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
Black Rat
Alliance Orthologs
More Info more info ...
Related Pseudogenes: Rps23-ps12  
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8223,814,517 - 23,816,087 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl223,814,497 - 23,816,088 (+)EnsemblGRCr8
mRatBN7.2222,079,339 - 22,080,909 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl222,079,302 - 22,080,918 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx229,122,505 - 29,124,075 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0227,222,852 - 27,224,422 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0222,038,786 - 22,040,355 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0219,823,234 - 19,824,804 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl219,823,234 - 19,824,804 (+)Ensemblrn6Rnor6.0
Rnor_5.0219,699,472 - 19,701,042 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4221,046,304 - 21,047,874 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera218,206,761 - 18,208,331 (+)NCBICelera
RGSC_v3.1220,966,672 - 20,968,243 (+)NCBI
Cytogenetic Map2q12NCBI
JBrowse:




Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction 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 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl223,814,497 - 23,816,088 (+)EnsemblGRCr8
mRatBN7.2222,079,339 - 22,080,909 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl222,079,302 - 22,080,918 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx229,122,505 - 29,124,075 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0227,222,852 - 27,224,422 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0222,038,786 - 22,040,355 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0219,823,234 - 19,824,804 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl219,823,234 - 19,824,804 (+)Ensemblrn6Rnor6.0
Rnor_5.0219,699,472 - 19,701,042 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4221,046,304 - 21,047,874 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera218,206,761 - 18,208,331 (+)NCBICelera
RGSC_v3.1220,966,672 - 20,968,243 (+)NCBI
Cytogenetic Map2q12NCBI
RPS23
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38582,273,320 - 82,278,354 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl582,273,320 - 82,278,414 (-)Ensemblhg38GRCh38
GRCh37581,569,139 - 81,574,173 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36581,604,895 - 81,609,991 (-)NCBIBuild 36Build 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 EnsemblGRCm39
GRCm381390,923,122 - 90,924,732 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1390,922,958 - 90,924,950 (+)Ensemblmm10GRCm38
MGSCv371391,062,727 - 91,064,337 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
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 (+)Ensembl
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 (+)EnsemblpanPan2panpan1.1
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 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha326,445,283 - 26,446,964 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0325,121,408 - 25,123,112 (+)NCBIROS_Cfam_1.0ROS_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_1.0UU_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
SpeTri2.0 EnsemblNW_0049364691,519,222 - 1,526,211 (-)EnsemblSpeTri2.0 Ensembl
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 (-)EnsemblsusScr11Sscrofa11.1
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 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
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_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046247432,663,474 - 2,665,508 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Rps23
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v13205,306,966 - 205,308,580 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Rps23
38 total Variants
miRNA Target Status (No longer updated)

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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1331764Bp205Blood pressure QTL 2053.476arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)21436870759368707Rat
10755430Coatc6Coat color QTL 60.02576coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)21332504158325041Rat
1600379Mcs18Mammary carcinoma susceptibility QTL 182.6mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)2962358144538110Rat
1331760Bp206Blood pressure QTL 2063.62454arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)24265106205135428Rat
61355Bp36Blood pressure QTL 362.9blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)27605533104774005Rat
10755499Bp389Blood pressure QTL 3892.61arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)220695736231474293Rat
1578664Bmd9Bone mineral QTL density 95femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)2573632550736325Rat
738010Lnnr3Liver neoplastic nodule remodeling QTL 32.94liver integrity trait (VT:0010547)liver remodeling tumorous lesion number (CMO:0001461)2142977529Rat
9590080Insglur4Insulin/glucose ratio QTL 428.70.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)2615276751152767Rat
1579916Bp270Blood pressure QTL 2700.003arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)21605188361051883Rat
731167Glom4Glomerulus QTL 42.40.0082kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)22203804467038044Rat
731166Mamtr2Mammary tumor resistance QTL 20.0001mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)2962358154623581Rat
61368Mcs1Mammary carcinoma susceptibility QTL 14.4mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)2962358125054526Rat
731184Mamtr4Mammary tumor resistance QTL 40.0003mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)21822713763227137Rat


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: ENSRNOT00000022348   ⟹   ENSRNOP00000022348
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl223,814,497 - 23,816,088 (+)Ensembl
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
GenBank Protein P62268 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_511172   ⟸   NM_078617
- UniProtKB: P62268 (UniProtKB/Swiss-Prot),   A6I4N9 (UniProtKB/TrEMBL)
- Sequence:
Ensembl 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, ENTREZGENE
Ensembl Transcript ENSRNOT00000022348 ENTREZGENE
Gene3D-CATH 2.40.50.140 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:6918484 IMAGE-MGC_LOAD
InterPro NA-bd_OB-fold UniProtKB/Swiss-Prot
  Ribosomal_S12/S23 UniProtKB/Swiss-Prot
  Ribosomal_S23_euk/arc UniProtKB/Swiss-Prot
KEGG Report rno:124323 UniProtKB/Swiss-Prot
MGC_CLONE MGC:72722 IMAGE-MGC_LOAD
NCBI Gene 124323 ENTREZGENE
PANTHER PTHR11652 UniProtKB/Swiss-Prot
Pfam Ribosom_S12_S23 UniProtKB/Swiss-Prot
PhenoGen Rps23 PhenoGen
PIRSF Ribosomal_S12/S23 UniProtKB/Swiss-Prot
PROSITE RIBOSOMAL_S12 UniProtKB/Swiss-Prot
RatGTEx ENSRNOG00000016580 RatGTEx
Superfamily-SCOP SSF50249 UniProtKB/Swiss-Prot
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