Ssb (small RNA binding exonuclease protection factor La) - Rat Genome Database

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Gene: Ssb (small RNA binding exonuclease protection factor La) Rattus norvegicus
Analyze
Symbol: Ssb
Name: small RNA binding exonuclease protection factor La
RGD ID: 620804
Description: Predicted to enable poly(U) RNA binding activity; sequence-specific mRNA binding activity; and tRNA binding activity. Involved in tRNA processing. Predicted to be located in cytoplasm. Predicted to be part of ribonucleoprotein complex. Predicted to be active in cytoplasmic stress granule; cytosol; and nucleus. Orthologous to human SSB (small RNA binding exonuclease protection factor La); PARTICIPATES IN tRNA maturation pathway; systemic lupus erythematosus pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran; 2,6-dinitrotoluene.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: la autoantigen homolog; la ribonucleoprotein; lupus La protein homolog; MGC93380; mRNA for autoantigen; Sjogren syndrome antigen B
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
GRCr8375,024,385 - 75,034,016 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl375,024,474 - 75,034,031 (+)EnsemblGRCr8
mRatBN7.2354,616,616 - 54,626,203 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl354,616,619 - 54,626,203 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx358,018,226 - 58,027,720 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0366,601,821 - 66,611,315 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0364,364,199 - 64,373,694 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0356,092,425 - 56,102,008 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl356,092,501 - 56,102,001 (+)Ensemblrn6Rnor6.0
Rnor_5.0362,727,433 - 62,737,034 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4352,001,106 - 52,010,611 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera354,176,184 - 54,185,689 (+)NCBICelera
RGSC_v3.1351,897,477 - 51,906,978 (+)NCBI
Cytogenetic Map3q21NCBI
JBrowse:




Disease Annotations     Click to see Annotation Detail View
COVID-19  (ISO)

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(1->4)-beta-D-glucan  (ISO)
17alpha-ethynylestradiol  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3,7,8-Tetrachlorodibenzofuran  (EXP)
2,6-dinitrotoluene  (EXP)
2-amino-14,16-dimethyloctadecan-3-ol  (ISO)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
3H-1,2-dithiole-3-thione  (EXP)
4,4'-sulfonyldiphenol  (EXP,ISO)
aflatoxin B1  (ISO)
aminoglutethimide  (ISO)
ammonium chloride  (EXP,ISO)
aristolochic acid A  (EXP,ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenous acid  (ISO)
benzo[a]pyrene  (ISO)
benzo[b]fluoranthene  (ISO)
beta-naphthoflavone  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
bisphenol AF  (ISO)
Bisphenol B  (ISO)
bisphenol F  (EXP,ISO)
Butylbenzyl phthalate  (EXP)
cadmium dichloride  (ISO)
caffeine  (ISO)
chloroquine  (ISO)
chlorpyrifos  (ISO)
chrysene  (ISO)
clofibric acid  (EXP)
cocaine  (EXP)
coumarin  (ISO)
cyclosporin A  (ISO)
DDE  (ISO)
deguelin  (ISO)
dexamethasone  (ISO)
diarsenic trioxide  (ISO)
dibutyl phthalate  (ISO)
dicrotophos  (ISO)
diethylstilbestrol  (ISO)
disodium selenite  (ISO)
enzyme inhibitor  (ISO)
epoxiconazole  (ISO)
ethyl methanesulfonate  (ISO)
flutamide  (EXP)
formaldehyde  (ISO)
FR900359  (ISO)
gentamycin  (EXP)
hypochlorous acid  (ISO)
indometacin  (ISO)
ivermectin  (ISO)
methyl methanesulfonate  (ISO)
mono(2-ethylhexyl) phthalate  (ISO)
nitrates  (ISO)
paracetamol  (EXP,ISO)
perfluorooctane-1-sulfonic acid  (ISO)
phenobarbital  (ISO)
potassium dichromate  (ISO)
resveratrol  (ISO)
SB 203580  (ISO)
sodium arsenite  (EXP,ISO)
sodium fluoride  (ISO)
succimer  (ISO)
tamoxifen  (ISO)
tebufenpyrad  (ISO)
testosterone enanthate  (ISO)
tetrachloromethane  (ISO)
tetraphene  (ISO)
thioacetamide  (EXP)
titanium dioxide  (ISO)
trichloroethene  (EXP)
triphenyl phosphate  (ISO)
vinclozolin  (EXP)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

