Ssx1 (SSX family member 1) - Rat Genome Database

Send us a Message
Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Search RGD Grant Resources Citing RGD About Us Contact Us
Genes Variants Community Projects QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Synteny Browser (VCMap) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) AllianceMine GViewer (Genome Viewer)
Aging & Age-Related Disease Behavioral & Substance Use Disorder Cancer & Neoplastic Disease Cardiovascular Disease Coronavirus Disease Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease
Find Models Genetic Models Autism Models Rat PhenoMiner (Quantitative Phenotypes) Chinchilla PhenoMiner Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive
Pathways
Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Presentations Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
Advanced Search (OLGA)
Gene: Ssx1 (SSX family member 1) Rattus norvegicus
Analyze
Symbol: Ssx1
Name: SSX family member 1
RGD ID: 1593374
Description: Predicted to enable transcription corepressor activity. Predicted to be involved in negative regulation of transcription by RNA polymerase II and spermatogenesis. Predicted to be located in sperm flagellum. Predicted to be active in nucleus. Human ortholog(s) of this gene implicated in X-linked spermatogenic failure 5 and synovial sarcoma. Orthologous to several human genes including SSX1 (SSX family member 1); SSX2 (SSX family member 2); and SSX2B (SSX family member 2B); INTERACTS WITH bisphenol A; paraquat; 2,3,7,8-tetrachlorodibenzodioxine (ortholog).
Type: protein-coding
RefSeq Status: MODEL
Previously known as: LOC691903; probable histone-lysine N-methyltransferase PRDM7; putative protein SSX9; similar to synovial sarcoma, X member B, breakpoint 10; synovial sarcoma, X breakpoint 1
RGD Orthologs
Human
Mouse
Dog
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X16,603,888 - 16,612,203 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 EnsemblX16,604,449 - 16,612,210 (-)EnsemblGRCr8
mRatBN7.2X13,931,433 - 13,939,732 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX13,931,470 - 13,939,720 (-)EnsemblmRatBN7.2
Rnor_6.0X14,903,854 - 14,911,999 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX14,905,337 - 14,910,778 (-)Ensemblrn6Rnor6.0
Rnor_5.0X15,690,056 - 15,698,574 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4X26,091,234 - 26,096,666 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
CeleraX40,574 - 48,714 (+)NCBICelera
Cytogenetic MapXq12NCBI
JBrowse:




Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
nucleus  (IBA,IEA,ISO)
sperm flagellum  (ISO)

Molecular Function

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. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
3. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
5. Comprehensive gene review and curation RGD comprehensive gene curation
Additional References at PubMed
PMID:21454665  


Genomics

Comparative Map Data
Ssx1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X16,603,888 - 16,612,203 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 EnsemblX16,604,449 - 16,612,210 (-)EnsemblGRCr8
mRatBN7.2X13,931,433 - 13,939,732 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX13,931,470 - 13,939,720 (-)EnsemblmRatBN7.2
Rnor_6.0X14,903,854 - 14,911,999 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX14,905,337 - 14,910,778 (-)Ensemblrn6Rnor6.0
Rnor_5.0X15,690,056 - 15,698,574 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4X26,091,234 - 26,096,666 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
CeleraX40,574 - 48,714 (+)NCBICelera
Cytogenetic MapXq12NCBI
SSX1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38X48,255,392 - 48,267,444 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 EnsemblX48,255,392 - 48,267,444 (+)Ensemblhg38GRCh38
GRCh37X48,114,827 - 48,126,879 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36X47,999,741 - 48,011,823 (+)NCBIBuild 36Build 36hg18NCBI36
Build 34X47,871,050 - 47,883,133NCBI
Cytogenetic MapXp11.23NCBI
HuRefX45,814,294 - 45,837,908 (+)NCBIHuRef
CHM1_1X48,146,383 - 48,158,691 (+)NCBICHM1_1
T2T-CHM13v2.0X47,664,400 - 47,676,453 (+)NCBIT2T-CHM13v2.0
Ssxb2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X8,320,582 - 8,327,965 (-)NCBIGRCm39GRCm39mm39
GRCm39 EnsemblX8,320,584 - 8,327,965 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm38X8,454,343 - 8,461,726 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX8,454,345 - 8,461,726 (-)Ensemblmm10GRCm38
MGSCv37X8,031,469 - 8,038,852 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv36X7,611,304 - 7,618,685 (-)NCBIMGSCv36mm8
CeleraX3,018,270 - 3,025,653 (+)NCBICelera
Cytogenetic MapXA1.1NCBI
cM MapX3.83NCBI
LOC612524
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X41,676,082 - 41,687,062 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_TashaX16,053,850 - 16,064,828 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0X41,813,709 - 41,824,717 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
UMICH_Zoey_3.1X41,800,742 - 41,811,722 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0X41,789,022 - 41,800,005 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0X41,882,569 - 41,893,561 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0

