Rps4x-ps13 (ribosomal protein S4, X-linked, pseudogene 13) - Rat Genome Database

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Gene: Rps4x-ps13 (ribosomal protein S4, X-linked, pseudogene 13) Rattus norvegicus
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Symbol: Rps4x-ps13
Name: ribosomal protein S4, X-linked, pseudogene 13
RGD ID: 1590988
Description: Predicted to enable RNA binding activity. Predicted to be a structural constituent of ribosome. Predicted to be involved in translation. Predicted to be located in nucleolus. Predicted to be part of cytosolic small ribosomal subunit. Orthologous to several human genes including RPS4Y2 (ribosomal protein S4 Y-linked 2); PARTICIPATES IN ribosome biogenesis pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 3-chloropropane-1,2-diol; 6-propyl-2-thiouracil.
Type: pseudo (Ensembl: protein-coding)
RefSeq Status: VALIDATED
Previously known as: LOC690845; ribosomal protein S4, Y-linked 2; Rps4y2; similar to 40S ribosomal protein S4, X isoform
RGD Orthologs
Human
Mouse
Bonobo
Alliance Orthologs
More Info more info ...
Related Functional Gene: Rps4x  
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr84183,000,913 - 183,001,846 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl4183,000,652 - 183,007,381 (+)EnsemblGRCr8
mRatBN7.24181,269,507 - 181,270,440 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl4181,269,081 - 181,270,349 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx4187,548,605 - 187,549,538 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.04183,333,151 - 183,334,084 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.04181,953,640 - 181,954,573 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.04182,745,448 - 182,746,381 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl4182,745,448 - 182,746,381 (+)Ensemblrn6Rnor6.0
Rnor_5.04246,879,802 - 246,880,735 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.44185,977,395 - 185,978,328 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera4169,754,542 - 169,755,475 (+)NCBICelera
Cytogenetic Map4q44NCBI
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. 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.
2. 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.
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
4. Comprehensive gene review and curation RGD comprehensive gene curation

Genomics

Comparative Map Data
Rps4x-ps13
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr84183,000,913 - 183,001,846 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl4183,000,652 - 183,007,381 (+)EnsemblGRCr8
mRatBN7.24181,269,507 - 181,270,440 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl4181,269,081 - 181,270,349 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx4187,548,605 - 187,549,538 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.04183,333,151 - 183,334,084 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.04181,953,640 - 181,954,573 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.04182,745,448 - 182,746,381 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl4182,745,448 - 182,746,381 (+)Ensemblrn6Rnor6.0
Rnor_5.04246,879,802 - 246,880,735 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.44185,977,395 - 185,978,328 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera4169,754,542 - 169,755,475 (+)NCBICelera
Cytogenetic Map4q44NCBI
RPS4Y2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38Y20,756,108 - 20,781,032 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 EnsemblY20,756,108 - 20,781,032 (+)Ensemblhg38GRCh38
GRCh37Y22,917,994 - 22,942,918 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36Y21,327,342 - 21,352,306 (+)NCBIBuild 36Build 36hg18NCBI36
Build 34Y21,256,787 - 21,281,043NCBI
CeleraY7,624,905 - 7,649,869 (+)NCBICelera
Cytogenetic MapYq11.223NCBI
HuRefY16,504,472 - 16,528,968 (+)NCBIHuRef
T2T-CHM13v2.0Y21,631,330 - 21,656,255 (+)NCBIT2T-CHM13v2.0
Rps4l
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm396148,256,154 - 148,257,094 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl6148,256,098 - 148,257,431 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm386148,354,656 - 148,355,596 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl6148,354,656 - 148,355,598 (+)Ensemblmm10GRCm38
MGSCv376148,303,178 - 148,304,118 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv366148,311,854 - 148,312,768 (+)NCBIMGSCv36mm8
Celera6151,386,921 - 151,387,861 (+)NCBICelera
Cytogenetic Map6G3NCBI
cM Map678.49NCBI
RPS4Y2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2Y35,532,435 - 35,558,025 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1Y11,369,086 - 11,394,568 (+)NCBINHGRI_mPanPan1

miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:35
Count of miRNA genes:34
Interacting mature miRNAs:35
Transcripts:ENSRNOT00000043543
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.


QTLs in Region (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
6478754Anxrr43Anxiety related response QTL 430.14035locomotor behavior trait (VT:0001392)distance moved per unit of time into, out of or within a discrete space in an experimental apparatus (CMO:0001493)4146370897184426481Rat
6478720Alc23Alcohol consumption QTL 230.00509drinking behavior trait (VT:0001422)ethanol drink intake rate to body weight ratio (CMO:0001616)4155834926184426481Rat
6478785Anxrr53Anxiety related response QTL 530.01397locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4155834926184426481Rat
6478693Anxrr32Anxiety related response QTL 320.00092locomotor behavior trait (VT:0001392)measurement of voluntary locomotion into, out of or within a discrete space in an experimental apparatus (CMO:0000957)4146370897184426481Rat
6478757Anxrr44Anxiety related response QTL 440.01087locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4155834926184426481Rat
6478728Anxrr36Anxiety related response QTL 360.01061locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4155834926184426481Rat
738016Alc16Alcohol consumption QTL 163.60.00015consumption behavior trait (VT:0002069)ethanol drink intake rate to body weight ratio (CMO:0001616)460916264184426481Rat
6478700Anxrr33Anxiety related response QTL 330.00896locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4146370897184426481Rat
1298524Oia8Oil induced arthritis QTL 8joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4140059299184426481Rat
6478733Anxrr37Anxiety related response QTL 370.00095locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4155834926184426481Rat
10053718Scort25Serum corticosterone level QTL 252.150.0097blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)4157292416184426481Rat
738009Sach4Saccharine consumption QTL 44.90.000016consumption behavior trait (VT:0002069)saccharin intake volume to total fluid intake volume ratio (CMO:0001601)460916264184426481Rat
61362Oia2Oil induced arthritis QTL 20.001joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4140059299184426481Rat
6478737Anxrr38Anxiety related response QTL 380.00159locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4155834926184426481Rat
2293659Bmd35Bone mineral density QTL 354.50.0001femur strength trait (VT:0010010)femoral neck ultimate force (CMO:0001703)4160623982184426481Rat
10401796Kidm48Kidney mass QTL 48kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)4147299608184426481Rat
6478718Anxrr34Anxiety related response QTL 340.00896locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4146370897184426481Rat
6478782Anxrr52Anxiety related response QTL 520.02091locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4155834926184426481Rat
6478748Anxrr42Anxiety related response QTL 420.28008locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4146370897184426481Rat