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. Aberrant nuclear trafficking of La protein leads to disordered processing of associated precursor tRNAs. Intine RV, etal., Mol Cell 2002 May;9(5):1113-23.
3. 3' processing of eukaryotic precursor tRNAs. Maraia RJ and Lamichhane TN, Wiley Interdiscip Rev RNA. 2011 May-Jun;2(3):362-75. doi: 10.1002/wrna.64.
4. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
5. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
6. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
7. GOA pipeline RGD automated data pipeline
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. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
11. Sumoylation in axons triggers retrograde transport of the RNA-binding protein La. van Niekerk EA, etal., Proc Natl Acad Sci U S A. 2007 Jul 31;104(31):12913-8. Epub 2007 Jul 23.
Additional References at PubMed
PMID:3192525   PMID:7916708   PMID:9154801   PMID:10983981   PMID:11817591   PMID:12384597   PMID:12842046   PMID:15004549   PMID:16387655   PMID:16449655   PMID:17308035   PMID:17971306  
PMID:19135898   PMID:19292454   PMID:20629309   PMID:22658674   PMID:22681889   PMID:24965446   PMID:28755400   PMID:31505169   PMID:38372104  


Genomics

Comparative Map Data
Ssb
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8375,024,385 - 75,034,016 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl375,024,474 - 75,034,031 (+)EnsemblGRCr8
mRatBN7.2354,616,616 - 54,626,203 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl354,616,619 - 54,626,203 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx358,018,226 - 58,027,720 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0366,601,821 - 66,611,315 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0364,364,199 - 64,373,694 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0356,092,425 - 56,102,008 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl356,092,501 - 56,102,001 (+)Ensemblrn6Rnor6.0
Rnor_5.0362,727,433 - 62,737,034 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4352,001,106 - 52,010,611 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera354,176,184 - 54,185,689 (+)NCBICelera
RGSC_v3.1351,897,477 - 51,906,978 (+)NCBI
Cytogenetic Map3q21NCBI
SSB
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382169,798,871 - 169,812,064 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl2169,791,933 - 169,812,091 (+)Ensemblhg38GRCh38
GRCh372170,655,381 - 170,668,574 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 362170,363,635 - 170,376,821 (+)NCBIBuild 36Build 36hg18NCBI36
Build 342170,480,895 - 170,494,082NCBI
Celera2164,271,755 - 164,284,947 (+)NCBICelera
Cytogenetic Map2q31.1NCBI
HuRef2162,543,375 - 162,556,636 (+)NCBIHuRef
CHM1_12170,659,176 - 170,674,430 (+)NCBICHM1_1
T2T-CHM13v2.02170,276,405 - 170,289,608 (+)NCBIT2T-CHM13v2.0
Ssb
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39269,691,963 - 69,702,185 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl269,691,906 - 69,702,190 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm38269,861,562 - 69,871,846 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl269,861,562 - 69,871,846 (+)Ensemblmm10GRCm38
MGSCv37269,699,619 - 69,709,903 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv36269,662,467 - 69,672,643 (+)NCBIMGSCv36mm8
Celera271,531,605 - 71,541,890 (+)NCBICelera
Cytogenetic Map2C2NCBI
cM Map240.95NCBI
Ssb
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_0049554494,806,468 - 4,815,175 (-)NCBIChiLan1.0ChiLan1.0
SSB
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21372,459,193 - 72,472,464 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan12B72,474,165 - 72,487,436 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v02B57,071,158 - 57,084,428 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.12B174,536,382 - 174,549,609 (+)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2B174,536,382 - 174,549,604 (+)EnsemblpanPan2panpan1.1
SSB
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13614,465,088 - 14,476,786 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3614,465,129 - 14,476,609 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha3614,477,215 - 14,488,515 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.03614,584,035 - 14,595,782 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl3614,584,083 - 14,597,032 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.13614,667,144 - 14,678,600 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.03614,659,402 - 14,670,867 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.03614,770,849 - 14,782,579 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Ssb
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405303131,732,490 - 131,741,876 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936509286,398 - 298,147 (+)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_004936509286,397 - 295,779 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SSB
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1576,088,641 - 76,100,785 (+)EnsemblsusScr11Sscrofa11.1
Sscrofa11.11576,088,587 - 76,099,517 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21585,205,395 - 85,216,312 (+)NCBISscrofa10.2Sscrofa10.2susScr3
SSB
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11055,325,975 - 55,339,317 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1055,262,897 - 55,339,008 (+)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_023666040144,196,826 - 144,210,322 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Ssb
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247877,292,549 - 7,301,190 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
