Ssna1 (SS nuclear autoantigen 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: Ssna1 (SS nuclear autoantigen 1) Rattus norvegicus
Analyze
Symbol: Ssna1
Name: SS nuclear autoantigen 1
RGD ID: 1310259
Description: Predicted to enable identical protein binding activity and microtubule binding activity. Predicted to be involved in axonogenesis; cell division; and microtubule nucleation. Predicted to act upstream of or within intraciliary transport; receptor clustering; and smoothened signaling pathway. Predicted to be located in cytoskeleton; midbody; and supramolecular fiber. Predicted to be active in axon; centrosome; and ciliary basal body. Orthologous to human SSNA1 (SS nuclear autoantigen 1); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,4,6-trinitrotoluene; 4,4'-sulfonyldiphenol.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC311802; microtubule nucleation factor SSNA1; Sjoegren syndrome nuclear autoantigen 1; Sjogren syndrome nuclear autoantigen 1; Sjogren's syndrome nuclear autoantigen 1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8328,483,107 - 28,484,571 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl328,483,107 - 28,484,608 (-)EnsemblGRCr8
mRatBN7.238,084,949 - 8,086,417 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl38,084,974 - 8,086,356 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx311,189,448 - 11,190,912 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0319,775,678 - 19,777,142 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0317,965,521 - 17,966,985 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.032,489,017 - 2,490,481 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl32,489,042 - 2,490,392 (-)Ensemblrn6Rnor6.0
Rnor_5.032,470,451 - 2,471,889 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.433,435,747 - 3,436,469 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera32,911,494 - 2,912,958 (-)NCBICelera
RGSC_v3.133,435,392 - 3,436,283 (-)NCBI
Cytogenetic Map3p13NCBI
JBrowse:




Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
axon  (IBA,ISO)
axoneme  (IEA,ISO)
centriole  (IEA,ISO)
centrosome  (IBA,IEA,ISO)
ciliary basal body  (IBA,IEA,ISO)
midbody  (IEA,ISO)
plasma membrane  (IEA)
supramolecular fiber  (IEA,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. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:11591653   PMID:12477932   PMID:21289087   PMID:21399614   PMID:21516116   PMID:25390646   PMID:25416956   PMID:27107012  


