RGD1565653 (similar to transcription elongation factor B (SIII), polypeptide 2) - Rat Genome Database

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Gene: RGD1565653 (similar to transcription elongation factor B (SIII), polypeptide 2) Rattus norvegicus
Analyze
No known orthologs.
Symbol: RGD1565653
Name: similar to transcription elongation factor B (SIII), polypeptide 2
RGD ID: 1565653
Description: Predicted to be involved in transcription elongation by RNA polymerase II promoter.
Type: pseudo (Ensembl: protein-coding)
RefSeq Status: INFERRED
Previously known as: elongin-B-like; LOC367176; transcription elongation factor B polypeptide 2-like
RGD Orthologs
Alliance Genes
More Info homologs ...
Related Functional Gene: Elob  
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.28110,990,032 - 110,995,705 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl8110,989,940 - 110,995,640 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.08119,280,608 - 119,286,094 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.08118,623,282 - 118,628,833 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.48115,408,074 - 115,413,469 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera8110,272,464 - 110,277,950 (+)NCBICelera
Cytogenetic Map8q32NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

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

Genomics

Variants

.
Variants in RGD1565653
82 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:44
Count of miRNA genes:42
Interacting mature miRNAs:44
Transcripts:ENSRNOT00000010249
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
631650Stl6Serum triglyceride level QTL 640.0019blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)810378157112202585Rat
1554321Bmd3Bone mineral density QTL 37.90.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)840952565123900184Rat
70197BpQTLcluster8Blood pressure QTL cluster 83.482arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)846531639119088624Rat
70197BpQTLcluster8Blood pressure QTL cluster 83.482arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)846531639119088624Rat
70197BpQTLcluster8Blood pressure QTL cluster 83.482arterial blood pressure trait (VT:2000000)absolute change in systolic blood pressure (CMO:0000607)846531639119088624Rat
70197BpQTLcluster8Blood pressure QTL cluster 83.482arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)846531639119088624Rat
2303171Bp331Blood pressure QTL 3315.570.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)861290298119084929Rat
631653Bp125Blood pressure QTL 1253.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)866142385111142385Rat
631210Bw3Body weight QTL35.9mesenteric fat pad mass (VT:0010427)mesenteric fat pad weight to body weight ratio (CMO:0000654)869349194112783834Rat
1300171Bp184Blood pressure QTL 1843.66arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)870513503118219066Rat
8694446Bw170Body weight QTL 17012.070.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)871888757116888757Rat
9590292Uminl3Urine mineral level QTL 33.620.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)871888757116888757Rat
8694200Abfw4Abdominal fat weight QTL 49.070.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)871888757116888757Rat
8694392Bw161Body weight QTL 1618.060.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)871888757116888757Rat
1549909Stresp11Stress response QTL 116.830.0019stress-related behavior trait (VT:0010451)number of approaches toward negative stimulus before onset of defensive burying response (CMO:0001960)873473045118473045Rat
2300181Bmd55Bone mineral density QTL 555.70.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)876468691121468691Rat
61437Cia6Collagen induced arthritis QTL 6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)882460758122812818Rat
2313400Anxrr25Anxiety related response QTL 25aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)889265192114019816Rat
738011Anxrr9Anxiety related response QTL 96.1exploratory behavior trait (VT:0010471)number of entries into a discrete space in an experimental apparatus (CMO:0000960)893535351123900184Rat
1358893Bp263Blood pressure QTL 2635.01arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)893965141123900184Rat
1358903Bp252Blood pressure QTL 25270.0001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)893965141123900184Rat
738014Anxrr15Anxiety related response QTL 153.60.005locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)895718998123900184Rat
2300182Bmd56Bone mineral density QTL 565.4femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)895718998123900184Rat
724539Cm19Cardiac mass QTL 192.6heart mass (VT:0007028)calculated heart weight (CMO:0000073)8100149864120994388Rat


Expression


Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000010249   ⟹   ENSRNOP00000010249
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl8110,989,940 - 110,995,640 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000040365   ⟹   ENSRNOP00000048876
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl8110,989,940 - 110,995,640 (+)Ensembl
RefSeq Acc Id: XM_017596137   ⟹   XP_017451626
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.28110,990,032 - 110,995,704 (+)NCBI
Rnor_6.08119,280,608 - 119,286,094 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039082669   ⟹   XP_038938597
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.28110,990,042 - 110,995,705 (+)NCBI
Protein Sequences
Protein RefSeqs XP_017451626 (Get FASTA)   NCBI Sequence Viewer  
  XP_038938597 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: XP_017451626   ⟸   XM_017596137
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_038938597   ⟸   XM_039082669
- Peptide Label: isoform X2
RefSeq Acc Id: ENSRNOP00000010249   ⟸   ENSRNOT00000010249
RefSeq Acc Id: ENSRNOP00000048876   ⟸   ENSRNOT00000040365
Protein Domains
Ubiquitin-like

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-F1M937-F1-model_v2 AlphaFold F1M937 1-117 view protein structure
AF-F1LZ51-F1-model_v2 AlphaFold F1LZ51 1-118 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)
BioCyc Gene G2FUF-29038 BioCyc
Ensembl Genes ENSRNOG00000062517 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000010249 ENTREZGENE
  ENSRNOP00000010249.4 UniProtKB/TrEMBL
  ENSRNOP00000048876 ENTREZGENE
  ENSRNOP00000048876.5 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000010249 ENTREZGENE
  ENSRNOT00000010249.4 UniProtKB/TrEMBL
  ENSRNOT00000040365 ENTREZGENE
  ENSRNOT00000040365.5 UniProtKB/TrEMBL
InterPro ELOB UniProtKB/TrEMBL
  Ubiquitin-like_dom UniProtKB/TrEMBL
  Ubiquitin-like_domsf UniProtKB/TrEMBL
NCBI Gene 367176 ENTREZGENE
PANTHER PTHR13248 UniProtKB/TrEMBL
Pfam ubiquitin UniProtKB/TrEMBL
PhenoGen RGD1565653 PhenoGen
PROSITE UBIQUITIN_2 UniProtKB/TrEMBL
SMART UBQ UniProtKB/TrEMBL
Superfamily-SCOP SSF54236 UniProtKB/TrEMBL
UniProt F1LZ51_RAT UniProtKB/TrEMBL
  F1M937_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2022-06-02 RGD1565653  similar to transcription elongation factor B (SIII), polypeptide 2  RGD1565653  similar to transcription elongation factor B (SIII), polypeptide 2  Data Merged 737654 PROVISIONAL
2021-08-09 RGD1565653  similar to transcription elongation factor B (SIII), polypeptide 2      Symbol and Name status set to provisional 45752 PROVISIONAL
2008-04-30 RGD1565653  similar to transcription elongation factor B (SIII), polypeptide 2   RGD1565653_predicted  similar to transcription elongation factor B (SIII), polypeptide 2 (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-07 RGD1565653_predicted  similar to transcription elongation factor B (SIII), polypeptide 2 (predicted)  LOC367176  similar to transcription elongation factor B (SIII), polypeptide 2  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC367176  similar to transcription elongation factor B (SIII), polypeptide 2      Symbol and Name status set to provisional 70820 PROVISIONAL