Rps16 (ribosomal protein S16) - Rat Genome Database

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Gene: Rps16 (ribosomal protein S16) Rattus norvegicus
Analyze
Symbol: Rps16
Name: ribosomal protein S16
RGD ID: 621031
Description: Predicted to enable RNA binding activity. Predicted to be a structural constituent of ribosome. Involved in liver regeneration. Part of cytosolic small ribosomal subunit. Orthologous to human RPS16 (ribosomal protein S16); PARTICIPATES IN ribosome biogenesis pathway; translation pathway; INTERACTS WITH 1-naphthyl isothiocyanate; 17beta-estradiol; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: 40S ribosomal protein S16
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2183,643,066 - 83,646,056 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl183,643,130 - 83,646,206 (+)Ensembl
Rnor_6.0185,405,499 - 85,408,444 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl185,405,512 - 85,408,444 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0186,620,608 - 86,623,555 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4183,444,204 - 83,463,592 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1183,538,778 - 83,541,448 (+)NCBI
Celera178,039,401 - 78,042,346 (+)NCBICelera
Cytogenetic Map1q21NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


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. Structures of the human and Drosophila 80S ribosome. Anger AM, etal., Nature. 2013 May 2;497(7447):80-5. doi: 10.1038/nature12104.
2. Molecular cloning and sequence analysis of the human ribosomal protein S16. Batra SK, etal., J Biol Chem. 1991 Apr 15;266(11):6830-3.
3. The primary structure of rat ribosomal protein S16. Chan YL, etal., FEBS Lett 1990 Apr 9;263(1):85-8.
4. Isolation of eukaryotic ribosomal proteins. Purification and characterization of the 40 S ribosomal subunit proteins Sa, Sc, S3a, S3b, S5', S9, S10, S11, S12, S14, S15, S15', S16, S17, S18, S19, S20, S21, S26, S27', and S29. Collatz E, etal., J Biol Chem. 1977 Dec 25;252(24):9071-80.
5. Coordinate regulation of ribosomal protein mRNA level in regenerating rat liver. Study with the corresponding mouse cloned cDNAs. Faliks D and Meyuhas O, Nucleic Acids Res. 1982 Feb 11;10(3):789-801.
6. 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.
7. Immunoelectron microscopic studies on the location of ribosomal proteins on the surface of the 40S ribosomal subunit from rat liver. Lutsch G, etal., Eur J Cell Biol. 1990 Feb;51(1):140-50.
8. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
9. Functional dichotomy of ribosomal proteins during the synthesis of mammalian 40S ribosomal subunits. O'Donohue MF, etal., J Cell Biol. 2010 Sep 6;190(5):853-66. doi: 10.1083/jcb.201005117.
10. GOA pipeline RGD automated data pipeline
11. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
12. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
13. Comprehensive gene review and curation RGD comprehensive gene curation
Additional References at PubMed
PMID:8706699   PMID:12477932   PMID:15883184   PMID:17881366   PMID:18697920   PMID:19946888   PMID:20439489   PMID:20458337   PMID:21423176   PMID:22681889   PMID:23106098   PMID:23979707  
PMID:24625528   PMID:24930395   PMID:26316108   PMID:29476059   PMID:30053369  


