Nuggc (nuclear GTPase, germinal center associated) - Rat Genome Database

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Gene: Nuggc (nuclear GTPase, germinal center associated) Rattus norvegicus
Analyze
Symbol: Nuggc
Name: nuclear GTPase, germinal center associated
RGD ID: 1562099
Description: Predicted to enable GTPase activity. Predicted to be involved in cellular response to lipopolysaccharide; negative regulation of apoptotic process; and regulation of nuclear cell cycle DNA replication. Predicted to act upstream of or within DNA damage response and somatic hypermutation of immunoglobulin genes. Predicted to be located in nucleus. Orthologous to human NUGGC (nuclear GTPase, germinal center associated); INTERACTS WITH 17beta-estradiol 3-benzoate; 2,3,7,8-tetrachlorodibenzodioxine; bisphenol A.
Type: protein-coding
RefSeq Status: MODEL
Previously known as: LOC290325; nuclear GTPase SLIP-GC; RGD1562099; similar to putative protein product of HMFN0672
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81543,997,446 - 44,041,716 (+)NCBIGRCr8
mRatBN7.21539,821,851 - 39,866,122 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1539,821,855 - 39,866,122 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.01549,011,951 - 49,055,246 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1549,010,492 - 49,055,237 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01552,749,593 - 52,794,085 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41545,027,370 - 45,069,708 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1539,496,861 - 39,539,609 (+)NCBICelera
Cytogenetic Map15p12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
nucleus  (ISO)

Molecular Function
GTPase activity  (IBA,ISO)

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. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:19734146   PMID:22833677  


