID:32219340   PMID:35640597   PMID:35905187   PMID:36289231   PMID:38060382  


Genomics

Comparative Map Data
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
(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
(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
(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
1043 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:1055
Count of miRNA genes:557
Interacting mature miRNAs:700
Transcripts:ENSMUST00000041126
Prediction methods:Miranda, 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 (GRCm39)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
5491196Mobq6_mmultigenic obesity QTL 6 (mouse)Not determined285724269180896594Mouse
1300867Lore2_mloss of righting induced by ethanol 2 (mouse)Not determined2144515861180896594Mouse
12790983Bwq12_mbody weight QTL 12 (mouse)2148238204181755017Mouse
4142211Nilac3_mnicotine induced locomotor activity 3 (mouse)Not determined2148664893181755017Mouse
1558917Gct8_mgranulosa cell tumorigenesis 8 (mouse)Not determined2149236907181755017Mouse
1300751Bdt1_mbone density traits 1 (mouse)Not determined2149988902181755017Mouse
1301085Lrnx10_mlearning-contextual 10 (mouse)Not determined2150212221181755017Mouse
11038701Ltpr2e_mLeishmania tropica response 2e (mouse)2150212221181755017Mouse
4142450Lmr16_mleishmaniasis resistance 16 (mouse)Not determined2150212221181755017Mouse
1301019Bmd6_mbone mineral density 6 (mouse)Not determined2151778297181755017Mouse
14747002Mancz3_mmandible centroid size 3 (mouse)2152329820181755017Mouse
1300622Cfld1_mcystic fibrosis lung disease 1 (mouse)Not determined2155823920181755017Mouse
1357537Lith12_mlithogenic gene 12 (mouse)Not determined2156196464181755017Mouse
1302003Sluc17_msusceptibility to lung cancer 17 (mouse)Not determined2162433493181755017Mouse
1301677Alcp6_malcohol preference locus 6 (mouse)Not determined2163486407181755017Mouse
1301348Alcp5_malcohol preference locus 5 (mouse)Not determined2163486407181755017Mouse
1300676Prdt2_mprion disease incubation time 2 (mouse)Not determined2164515154181755017Mouse
1558748Vacq1_mvoluntary alcohol consumption QTL 1 (mouse)Not determined2178442338181515280Mouse


Expression


Sequence


Reference Sequences
RefSeq Acc Id: ENSMUST00000041126   ⟹   ENSMUSP00000041288
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl2179,684,302 - 179,711,994 (+)Ensembl
GRCm38.p6 Ensembl2180,042,509 - 180,070,201 (+)Ensembl
RefSeq Acc Id: NM_178750   ⟹   NP_848865
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm392179,684,276 - 179,711,994 (+)NCBI
GRCm382180,042,483 - 180,070,201 (+)ENTREZGENE
MGSCv372179,777,188 - 179,804,906 (+)RGD
Celera2184,127,089 - 184,152,510 (+)RGD
cM Map2 ENTREZGENE
Sequence:
RefSeq Acc Id: XM_006500631   ⟹   XP_006500694
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm392179,685,006 - 179,711,994 (+)NCBI
GRCm382180,043,202 - 180,070,201 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006500632   ⟹   XP_006500695
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm392179,684,565 - 179,711,994 (+)NCBI
GRCm382180,053,369 - 180,070,201 (+)NCBI
Sequence:
Reference Protein Sequences
RefSeq Acc Id: NP_848865   ⟸   NM_178750
- UniProtKB: Q7TQF3 (UniProtKB/Swiss-Prot),   Q6A014 (UniProtKB/Swiss-Prot),   Q8BYQ7 (UniProtKB/Swiss-Prot),   Q8BW22 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006500694   ⟸   XM_006500631
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_006500695   ⟸   XM_006500632
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: ENSMUSP00000041288   ⟸   ENSMUST00000041126

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q8BW22-F1-model_v2 AlphaFold Q8BW22 1-402 view protein structure

Promoters
RGD ID:6832842
Promoter ID:MM_KWN:33517
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:3T3L1_Day0,   3T3L1_Day1,   BoneMarrow_0Hour,   BoneMarrow_2Hour,   BoneMarrow_4Hour,   Brain,   ES_Cell,   Kidney,   Liver,   Lung,   MEF_B4,   Spleen
Transcripts:OTTMUST00000038893,   OTTMUST00000038904,   OTTMUST00000038905,   OTTMUST00000038906
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv362179,776,081 - 179,777,577 (+)MPROMDB
RGD ID:6880040
Promoter ID:EPDNEW_M3468
Type:initiation region
Name:Ss18l1_1
Description:Mus musculus SS18, nBAF chromatin remodeling complex subunitlike 1 , mRNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_M3469  
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm382180,042,506 - 180,042,566EPDNEW
RGD ID:6880036
Promoter ID:EPDNEW_M3469
Type:initiation region
Name:Ss18l1_2
Description:Mus musculus SS18, nBAF chromatin remodeling complex subunitlike 1 , mRNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_M3468  
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm382180,042,721 - 180,042,781EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:2444061 AgrOrtholog
Ensembl Genes ENSMUSG00000039086 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSMUST00000041126 ENTREZGENE
  ENSMUST00000041126.9 UniProtKB/Swiss-Prot
InterPro SS18 UniProtKB/Swiss-Prot
  SS18_fam UniProtKB/Swiss-Prot
KEGG Report mmu:269397 UniProtKB/Swiss-Prot
MGD MGI:2444061 ENTREZGENE
NCBI Gene 269397 ENTREZGENE
PANTHER CALCIUM-RESPONSIVE TRANSACTIVATOR UniProtKB/Swiss-Prot
  PTHR23107 UniProtKB/Swiss-Prot
Pfam SSXT UniProtKB/Swiss-Prot
PhenoGen Ss18l1 PhenoGen
UniProt CREST_MOUSE UniProtKB/Swiss-Prot
  Q6A014 ENTREZGENE
  Q7TQF3 ENTREZGENE
  Q8BW22 ENTREZGENE
  Q8BYQ7 ENTREZGENE
UniProt Secondary Q6A014 UniProtKB/Swiss-Prot
  Q7TQF3 UniProtKB/Swiss-Prot
  Q8BYQ7 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-11-08 Ss18l1  SS18, nBAF chromatin remodeling complex subunit like 1    synovial sarcoma translocation gene on chromosome 18-like 1  Symbol and/or name change 5135510 APPROVED