Genomics

Comparative Map Data
Rps16
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2183,643,066 - 83,646,056 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl183,643,130 - 83,646,206 (+)Ensembl
Rnor_6.0185,405,499 - 85,408,444 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl185,405,512 - 85,408,444 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0186,620,608 - 86,623,555 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4183,444,204 - 83,463,592 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1183,538,778 - 83,541,448 (+)NCBI
Celera178,039,401 - 78,042,346 (+)NCBICelera
Cytogenetic Map1q21NCBI
RPS16
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381939,433,137 - 39,435,949 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl1939,433,137 - 39,435,949 (-)EnsemblGRCh38hg38GRCh38
GRCh371939,923,777 - 39,926,589 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361944,615,687 - 44,618,458 (-)NCBINCBI36hg18NCBI36
Build 341944,615,691 - 44,618,478NCBI
Celera1936,725,537 - 36,728,308 (-)NCBI
Cytogenetic Map19q13.2NCBI
HuRef1936,370,438 - 36,373,209 (-)NCBIHuRef
CHM1_11939,924,493 - 39,927,264 (-)NCBICHM1_1
T2T-CHM13v2.01942,237,400 - 42,240,212 (-)NCBI
Rps16
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39728,050,114 - 28,052,123 (+)NCBIGRCm39mm39
GRCm39 Ensembl728,050,077 - 28,052,580 (+)Ensembl
GRCm38728,350,689 - 28,352,698 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl728,350,652 - 28,353,155 (+)EnsemblGRCm38mm10GRCm38
MGSCv37729,135,708 - 29,137,717 (+)NCBIGRCm37mm9NCBIm37
MGSCv36728,059,510 - 28,061,456 (+)NCBImm8
Celera722,912,329 - 22,914,338 (+)NCBICelera
Cytogenetic Map7A3NCBI
Rps16
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955468130,244 - 132,258 (+)EnsemblChiLan1.0
ChiLan1.0NW_004955468130,244 - 132,258 (+)NCBIChiLan1.0ChiLan1.0
RPS16
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11945,079,106 - 45,081,985 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1945,079,106 - 45,085,351 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01936,531,284 - 36,534,156 (-)NCBIMhudiblu_PPA_v0panPan3
RPS16
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11113,795,239 - 113,798,380 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1113,644,100 - 113,828,488 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1113,198,999 - 113,202,134 (+)NCBI
ROS_Cfam_1.01114,396,221 - 114,399,355 (+)NCBI
ROS_Cfam_1.0 Ensembl1114,396,295 - 114,429,130 (+)Ensembl
UMICH_Zoey_3.11113,955,179 - 113,958,155 (+)NCBI
UNSW_CanFamBas_1.01113,588,188 - 113,591,111 (+)NCBI
UU_Cfam_GSD_1.01114,582,841 - 114,585,969 (+)NCBI
Rps16
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934913,843,678 - 13,846,698 (-)NCBI
SpeTri2.0NW_0049366612,271,747 - 2,274,769 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
RPS16
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl648,085,678 - 48,088,423 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1648,085,684 - 48,088,368 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.214143,655,447 - 143,658,128 (+)NCBISscrofa10.2Sscrofa10.2susScr3
RPS16
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1634,039,470 - 34,042,278 (-)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl634,039,251 - 34,042,313 (-)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366607312,060,718 - 12,063,569 (-)NCBIVero_WHO_p1.0
Rps16
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462479412,754,849 - 12,760,528 (-)EnsemblHetGla_female_1.0hetGla2
HetGla 1.0NW_00462479412,758,224 - 12,760,482 (-)NCBIHetGla_female_1.0hetGla2