Genomics

Comparative Map Data
Nuggc
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81543,997,446 - 44,041,716 (+)NCBIGRCr8
mRatBN7.21539,821,851 - 39,866,122 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1539,821,855 - 39,866,122 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.01549,011,951 - 49,055,246 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1549,010,492 - 49,055,237 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01552,749,593 - 52,794,085 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41545,027,370 - 45,069,708 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1539,496,861 - 39,539,609 (+)NCBICelera
Cytogenetic Map15p12NCBI
NUGGC
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38828,021,964 - 28,083,936 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl828,021,964 - 28,083,936 (-)EnsemblGRCh38hg38GRCh38
GRCh37827,879,481 - 27,941,453 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36827,935,400 - 27,997,307 (-)NCBINCBI36Build 36hg18NCBI36
Celera826,839,322 - 26,901,233 (-)NCBICelera
Cytogenetic Map8p21.1NCBI
HuRef826,424,993 - 26,486,840 (-)NCBIHuRef
CHM1_1828,081,599 - 28,143,480 (-)NCBICHM1_1
T2T-CHM13v2.0828,300,186 - 28,362,146 (-)NCBIT2T-CHM13v2.0
Nuggc
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391465,830,901 - 65,885,893 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1465,835,995 - 65,885,980 (+)EnsemblGRCm39 Ensembl
GRCm381465,593,499 - 65,648,444 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1465,598,546 - 65,648,531 (+)EnsemblGRCm38mm10GRCm38
MGSCv371466,220,118 - 66,267,281 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361466,224,104 - 66,267,281 (+)NCBIMGSCv36mm8
Celera1463,352,688 - 63,399,760 (+)NCBICelera
Cytogenetic Map14D1NCBI
cM Map1434.34NCBI
Nuggc
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540350,507,116 - 50,558,826 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495540350,507,971 - 50,558,881 (-)NCBIChiLan1.0ChiLan1.0
NUGGC
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2746,559,069 - 46,622,123 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1822,273,393 - 22,336,451 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0827,299,051 - 27,351,350 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1824,500,131 - 24,551,201 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl824,500,131 - 24,551,201 (-)Ensemblpanpan1.1panPan2
NUGGC
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12529,507,198 - 29,561,565 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2529,520,921 - 29,561,349 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2530,157,005 - 30,214,820 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02529,699,802 - 29,754,149 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2529,662,666 - 29,754,172 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12529,625,902 - 29,683,686 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02529,510,420 - 29,564,816 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02529,676,646 - 29,731,112 (+)NCBIUU_Cfam_GSD_1.0
Nuggc
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_0244049437,654,241 - 7,701,142 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936675885,039 - 920,253 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_004936675885,015 - 931,657 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
NUGGC
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1411,775,704 - 11,826,096 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11411,775,684 - 11,826,162 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21413,007,019 - 13,059,552 (-)NCBISscrofa10.2Sscrofa10.2susScr3
NUGGC
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1826,129,593 - 26,190,881 (-)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366605215,945,271 - 16,010,485 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Nuggc
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462475822,777,612 - 22,838,061 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462475822,777,511 - 22,838,082 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Nuggc
123 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:92
Count of miRNA genes:82
Interacting mature miRNAs:84
Transcripts:ENSRNOT00000024527
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.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
731170Pur3Proteinuria QTL 32.30.0005urine protein amount (VT:0005160)urine protein excretion rate (CMO:0000759)15141686771Rat
1641887Alcrsp14Alcohol response QTL 14response to alcohol trait (VT:0010489)brain neurotensin receptor 1 density (CMO:0002068)15142356671Rat
2298549Neuinf12Neuroinflammation QTL 123.5nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)15155302115Rat
10401805Kidm51Kidney mass QTL 51kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)1530632945306329Rat
738017Hcas7Hepatocarcinoma susceptibility QTL 72.91liver integrity trait (VT:0010547)liver nonremodeling tumorous lesion volume to total liver volume ratio (CMO:0001464)15226636846921453Rat
1582251Gluco24Glucose level QTL 243.20.0008blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)15553075650530756Rat
631273Lecl2Lens clarity QTL 20.001lens clarity trait (VT:0001304)age of onset/diagnosis of cataract (CMO:0001584)151059608955596089Rat
2300167Bmd63Bone mineral density QTL 635.90.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)151111114256111142Rat
2300173Bmd62Bone mineral density QTL 6212.80.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)151111114256111142Rat
2293688Bss29Bone structure and strength QTL 295.310.0001femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)151111114256111142Rat
2317750Glom26Glomerulus QTL 264.3urine protein amount (VT:0005160)urine protein level (CMO:0000591)151249614165205939Rat
61424Scl1Serum cholesterol level QTL 17.70.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)151672552880672115Rat
1331729Rf42Renal function QTL 423.071kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)151736289773690657Rat
2324620Coatc3Coat color QTL 3coat/hair pigmentation trait (VT:0010463)pigmented coat/hair area to total coat/hair area ratio (CMO:0001810)151985656646187442Rat
10054130Srcrt8Stress Responsive Cort QTL 82.180.0085blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)152211793367117933Rat
1578646Bmd18Bone mineral density QTL 185.2femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)152280624098288169Rat
1578647Bmd17Bone mineral density QTL 174femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)152280624098288169Rat
1578660Bss19Bone structure and strength QTL 194.3femur morphology trait (VT:0000559)bone trabecular cross-sectional area (CMO:0002311)152280624098288169Rat
1582214Stl21Serum triglyceride level QTL 213.10.022blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)152803066582262678Rat
1582227Gluco30Glucose level QTL 303.60.0003blood glucose amount (VT:0000188)absolute change in blood glucose level area under curve (CMO:0002034)152803066582262678Rat
1582228Epfw3Epididymal fat weight QTL 34.10.0002epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)152803066582262678Rat
1582242Gluco28Glucose level QTL 283.30.0008blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)152803066582262678Rat
1582244Bw79Body weight QTL 7940.0002epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)152803066582262678Rat
2293691Bmd37Bone mineral density QTL 376.60.0001femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)153361105871477291Rat
2293686Bmd36Bone mineral density QTL 367.40.0001femur strength trait (VT:0010010)femoral neck ultimate force (CMO:0001703)153361105871477291Rat
1598828Glom14Glomerulus QTL 142.5kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)153405413979054139Rat

