Rpsa (ribosomal protein SA) - Rat Genome Database

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Gene: Rpsa (ribosomal protein SA) Rattus norvegicus
Analyze
Symbol: Rpsa
Name: ribosomal protein SA
RGD ID: 71026
Description: Predicted to have laminin binding activity and ribosome binding activity. Predicted to be a structural constituent of ribosome. Involved in cell-cell adhesion and epithelial cell differentiation. Localizes to several cellular components, including basement membrane; cytosolic small ribosomal subunit; and neuronal cell body. Biomarker of irritable bowel syndrome and sciatic neuropathy. Orthologous to human RPSA (ribosomal protein SA); PARTICIPATES IN ribosome biogenesis pathway; translation pathway; INTERACTS WITH 1,1,1-Trichloro-2-(o-chlorophenyl)-2-(p-chlorophenyl)ethane; 1-naphthyl isothiocyanate; 17beta-estradiol.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: 37 kDa laminin receptor; 37 kDa laminin receptor precursor; 37/67 kDa laminin receptor; 37LRP; 40S ribosomal protein SA; 67 kDa laminin receptor; 67LR; laminin receptor 1 (67kD, ribosomal protein SA); laminin receptor 1 (ribosomal protein SA); laminin-binding protein precursor p40; lamR; Lamr1; LBP/p40; LRP/LR
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.28119,851,225 - 119,855,103 (+)NCBI
Rnor_6.0 Ensembl8128,806,129 - 128,809,986 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.08128,806,053 - 128,809,987 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.08128,006,814 - 128,010,671 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.48125,100,239 - 125,104,096 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.18125,119,975 - 125,123,833 (+)NCBI
Celera8118,996,237 - 119,000,094 (+)NCBICelera
Cytogenetic Map8q32NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(Z)-3-butylidenephthalide  (ISO)
1,1,1-Trichloro-2-(o-chlorophenyl)-2-(p-chlorophenyl)ethane  (EXP)
1,2-dichloroethane  (ISO)
1,2-dimethylhydrazine  (ISO)
1-naphthyl isothiocyanate  (EXP)
17alpha-ethynylestradiol  (ISO)
17beta-estradiol  (EXP,ISO)
17beta-hydroxy-17-methylestra-4,9,11-trien-3-one  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2,4,6-trinitrotoluene  (EXP)
2,4-dibromophenyl 2,4,5-tribromophenyl ether  (EXP,ISO)
2-nitrofluorene  (EXP)
3,3',5,5'-tetrabromobisphenol A  (ISO)
3-chloropropane-1,2-diol  (EXP)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
3H-1,2-dithiole-3-thione  (EXP)
4,4'-sulfonyldiphenol  (ISO)
4-(N-nitrosomethylamino)-1-(3-pyridyl)butan-1-one  (EXP)
5-aza-2'-deoxycytidine  (ISO)
5-azacytidine  (ISO)
6-propyl-2-thiouracil  (EXP)
7,12-dimethyltetraphene  (EXP)
aflatoxin B1  (EXP,ISO)
aldehydo-D-glucose  (EXP,ISO)
all-trans-retinoic acid  (ISO)
ammonium chloride  (EXP)
antirheumatic drug  (ISO)
Aroclor 1254  (ISO)
arsenous acid  (ISO)
bexarotene  (EXP)
bisphenol A  (EXP,ISO)
Brodifacoum  (EXP)
bucladesine  (ISO)
bufalin  (ISO)
C60 fullerene  (EXP)
carbon nanotube  (ISO)
chlorohydrocarbon  (EXP)
chloropicrin  (ISO)
choline  (ISO)
chromium(6+)  (ISO)
cisplatin  (ISO)
clofibrate  (ISO)
clofibric acid  (EXP)
cocaine  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
crocidolite asbestos  (ISO)
CU-O LINKAGE  (ISO)
cypermethrin  (EXP)
D-glucose  (EXP,ISO)
dexamethasone  (ISO)
diarsenic trioxide  (ISO)
dibutyl phthalate  (EXP)
dicrotophos  (ISO)
diethylstilbestrol  (EXP)
dioxygen  (EXP)
disodium selenite  (ISO)
dopamine  (ISO)
enzyme inhibitor  (ISO)
ethanol  (EXP,ISO)
fipronil  (EXP)
flutamide  (EXP)
folic acid  (ISO)
furan  (EXP)
gentamycin  (EXP)
glafenine  (EXP)
glucose  (EXP,ISO)
indometacin  (ISO)
L-ascorbic acid  (ISO)
L-methionine  (ISO)
lovastatin  (ISO)
medroxyprogesterone acetate  (ISO)
methapyrilene  (EXP)
methoxyacetic acid  (ISO)
methylseleninic acid  (ISO)
microcystin  (EXP)
N-methyl-4-phenylpyridinium  (ISO)
N-methyl-N'-nitro-N-nitrosoguanidine  (ISO)
N-nitrosodiethylamine  (EXP)
N-nitrosodimethylamine  (EXP)
naphthalene  (ISO)
nefazodone  (EXP)
nimesulide  (EXP)
paracetamol  (EXP,ISO)
perfluorooctanoic acid  (EXP,ISO)
phenobarbital  (EXP)
phenytoin  (ISO)
PhIP  (EXP)
piperonyl butoxide  (EXP)
pirinixic acid  (EXP,ISO)
pregnenolone 16alpha-carbonitrile  (ISO)
pyrogallol  (ISO)
quercetin  (ISO)
silicon dioxide  (ISO)
sodium fluoride  (ISO)
sulforaphane  (ISO)
T-2 toxin  (EXP)
tetrachloromethane  (EXP)
trimellitic anhydride  (ISO)
tungsten  (ISO)
valproic acid  (ISO)
vinclozolin  (EXP)
vorinostat  (ISO)
warfarin  (ISO)
zinc atom  (ISO)
zinc(0)  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:2146686   PMID:8452943   PMID:8706699   PMID:10079194   PMID:15489334   PMID:16263087   PMID:18056256   PMID:19946888   PMID:20458337   PMID:22681889   PMID:22871113   PMID:23106098  
PMID:23376485   PMID:24508265   PMID:24625528   PMID:24930395   PMID:25002582   PMID:29476059   PMID:31795399   PMID:31904090   PMID:32664509  


