Gpn3 (GPN-loop GTPase 3) - Rat Genome Database

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Gene: Gpn3 (GPN-loop GTPase 3) Rattus norvegicus
Analyze
Symbol: Gpn3
Name: GPN-loop GTPase 3
RGD ID: 1303034
Description: Predicted to enable GTPase activity. Predicted to be part of protein-containing complex. Orthologous to human GPN3 (GPN-loop GTPase 3); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,6-dinitrotoluene; 4,4'-sulfonyldiphenol.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: ATP binding domain 1 family, member C; ATP-binding domain 1 family member C; Atpbd1c; LOC360810; similar to RIKEN cDNA A930018B01
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81239,850,070 - 39,859,032 (-)NCBIGRCr8
mRatBN7.21234,189,285 - 34,198,251 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1234,189,577 - 34,198,206 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1235,361,706 - 35,370,669 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01235,973,115 - 35,982,079 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01235,025,439 - 35,034,403 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01239,670,746 - 39,679,364 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1239,670,453 - 39,679,510 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01241,551,264 - 41,559,994 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41235,384,028 - 35,392,646 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11235,247,415 - 35,256,034 (-)NCBI
Celera1235,860,509 - 35,869,119 (-)NCBICelera
Cytogenetic Map12q16NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

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. GOA pipeline RGD automated data pipeline
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions

