Rps4x-ps9 (ribosomal protein S4, X-linked, pseudogene 9) - Rat Genome Database

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Gene: Rps4x-ps9 (ribosomal protein S4, X-linked, pseudogene 9) Rattus norvegicus
Analyze
No known orthologs.
Symbol: Rps4x-ps9 (Ensembl: Rps4x)
Name: ribosomal protein S4, X-linked, pseudogene 9
RGD ID: 3600
Description: Predicted to enable rRNA binding activity; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; gentamycin; paracetamol.
Type: pseudo (Ensembl: protein-coding)
RefSeq Status: INFERRED
Previously known as: 40S ribosomal protein S4, X isoform; MGC105788; ribosomal protein S4, X-linked; Rps4x
RGD Orthologs
Alliance Genes
More Info homologs ...
Related Functional Gene: Rps4x  
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2437,758,373 - 37,759,289 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl437,758,363 - 37,759,291 (-)EnsemblmRatBN7.2 Ensembl
Rnor_6.0435,729,619 - 35,730,535 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl435,729,628 - 35,730,599 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0435,587,239 - 35,588,132 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera433,242,260 - 33,243,176 (-)NCBICelera
Cytogenetic Map4q21NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


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

References

References - curated
# Reference Title Reference Citation
1. The primary structure of rat ribosomal protein S4. Devi KR, etal., Biochim Biophys Acta 1989 Jul 7;1008(2):258-62.
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. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
4. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
5. GOA pipeline RGD automated data pipeline
6. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
7. Comprehensive gene review and curation RGD comprehensive gene curation
Additional References at PubMed
PMID:12477932   PMID:15057822   PMID:15489334  


Genomics

Variants

.
Variants in Rps4x-ps9
11 total Variants

QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
61415Eae11Experimental allergic encephalomyelitis QTL 112.9nervous system integrity trait (VT:0010566)post-insult time to onset of experimental autoimmune encephalomyelitis (CMO:0001422)4139505420Rat
634323Hc2Hypercalciuria QTL 22.15urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)421079645210796Rat
619616Bp79Blood pressure QTL 790.0292arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)4521460278882945Rat
2303168Bp330Blood pressure QTL 3304.250.017arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)45214602146446691Rat
2302371Stl22Serum triglyceride level QTL 225.15blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)4521829457114705Rat
1358203Stl19Serum triglyceride level QTL 192.80.002blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)4521829465958103Rat
631642Stl2Serum triglyceride level QTL 23.3blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)4521917856647776Rat
631209Bw2Body weight QTL24.2retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)4994088544463908Rat
1300141Bp178Blood pressure QTL 178arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)41002490139524530Rat
6478724Anxrr35Anxiety related response QTL 350.00449defecation behavior trait (VT:0010462)defecation measurement (CMO:0000997)41008408955084089Rat
6478766Anxrr47Anxiety related response QTL 470.09637locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)41008408955084089Rat
6478769Anxrr48Anxiety related response QTL 480.02514locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)41008408955084089Rat
8694374Bw155Body weight QTL 1553.390.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)41008408955084089Rat
9590304Scort17Serum corticosterone level QTL 174.960.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)41008408955084089Rat
8552906Pigfal3Plasma insulin-like growth factor 1 level QTL 3blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)41008408955084089Rat
631261Tcas3Tongue tumor susceptibility QTL 36.88tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)41081417091360527Rat
2316958Gluco58Glucose level QTL 5810blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)411320076180699135Rat
2303585Bw86Body weight QTL 864body mass (VT:0001259)body weight (CMO:0000012)41467806559678065Rat
2313401Anxrr27Anxiety related response QTL 27aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)41793350862933508Rat
70222Eae2Experimental allergic encephalomyelitis QTL 24.3nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)42133334339505420Rat
1354665Stl10Serum triglyceride level QTL 103.57blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)42133334344463908Rat
61412Pia2Pristane induced arthritis QTL 23.9joint integrity trait (VT:0010548)post-insult time to onset of experimental arthritis (CMO:0001450)42133334362278020Rat
6909122Insul22Insulin level QTL 224.63blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)42690728575585128Rat
6909128Pancm4Pancreatic morphology QTL 411.35pancreas mass (VT:0010144)pancreas wet weight (CMO:0000626)42690728575585128Rat
8655906Rf60Renal function QTL 603.8blood creatinine amount (VT:0005328)creatinine clearance (CMO:0000765)42949419581006281Rat
12798520Anxrr55Anxiety related response QTL 554.450.01locomotor behavior trait (VT:0001392)number of rearing movements with lid-pushing in an experimental apparatus (CMO:0002715)432583980114627242Rat
11530004Niddm71Non-insulin dependent diabetes mellitus QTL 710.001blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)43258419952754138Rat
8655949Rf62Renal function QTL 6222blood urea nitrogen amount (VT:0005265)plasma urea nitrogen level (CMO:0000586)43443011944463908Rat
8552782Vie1Viral induced encephalitis QTL 126.4brain integrity trait (VT:0010579)encephalitis incidence/prevalence measurement (CMO:0002361)43443048482490359Rat
8552801Bw143Body weight QTL 1437.3body mass (VT:0001259)change in body weight to body weight ratio (CMO:0002216)43443048482490359Rat
8552809Vie5Viral induced encephalitis QTL 525.3brain integrity trait (VT:0010579)encephalitis incidence/prevalence measurement (CMO:0002361)43443048482490359Rat
8655961Kidm43Kidney mass QTL 4318kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)436303261103194984Rat
4889511Gluco61Glucose level QTL 614.70.001blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)43717795040869000Rat
2290374Gluco32Glucose level QTL 326.27blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)43717795044463908Rat