Genomics

Comparative Map Data
Rpsa
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.28119,851,225 - 119,855,103 (+)NCBI
Rnor_6.0 Ensembl8128,806,129 - 128,809,986 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.08128,806,053 - 128,809,987 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.08128,006,814 - 128,010,671 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.48125,100,239 - 125,104,096 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.18125,119,975 - 125,123,833 (+)NCBI
Celera8118,996,237 - 119,000,094 (+)NCBICelera
Cytogenetic Map8q32NCBI
RPSA
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl339,406,716 - 39,412,542 (+)EnsemblGRCh38hg38GRCh38
GRCh38339,406,720 - 39,412,542 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37339,448,211 - 39,454,033 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36339,422,917 - 39,429,037 (+)NCBINCBI36hg18NCBI36
Build 34339,423,189 - 39,429,034NCBI
Celera339,389,788 - 39,395,643 (+)NCBI
Cytogenetic Map3p22.1NCBI
HuRef339,491,541 - 39,497,373 (+)NCBIHuRef
CHM1_1339,399,293 - 39,405,084 (+)NCBICHM1_1
Rpsa
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm399119,956,832 - 119,961,435 (+)NCBIGRCm39mm39
GRCm39 Ensembl9119,956,755 - 119,961,435 (+)Ensembl
GRCm389120,127,766 - 120,132,369 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl9120,127,689 - 120,132,369 (+)EnsemblGRCm38mm10GRCm38
MGSCv379120,036,884 - 120,041,487 (+)NCBIGRCm37mm9NCBIm37
MGSCv369119,976,486 - 119,981,067 (+)NCBImm8
Celera9120,596,577 - 120,601,180 (+)NCBICelera
Cytogenetic Map9F4NCBI
cM Map971.41NCBI
Rpsa
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_00495542029,978,160 - 29,983,544 (-)NCBIChiLan1.0ChiLan1.0
RPSA
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1339,591,012 - 39,596,745 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl339,591,012 - 39,596,748 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0339,311,321 - 39,317,083 (+)NCBIMhudiblu_PPA_v0panPan3
RPSA
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1239,070,953 - 9,077,058 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl239,070,953 - 9,077,057 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha239,106,400 - 9,112,506 (+)NCBI
ROS_Cfam_1.0239,355,693 - 9,361,799 (+)NCBI
UMICH_Zoey_3.1239,168,769 - 9,174,877 (+)NCBI
UNSW_CanFamBas_1.0239,311,676 - 9,317,784 (+)NCBI
UU_Cfam_GSD_1.0239,305,292 - 9,311,400 (+)NCBI
Rpsa
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118195,485,476 - 195,489,915 (+)NCBI
SpeTri2.0NW_00493647328,624,110 - 28,628,488 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
RPSA
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1324,072,527 - 24,083,686 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11324,072,551 - 24,081,536 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21326,315,726 - 26,319,088 (-)NCBISscrofa10.2Sscrofa10.2susScr3
Sscrofa10.21326,391,337 - 26,393,313 (+)NCBISscrofa10.2Sscrofa10.2susScr3
RPSA
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11523,915 - 29,889 (-)NCBI
Rpsa
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462473078,808,270 - 78,813,782 (-)NCBI