Genomics

Comparative Map Data
Gpn3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81239,850,070 - 39,859,032 (-)NCBIGRCr8
mRatBN7.21234,189,285 - 34,198,251 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1234,189,577 - 34,198,206 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1235,361,706 - 35,370,669 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01235,973,115 - 35,982,079 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01235,025,439 - 35,034,403 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01239,670,746 - 39,679,364 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1239,670,453 - 39,679,510 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01241,551,264 - 41,559,994 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41235,384,028 - 35,392,646 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11235,247,415 - 35,256,034 (-)NCBI
Celera1235,860,509 - 35,869,119 (-)NCBICelera
Cytogenetic Map12q16NCBI
GPN3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh3812110,452,486 - 110,468,721 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl12110,452,486 - 110,469,268 (-)EnsemblGRCh38hg38GRCh38
GRCh3712110,890,291 - 110,906,526 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 3612109,374,674 - 109,390,447 (-)NCBINCBI36Build 36hg18NCBI36
Celera12110,517,052 - 110,533,287 (-)NCBICelera
Cytogenetic Map12q24.11NCBI
HuRef12107,908,631 - 107,924,854 (-)NCBIHuRef
CHM1_112110,858,121 - 110,874,356 (-)NCBICHM1_1
T2T-CHM13v2.012110,430,179 - 110,446,415 (-)NCBIT2T-CHM13v2.0
Gpn3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm395122,510,571 - 122,520,834 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl5122,509,939 - 122,520,965 (+)EnsemblGRCm39 Ensembl
GRCm385122,372,508 - 122,382,771 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl5122,371,876 - 122,382,902 (+)EnsemblGRCm38mm10GRCm38
MGSCv375122,822,517 - 122,832,780 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv365122,633,123 - 122,643,388 (+)NCBIMGSCv36mm8
Celera5119,454,962 - 119,465,226 (+)NCBICelera
Cytogenetic Map5FNCBI
cM Map562.33NCBI
Gpn3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554827,367,000 - 7,383,951 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554827,367,000 - 7,383,951 (-)NCBIChiLan1.0ChiLan1.0
GPN3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v210118,516,443 - 118,532,512 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan112118,512,844 - 118,529,195 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v012108,025,450 - 108,041,876 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.112111,417,321 - 111,433,434 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl12111,417,255 - 111,433,369 (-)Ensemblpanpan1.1panPan2
GPN3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1268,279,100 - 8,291,584 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl268,279,499 - 8,291,238 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha268,442,731 - 8,455,418 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0268,536,779 - 8,549,472 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl268,536,776 - 8,548,975 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1268,496,120 - 8,508,709 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0268,554,838 - 8,567,503 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0268,510,061 - 8,522,976 (-)NCBIUU_Cfam_GSD_1.0
Gpn3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118156,043,634 - 156,054,203 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365583,424,064 - 3,435,975 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365583,424,832 - 3,436,376 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
GPN3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1431,836,741 - 31,849,945 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11431,836,733 - 31,849,559 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21433,759,997 - 33,771,083 (-)NCBISscrofa10.2Sscrofa10.2susScr3
GPN3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.111105,688,067 - 105,704,409 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl11105,688,064 - 105,703,976 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_023666037139,415,729 - 139,431,692 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Gpn3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462474721,420,602 - 21,435,299 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462474721,420,619 - 21,437,928 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Gpn3
59 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:75
Count of miRNA genes:66
Interacting mature miRNAs:70
Transcripts:ENSRNOT00000001722
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
631560Apr1Acute phase response QTL 16.1orosomucoid 1 amount (VT:0010541)plasma orosomucoid 1 level (CMO:0001467)122480502252308831Rat
70213Niddm27Non-insulin dependent diabetes mellitus QTL 273.72blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)121120049452308831Rat
8552964Pigfal17Plasma insulin-like growth factor 1 level QTL 173.5blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)121120049452308831Rat
7411641Foco19Food consumption QTL 1927.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)121120049452308831Rat
7411643Foco20Food consumption QTL 200.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)122598935552308831Rat
5684888Pia42Pristane induced arthritis QTL 42joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)12348941648489416Rat
1641928Alcrsp5Alcohol response QTL 5response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)121847304152308831Rat
1300162Bp188Blood pressure QTL 1883.19arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)123776414551558799Rat
8552912Pigfal6Plasma insulin-like growth factor 1 level QTL 65blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)121120049752308831Rat
1549829Scl48Serum cholesterol level QTL 485blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)121526424852308831Rat
10059594Kidm46Kidney mass QTL 463.790.025kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)121174352852308831Rat
8552918Pigfal7Plasma insulin-like growth factor 1 level QTL 7blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)121120049452308831Rat
70169Eae13Experimental allergic encephalomyelitis QTL 130.032nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)122977552242298555Rat
1600386Calcic2Intracellular calcium level QTL 20.001platelet physiology trait (VT:0005464)platelet intracellular calcium level (CMO:0000922)123370043246784661Rat
61404Bw120Body weight QTL 1205.1body mass (VT:0001259)body mass index (BMI) (CMO:0000105)121746497946784661Rat
1556747Calcic1Intracellular calcium level QTL 13.6platelet calcium amount (VT:0010500)platelet intracellular calcium level (CMO:0000922)123370043246784661Rat
1300175Cm5Cardiac mass QTL 53.78heart mass (VT:0007028)heart left ventricle weight to body weight ratio (CMO:0000530)123370043251558799Rat
631829Alc6Alcohol consumption QTL 64.7consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)123424347543352593Rat
1331786Kidm11Kidney mass QTL 113.571kidney mass (VT:0002707)right kidney wet weight (CMO:0000082)121618743852308831Rat
2293699Bss49Bone structure and strength QTL 495.610.0001lumbar vertebra size trait (VT:0010518)lumbar vertebra trabecular cross-sectional area (CMO:0001692)121613502952308831Rat
1331761Bp218Blood pressure QTL 2182.973arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)121618743851213550Rat
1331763Wbc2White blood cell count QTL 23.162leukocyte quantity (VT:0000217)total white blood cell count (CMO:0000365)121120049452308831Rat
7411547Bw129Body weight QTL 1290.001body mass (VT:0001259)body weight gain (CMO:0000420)61120049452308831Rat
1298081Cia25Collagen induced arthritis QTL 254.7joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)12274769447747694Rat
2303569Gluco44Glucose level QTL 442blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)121847304152308831Rat
2303575Insul14Insulin level QTL 144blood insulin amount (VT:0001560)blood insulin level (CMO:0000349)12308718048087180Rat
7411588Foco6Food consumption QTL 60.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)121120049452308831Rat
7243862Mcs30Mammary carcinoma susceptibility QTL 308.62mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)12563330650633306Rat
2300186Bmd59Bone mineral density QTL 597.10.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)121613502952308831Rat
7411597Foco10Food consumption QTL 100.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)121120049452308831Rat


