Rpl23a-ps20 (ribosomal protein L23a, pseudogene 20) - Rat Genome Database

Send us a Message
Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Search RGD Grant Resources Citing RGD About Us Contact Us
Genes Variants Community Projects QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Synteny Browser (VCMap) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) AllianceMine GViewer (Genome Viewer)
Aging & Age-Related Disease Cancer & Neoplastic Disease Cardiovascular Disease Coronavirus Disease Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease
Find Models Genetic Models Autism Models Rat PhenoMiner (Quantitative Phenotypes) Chinchilla PhenoMiner Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive
Pathways
Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Presentations Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
Advanced Search (OLGA)
Gene: Rpl23a-ps20 (ribosomal protein L23a, pseudogene 20) Rattus norvegicus
Analyze
No known orthologs.
Symbol: Rpl23a-ps20 (Ensembl: LOC689899)
Name: ribosomal protein L23a, pseudogene 20 (Ensembl:similar to 60S ribosomal protein L23a)
RGD ID: 1587481
Description:
Type: pseudo (Ensembl: protein-coding)
RefSeq Status: INFERRED
Previously known as: 60S ribosomal protein L23a-like; LOC689899; similar to 60S ribosomal protein L23a
RGD Orthologs
Alliance Orthologs
More Info homologs ...
Related Functional Gene: Rpl23a  
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81421,733,873 - 21,734,412 (-)NCBIGRCr8
mRatBN7.21421,379,049 - 21,379,588 (-)NCBImRatBN7.2mRatBN7.2
Rnor_6.01424,129,598 - 24,130,134 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1424,129,592 - 24,130,122 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01423,966,461 - 23,966,994 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41423,002,097 - 23,002,613 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1420,869,907 - 20,870,443 (-)NCBICelera
Cytogenetic Map14p21NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


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. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions

Genomics

Variants

.
Variants in Rpl23a-ps20
24 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:8
Count of miRNA genes:8
Interacting mature miRNAs:8
Transcripts:ENSRNOT00000040647
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
1581500Renag1Renal agenesis QTL 1kidney development trait (VT:0000527)percentage of study population developing unilateral renal agenesis during a period of time (CMO:0000940)14817066868298175Rat
731183Pia20Pristane induced arthritis QTL 203.55joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)14908897839057237Rat
631212Bw5Body weight QTL55.43retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)141103081230320092Rat
2302277Gluco38Glucose level QTL 385.8blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)141103062228035204Rat
10755459Coatc15Coat color QTL 150.01681coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)141983694464836944Rat
1331740Bw26Body weight QTL 263.028body mass (VT:0001259)body weight (CMO:0000012)14381307430767156Rat
619619Rf4Renal disease susceptibility QTL 44.10.002urine total protein amount (VT:0000032)urine protein excretion rate to body weight ratio (CMO:0001099)14132754612Rat
1358296Ael3Aortic elastin QTL 33.70.00051aorta elastin amount (VT:0003905)aortic elastin14826709053267090Rat
71117Niddm17Non-insulin dependent diabetes mellitus QTL 172.35blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)141759376142336881Rat
61420Pia6Pristane induced arthritis QTL 64.9joint integrity trait (VT:0010548)arthritic paw count (CMO:0001460)141863134542337007Rat
70195Mcs8Mammary carcinoma susceptibility QTL 84.28mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)14381307424531477Rat
2300183Bmd60Bone mineral density QTL 605.70.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)14126541967Rat
631839Niddm37Non-insulin dependent diabetes mellitus QTL 373.37blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)141103062295876975Rat
2313397Coatc1Coat color QTL1coat/hair pigmentation trait (VT:0010463)coat/hair color measurement (CMO:0001808)141854133263541332Rat
631262Tcas4Tongue tumor susceptibility QTL 47.29tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)141762256142337007Rat
634352Apr6Acute phase response QTL 63.7blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)14141131407Rat
2300159Bmd61Bone mineral density QTL 615.30.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)14126541967Rat
2302045Pia39Pristane induced arthritis QTL 394.90.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G2a level (CMO:0002116)14826709053267090Rat
1300140Srn3Serum renin concentration QTL 33.19blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)141487516830883947Rat

Markers in Region
D14Wox3  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21421,379,546 - 21,379,735 (-)MAPPERmRatBN7.2
Rnor_6.01424,129,442 - 24,129,630NCBIRnor6.0
Rnor_5.01423,966,305 - 23,966,493UniSTSRnor5.0
RGSC_v3.41423,002,588 - 23,002,775RGDRGSC3.4
RGSC_v3.41423,002,587 - 23,002,775UniSTSRGSC3.4
RGSC_v3.11423,002,588 - 23,002,775RGD
Celera1420,870,411 - 20,870,601UniSTS
RH 3.4 Map14245.5UniSTS
RH 3.4 Map14245.5RGD
Cytogenetic Map14p21UniSTS


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
nervous system
renal system
reproductive system
respiratory system
9 4 28 65 54 57 35 17 35 6 131 59 53 26 42 22

Sequence


Ensembl Acc Id: ENSRNOT00000040647   ⟹   ENSRNOP00000049652
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1424,129,592 - 24,130,122 (+)Ensembl
RefSeq Acc Id: XM_039092689   ⟹   XP_038948617
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21421,379,046 - 21,379,585 (-)NCBI
Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZTH8-F1-model_v2 AlphaFold D3ZTH8 1-156 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1587481 AgrOrtholog
BioCyc Gene G2FUF-16080 BioCyc
Ensembl Genes ENSRNOG00000030614 Ensembl
NCBI Gene 689899 ENTREZGENE
PhenoGen Rpl23a-ps20 PhenoGen
RatGTEx ENSRNOG00000030614 RatGTEx


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2022-07-15 Rpl23a-ps20  ribosomal protein L23a, pseudogene 20  LOC689899  similar to 60S ribosomal protein L23a  Name and Symbol and Type changed (type changed from [protein-coding] to [pseudo]) 629549 APPROVED
2008-01-09 LOC689899  similar to 60S ribosomal protein L23a  LOC686564  similar to 60S ribosomal protein L23a  Data merged from RGD:1596335 1643240 APPROVED
2006-11-20 LOC686564  similar to 60S ribosomal protein L23a      Symbol and Name status set to provisional 70820 PROVISIONAL
2006-11-19 LOC689899  similar to 60S ribosomal protein L23a      Symbol and Name status set to provisional 70820 PROVISIONAL