Ssb
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v1547,153,336 - 47,162,803 (+)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Ssb
189 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:46
Count of miRNA genes:36
Interacting mature miRNAs:43
Transcripts:ENSRNOT00000011174
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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1300178Hrtrt4Heart rate QTL 43.74heart pumping trait (VT:2000009)heart rate (CMO:0000002)351490129111359995Rat
61377Edpm3Estrogen-dependent pituitary mass QTL 37.050.038pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)373592611110333156Rat
1358293Bw38Body weight QTL 3860.0000031body mass (VT:0001259)body weight (CMO:0000012)374364268119364268Rat
1582238Bw68Body weight QTL 683.20.0064body mass (VT:0001259)body weight (CMO:0000012)373592512136118980Rat
1331795Rf30Renal function QTL 303.708urine potassium amount (VT:0010539)urine potassium level (CMO:0000128)35986366387321459Rat
1582239Epfw1Epididymal fat weight QTL 14.50.0006epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)373592512136118980Rat
70216Cm14Cardiac mass QTL 142.1heart mass (VT:0007028)heart wet weight (CMO:0000069)351581665184004958Rat
1354589Bw31Body weight QTL 313.3body mass (VT:0001259)body weight (CMO:0000012)35365182698651826Rat
2303593Gluco46Glucose level QTL 463blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)34887661993876619Rat
1354590Despr11Despair related QTL 110.000031locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)34887661993876619Rat
2298542Neuinf11Neuroinflammation QTL 113.9nervous system integrity trait (VT:0010566)spinal cord complement component 1, q subcomponent, B chain mRNA level (CMO:0002126)33540319997383526Rat
2292591Esta4Estrogen-induced thymic atrophy QTL 4thymus mass (VT:0004954)thymus wet weight (CMO:0000855)367641776167835660Rat
1358362Srcrt2Stress Responsive Cort QTL 22.78blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)358601291153936591Rat
631832Sach1Saccharin preference QTL 12.70.02consumption behavior trait (VT:0002069)calculated saccharin drink intake volume (CMO:0001600)34790417292904172Rat
737818Hcar12Hepatocarcinoma resistance QTL 122.6liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)349872657138829559Rat
1582218Bw74Body weight QTL 743.90.0021body mass (VT:0001259)body weight (CMO:0000012)373592512136118980Rat
1331777Bw24Body weight QTL 243.503body mass (VT:0001259)body weight (CMO:0000012)35986366387321459Rat
631647Bp122Blood pressure QTL 1226.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)35109256196092561Rat
1300169Bp177Blood pressure QTL 1772.96arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)33642511681425116Rat
9590286Uminl1Urine mineral level QTL 13.50.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)34865774493657744Rat
724523Tsu1Thymus enlargement suppressive QTL 13.84thymus mass (VT:0004954)thymus weight to body weight ratio (CMO:0000612)370845569136091483Rat
4889966Bss95Bone structure and strength QTL 954.4tibia area (VT:1000281)tibia-fibula cross-sectional area (CMO:0001718)33779691982796919Rat
2302276Bw82Body weight QTL 824.32body mass (VT:0001259)body weight (CMO:0000012)35986366383358329Rat
2292613Ept16Estrogen-induced pituitary tumorigenesis QTL 168.3pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)367641995130815812Rat
738019Anxrr10Anxiety related response QTL 103.9exploratory behavior trait (VT:0010471)number of entries into a discrete space in an experimental apparatus (CMO:0000960)358925062103925062Rat
631841Niddm39Non-insulin dependent diabetes mellitus QTL 393.36blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)370311536115311536Rat
9590136Scort3Serum corticosterone level QTL 323.370.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)34865774493657744Rat
61419Cia11Collagen induced arthritis QTL 115.6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)35076614595766145Rat
61356Bp37Blood pressure QTL 373blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)35109256196092561Rat
1358905Hrtrt17Heart rate QTL 175.90.000014heart pumping trait (VT:2000009)heart rate (CMO:0000002)336721849110333156Rat
1558650Cm48Cardiac mass QTL 4840.0001heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)35076614595766145Rat
8694196Abfw2Abdominal fat weight QTL 216.580.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)34865774493657744Rat
1358885Bp251Blood pressure QTL 2513.8arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)31141509147Rat
1354597Kidm13Kidney mass QTL 132.9kidney mass (VT:0002707)right kidney wet weight (CMO:0000082)342158111124558371Rat
1582249Bw77Body weight QTL 773.20.0025epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)37359251285062403Rat
2325840Bp345Blood pressure QTL 3450.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)33870893183708931Rat
8552950Pigfal12Plasma insulin-like growth factor 1 level QTL 127.3blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)34865774493657744Rat
631676Cm8Cardiac mass QTL 87.030.0001aorta mass (VT:0002845)aorta weight (CMO:0000076)33736373482363734Rat
2290452Scl56Serum cholesterol level QTL 562.26blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)33610140381101403Rat
8694386Bw159Body weight QTL 1594.520.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)34865774493657744Rat
1354604Bw36Body weight QTL 362.9body mass (VT:0001259)body weight (CMO:0000012)342158111124558371Rat
1358888Bp264Blood pressure QTL 2644.43arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)35675975141509147Rat
1358186Ept2Estrogen-induced pituitary tumorigenesis QTL 28.3pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)367641995130815812Rat