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
738011Anxrr9Anxiety related response QTL 96.1exploratory behavior trait (VT:0010471)number of entries into a discrete space in an experimental apparatus (CMO:0000960)8102051964133307652Rat
738014Anxrr15Anxiety related response QTL 153.60.005locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)8104682575133307652Rat
1358893Bp263Blood pressure QTL 2635.01arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)8100873811133307652Rat
1358903Bp252Blood pressure QTL 25270.0001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)8100873811133307652Rat
61437Cia6Collagen induced arthritis QTL 6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)889058229132243842Rat
2300181Bmd55Bone mineral density QTL 555.70.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)883894304128894304Rat
2300182Bmd56Bone mineral density QTL 565.4femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)8104682575133307652Rat
724539Cm19Cardiac mass QTL 192.6heart mass (VT:0007028)calculated heart weight (CMO:0000073)8107769005129956433Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:43
Count of miRNA genes:42
Interacting mature miRNAs:43
Transcripts:ENSRNOT00000025225
Prediction methods:Miranda, 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.


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High 8 28 25 20 8 20 51 20 28 2
Medium 1 15 36 21 11 21 8 11 23 15 13 9 8
Low
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_017138 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008766672 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide BC060578 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473954 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  D25224 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FJ386454 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ209396 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ209463 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ209469 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ209490 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ209667 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ209729 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ210331 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ211189 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ212660 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ212893 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ213275 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ213317 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ213334 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ213623 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ213835 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ213894 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ214765 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ215242 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ215292 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ216063 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ216085 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ216130 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ216245 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ216788 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ216997 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ217664 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ219586 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ219785 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ220012 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ220017 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ220075 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ220084 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ220126 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ220134 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ220171 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ220184 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ220347 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ220461 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ220468 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ220661 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ220822 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ220904 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ220964 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ221103 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ221334 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ221443 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ221672 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ222093 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ222280 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ222542 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ222757 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ223223 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ224747 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ224954 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ225510 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ226054 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ226408 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ226780 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ227028 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ227056 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ227293 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ227600 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ228002 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ228212 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ229290 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ229305 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ229367 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ229516 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ229579 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ229598 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ229712 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ229787 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ229850 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ229859 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ229890 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ229918 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ229945 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ229970 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ230088 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ230106 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ230180 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ230258 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ231469 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ231622 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ232305 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ232568 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ233068 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ233112 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ233231 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ233340 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ233547 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ233919 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ234511 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ234563 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ234742 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ234765 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ234772 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000200 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  U04942 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000025225   ⟹   ENSRNOP00000025224
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl8128,806,129 - 128,809,986 (+)Ensembl
RefSeq Acc Id: NM_017138   ⟹   NP_058834
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.28119,851,246 - 119,855,103 (+)NCBI
Rnor_6.08128,806,129 - 128,809,986 (+)NCBI
Rnor_5.08128,006,814 - 128,010,671 (+)NCBI
RGSC_v3.48125,100,239 - 125,104,096 (+)RGD
Celera8118,996,237 - 119,000,094 (+)RGD
Sequence:
RefSeq Acc Id: XM_008766672   ⟹   XP_008764894
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.28119,851,225 - 119,855,103 (+)NCBI
Rnor_6.08128,806,053 - 128,809,987 (+)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_058834   ⟸   NM_017138
- UniProtKB: P38983 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_008764894   ⟸   XM_008766672
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000025224   ⟸   ENSRNOT00000025225