Genomics

Comparative Map Data
Ssna1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8328,483,107 - 28,484,571 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl328,483,107 - 28,484,608 (-)EnsemblGRCr8
mRatBN7.238,084,949 - 8,086,417 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl38,084,974 - 8,086,356 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx311,189,448 - 11,190,912 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0319,775,678 - 19,777,142 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0317,965,521 - 17,966,985 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.032,489,017 - 2,490,481 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl32,489,042 - 2,490,392 (-)Ensemblrn6Rnor6.0
Rnor_5.032,470,451 - 2,471,889 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.433,435,747 - 3,436,469 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera32,911,494 - 2,912,958 (-)NCBICelera
RGSC_v3.133,435,392 - 3,436,283 (-)NCBI
Cytogenetic Map3p13NCBI
SSNA1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh389137,188,676 - 137,190,366 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl9137,188,657 - 137,190,370 (+)Ensemblhg38GRCh38
GRCh379140,083,128 - 140,084,818 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 369139,202,954 - 139,204,639 (+)NCBIBuild 36Build 36hg18NCBI36
Build 349137,358,969 - 137,360,652NCBI
Celera9110,597,085 - 110,598,853 (+)NCBICelera
Cytogenetic Map9q34.3NCBI
HuRef9109,543,071 - 109,544,839 (+)NCBIHuRef
CHM1_19140,231,743 - 140,233,511 (+)NCBICHM1_1
T2T-CHM13v2.09149,426,339 - 149,428,029 (+)NCBIT2T-CHM13v2.0
Ssna1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39225,161,051 - 25,162,430 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl225,161,051 - 25,162,450 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm38225,271,039 - 25,272,418 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl225,271,039 - 25,272,438 (-)Ensemblmm10GRCm38
MGSCv37225,126,559 - 25,127,938 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv36225,087,542 - 25,094,421 (-)NCBIMGSCv36mm8
Celera224,998,730 - 25,000,109 (-)NCBICelera
Cytogenetic Map2A3NCBI
cM Map217.12NCBI
Ssna1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555135,194,308 - 5,195,721 (+)Ensembl
ChiLan1.0NW_0049555135,194,308 - 5,195,721 (+)NCBIChiLan1.0ChiLan1.0
SSNA1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan192,211,584 - 2,213,367 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v09108,248,263 - 108,250,002 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.19137,217,653 - 137,219,406 (+)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl9137,217,653 - 137,219,406 (+)EnsemblpanPan2panpan1.1
SSNA1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1948,474,132 - 48,475,731 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl948,474,139 - 48,475,691 (-)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha947,664,954 - 47,666,564 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0949,339,809 - 49,341,406 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl949,339,811 - 49,341,350 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1948,116,208 - 48,117,818 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0948,415,021 - 48,416,631 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0948,462,180 - 48,463,790 (-)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Ssna1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404947202,577,630 - 202,579,125 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936669795,950 - 797,422 (-)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_004936669795,929 - 797,422 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SSNA1
(Sus scrofa - pig)		 No map positions available.
SSNA1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.112999,142 - 1,000,877 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl12999,327 - 1,000,831 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_0236660584,304,376 - 4,306,111 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Ssna1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_004624760759,469 - 760,797 (-)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_004624760759,471 - 760,797 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Ssna1
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v1511,911,270 - 11,912,717 (+)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Ssna1
6 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:108
Count of miRNA genes:91
Interacting mature miRNAs:99
Transcripts:ENSRNOT00000014993
Prediction methods:Microtar, 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
1558647Cm46Cardiac mass QTL 465.40.0000055heart mass (VT:0007028)heart wet weight (CMO:0000069)32267715050766390Rat
6893355Bw101Body weight QTL 1010.40.38body mass (VT:0001259)body weight (CMO:0000012)3576639050766390Rat
10450811Scl73Serum cholesterol level QTL 734.70.001blood LDL cholesterol amount (VT:0000181)blood low density lipoprotein cholesterol level (CMO:0000053)3290432947904329Rat
2292615Ept17Estrogen-induced pituitary tumorigenesis QTL 176.7pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)3655634751556347Rat
10450808Scl72Serum cholesterol level QTL 724.40.001blood LDL cholesterol amount (VT:0000181)blood low density lipoprotein cholesterol level (CMO:0000053)3290432947904329Rat
10450806Scl71Serum cholesterol level QTL 715.80.001blood LDL cholesterol amount (VT:0000181)blood low density lipoprotein cholesterol level (CMO:0000053)3290432947904329Rat
1558654Bw56Body weight QTL 564.50.0000171body mass (VT:0001259)body weight (CMO:0000012)3576639050766390Rat
1298526Arunc3Aerobic running capacity QTL 32.2exercise endurance trait (VT:0002332)longest distance run on treadmill (CMO:0001406)3612543751125437Rat
631545Bp85Blood pressure QTL 853.1arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3136721849Rat
1358885Bp251Blood pressure QTL 2513.8arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)31141509147Rat
631679Cm10Cardiac mass QTL 107.340.0001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)3655634751556347Rat
1558657Cm43Cardiac mass QTL 436.63e-08heart mass (VT:0007028)heart wet weight (CMO:0000069)32267715050766390Rat
631568Bp92Blood pressure QTL 922.20.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)31527234860272348Rat
6893363Bw105Body weight QTL 1052.60.0036body mass (VT:0001259)body weight (CMO:0000012)3576639050766390Rat
1358888Bp264Blood pressure QTL 2644.43arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)35675975141509147Rat
1358185Ept6Estrogen-induced pituitary tumorigenesis QTL 66.7pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)3655634751556347Rat

Markers in Region
RH128511  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.238,085,113 - 8,085,304 (+)MAPPERmRatBN7.2
Rnor_6.032,489,182 - 2,489,372NCBIRnor6.0
Rnor_5.032,470,595 - 2,470,785UniSTSRnor5.0
RGSC_v3.433,435,213 - 3,435,403UniSTSRGSC3.4
Celera32,911,659 - 2,911,849UniSTS
Cytogenetic Map3p13UniSTS