Position Markers
RH134025  
Rat AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map1q21UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1554320Bmd1Bone mineral density QTL 112.20.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)150910886060548Rat
631688Hcas2Hepatocarcinoma susceptibility QTL 230.0001liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)15925874115540829Rat
631495Bp96Blood pressure QTL 964.52arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)122340647102268831Rat
1358359Sradr1Stress Responsive Adrenal Weight QTL 14.74adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)130882023123479925Rat
70225Bp58Blood pressure QTL 583.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)132356093162846471Rat
1300172Bp172Blood pressure QTL 1723.56arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)13273727390665040Rat
10059597Bp377Blood pressure QTL 3773.420.025arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)132737458199368955Rat
2313051Bss57Bone structure and strength QTL 573.70.0001tibia strength trait (VT:1000284)bone polar moment of inertia (CMO:0001558)143284731118944897Rat
2313059Bss55Bone structure and strength QTL 553.20.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)143284731118944897Rat
2313072Bss53Bone structure and strength QTL 534.30.0001tibia length (VT:0004357)tibia length (CMO:0000450)143284731118944897Rat
2313078Bss54Bone structure and strength QTL 543.50.0001tibia area (VT:1000281)tibia midshaft cross-sectional area (CMO:0001717)143284731118944897Rat
2313094Bss58Bone structure and strength QTL 583.70.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)143284731118944897Rat
2313098Bmd70Bone mineral density QTL 703.60.0001tibia mineral mass (VT:1000283)cortical volumetric bone mineral density (CMO:0001730)143284731118944897Rat
2313099Bss56Bone structure and strength QTL 562.40.0001tibia size trait (VT:0100001)tibia midshaft endosteal cross-sectional area (CMO:0001716)143284731118944897Rat
2302059Pia36Pristane induced arthritis QTL 363.80.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G1 level (CMO:0002115)14333300288333002Rat
2313402Anxrr24Anxiety related response QTL 24aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)148963584144267916Rat
1578649Bmd8Bone mineral density QTL 84.9femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)14939317294393172Rat
1578654Bss10Bone structure and strength QTL 104femur morphology trait (VT:0000559)femoral neck cortical cross-sectional area (CMO:0001702)149393172159356837Rat
634314Niddm44Non-insulin dependent diabetes mellitus QTL 44blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)149393289199050459Rat
6903308Scl36Serum cholesterol QTL 3620.0125blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)15386304190532583Rat
61342Bp27Blood pressure QTL 273.40.0006arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)15673266898773277Rat
2300164Bmd44Bone mineral density QTL 445.40.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)156949932101949932Rat
2298545Neuinf8Neuroinflammation QTL 84.6nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)157336763151090257Rat
1300121Hrtrt1Heart rate QTL 13.7heart pumping trait (VT:2000009)heart rate (CMO:0000002)165789093115540829Rat
7421628Bp361Blood pressure QTL 3610.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)166023617118608521Rat
631512Scl6Serum cholesterol level QTL 69.6blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)17219768090508767Rat
1358192Ept13Estrogen-induced pituitary tumorigenesis QTL 133.4pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)177494165122494165Rat
10054135Gmadr2Adrenal mass QTL 21.970.0129adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)177857876122857876Rat
1549903Bp267Blood pressure QTL 267arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)177876254106047988Rat
61344Bp29Blood pressure QTL 297.5arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)178350581123350581Rat
7411712Strs4Sensitivity to stroke QTL 48.7cerebrum integrity trait (VT:0010549)percentage of study population developing cerebrovascular lesions during a period of time (CMO:0000932)178430536123430536Rat
61433Cia2Collagen induced arthritis QTL 25joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)17843075491209302Rat
1582234Gluco18Glucose level QTL 183.40.0003blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)178479925123479925Rat
4889494Scort2Serum corticosterone level QTL 24.2blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)180592172125592172Rat
1578780Cm52Cardiac mass QTL 523.30.0001heart mass (VT:0007028)heart wet weight (CMO:0000069)181591954219808434Rat
2313083Bmd74Bone mineral density QTL 7440.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)182174743118944897Rat
738022Anxrr13Anxiety related response QTL 134.60.00039locomotor behavior trait (VT:0001392)number of 20 x 20 cm floor squares crossed into, out of or within a discrete space in an experimental apparatus (CMO:0001514)183547917128547917Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:40
Count of miRNA genes:35
Interacting mature miRNAs:39
Transcripts:ENSRNOT00000026576
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.


