RGD1564606 (similar to 60S ribosomal protein L23a) - Rat Genome Database

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Gene: RGD1564606 (similar to 60S ribosomal protein L23a) Rattus norvegicus
Analyze
No known orthologs.
Symbol: RGD1564606
Name: similar to 60S ribosomal protein L23a
RGD ID: 1564606
Description: Predicted to be a structural constituent of ribosome. Predicted to be involved in ribosomal large subunit assembly. Predicted to be part of cytosolic large ribosomal subunit; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; cefaloridine.
Type: protein-coding
RefSeq Status: MODEL
Previously known as: 60S ribosomal protein L23a-like; LOC499523
RGD Orthologs
Alliance Genes
More Info homologs ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2238,452,814 - 38,453,384 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl238,451,401 - 38,453,417 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.0238,230,697 - 38,231,287 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl238,230,757 - 38,231,227 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0257,324,892 - 57,325,451 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4238,164,306 - 38,165,356 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera234,320,547 - 34,321,137 (+)NCBICelera
Cytogenetic Map2q14NCBI
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. 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. GOA pipeline RGD automated data pipeline
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:22082260   PMID:25931508  


Genomics

Variants

.
Variants in RGD1564606
2 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:57
Count of miRNA genes:53
Interacting mature miRNAs:53
Transcripts:ENSRNOT00000048598
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
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
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
10402051Gdil2Gastrointestinal dilation QTL 2enteric ganglion morphology trait (VT:0001045)length of intestine affected by colonic aganglionosis to total length of colon ratio (CMO:0001836)22490385374786777Rat
1302794Stl27Serum triglyceride level QTL 274.40.0001blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)225413423143657569Rat
1358894Kidm24Kidney mass QTL 244.03kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)225413423157142209Rat
1358899Kidm23Kidney mass QTL 233.88kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)225413423157142209Rat
1358901Cm38Cardiac mass QTL 382heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)225413423157142209Rat
1358904Cm39Cardiac mass QTL 392.26heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)225413423157142209Rat
1358910Kidm27Kidney mass QTL 275.77kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)225413423157142209Rat
1358911Kidm28Kidney mass QTL 285.42kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)225413423157142209Rat
1358913Cm41Cardiac mass QTL 412.73heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)225413423203928301Rat
1358917Cm42Cardiac mass QTL 422.82heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)225413423203928301Rat
1358887Bw50Body weight QTL 502.39body mass (VT:0001259)body weight (CMO:0000012)225413652157142078Rat
1358908Bw49Body weight QTL 493.36body mass (VT:0001259)body weight (CMO:0000012)225413652157142078Rat
1354617Bp240Blood pressure QTL 2404arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)22691781781754745Rat
1354617Bp240Blood pressure QTL 2404arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)22691781781754745Rat
1354617Bp240Blood pressure QTL 2404arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)22691781781754745Rat
1354603Bp243Blood pressure QTL 2433.9arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)226917817127469484Rat
2290453Scl55Serum cholesterol level QTL 552.83blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)226917817136917119Rat
1331764Bp205Blood pressure QTL 2053.476arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)22699957143154682Rat
1643006Pain1Pain QTL 13.630.005mechanical nociception trait (VT:0002734)self mutilation severity score (CMO:0002145)22699957148268661Rat
9590095Sffal3Serum free fatty acids level QTL 36.780.001blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)22715716072157160Rat
1300160Hrtrt3Heart rate QTL 33.62heart pumping trait (VT:2000009)absolute change in heart rate (CMO:0000534)22997159351729300Rat
10755434Coatc7Coat color QTL 70.04794coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)23064806575648065Rat
731179Mamtr3Mammary tumor resistance QTL 30.0001mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)23237377043665178Rat
10755436Coatc8Coat color QTL 80.02431coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)23502311780023117Rat
61371Edpm1Estrogen-dependent pituitary mass QTL 140.05pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)23513484188029593Rat


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
Low 1 24 23 22 2 22 54 20 31 1
Below cutoff 1 10 21 12 12 12 4 6 13 11 8 7 4

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000048598   ⟹   ENSRNOP00000043004
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl238,451,401 - 38,453,417 (+)Ensembl
Rnor_6.0 Ensembl238,230,757 - 38,231,227 (+)Ensembl
RefSeq Acc Id: XM_039103498   ⟹   XP_038959426
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2238,452,814 - 38,453,384 (+)NCBI
Protein Sequences
Protein RefSeqs XP_038959426 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: ENSRNOP00000043004   ⟸   ENSRNOT00000048598
RefSeq Acc Id: XP_038959426   ⟸   XM_039103498
- UniProtKB: F1LT35 (UniProtKB/TrEMBL)
Protein Domains
Ribosomal_L23eN

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-F1LT35-F1-model_v2 AlphaFold F1LT35 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:1564606 AgrOrtholog
BioCyc Gene G2FUF-54523 BioCyc
Ensembl Genes ENSRNOG00000029670 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000043004 ENTREZGENE
  ENSRNOP00000043004.2 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000048598 ENTREZGENE
  ENSRNOT00000048598.2 UniProtKB/TrEMBL
Gene3D-CATH 3.30.70.330 UniProtKB/TrEMBL
InterPro Nucleotide-bd_a/b_plait_sf UniProtKB/TrEMBL
  Ribosomal_L23 UniProtKB/TrEMBL
  Ribosomal_L23/L15e UniProtKB/TrEMBL
  Ribosomal_L23/L25_CS UniProtKB/TrEMBL
  Ribosomal_L23/L25_N UniProtKB/TrEMBL
  Ribosomal_L25/23 UniProtKB/TrEMBL
NCBI Gene 499523 ENTREZGENE
PANTHER PTHR11620 UniProtKB/TrEMBL
Pfam Ribosomal_L23 UniProtKB/TrEMBL
  Ribosomal_L23eN UniProtKB/TrEMBL
PhenoGen RGD1564606 PhenoGen
PROSITE RIBOSOMAL_L23 UniProtKB/TrEMBL
Superfamily-SCOP L23_L15e_core UniProtKB/TrEMBL
TIGRFAMs L23_arch UniProtKB/TrEMBL
UniProt F1LT35 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 RGD1564606  similar to 60S ribosomal protein L23a   RGD1564606_predicted  similar to 60S ribosomal protein L23a (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-07 RGD1564606_predicted  similar to 60S ribosomal protein L23a (predicted)  LOC499523  similar to 60S ribosomal protein L23a  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC499523  similar to 60S ribosomal protein L23a      Symbol and Name status set to provisional 70820 PROVISIONAL