Markers in Region
AI232705  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2354,625,630 - 54,625,850 (+)MAPPERmRatBN7.2
Rnor_6.0356,101,438 - 56,101,657NCBIRnor6.0
Rnor_5.0362,736,446 - 62,736,665UniSTSRnor5.0
RGSC_v3.4352,010,043 - 52,010,262UniSTSRGSC3.4
Celera354,185,121 - 54,185,340UniSTS
Cytogenetic Map3q24-q32UniSTS
Cytogenetic Map3q21UniSTS
RH130588  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2354,625,102 - 54,625,289 (+)MAPPERmRatBN7.2
Rnor_6.0356,100,910 - 56,101,096NCBIRnor6.0
Rnor_5.0362,735,918 - 62,736,104UniSTSRnor5.0
RGSC_v3.4352,009,515 - 52,009,701UniSTSRGSC3.4
Celera354,184,593 - 54,184,779UniSTS
Cytogenetic Map3q24-q32UniSTS
RH133554  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2354,623,883 - 54,624,033 (+)MAPPERmRatBN7.2
Rnor_6.0356,099,691 - 56,099,840NCBIRnor6.0
Rnor_5.0362,734,699 - 62,734,848UniSTSRnor5.0
RGSC_v3.4352,008,296 - 52,008,445UniSTSRGSC3.4
Celera354,183,374 - 54,183,523UniSTS
RH 3.4 Map4528.52UniSTS
Cytogenetic Map3q24-q32UniSTS
UniSTS:479281  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24149,078,400 - 149,079,060 (+)MAPPERmRatBN7.2
Rnor_6.04147,930,023 - 147,930,682NCBIRnor6.0
Rnor_5.04211,213,427 - 211,214,086UniSTSRnor5.0
RGSC_v3.44152,156,876 - 152,157,535UniSTSRGSC3.4
Celera4137,967,943 - 137,968,602UniSTS
Cytogenetic Map3q24-q32UniSTS
Cytogenetic Map4q42UniSTS


