RGD1565959 (RGD1565959) - Rat Genome Database

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Pathways
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Gene: RGD1565959 (RGD1565959) Rattus norvegicus
Analyze
Symbol: RGD1565959
Name: RGD1565959
RGD ID: 1565959
Description: ASSOCIATED WITH Hepatomegaly; INTERACTS WITH bisphenol A; chlorpyrifos; fenvalerate
Type: protein-coding
RefSeq Status: PREDICTED
Previously known as: hypothetical LOC301230; hypothetical protein LOC301230; LOC301230; uncharacterized protein LOC301230
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8920,371,212 - 20,383,992 (+)NCBIGRCr8
mRatBN7.2912,873,697 - 12,886,364 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl912,873,697 - 12,886,364 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx921,453,276 - 21,465,963 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0926,519,505 - 26,532,186 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0924,816,643 - 24,829,368 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0914,883,241 - 14,896,662 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl914,883,296 - 14,895,960 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0913,807,032 - 13,819,694 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.498,282,628 - 8,295,293 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera910,622,607 - 10,642,780 (+)NCBICelera
Cytogenetic Map9q12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View
Hepatomegaly  (EXP)

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions

Genomics

Variants

.
Variants in RGD1565959
142 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:38
Count of miRNA genes:36
Interacting mature miRNAs:38
Transcripts:ENSRNOT00000065800
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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
10054141Gmadr4Adrenal mass QTL 42.450.0074adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)9114209783Rat
70226Eae4Experimental allergic encephalomyelitis QTL 4nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)9125661317Rat
9589055Scfw5Subcutaneous fat weight QTL 55.550.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)9137999212Rat
7411592Foco8Food consumption QTL 87.40.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)9137999212Rat
9589158Gluco65Glucose level QTL 656.820.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)9137999212Rat
1300124Cm4Cardiac mass QTL 43.55heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)9140594091Rat
1298088Edpm11Estrogen-dependent pituitary mass QTL 112.5pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)9143718459Rat
1641911Alcrsp13Alcohol response QTL 13response to alcohol trait (VT:0010489)brain neurotensin receptor 1 density (CMO:0002068)9143718459Rat
10054125Srcrt7Stress Responsive Cort QTL 73.330.0011blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)9187073594Rat
1331757Cdexp1CD45RC expression in CD8 T cells QTL 14.3CD8-positive T cell quantity (VT:0008077)blood CD45RC(high) CD8 T cell count to CD45RC(low) CD8 T cell count ratio (CMO:0001990)9102453767509080Rat
1354650Despr5Despair related QTL 54.010.0017locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)9125408446254084Rat
2303559Gluco54Glucose level QTL 542blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)9125408446254084Rat
1578675Bss17Bone structure and strength QTL 173.8femur morphology trait (VT:0000559)femoral neck cortical cross-sectional area (CMO:0001702)9336865213533896Rat
61425Cia15Collagen induced arthritis QTL 154.6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)9510982642921101Rat
631211Bw4Body weight QTL45.31retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)9510982650109826Rat
11353947Bp392Blood pressure QTL 392arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)9728325252283252Rat
61450Ciaa3CIA Autoantibody QTL 36.5blood autoantibody amount (VT:0003725)calculated serum anti-type 2 collagen antibody titer (CMO:0001279)9795472022071169Rat
9589133Insul26Insulin level QTL 2617.960.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)9895256053952560Rat
7411609Foco16Food consumption QTL 1625.60.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)9895256053952560Rat


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 hemolymphoid system reproductive system
High
Medium 6
Low 2 1
Below cutoff 2 9 8

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000065800   ⟹   ENSRNOP00000062876
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl912,873,697 - 12,886,364 (+)Ensembl
Rnor_6.0 Ensembl914,883,296 - 14,895,960 (+)Ensembl
RefSeq Acc Id: NM_001106886   ⟹   NP_001100356
RefSeq Status: PREDICTED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8920,371,287 - 20,383,956 (+)NCBI
mRatBN7.2912,873,697 - 12,886,364 (+)NCBI
Rnor_6.0914,883,296 - 14,895,960 (+)NCBI
Rnor_5.0913,807,032 - 13,819,694 (+)NCBI
RGSC_v3.498,282,628 - 8,295,293 (+)RGD
Celera910,622,607 - 10,642,780 (+)RGD
Sequence:
RefSeq Acc Id: XM_063266845   ⟹   XP_063122915
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8920,371,212 - 20,383,992 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001100356 (Get FASTA)   NCBI Sequence Viewer  
  XP_063122915 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDM18915 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000062876
  ENSRNOP00000062876.1
Reference Protein Sequences
RefSeq Acc Id: NP_001100356   ⟸   NM_001106886
- Peptide Label: precursor
- UniProtKB: D3ZB01 (UniProtKB/TrEMBL),   A6JIG7 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000062876   ⟸   ENSRNOT00000065800
RefSeq Acc Id: XP_063122915   ⟸   XM_063266845
- Peptide Label: isoform X1

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZB01-F1-model_v2 AlphaFold D3ZB01 1-121 view protein structure

Transcriptome

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

Promoters
RGD ID:13696490
Promoter ID:EPDNEW_R7015
Type:initiation region
Name:RGD1565959_1
Description:RGD1565959
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_6.0914,883,255 - 14,883,315EPDNEW

Additional Information

Database Acc Id Source(s)
BioCyc Gene G2FUF-28290 BioCyc
Ensembl Genes ENSRNOG00000042054 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000065800 ENTREZGENE
  ENSRNOT00000065800.2 UniProtKB/TrEMBL
KEGG Report rno:301230 UniProtKB/TrEMBL
NCBI Gene 301230 ENTREZGENE
PhenoGen RGD1565959 PhenoGen
RatGTEx ENSRNOG00000042054 RatGTEx
UniProt A6JIG7 ENTREZGENE, UniProtKB/TrEMBL
  D3ZB01 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 RGD1565959  RGD1565959   RGD1565959_predicted  RGD1565959 (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-07 RGD1565959_predicted  RGD1565959 (predicted)  LOC301230  hypothetical LOC301230  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC301230  hypothetical LOC301230      Symbol and Name status set to provisional 70820 PROVISIONAL