Markers in Region
GDB:194748  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2437,758,608 - 37,759,229 (+)MAPPERmRatBN7.2
Rnor_6.0435,729,855 - 35,730,475NCBIRnor6.0
Rnor_5.0435,587,475 - 35,588,095UniSTSRnor5.0
RGSC_v3.4434,793,919 - 34,794,539UniSTSRGSC3.4
Celera433,242,496 - 33,243,116UniSTS
Cytogenetic MapXq31UniSTS
GDB:194747  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X67,301,536 - 67,301,970 (+)MAPPERmRatBN7.2
mRatBN7.2437,759,098 - 37,759,229 (+)MAPPERmRatBN7.2
Rnor_6.0435,730,345 - 35,730,475NCBIRnor6.0
Rnor_6.0X72,077,123 - 72,077,556NCBIRnor6.0
Rnor_5.0435,587,965 - 35,588,095UniSTSRnor5.0
Rnor_5.0X72,919,045 - 72,919,478UniSTSRnor5.0
RGSC_v3.4X90,252,389 - 90,252,822UniSTSRGSC3.4
RGSC_v3.4434,794,409 - 34,794,539UniSTSRGSC3.4
Celera433,242,986 - 33,243,116UniSTS
CeleraX67,655,319 - 67,655,752UniSTS
Cytogenetic MapXq31UniSTS


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
Medium 2 23 13 13 3 13 1 23 11 16 2
Low 1 12 29 23 13 23 3 5 44 17 22 5 3
Below cutoff 7 15 5 3 5 5 5 6 7 1 4 5

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000051149   ⟹   ENSRNOP00000043988
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl437,758,363 - 37,759,291 (-)Ensembl
Rnor_6.0 Ensembl435,729,628 - 35,730,599 (-)Ensembl
Protein Sequences
GenBank Protein EDL95869 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: ENSRNOP00000043988   ⟸   ENSRNOT00000051149
Protein Domains
S4

Transcriptome

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

Promoters
RGD ID:13692885
Promoter ID:EPDNEW_R3402
Type:multiple initiation site
Name:Rps4x_1
Description:ribosomal protein S4, X-linked
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R12407  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0435,730,535 - 35,730,595EPDNEW

Additional Information

Database Acc Id Source(s)
BioCyc Gene G2FUF-45650 BioCyc
Ensembl Genes ENSRNOG00000029574 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000043988 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000051149 UniProtKB/TrEMBL
Gene3D-CATH 2.30.30.30 UniProtKB/TrEMBL
  2.40.50.740 UniProtKB/TrEMBL
  3.10.290.10 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7303578 IMAGE-MGC_LOAD
InterPro 40S_S4_C UniProtKB/TrEMBL
  KOW UniProtKB/TrEMBL
  KOW_RPS4 UniProtKB/TrEMBL
  Rib_L2_dom2 UniProtKB/TrEMBL
  Ribosomal_S4e UniProtKB/TrEMBL
  Ribosomal_S4e_central_region UniProtKB/TrEMBL
  Ribosomal_S4e_central_sf UniProtKB/TrEMBL
  Ribosomal_S4e_N UniProtKB/TrEMBL
  Ribosomal_S4e_N_CS UniProtKB/TrEMBL
  S4_RNA-bd UniProtKB/TrEMBL
  S4_RNA-bd_sf UniProtKB/TrEMBL
MGC_CLONE MGC:105788 IMAGE-MGC_LOAD
NCBI Gene 29426 ENTREZGENE
PANTHER PTHR11581 UniProtKB/TrEMBL
Pfam 40S_S4_C UniProtKB/TrEMBL
  KOW UniProtKB/TrEMBL
  PF01479 UniProtKB/TrEMBL
  Ribosomal_S4e UniProtKB/TrEMBL
  RS4NT UniProtKB/TrEMBL
PhenoGen Rps4x-ps9 PhenoGen
PIRSF Ribosomal_S4 UniProtKB/TrEMBL
PROSITE RIBOSOMAL_S4E UniProtKB/TrEMBL
SMART SM00363 UniProtKB/TrEMBL
UniProt A0A0H2UHX3_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-04-09 Rps4x-ps9  ribosomal protein S4, X-linked, pseudogene 9  Rps4xl1  ribosomal protein S4, X-linked-like 1  Name and Symbol changed 629549 APPROVED
2015-04-09 Rps4x-ps9  ribosomal protein S4, X-linked, pseudogene 9  Rps4x-ps9  ribosomal protein S4, X-linked, pseudogene 9  Type changed (type changed from [protein-coding] to [pseudo]) 629549 APPROVED
2015-04-08 Rps4xl1  ribosomal protein S4, X-linked-like 1  Rps4x  ribosomal protein S4, X-linked  Name and Symbol changed 629549 APPROVED
2002-06-10 Rps4x  ribosomal protein S4, X-linked       Name updated 70584 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_other 7-11 copies of the gene 69970
gene_protein 282 amino acids 69970