Markers in Region
AI104090  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24181,270,223 - 181,270,369 (+)MAPPERmRatBN7.2
Rnor_6.04182,746,165 - 182,746,310NCBIRnor6.0
Rnor_5.04246,880,519 - 246,880,664UniSTSRnor5.0
RGSC_v3.44185,978,112 - 185,978,257UniSTSRGSC3.4
Celera4169,755,259 - 169,755,404UniSTS
RH 3.4 Map2055.73UniSTS
Cytogenetic Map4q44UniSTS


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 67 162 91 90 59 92 59 6 356 192 11 141 81 91 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000043543   ⟹   ENSRNOP00000049546
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl4183,000,688 - 183,003,946 (+)Ensembl
mRatBN7.2 Ensembl4181,269,081 - 181,270,349 (+)Ensembl
Rnor_6.0 Ensembl4182,745,448 - 182,746,381 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000051149   ⟹   ENSRNOP00000043988
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl4183,000,652 - 183,007,381 (+)Ensembl
RefSeq Acc Id: NM_001109612   ⟹   NP_001103082
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr84183,000,913 - 183,001,846 (+)NCBI
mRatBN7.24181,269,507 - 181,270,440 (+)NCBI
Rnor_6.04182,745,448 - 182,746,381 (+)NCBI
Rnor_5.04246,879,802 - 246,880,735 (+)NCBI
RGSC_v3.44185,977,395 - 185,978,328 (+)RGD
Celera4169,754,542 - 169,755,475 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001103082 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDM01382 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000049546.4
RefSeq Acc Id: NP_001103082   ⟸   NM_001109612
- Sequence:
Ensembl Acc Id: ENSRNOP00000049546   ⟸   ENSRNOT00000043543
Ensembl Acc Id: ENSRNOP00000043988   ⟸   ENSRNOT00000051149
Protein Domains
RNA-binding S4

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZX01-F1-model_v2 AlphaFold D3ZX01 1-262 view protein structure

Transcriptome

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

Promoters
RGD ID:13693513
Promoter ID:EPDNEW_R4038
Type:initiation region
Name:Rps4y2_1
Description:ribosomal protein S4, Y-linked 2
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_6.04182,745,449 - 182,745,509EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1590988 AgrOrtholog
BioCyc Gene G2FUF-42401 BioCyc
Ensembl Genes ENSRNOG00000031041 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000043543.4 UniProtKB/TrEMBL
Gene3D-CATH 2.30.30.30 UniProtKB/TrEMBL
  2.40.50.740 UniProtKB/TrEMBL
  3.10.290.10 UniProtKB/TrEMBL
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 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
KEGG Report rno:690845 UniProtKB/TrEMBL
NCBI Gene 690845 ENTREZGENE
PANTHER Ribosomal_S4E UniProtKB/TrEMBL
  SMALL RIBOSOMAL SUBUNIT PROTEIN ES4 UniProtKB/TrEMBL
Pfam 40S_S4_C UniProtKB/TrEMBL
  KOW UniProtKB/TrEMBL
  PF01479 UniProtKB/TrEMBL
  Ribosomal_S4e UniProtKB/TrEMBL
  RS4NT UniProtKB/TrEMBL
PhenoGen Rps4x-ps13 PhenoGen
PIRSF Ribosomal_S4 UniProtKB/TrEMBL
PROSITE PS50889 UniProtKB/TrEMBL
  RIBOSOMAL_S4E UniProtKB/TrEMBL
RatGTEx ENSRNOG00000031041 RatGTEx
SMART SM00363 UniProtKB/TrEMBL
Superfamily-SCOP Alpha-L RNA-binding motif UniProtKB/TrEMBL
UniProt A6IN57_RAT UniProtKB/TrEMBL
  D3ZX01_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2024-08-29 Rps4x-ps13  ribosomal protein S4, X-linked, pseudogene 13  Rps4y2  ribosomal protein S4, Y-linked 2  Name and Symbol and Type changed (type changed from [protein-coding] to [pseudo]) 629549 APPROVED
2008-03-06 Rps4y2  ribosomal protein S4, Y-linked 2  LOC690845  similar to 40S ribosomal protein S4, X isoform  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-01-09 LOC690845  similar to 40S ribosomal protein S4, X isoform  LOC686587  similar to 40S ribosomal protein S4, X isoform  Data merged from RGD:1596316 1643240 APPROVED
2006-11-20 LOC690845  similar to 40S ribosomal protein S4, X isoform      Symbol and Name status set to provisional 70820 PROVISIONAL
2006-11-20 LOC686587  similar to 40S ribosomal protein S4, X isoform      Symbol and Name status set to provisional 70820 PROVISIONAL