Variants

.
Variants in Ssx1
13 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:73
Count of miRNA genes:68
Interacting mature miRNAs:70
Transcripts:ENSRNOT00000030146
Prediction methods:Microtar, Miranda, Pita, Rnahybrid
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
70165Bp64Blood pressure QTL 645.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)X400149344939387Rat
731181Uae27Urinary albumin excretion QTL 272.70.0059urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)X197044046970440Rat
631666Iddm5Insulin dependent diabetes mellitus QTL 5blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)X811148653111486Rat
634325Bw13Body weight QTL 130body mass (VT:0001259)body weight (CMO:0000012)X400149324470521Rat


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
sensory system
visual system
9 11 17 48 49 48 17 26 17 6 112 64 29 14 28 31 6 6

Sequence


Ensembl Acc Id: ENSRNOT00000030146   ⟹   ENSRNOP00000037344
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 EnsemblX16,604,449 - 16,612,210 (-)Ensembl
mRatBN7.2 EnsemblX13,931,470 - 13,939,720 (-)Ensembl
Rnor_6.0 EnsemblX14,905,337 - 14,910,778 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000085079   ⟹   ENSRNOP00000072628
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX13,931,988 - 13,938,955 (-)Ensembl
Rnor_6.0 EnsemblX14,905,337 - 14,910,727 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000093905   ⟹   ENSRNOP00000087992
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 EnsemblX16,604,453 - 16,612,210 (-)Ensembl
mRatBN7.2 EnsemblX13,931,988 - 13,939,720 (-)Ensembl
RefSeq Acc Id: XM_039100571   ⟹   XP_038956499
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X16,603,888 - 16,609,911 (-)NCBI
mRatBN7.2X13,931,433 - 13,939,732 (-)NCBI
RefSeq Acc Id: XM_039100572   ⟹   XP_038956500
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X16,603,888 - 16,612,203 (-)NCBI
mRatBN7.2X13,931,433 - 13,939,732 (-)NCBI
Protein Sequences
Protein RefSeqs XP_038956499 (Get FASTA)   NCBI Sequence Viewer  
  XP_038956500 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000037344
  ENSRNOP00000037344.6
  ENSRNOP00000087992.2
Ensembl Acc Id: ENSRNOP00000072628   ⟸   ENSRNOT00000085079
Ensembl Acc Id: ENSRNOP00000037344   ⟸   ENSRNOT00000030146
RefSeq Acc Id: XP_038956500   ⟸   XM_039100572
- Peptide Label: isoform X2
- UniProtKB: F1M0F5 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038956499   ⟸   XM_039100571
- Peptide Label: isoform X1
- UniProtKB: F1M0F5 (UniProtKB/TrEMBL)
Ensembl Acc Id: ENSRNOP00000087992   ⟸   ENSRNOT00000093905
Protein Domains
KRAB   KRAB-related

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-F1M0F5-F1-model_v2 AlphaFold F1M0F5 1-184 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:1593374 AgrOrtholog
BioCyc Gene G2FUF-2959 BioCyc
Ensembl Genes ENSRNOG00000027850 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000030146 ENTREZGENE
  ENSRNOT00000030146.8 UniProtKB/TrEMBL
  ENSRNOT00000093905.2 UniProtKB/TrEMBL
Gene3D-CATH 6.10.140.140 UniProtKB/TrEMBL
InterPro KRAB UniProtKB/TrEMBL
  KRAB_dom_sf UniProtKB/TrEMBL
  Krueppel-associated_box-rel UniProtKB/TrEMBL
  SSXRD_motif UniProtKB/TrEMBL
NCBI Gene 691903 ENTREZGENE
PANTHER PTHR14112 UniProtKB/TrEMBL
  SSXB10 PROTEIN-RELATED UniProtKB/TrEMBL
Pfam KRAB UniProtKB/TrEMBL
  SSXRD UniProtKB/TrEMBL
PharmGKB SSX1 RGD
PhenoGen Ssx1 PhenoGen
PROSITE KRAB UniProtKB/TrEMBL
  KRAB_RELATED UniProtKB/TrEMBL
RatGTEx ENSRNOG00000027850 RatGTEx
SMART KRAB UniProtKB/TrEMBL
Superfamily-SCOP SSF109640 UniProtKB/TrEMBL
UniProt A0A8I6A9U9_RAT UniProtKB/TrEMBL
  F1M0F5 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-06-03 Ssx1  SSX family member 1  Ssx1  synovial sarcoma, X breakpoint 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2010-05-05 Ssx1  synovial sarcoma, X breakpoint 1  LOC691903  similar to synovial sarcoma, X member B, breakpoint 10  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-01-09 LOC691903  similar to synovial sarcoma, X member B, breakpoint 10  LOC679104  similar to synovial sarcoma, X member B, breakpoint 10  Data merged from RGD:1591888 1643240 APPROVED
2006-11-20 LOC691903  similar to synovial sarcoma, X member B, breakpoint 10      Symbol and Name status set to provisional 70820 PROVISIONAL
2006-11-20 LOC679104  similar to synovial sarcoma, X member B, breakpoint 10      Symbol and Name status set to provisional 70820 PROVISIONAL