Rps23 (ribosomal protein S23) - Rat Genome Database

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Gene: Rps23 (ribosomal protein S23) Rattus norvegicus
Analyze
Symbol: Rps23
Name: ribosomal protein S23
RGD ID: 621039
Description: Predicted to be a structural constituent of ribosome. Predicted to be involved in ribosomal small subunit biogenesis; stress granule assembly; and translation. Part of cytosolic small ribosomal subunit. Human ortholog(s) of this gene implicated in brachycephaly, trichomegaly, and developmental delay. Orthologous to human RPS23 (ribosomal protein S23); PARTICIPATES IN ribosome biogenesis pathway; translation pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran; 4,4'-sulfonyldiphenol.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: 40S ribosomal protein S23; small ribosomal subunit protein uS12
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Related Pseudogenes: Rps23-ps12  
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8223,814,517 - 23,816,087 (+)NCBIGRCr8
mRatBN7.2222,079,339 - 22,080,909 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl222,079,302 - 22,080,918 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx229,122,505 - 29,124,075 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0227,222,852 - 27,224,422 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0222,038,786 - 22,040,355 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0219,823,234 - 19,824,804 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl219,823,234 - 19,824,804 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0219,699,472 - 19,701,042 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4221,046,304 - 21,047,874 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1220,966,672 - 20,968,243 (+)NCBI
Celera218,206,761 - 18,208,331 (+)NCBICelera
Cytogenetic Map2q12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

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. 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.
3. The primary structure of rat ribosomal protein S23. Kitaoka Y, etal., Biochem Biophys Res Commun 1994 Jul 15;202(1):314-20.
4. Localization of proteins S1, S2, S16 and S23 on the surface of small subunits of rat liver ribosomes by immune electron microscopy. Lutsch G, etal., Mol Gen Genet. 1979 Oct 3;176(2):281-91.
5. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
6. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
7. 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.
8. GOA pipeline RGD automated data pipeline
9. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
10. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
11. Comprehensive gene review and curation RGD comprehensive gene curation
12. 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.
13. The EARP Complex and Its Interactor EIPR-1 Are Required for Cargo Sorting to Dense-Core Vesicles. Topalidou I, etal., PLoS Genet. 2016 May 18;12(5):e1006074. doi: 10.1371/journal.pgen.1006074. eCollection 2016 May.
Additional References at PubMed
PMID:8706699   PMID:15489334   PMID:15883184   PMID:16452087   PMID:16854843   PMID:19946888   PMID:22681889   PMID:24930395   PMID:25957688   PMID:28257692   PMID:30053369  


Genomics

Comparative Map Data
Rps23
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8223,814,517 - 23,816,087 (+)NCBIGRCr8
mRatBN7.2222,079,339 - 22,080,909 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl222,079,302 - 22,080,918 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx229,122,505 - 29,124,075 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0227,222,852 - 27,224,422 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0222,038,786 - 22,040,355 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0219,823,234 - 19,824,804 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl219,823,234 - 19,824,804 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0219,699,472 - 19,701,042 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4221,046,304 - 21,047,874 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1220,966,672 - 20,968,243 (+)NCBI
Celera218,206,761 - 18,208,331 (+)NCBICelera
Cytogenetic Map2q12NCBI
RPS23
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38582,273,320 - 82,278,354 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl582,273,320 - 82,278,396 (-)EnsemblGRCh38hg38GRCh38
GRCh37581,569,139 - 81,574,173 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36581,604,895 - 81,609,991 (-)NCBINCBI36Build 36hg18NCBI36
Build 34581,607,203 - 81,610,080NCBI
Celera577,474,126 - 77,479,222 (-)NCBICelera
Cytogenetic Map5q14.2NCBI
HuRef576,777,631 - 76,782,727 (-)NCBIHuRef
CHM1_1581,002,316 - 81,007,417 (-)NCBICHM1_1
T2T-CHM13v2.0582,759,105 - 82,764,144 (-)NCBIT2T-CHM13v2.0
Rps23
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391391,071,241 - 91,072,851 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1391,071,077 - 91,073,069 (+)EnsemblGRCm39 Ensembl
GRCm381390,923,122 - 90,924,732 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1390,922,958 - 90,924,950 (+)EnsemblGRCm38mm10GRCm38
MGSCv371391,062,727 - 91,064,337 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361391,397,415 - 91,398,969 (+)NCBIMGSCv36mm8
Celera1394,539,233 - 94,557,826 (+)NCBICelera
Cytogenetic Map13C3NCBI
cM Map1346.46NCBI
Rps23
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541828,106,333 - 28,108,271 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495541828,106,333 - 28,108,276 (+)NCBIChiLan1.0ChiLan1.0
RPS23
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2433,028,070 - 33,033,140 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1531,181,696 - 31,186,766 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0533,005,488 - 33,007,881 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1533,323,233 - 33,325,775 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl533,323,233 - 33,326,569 (+)Ensemblpanpan1.1panPan2
RPS23
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1325,208,812 - 25,210,492 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl325,208,920 - 25,210,489 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha326,445,283 - 26,446,964 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0325,121,408 - 25,123,112 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl325,121,147 - 25,123,111 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1325,075,589 - 25,077,271 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0325,043,375 - 25,045,060 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0325,324,171 - 25,325,845 (+)NCBIUU_Cfam_GSD_1.0
Rps23
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024407213181,099,875 - 181,101,903 (+)NCBIHiC_Itri_2
SpeTri2.0NW_0049364691,523,667 - 1,525,830 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
RPS23
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl290,679,000 - 90,680,765 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1290,679,038 - 90,680,681 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2292,675,140 - 92,676,784 (-)NCBISscrofa10.2Sscrofa10.2susScr3
RPS23
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1476,394,049 - 76,396,435 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl476,392,625 - 76,396,331 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604925,271,999 - 25,274,564 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Rps23
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247432,663,479 - 2,665,493 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247432,663,474 - 2,665,508 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Rps23
23 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:90
Count of miRNA genes:78
Interacting mature miRNAs:81
Transcripts:ENSRNOT00000022348
Prediction methods:Microtar, 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.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
631682Bp115Blood pressure QTL 1154.30.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2137410502Rat
738010Lnnr3Liver neoplastic nodule remodeling QTL 32.94liver integrity trait (VT:0010547)liver remodeling tumorous lesion number (CMO:0001461)2141244106Rat
61355Bp36Blood pressure QTL 362.9blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)25873687102844969Rat
61368Mcs1Mammary carcinoma susceptibility QTL 14.4mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)2788777223319447Rat
1600379Mcs18Mammary carcinoma susceptibility QTL 182.6mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)2788777242804738Rat
738012Anxrr3Anxiety related response QTL 33.8exploratory behavior trait (VT:0010471)percentage of entries into a discrete space in an experimental apparatus (CMO:0000961)2902351954023519Rat
10755430Coatc6Coat color QTL 60.02576coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)21159110056591100Rat
1578664Bmd9Bone mineral QTL density 95femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)21185206249003364Rat
731184Mamtr4Mammary tumor resistance QTL 40.0003mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)21649174061491740Rat
1357990Ael1Aortic elastin QTL 13.10.00091aorta elastin amount (VT:0003905)aortic elastin21907682564076825Rat
731167Glom4Glomerulus QTL 42.40.0082kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)22030467265304672Rat
2300168Bmd47Bone mineral density QTL 476.60.0001femur mineral mass (VT:0010011)bone mineral density (CMO:0001226)22066244865662448Rat