Transcriptome

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

Promoters
RGD ID:13696382
Promoter ID:EPDNEW_R6906
Type:multiple initiation site
Name:Rpsa_1
Description:ribosomal protein SA
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_6.08128,806,115 - 128,806,175EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Damaging Variants


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
8 128008202 128008203 G C snv IS-Tlk/Kyo (KyushuU), BDIX/NemOda (KyushuU), LE/Stm (KyushuU), IS/Kyo (KyushuU), HWY/Slc (KyushuU), LEC/Tj (KyushuU)
8 128008205 128008206 A T snv IS/Kyo (KyushuU), IS-Tlk/Kyo (KyushuU), LE/Stm (KyushuU), HWY/Slc (KyushuU), BDIX/NemOda (KyushuU), LEC/Tj (KyushuU)
8 128008240 128008241 C T snv LEC/Tj (KyushuU), BDIX/NemOda (KyushuU), BDIX.Cg-Tal/NemOda (KyushuU), IS-Tlk/Kyo (KyushuU), IS/Kyo (KyushuU), KFRS3B/Kyo (KyushuU), HWY/Slc (KyushuU), F344/Jcl (KyushuU), LE/Stm (KyushuU), HTX/Kyo (KyushuU)


Assembly: RGSC_v3.4

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
8 125100976 125100977 C T snv LCR/1Mco (UMich), FHL/EurMcwi (MCW), HCR/2Mco (UMich), FHH/EurMcwi (MCW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:71026 AgrOrtholog
Ensembl Genes ENSRNOG00000018645 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000025224 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000025225 ENTREZGENE, UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:6919235 IMAGE-MGC_LOAD
InterPro 40S_ribosomal_SA UniProtKB/Swiss-Prot
  40S_SA_C UniProtKB/Swiss-Prot
  Ribosomal_S2 UniProtKB/Swiss-Prot
  Ribosomal_S2_CS UniProtKB/Swiss-Prot
  Ribosomal_S2_euk UniProtKB/Swiss-Prot
  Ribosomal_S2_euk/arc UniProtKB/Swiss-Prot
  Ribosomal_S2_flav_dom_sf UniProtKB/Swiss-Prot
KEGG Report rno:29236 UniProtKB/Swiss-Prot
MGC_CLONE MGC:72885 IMAGE-MGC_LOAD
NCBI Gene 29236 ENTREZGENE
PANTHER PTHR11489 UniProtKB/Swiss-Prot
Pfam 40S_SA_C UniProtKB/Swiss-Prot
  Ribosomal_S2 UniProtKB/Swiss-Prot
PhenoGen Rpsa PhenoGen
PRINTS RIBOSOMALS2 UniProtKB/Swiss-Prot
PROSITE RIBOSOMAL_S2_1 UniProtKB/Swiss-Prot
  RIBOSOMAL_S2_2 UniProtKB/Swiss-Prot
Superfamily-SCOP SSF52313 UniProtKB/Swiss-Prot
TIGRFAMs uS2_euk_arch UniProtKB/Swiss-Prot
UniProt P38983 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary B6ZB78 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2006-03-30 Rpsa  ribosomal protein SA  Lamr1  laminin receptor 1 (ribosomal protein SA)  Symbol and Name updated 1299863 APPROVED
2005-11-17 Lamr1  laminin receptor 1 (ribosomal protein SA)      Name updated 1299863 APPROVED
2002-07-09 Lamr1  laminin receptor 1 (67kD, ribosomal protein SA)      Symbol and Name updated to reflect Human and Mouse nomenclature 70877 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_expression expressed during the development and differentiation of the intestine and liver, and undifferentiated, mitotically active crypt cells 633045
gene_protein 67 kDa protein 633045