RGD1560821 (similar to small nuclear ribonucleoparticle-associated protein) - Rat Genome Database

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Gene: RGD1560821 (similar to small nuclear ribonucleoparticle-associated protein) Rattus norvegicus
Analyze
No known orthologs.
Symbol: RGD1560821
Name: similar to small nuclear ribonucleoparticle-associated protein
RGD ID: 1560821
Description: Predicted to enable mRNA binding activity. Predicted to be a structural constituent of ribosome. Predicted to be involved in cytoplasmic translation. Predicted to be part of cytosolic large ribosomal subunit; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran; 3-chloropropane-1,2-diol.
Type: protein-coding
RefSeq Status: MODEL
Previously known as: 60S ribosomal protein L24-like; LOC367865
RGD Orthologs
Alliance Genes
More Info homologs ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2X71,880,236 - 71,880,917 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX71,880,204 - 71,880,879 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.0X77,885,562 - 77,886,179 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX77,885,586 - 77,886,170 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X78,083,776 - 78,084,382 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X95,019,866 - 95,022,619 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
CeleraX73,180,766 - 73,181,383 (+)NCBICelera
Cytogenetic MapXq22NCBI
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. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions

Genomics

Variants

.
Variants in RGD1560821
8 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:19
Count of miRNA genes:17
Interacting mature miRNAs:19
Transcripts:ENSRNOT00000034329
Prediction methods:Miranda, Pita, 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
61430Cia18Collagen induced arthritis QTL 183.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X14843113120568734Rat
1598837Memor13Memory QTL 133.2exploratory behavior trait (VT:0010471)difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)X41052407146860749Rat
738035Stresp1Stress response QTL 14.960.000011stress-related behavior trait (VT:0010451)defensive burying - copingX41304447112935181Rat
61431Cia19Collagen induced arthritis QTL 194.4joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X65612192120568734Rat


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 3 12 29 13 18 13 8 10 10 12 13 11 8
Low 31 28 28 1 28 1 64 23 28
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000034329   ⟹   ENSRNOP00000066863
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX71,880,204 - 71,880,879 (+)Ensembl
Rnor_6.0 EnsemblX77,885,586 - 77,886,170 (+)Ensembl
RefSeq Acc Id: XM_039100356   ⟹   XP_038956284
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X71,880,236 - 71,880,917 (+)NCBI
Protein Sequences
Protein RefSeqs XP_038956284 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: ENSRNOP00000066863   ⟸   ENSRNOT00000034329
RefSeq Acc Id: XP_038956284   ⟸   XM_039100356
Protein Domains
TRASH

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-M0RBD1-F1-model_v2 AlphaFold M0RBD1 1-158 view protein structure

Transcriptome

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

Promoters
RGD ID:13701912
Promoter ID:EPDNEW_R12429
Type:initiation region
Name:RGD1560821_1
Description:similar to small nuclear ribonucleoparticle-associated protein
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_6.0X77,885,561 - 77,885,621EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1560821 AgrOrtholog
BioCyc Gene G2FUF-1904 BioCyc
Ensembl Genes ENSRNOG00000023733 Ensembl, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000066863.3 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000034329.6 UniProtKB/TrEMBL
Gene3D-CATH 2.30.170.20 UniProtKB/TrEMBL
InterPro L24e/L24_sf UniProtKB/TrEMBL
  Ribosomal_L24e-rel UniProtKB/TrEMBL
  Ribosomal_L24e_CS UniProtKB/TrEMBL
  TRASH_dom UniProtKB/TrEMBL
NCBI Gene 367865 ENTREZGENE
PANTHER PTHR10792 UniProtKB/TrEMBL
Pfam Ribosomal_L24e UniProtKB/TrEMBL
PhenoGen RGD1560821 PhenoGen
PROSITE RIBOSOMAL_L24E UniProtKB/TrEMBL
SMART TRASH UniProtKB/TrEMBL
UniProt M0RBD1_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 RGD1560821  similar to small nuclear ribonucleoparticle-associated protein   RGD1560821_predicted  similar to small nuclear ribonucleoparticle-associated protein (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-07 RGD1560821_predicted  similar to small nuclear ribonucleoparticle-associated protein (predicted)  LOC367865  similar to small nuclear ribonucleoparticle-associated protein  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC367865  similar to small nuclear ribonucleoparticle-associated protein      Symbol and Name status set to provisional 70820 PROVISIONAL