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

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Gene: Nuggc (nuclear GTPase, germinal center associated) Rattus norvegicus
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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
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81543,997,446 - 44,041,716 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1543,997,438 - 44,041,643 (+)EnsemblGRCr8
mRatBN7.21539,821,851 - 39,866,122 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1539,821,855 - 39,866,122 (+)EnsemblmRatBN7.2
Rnor_6.01549,011,951 - 49,055,246 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1549,010,492 - 49,055,237 (+)Ensemblrn6Rnor6.0
Rnor_5.01552,749,593 - 52,794,085 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41545,027,370 - 45,069,708 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1539,496,861 - 39,539,609 (+)NCBICelera
Cytogenetic Map15p12NCBI
JBrowse:




Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
nuclear speck  (IEA,ISO)
nucleus  (IEA,ISO)

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. 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 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1543,997,438 - 44,041,643 (+)EnsemblGRCr8
mRatBN7.21539,821,851 - 39,866,122 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1539,821,855 - 39,866,122 (+)EnsemblmRatBN7.2
Rnor_6.01549,011,951 - 49,055,246 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1549,010,492 - 49,055,237 (+)Ensemblrn6Rnor6.0
Rnor_5.01552,749,593 - 52,794,085 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41545,027,370 - 45,069,708 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
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 (-)Ensemblhg38GRCh38
GRCh37827,879,481 - 27,941,453 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36827,935,400 - 27,997,307 (-)NCBIBuild 36Build 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 EnsemblGRCm39
GRCm381465,593,499 - 65,648,444 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1465,598,546 - 65,648,531 (+)Ensemblmm10GRCm38
MGSCv371466,224,104 - 66,267,281 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv361466,224,104 - 66,267,281 (+)NCBIMGSCv36mm8
Celera1463,356,716 - 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 (-)Ensembl
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 (-)EnsemblpanPan2panpan1.1
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 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha2530,157,005 - 30,214,820 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.02529,699,802 - 29,754,149 (+)NCBIROS_Cfam_1.0ROS_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_1.0UU_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 (-)EnsemblSpeTri2.0 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 (-)EnsemblsusScr11Sscrofa11.1
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_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_00462475822,777,511 - 22,838,082 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Nuggc
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v11258,792,446 - 58,827,680 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Nuggc
87 total Variants
miRNA Target Status (No longer updated)

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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1641913Colcr2Colorectal carcinoma resistance QTL 26.570.0197intestine integrity trait (VT:0010554)poorly differentiated malignant colorectal tumor number (CMO:0002076)15231575947315759Rat
1641887Alcrsp14Alcohol response QTL 14response to alcohol trait (VT:0010489)brain neurotensin receptor 1 density (CMO:0002068)15144836456Rat
738017Hcas7Hepatocarcinoma susceptibility QTL 72.91liver integrity trait (VT:0010547)liver nonremodeling tumorous lesion volume to total liver volume ratio (CMO:0001464)15231575953331089Rat
152025253Hrtrt24Heart rate QTL 243.82heart pumping trait (VT:2000009)153185580392671517Rat
1582227Gluco30Glucose level QTL 303.60.0003blood glucose amount (VT:0000188)absolute change in blood glucose level area under curve (CMO:0002034)154367724488677244Rat
10054130Srcrt8Stress Responsive Cort QTL 82.180.0085blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)152852773273527732Rat
1582228Epfw3Epididymal fat weight QTL 34.10.0002epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)154367724488677244Rat
1578646Bmd18Bone mineral density QTL 185.2femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)1525285835104695021Rat
2324620Coatc3Coat color QTL 3coat/hair pigmentation trait (VT:0010463)pigmented coat/hair area to total coat/hair area ratio (CMO:0001810)152233635152597086Rat
1578647Bmd17Bone mineral density QTL 174femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)1525285835104695021Rat
61424Scl1Serum cholesterol level QTL 17.70.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)151915576287086765Rat
10401805Kidm51Kidney mass QTL 51kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)15278592347785923Rat
1598828Glom14Glomerulus QTL 142.5kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)154046315285463152Rat
2317750Glom26Glomerulus QTL 264.3urine protein amount (VT:0005160)urine protein level (CMO:0000591)151492659471614418Rat
631550Bw7Body weight QTL 73.6body mass (VT:0001259)body weight (CMO:0000012)152233635167336351Rat
1582242Gluco28Glucose level QTL 283.30.0008blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)154367724488677244Rat
1582244Bw79Body weight QTL 7940.0002epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)154367724488677244Rat
1578660Bss19Bone structure and strength QTL 194.3femur morphology trait (VT:0000559)bone trabecular cross-sectional area (CMO:0002311)1525285835104695021Rat
1582214Stl21Serum triglyceride level QTL 213.10.022blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)154367724488677244Rat

Markers in Region
D15Rat17  
Rat AssemblyChrPosition (strand)SourceJBrowse
GRCr81544,014,376 - 44,014,576 (+)Marker Load Pipeline
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
Celera1539,512,159 - 39,512,358UniSTS
RGSC_v3.11545,058,374 - 45,058,574RGD
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

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
11 1 4 43 33 42 15 78 15 1 176 98 11 30 52 58 27 1 1

Sequence


Ensembl Acc Id: ENSRNOT00000024527   ⟹   ENSRNOP00000042169
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1543,997,438 - 44,041,643 (+)Ensembl
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:
Ensembl 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 ENTREZGENE
  ENSRNOT00000024527.9 UniProtKB/TrEMBL
Gene3D-CATH 3.40.50.300 UniProtKB/TrEMBL
InterPro Dynamin_N UniProtKB/TrEMBL
  Nuclear_GTPase_SLIP-GC 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