Markers in Region
D15Rat17  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21539,838,783 - 39,838,985 (+)MAPPERmRatBN7.2
Rnor_6.01549,027,416 - 49,027,615NCBIRnor6.0
Rnor_5.01552,766,530 - 52,766,729UniSTSRnor5.0
RGSC_v3.41545,042,674 - 45,042,874RGDRGSC3.4
RGSC_v3.41545,042,675 - 45,042,874UniSTSRGSC3.4
RGSC_v3.11545,058,374 - 45,058,574RGD
Celera1539,512,159 - 39,512,358UniSTS
RH 2.0 Map15273.1RGD
SHRSP x BN Map1533.5099RGD
FHH x ACI Map1546.36RGD
Cytogenetic Map15p12UniSTS
D15Got230  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21539,824,594 - 39,824,738 (+)MAPPERmRatBN7.2
Rnor_6.01549,013,223 - 49,013,364NCBIRnor6.0
Rnor_5.01552,752,337 - 52,752,478UniSTSRnor5.0
RGSC_v3.41545,028,488 - 45,028,629UniSTSRGSC3.4
Celera1539,498,133 - 39,498,274UniSTS
Cytogenetic Map15p12UniSTS


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 endocrine system exocrine system hemolymphoid system hepatobiliary system nervous system renal system reproductive system respiratory system
High
Medium 2
Low 8 19 4 8
Below cutoff 1 1 1 1 14 23 24 11

Sequence


RefSeq Acc Id: ENSRNOT00000024527   ⟹   ENSRNOP00000042169
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1539,821,855 - 39,866,122 (+)Ensembl
Rnor_6.0 Ensembl1549,010,492 - 49,055,237 (+)Ensembl
RefSeq Acc Id: XM_008770806   ⟹   XP_008769028
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81543,998,913 - 44,041,716 (+)NCBI
mRatBN7.21539,823,319 - 39,866,122 (+)NCBI
Rnor_6.01549,011,951 - 49,055,246 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039093929   ⟹   XP_038949857
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81543,997,446 - 44,041,716 (+)NCBI
mRatBN7.21539,821,851 - 39,866,122 (+)NCBI
Protein Sequences
Protein RefSeqs XP_008769028 (Get FASTA)   NCBI Sequence Viewer  
  XP_038949857 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000042169
  ENSRNOP00000042169.5
RefSeq Acc Id: XP_008769028   ⟸   XM_008770806
- UniProtKB: F1M575 (UniProtKB/TrEMBL),   A6K6K1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000042169   ⟸   ENSRNOT00000024527
RefSeq Acc Id: XP_038949857   ⟸   XM_039093929
- UniProtKB: F1M575 (UniProtKB/TrEMBL),   A6K6K1 (UniProtKB/TrEMBL)
Protein Domains
Dynamin N-terminal

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-F1M575-F1-model_v2 AlphaFold F1M575 1-796 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:1562099 AgrOrtholog
BioCyc Gene G2FUF-13352 BioCyc
Ensembl Genes ENSRNOG00000018238 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000024527.8 UniProtKB/TrEMBL
Gene3D-CATH 3.40.50.300 UniProtKB/TrEMBL
InterPro Dynamin_N UniProtKB/TrEMBL
  P-loop_NTPase UniProtKB/TrEMBL
KEGG Report rno:290325 UniProtKB/TrEMBL
NCBI Gene 290325 ENTREZGENE
PANTHER NUCLEAR GTPASE SLIP-GC UniProtKB/TrEMBL
  NUCLEAR GTPASE SLIP-GC UniProtKB/TrEMBL
Pfam Dynamin_N UniProtKB/TrEMBL
PhenoGen Nuggc PhenoGen
RatGTEx ENSRNOG00000018238 RatGTEx
Superfamily-SCOP SSF52540 UniProtKB/TrEMBL
UniProt A6K6K1 ENTREZGENE, UniProtKB/TrEMBL
  F1M575 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2013-01-22 Nuggc  nuclear GTPase, germinal center associated  RGD1562099  similar to putative protein product of HMFN0672  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 RGD1562099  similar to putative protein product of HMFN0672   RGD1562099_predicted  similar to putative protein product of HMFN0672 (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-07 RGD1562099_predicted  similar to putative protein product of HMFN0672 (predicted)  LOC290325  similar to putative protein product of HMFN0672  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC290325  similar to putative protein product of HMFN0672      Symbol and Name status set to provisional 70820 PROVISIONAL