Urgcp (upregulator of cell proliferation) - Chinchilla Research Resource Database
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Gene: Urgcp (upregulator of cell proliferation) Rattus norvegicus
Analyze
Symbol: Urgcp
Name: upregulator of cell proliferation
CRRD ID: 1564681
Description: Predicted to have GTP binding activity. Predicted to localize to cytosol. Orthologous to human URGCP (upregulator of cell proliferation); INTERACTS WITH bisphenol A; flutamide; genistein.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: LOC498406; RGD1564681; similar to mitochondrial ribosomal protein S24; up-regulated gene 4; Urg4
Orthologs:
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.01485,957,726 - 86,002,227 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1485,957,716 - 85,991,211 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01486,649,967 - 86,694,245 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41486,367,017 - 86,392,064 (-)NCBIRGSC3.4rn4RGSC3.4
Celera1479,479,557 - 79,504,606 (-)NCBICelera
Cytogenetic Map14q21NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

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

Cellular Component
cytoplasm  (IEA)
cytosol  (IEA,ISO)
nucleus  (IEA)

Molecular Function
GTP binding  (IEA)

References

Additional References at PubMed
PMID:8889548  


Genomics

Comparative Map Data
Urgcp
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.01485,957,726 - 86,002,227 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1485,957,716 - 85,991,211 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01486,649,967 - 86,694,245 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41486,367,017 - 86,392,064 (-)NCBIRGSC3.4rn4RGSC3.4
Celera1479,479,557 - 79,504,606 (-)NCBICelera
Cytogenetic Map14q21NCBI
URGCP
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl743,875,894 - 43,926,411 (-)EnsemblGRCh38hg38GRCh38
GRCh38743,875,913 - 43,926,726 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37743,915,485 - 43,965,996 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36743,882,026 - 43,932,521 (-)NCBINCBI36hg18NCBI36
Celera743,905,366 - 43,955,861 (-)NCBI
Cytogenetic Map7p13NCBI
HuRef743,800,542 - 43,850,705 (-)NCBIHuRef
CHM1_1743,919,387 - 43,969,925 (-)NCBICHM1_1
CRA_TCAGchr7v2743,955,001 - 44,005,497 (-)NCBI
Urgcp
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39115,663,417 - 5,712,376 (-)NCBI
GRCm38115,713,417 - 5,762,376 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl115,713,417 - 5,762,376 (-)EnsemblGRCm38mm10GRCm38
MGSCv37115,613,420 - 5,662,379 (-)NCBIGRCm37mm9NCBIm37
MGSCv36115,614,188 - 5,641,153 (-)NCBImm8
Celera116,203,912 - 6,252,767 (-)NCBICelera
Cytogenetic Map11A1NCBI
URGCP
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1740,408,771 - 40,421,002 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl740,405,063 - 40,421,002 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0740,324,724 - 40,375,428 (+)NCBIMhudiblu_PPA_v0panPan3
LOC610578
(Canis lupus familiaris - dog)
No map positions available.
LOC100525140
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1848,780,576 - 48,821,582 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11848,780,521 - 48,817,058 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21853,469,534 - 53,527,955 (+)NCBISscrofa10.2Sscrofa10.2susScr3

Position Markers
D14Rat108  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01485,964,092 - 85,964,243NCBIRnor6.0
Rnor_5.01486,656,332 - 86,656,484NCBIRnor5.0
RGSC_v3.41486,373,380 - 86,373,531UniSTSRGSC3.4
Celera1479,485,924 - 79,486,075UniSTS
Cytogenetic Map14q21UniSTS
RH 3.4 Map14573.5UniSTS
RH 3.4 Map14573.5RGD
RH 2.0 Map14706.8RGD
SHRSP x BN Map1445.59RGD
AA800188  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01485,958,065 - 85,958,186NCBIRnor6.0
Rnor_5.01486,650,306 - 86,650,427UniSTSRnor5.0
RGSC_v3.41486,367,353 - 86,367,474UniSTSRGSC3.4
Celera1479,479,893 - 79,480,014UniSTS
Cytogenetic Map14q21UniSTS
RH 3.4 Map14576.9UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
CRRD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
631839Niddm37Non-insulin dependent diabetes mellitus QTL 373.37blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1412680424106641756Rat
70187Pancm5Pancreatic morphology QTL 516.7pancreas mass (VT:0010144)pancreas weight to body weight ratio (CMO:0000630)143259392686191589Rat
631523Pia13Pristane induced arthritis QTL 133.3joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1442442731108833671Rat
1300136Rf22Renal function QTL 223.9renal blood flow trait (VT:2000006)absolute change in renal vascular resistance (CMO:0001900)1443910761105074364Rat
1549834Scl45Serum cholesterol level QTL 455.8blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)1451818462105074364Rat
9590294Uminl4Urine mineral level QTL 45.660.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)1460980905105980905Rat
9589034Epfw11Epididymal fat weight QTL 1160.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)1460980905105980905Rat
738037Hcas6Hepatocarcinoma susceptibility QTL 62.93liver integrity trait (VT:0010547)liver nonremodeling tumorous lesion volume to total liver volume ratio (CMO:0001464)146187332388870994Rat
2317879Alcrsp27Alcohol response QTL 273.30.63response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)1461993178106993178Rat
634328Hc5Hypercalciuria QTL 52.3urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)1463548095108548095Rat
70153Bp59Blood pressure QTL 593.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)147339146788870994Rat
1582236Gluco22Glucose level QTL 223.30.0164blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1478172765102549388Rat
1582255Gluco29Glucose level QTL 293.10.0025blood glucose amount (VT:0000188)absolute change in blood glucose level area under curve (CMO:0002034)1478172765102549388Rat
1582197Gluco27Glucose level QTL 273.40.0006blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1478172765102549388Rat
1582209Gluco20Glucose level QTL 203.80.0005blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1478172765102549388Rat
1582250Gluco26Glucose level QTL 263.30.0009blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1478172765106641756Rat
2300197Scl59Serum cholesterol level QTL 59blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)1478446303110402569Rat
1582259Gluco23Glucose level QTL 233.10.0008blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1480049285115493446Rat
1641900Alcrsp11Alcohol response QTL 11alcohol metabolism trait (VT:0015089)blood ethanol level (CMO:0000535)1480049285115493446Rat
631213Bw60Body weight QTL604.51retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)1485307663106641756Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:426
Count of miRNA genes:228
Interacting mature miRNAs:270
Transcripts:ENSRNOT00000016468
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
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.