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 67 165 91 90 59 92 59 6 356 192 11 144 81 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000011174   ⟹   ENSRNOP00000011175
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl375,024,474 - 75,034,031 (+)Ensembl
mRatBN7.2 Ensembl354,616,619 - 54,626,198 (+)Ensembl
Rnor_6.0 Ensembl356,092,501 - 56,102,001 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000100130   ⟹   ENSRNOP00000092285
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl354,616,699 - 54,626,082 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000105351   ⟹   ENSRNOP00000090563
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl354,616,619 - 54,626,203 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000112148   ⟹   ENSRNOP00000083561
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl375,026,120 - 75,034,031 (+)Ensembl
mRatBN7.2 Ensembl354,616,654 - 54,626,124 (+)Ensembl
RefSeq Acc Id: NM_031119   ⟹   NP_112381
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8375,024,509 - 75,034,014 (+)NCBI
mRatBN7.2354,616,693 - 54,626,199 (+)NCBI
Rnor_6.0356,092,501 - 56,102,006 (+)NCBI
Rnor_5.0362,727,433 - 62,737,034 (+)NCBI
RGSC_v3.4352,001,106 - 52,010,611 (+)RGD
Celera354,176,184 - 54,185,689 (+)RGD
Sequence:
RefSeq Acc Id: XM_006234321   ⟹   XP_006234383
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8375,024,385 - 75,034,016 (+)NCBI
mRatBN7.2354,616,616 - 54,626,203 (+)NCBI
Rnor_6.0356,092,425 - 56,102,008 (+)NCBI
Rnor_5.0362,727,433 - 62,737,034 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006234322   ⟹   XP_006234384
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8375,024,385 - 75,034,016 (+)NCBI
mRatBN7.2354,616,616 - 54,626,203 (+)NCBI
Rnor_6.0356,092,425 - 56,102,008 (+)NCBI
Rnor_5.0362,727,433 - 62,737,034 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006234323   ⟹   XP_006234385
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8375,024,385 - 75,034,016 (+)NCBI
mRatBN7.2354,616,616 - 54,626,203 (+)NCBI
Rnor_6.0356,092,425 - 56,102,008 (+)NCBI
Rnor_5.0362,727,433 - 62,737,034 (+)NCBI
Sequence:
RefSeq Acc Id: XM_063284632   ⟹   XP_063140702
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8375,024,385 - 75,034,016 (+)NCBI
RefSeq Acc Id: NP_112381   ⟸   NM_031119
- UniProtKB: P38656 (UniProtKB/Swiss-Prot),   Q66HM7 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006234383   ⟸   XM_006234321
- Peptide Label: isoform X2
- UniProtKB: P38656 (UniProtKB/Swiss-Prot),   F7FK94 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006234385   ⟸   XM_006234323
- Peptide Label: isoform X4
- UniProtKB: A0A8I6AH92 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006234384   ⟸   XM_006234322
- Peptide Label: isoform X3
- UniProtKB: A6HM21 (UniProtKB/TrEMBL),   A0A8I6AH92 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000011175   ⟸   ENSRNOT00000011174
Ensembl Acc Id: ENSRNOP00000092285   ⟸   ENSRNOT00000100130
Ensembl Acc Id: ENSRNOP00000090563   ⟸   ENSRNOT00000105351
Ensembl Acc Id: ENSRNOP00000083561   ⟸   ENSRNOT00000112148
RefSeq Acc Id: XP_063140702   ⟸   XM_063284632
- Peptide Label: isoform X1
- UniProtKB: A0A8I6AH92 (UniProtKB/TrEMBL)
Protein Domains
HTH La-type RNA-binding   RRM   XRRM