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
nervous system
renal system
reproductive system
respiratory system
9 11 49 113 91 90 59 25 59 6 218 97 93 45 60 31

Sequence


Ensembl Acc Id: ENSRNOT00000001722   ⟹   ENSRNOP00000001722
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1234,189,577 - 34,198,206 (-)Ensembl
Rnor_6.0 Ensembl1239,670,453 - 39,679,510 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000096380   ⟹   ENSRNOP00000086801
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1234,189,577 - 34,193,913 (-)Ensembl
RefSeq Acc Id: NM_001393837   ⟹   NP_001380766
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81239,850,070 - 39,859,032 (-)NCBI
mRatBN7.21234,189,285 - 34,198,251 (-)NCBI
RefSeq Acc Id: NM_201991   ⟹   NP_973720
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81239,850,070 - 39,859,032 (-)NCBI
mRatBN7.21234,189,285 - 34,198,251 (-)NCBI
Rnor_6.01239,670,746 - 39,679,364 (-)NCBI
Rnor_5.01241,551,264 - 41,559,994 (-)NCBI
RGSC_v3.41235,384,028 - 35,392,646 (-)RGD
Celera1235,860,509 - 35,869,119 (-)RGD
Sequence:
RefSeq Acc Id: XM_063271534   ⟹   XP_063127604
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81239,850,070 - 39,858,965 (-)NCBI
RefSeq Acc Id: NP_973720   ⟸   NM_201991
- Peptide Label: isoform 1
- UniProtKB: Q6R518 (UniProtKB/Swiss-Prot),   G3V652 (UniProtKB/TrEMBL),   A6J199 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000001722   ⟸   ENSRNOT00000001722
Ensembl Acc Id: ENSRNOP00000086801   ⟸   ENSRNOT00000096380
RefSeq Acc Id: NP_001380766   ⟸   NM_001393837
- Peptide Label: isoform 2
- UniProtKB: Q6R518 (UniProtKB/Swiss-Prot)
RefSeq Acc Id: XP_063127604   ⟸   XM_063271534
- Peptide Label: isoform X1
- UniProtKB: Q6R518 (UniProtKB/Swiss-Prot)

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q6R518-F1-model_v2 AlphaFold Q6R518 1-284 view protein structure

Transcriptome

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

Promoters
RGD ID:13698647
Promoter ID:EPDNEW_R9170
Type:multiple initiation site
Name:Gpn3_1
Description:GPN-loop GTPase 3
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_6.01239,679,342 - 39,679,402EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1303034 AgrOrtholog
BioCyc Gene G2FUF-19246 BioCyc
Ensembl Genes ENSRNOG00000001278 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000001722 ENTREZGENE
  ENSRNOT00000001722.6 UniProtKB/TrEMBL
  ENSRNOT00000096380.1 UniProtKB/TrEMBL
Gene3D-CATH 3.40.50.300 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro Gpn UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Gpn3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  P-loop_NTPase UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:360810 UniProtKB/Swiss-Prot
NCBI Gene 360810 ENTREZGENE
PANTHER PTHR21231 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR21231:SF7 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam ATP_bind_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Gpn3 PhenoGen
RatGTEx ENSRNOG00000001278 RatGTEx
Superfamily-SCOP SSF52540 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A8I6A318_RAT UniProtKB/TrEMBL
  A6J199 ENTREZGENE, UniProtKB/TrEMBL
  G3V652 ENTREZGENE, UniProtKB/TrEMBL
  GPN3_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-05-19 Gpn3  GPN-loop GTPase 3  Atpbd1c  ATP binding domain 1 family, member C  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-30 Atpbd1c  ATP binding domain 1 family, member C  LOC360810  similar to RIKEN cDNA A930018B01  Symbol and Name updated 1299863 APPROVED
2005-09-30 LOC360810        Symbol and Name status set to provisional 70820 PROVISIONAL