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 43 27 11 19 11 8 11 64 29 35 11 8
Low 30 30 30 10 6 6
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001077660 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006251312 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006251313 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006251315 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017599224 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AAHX01080901 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AC128636 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BI285944 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CB720935 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CB757259 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CB809919 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473963 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DN931704 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DN934843 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  EX490902 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FM041979 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FM044330 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FM046879 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FM056971 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ209875 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ222248 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ223767 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000016468   ⟹   ENSRNOP00000016468
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1485,957,730 - 85,968,037 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000076740   ⟹   ENSRNOP00000068129
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1485,957,716 - 85,982,771 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000076811
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1485,960,906 - 85,991,211 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000076874   ⟹   ENSRNOP00000067978
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1485,957,729 - 85,982,794 (-)Ensembl
RefSeq Acc Id: NM_001077660   ⟹   NP_001071128
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01485,957,729 - 85,982,774 (-)NCBI
Rnor_5.01486,649,967 - 86,694,245 (-)NCBI
RGSC_v3.41486,367,017 - 86,392,064 (-)RGD
Celera1479,479,557 - 79,504,606 (-)RGD
Sequence:
RefSeq Acc Id: XM_006251312   ⟹   XP_006251374
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01485,957,729 - 86,002,227 (-)NCBI
Rnor_5.01486,649,967 - 86,694,245 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006251313   ⟹   XP_006251375
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01485,957,729 - 86,002,227 (-)NCBI
Rnor_5.01486,649,967 - 86,694,245 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006251315   ⟹   XP_006251377
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01485,957,726 - 85,982,857 (-)NCBI
Rnor_5.01486,649,967 - 86,694,245 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017599224   ⟹   XP_017454713
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01485,957,729 - 85,971,153 (-)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_001071128   ⟸   NM_001077660
- UniProtKB: A0A096MJ37 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006251377   ⟸   XM_006251315
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_006251375   ⟸   XM_006251313
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_006251374   ⟸   XM_006251312
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_017454713   ⟸   XM_017599224
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000016468   ⟸   ENSRNOT00000016468
RefSeq Acc Id: ENSRNOP00000067978   ⟸   ENSRNOT00000076874
RefSeq Acc Id: ENSRNOP00000068129   ⟸   ENSRNOT00000076740
Protein Domains
VLIG-type G

Transcriptome

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

Promoters
RGD ID:13699471
Promoter ID:EPDNEW_R9984
Type:initiation region
Name:Urgcp_1
Description:upregulator of cell proliferation
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_6.01485,982,761 - 85,982,821EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1564681 AgrOrtholog
Ensembl Genes ENSRNOG00000012184 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000016468 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000067978 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000068129 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000016468 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000076740 UniProtKB/TrEMBL
  ENSRNOT00000076874 ENTREZGENE, UniProtKB/TrEMBL
InterPro G_VLIG_dom UniProtKB/TrEMBL
  GTP1_OBG UniProtKB/TrEMBL
  P-loop_NTPase UniProtKB/TrEMBL
KEGG Report rno:305493 UniProtKB/TrEMBL
NCBI Gene 305493 ENTREZGENE
PhenoGen Urgcp PhenoGen
PRINTS GTP1OBG UniProtKB/TrEMBL
PROSITE G_VLIG UniProtKB/TrEMBL
Superfamily-SCOP SSF52540 UniProtKB/TrEMBL
UniGene Rn.138962 ENTREZGENE
UniProt A0A096MJ37 ENTREZGENE, UniProtKB/TrEMBL
  A0A096MJH4_RAT UniProtKB/TrEMBL
  F1M5F4_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2011-08-01 Urgcp  upregulator of cell proliferation  Urg4  up-regulated gene 4  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-07 Urg4  up-regulated gene 4  RGD1564681_predicted  similar to mitochondrial ribosomal protein S24 (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-07 RGD1564681_predicted  similar to mitochondrial ribosomal protein S24 (predicted)  LOC498406  similar to mitochondrial ribosomal protein S24  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC498406  similar to mitochondrial ribosomal protein S24      Symbol and Name status set to provisional 70820 PROVISIONAL