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
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
16 12 67 164 91 90 59 92 59 6 356 192 11 143 81 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000014993   ⟹   ENSRNOP00000014993
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl328,483,107 - 28,484,571 (-)Ensembl
mRatBN7.2 Ensembl38,084,974 - 8,086,352 (-)Ensembl
Rnor_6.0 Ensembl32,489,042 - 2,490,392 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000119530   ⟹   ENSRNOP00000090440
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl328,483,107 - 28,484,608 (-)Ensembl
mRatBN7.2 Ensembl38,084,974 - 8,086,356 (-)Ensembl
RefSeq Acc Id: NM_001303617   ⟹   NP_001290546
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8328,483,107 - 28,484,571 (-)NCBI
mRatBN7.238,084,949 - 8,086,413 (-)NCBI
Rnor_6.032,489,017 - 2,490,481 (-)NCBI
Celera32,911,494 - 2,912,958 (-)NCBI
Sequence:
RefSeq Acc Id: NR_130647
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8328,483,107 - 28,484,571 (-)NCBI
mRatBN7.238,084,949 - 8,086,413 (-)NCBI
Rnor_6.032,489,017 - 2,490,481 (-)NCBI
Celera32,911,494 - 2,912,958 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039105201   ⟹   XP_038961129
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8328,483,128 - 28,484,548 (-)NCBI
mRatBN7.238,084,970 - 8,086,417 (-)NCBI
RefSeq Acc Id: NP_001290546   ⟸   NM_001303617
- UniProtKB: B2RZ20 (UniProtKB/TrEMBL),   F7FL58 (UniProtKB/TrEMBL),   A0A9K3Y6S6 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000014993   ⟸   ENSRNOT00000014993
RefSeq Acc Id: XP_038961129   ⟸   XM_039105201
- Peptide Label: isoform X1
Ensembl Acc Id: ENSRNOP00000090440   ⟸   ENSRNOT00000119530

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-B2RZ20-F1-model_v2 AlphaFold B2RZ20 1-119 view protein structure

Transcriptome

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

Promoters
RGD ID:13691905
Promoter ID:EPDNEW_R2391
Type:multiple initiation site
Name:Ssna1_1
Description:SS nuclear autoantigen 1
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_6.032,490,438 - 2,490,498EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1310259 AgrOrtholog
BioCyc Gene G2FUF-50466 BioCyc
Ensembl Genes ENSRNOG00000011093 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000014993 ENTREZGENE
  ENSRNOT00000014993.8 UniProtKB/TrEMBL
  ENSRNOT00000119530.2 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7304458 IMAGE-MGC_LOAD
InterPro SSNA1_fam UniProtKB/TrEMBL
KEGG Report rno:311802 UniProtKB/TrEMBL
MGC_CLONE MGC:189140 IMAGE-MGC_LOAD
NCBI Gene 311802 ENTREZGENE
PANTHER PTHR28661 UniProtKB/TrEMBL
  SJOEGREN SYNDROME NUCLEAR AUTOANTIGEN 1 UniProtKB/TrEMBL
PhenoGen Ssna1 PhenoGen
RatGTEx ENSRNOG00000011093 RatGTEx
UniProt A0A8I6ACI2_RAT UniProtKB/TrEMBL
  A0A9K3Y6S6 ENTREZGENE, UniProtKB/TrEMBL
  B2RZ20 ENTREZGENE, UniProtKB/TrEMBL
  F7FL58 ENTREZGENE
UniProt Secondary F7FL58 UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-06-03 Ssna1  SS nuclear autoantigen 1  Ssna1  Sjogren syndrome nuclear autoantigen 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-10-23 Ssna1  Sjogren syndrome nuclear autoantigen 1  Ssna1  Sjogren's syndrome nuclear autoantigen 1   Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Ssna1  Sjogren's syndrome nuclear autoantigen 1   Ssna1_predicted  Sjogren's syndrome nuclear autoantigen 1 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Ssna1_predicted  Sjogren's syndrome nuclear autoantigen 1 (predicted)      Symbol and Name status set to approved 70820 APPROVED