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 16 18 18 3 18 30 18 28 1
Medium 1 27 39 23 16 23 8 11 44 17 13 10 8
Low
Below cutoff

Sequence


RefSeq Acc Id: ENSRNOT00000022348   ⟹   ENSRNOP00000022348
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl222,079,302 - 22,080,918 (+)Ensembl
Rnor_6.0 Ensembl219,823,234 - 19,824,804 (+)Ensembl
RefSeq Acc Id: NM_078617   ⟹   NP_511172
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8223,814,517 - 23,816,087 (+)NCBI
mRatBN7.2222,079,339 - 22,080,909 (+)NCBI
Rnor_6.0219,823,234 - 19,824,804 (+)NCBI
Rnor_5.0219,699,472 - 19,701,042 (+)NCBI
RGSC_v3.4221,046,304 - 21,047,874 (+)RGD
Celera218,206,761 - 18,208,331 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_511172 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH58134 (Get FASTA)   NCBI Sequence Viewer  
  CAA54584 (Get FASTA)   NCBI Sequence Viewer  
  EDM09997 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000022348.5
  ENSRNOP00065031578
  ENSRNOP00065037830
GenBank Protein P62268 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_511172   ⟸   NM_078617
- UniProtKB: P62268 (UniProtKB/Swiss-Prot),   A6I4N9 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000022348   ⟸   ENSRNOT00000022348

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-P62268-F1-model_v2 AlphaFold P62268 1-143 view protein structure

Transcriptome

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

Promoters
RGD ID:13691053
Promoter ID:EPDNEW_R1578
Type:multiple initiation site
Name:Rps23_1
Description:ribosomal protein S23
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_6.0219,823,242 - 19,823,302EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:621039 AgrOrtholog
BioCyc Gene G2FUF-54894 BioCyc
Ensembl Genes ENSRNOG00000016580 Ensembl, UniProtKB/TrEMBL
  ENSRNOG00065022794 UniProtKB/Swiss-Prot
  ENSRNOG00065026736 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000022348.7 UniProtKB/TrEMBL
  ENSRNOT00065038921 UniProtKB/Swiss-Prot
  ENSRNOT00065046110 UniProtKB/Swiss-Prot
Gene3D-CATH 2.40.50.140 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:6918484 IMAGE-MGC_LOAD
InterPro NA-bd_OB-fold UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ribosomal_S12/S23 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ribosomal_S23_euk/arc UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:124323 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
MGC_CLONE MGC:72722 IMAGE-MGC_LOAD
NCBI Gene 124323 ENTREZGENE
PANTHER 40S RIBOSOMAL PROTEIN S23 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR11652 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Ribosom_S12_S23 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Rps23 PhenoGen
PIRSF Ribosomal_S12/S23 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE RIBOSOMAL_S12 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
RatGTEx ENSRNOG00000016580 RatGTEx
  ENSRNOG00065022794 RatGTEx
  ENSRNOG00065026736 RatGTEx
Superfamily-SCOP SSF50249 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A8L2UJT5_RAT UniProtKB/TrEMBL
  A6I4N9 ENTREZGENE, UniProtKB/TrEMBL
  P62268 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary P39028 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2004-09-10 Rps23  ribosomal protein S23      Symbol and Name status set to approved 1299863 APPROVED
2002-08-07 Rps23  ribosomal protein S23      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_protein 142 amino acids 634017