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 2 3 4 2 1
Medium 1 43 57 41 16 41 8 11 74 31 39 10 8
Low
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001169146 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006228612 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide BC064030 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC084715 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC159438 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473979 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ211832 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ221089 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ221637 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ221660 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ221692 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ222913 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ223100 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ223384 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ223396 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ224101 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ228433 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ229060 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ231245 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000033 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000026576   ⟹   ENSRNOP00000026576
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl183,643,130 - 83,646,206 (+)Ensembl
Rnor_6.0 Ensembl185,405,512 - 85,408,444 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000093203
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl185,407,402 - 85,408,423 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000093351
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl185,405,751 - 85,406,493 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000093558   ⟹   ENSRNOP00000076119
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl183,643,130 - 83,646,206 (+)Ensembl
Rnor_6.0 Ensembl185,405,773 - 85,408,413 (-)Ensembl
RefSeq Acc Id: NM_001169146   ⟹   NP_001162617
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2183,643,111 - 83,646,056 (+)NCBI
Rnor_6.0185,405,499 - 85,408,444 (-)NCBI
Rnor_5.0186,620,608 - 86,623,555 (-)NCBI
Celera178,039,401 - 78,042,346 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006228612   ⟹   XP_006228674
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2183,643,066 - 83,645,802 (+)NCBI
Rnor_6.0185,405,751 - 85,408,443 (-)NCBI
Rnor_5.0186,620,608 - 86,623,555 (-)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_001162617   ⟸   NM_001169146
- UniProtKB: P62250 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006228674   ⟸   XM_006228612
- Peptide Label: isoform X1
- UniProtKB: A0A1W2Q631 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000026576   ⟸   ENSRNOT00000026576
RefSeq Acc Id: ENSRNOP00000076119   ⟸   ENSRNOT00000093558

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-P62250-F1-model_v2 AlphaFold P62250 1-146 view protein structure

Transcriptome

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

Promoters
RGD ID:13689875
Promoter ID:EPDNEW_R398
Type:multiple initiation site
Name:Rps16_1
Description:ribosomal protein S16
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_6.0185,408,426 - 85,408,486EPDNEW

Strain Variation

Strain Sequence Variants (mRatBN7.2)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN-Lx/CubMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BUF/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
DA/OlaHsd (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE16/Stm (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/FarMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB10/IpcvMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF10A/StmMcwi (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrcAek (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrcAek (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrcAek (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/NRrrcMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MWF/Hsd (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHR/OlalpcvMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WAG/RijCrl (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/N (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Damaging Variants


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
1 86620949 86620950 C G snv IS-Tlk/Kyo (KyushuU), IS/Kyo (KyushuU)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:621031 AgrOrtholog
BioCyc Gene G2FUF-60250 BioCyc
Ensembl Genes ENSRNOG00000019578 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000026576 ENTREZGENE
  ENSRNOP00000076119 ENTREZGENE
  ENSRNOP00000076119.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000026576 ENTREZGENE
  ENSRNOT00000093558 ENTREZGENE
  ENSRNOT00000093558.2 UniProtKB/TrEMBL
Gene3D-CATH 3.30.230.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:6887619 IMAGE-MGC_LOAD
  IMAGE:7311638 IMAGE-MGC_LOAD
  IMAGE:8375510 IMAGE-MGC_LOAD
InterPro Ribosomal_S5_D2-typ_fold UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ribosomal_S5_D2-typ_fold_subgr UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ribosomal_S9 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ribosomal_S9_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:140655 UniProtKB/Swiss-Prot
MGC_CLONE MGC:105803 IMAGE-MGC_LOAD
  MGC:188783 IMAGE-MGC_LOAD
  MGC:72948 IMAGE-MGC_LOAD
NCBI Gene 140655 ENTREZGENE
PANTHER PTHR21569 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Ribosomal_S9 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Rps16 PhenoGen
PROSITE RIBOSOMAL_S9 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF54211 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A1W2Q631 ENTREZGENE, UniProtKB/TrEMBL
  B0K038_RAT UniProtKB/TrEMBL
  P62250 ENTREZGENE
  Q5XFV9_RAT UniProtKB/TrEMBL
  Q6P3E1_RAT UniProtKB/TrEMBL
  RS16_RAT UniProtKB/Swiss-Prot
UniProt Secondary P17008 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2004-02-26 Rps16  ribosomal protein S16      Symbol and Name status set to approved 625702 APPROVED
2002-08-07 Rps16  ribosomal protein S16      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_other 11-13 copies of the gene 634013
gene_protein 145 amino acids 634013