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-P38656-F1-model_v2 AlphaFold P38656 1-415 view protein structure

Transcriptome

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

Promoters
RGD ID:13692124
Promoter ID:EPDNEW_R2648
Type:initiation region
Name:Ssb_1
Description:Sjogren syndrome antigen B
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_6.0356,092,483 - 56,092,543EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:620804 AgrOrtholog
BioCyc Gene G2FUF-49498 BioCyc
Ensembl Genes ENSRNOG00000007998 Ensembl, ENTREZGENE
Ensembl Transcript ENSRNOT00000011174 ENTREZGENE
Gene3D-CATH 1.10.10.10 UniProtKB/Swiss-Prot
  3.30.70.330 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7192454 IMAGE-MGC_LOAD
InterPro La_dom_prot UniProtKB/Swiss-Prot
  La_HTH UniProtKB/Swiss-Prot
  La_RRM UniProtKB/Swiss-Prot
  Lupus_La UniProtKB/Swiss-Prot
  Nucleotide-bd_a/b_plait_sf UniProtKB/Swiss-Prot
  RBD_domain_sf UniProtKB/Swiss-Prot
  RRM_dom UniProtKB/Swiss-Prot
  WH-like_DNA-bd_sf UniProtKB/Swiss-Prot
  WH_DNA-bd_sf UniProtKB/Swiss-Prot
MGC_CLONE MGC:93380 IMAGE-MGC_LOAD
NCBI Gene 81783 ENTREZGENE
PANTHER LUPUS LA PROTEIN HOMOLOG UniProtKB/Swiss-Prot
  PTHR22792 UniProtKB/Swiss-Prot
Pfam PF05383 UniProtKB/Swiss-Prot
  RRM_1 UniProtKB/Swiss-Prot
  RRM_3 UniProtKB/Swiss-Prot
PhenoGen Ssb PhenoGen
PRINTS LUPUSLA UniProtKB/Swiss-Prot
PROSITE HTH_LA UniProtKB/Swiss-Prot
  RRM UniProtKB/Swiss-Prot
  XRRM UniProtKB/Swiss-Prot
RatGTEx ENSRNOG00000007998 RatGTEx
SMART RRM UniProtKB/Swiss-Prot
  SM00715 UniProtKB/Swiss-Prot
Superfamily-SCOP SSF46785 UniProtKB/Swiss-Prot
  SSF54928 UniProtKB/Swiss-Prot
UniProt A0A8I5ZZL0_RAT UniProtKB/TrEMBL
  A0A8I6AH92 ENTREZGENE
  A6HM21 ENTREZGENE, UniProtKB/TrEMBL
  A6HM23_RAT UniProtKB/TrEMBL
  A6HM24_RAT UniProtKB/TrEMBL
  F7FK94 ENTREZGENE, UniProtKB/TrEMBL
  LA_RAT UniProtKB/Swiss-Prot, ENTREZGENE
  Q4V8Q3_RAT UniProtKB/TrEMBL
  Q66HM7 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2019-04-02 Ssb  small RNA binding exonuclease protection factor La  Ssb  Sjogren syndrome antigen B  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-01-20 Ssb  Sjogren syndrome antigen B      Symbol and Name status set to approved 1299863 APPROVED
2002-08-07 Ssb  Sjogren syndrome antigen B      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_function interacts with pre-tRNAs and other nascent transcripts 737671