Gpnmb (glycoprotein nmb) - Rat Genome Database

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Gene: Gpnmb (glycoprotein nmb) Rattus norvegicus
Analyze
Symbol: Gpnmb
Name: glycoprotein nmb
RGD ID: 71008
Description: Predicted to enable heparin binding activity; signaling receptor binding activity; and syndecan binding activity. Involved in bone mineralization and osteoblast differentiation. Predicted to be located in cytoplasmic vesicle and membrane. Predicted to be active in plasma membrane. Biomarker of brain infarction. Human ortholog(s) of this gene implicated in primary localized cutaneous amyloidosis 3. Orthologous to human GPNMB (glycoprotein nmb); INTERACTS WITH 1,2-dimethylhydrazine; 1-(3-(trifluoromethyl)phenyl)piperazine; 1-[(4-chlorophenyl)-phenylmethyl]-4-methylpiperazine.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: glycoprotein (transmembrane) nmb; osteoactivin; transmembrane glycoprotein NMB
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
GRCr8479,341,128 - 79,362,366 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl479,341,021 - 79,380,240 (+)EnsemblGRCr8
mRatBN7.2478,010,247 - 78,031,491 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl478,010,197 - 78,049,367 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx483,217,702 - 83,238,961 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0478,993,176 - 79,014,437 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0477,433,480 - 77,454,739 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0478,694,447 - 78,715,685 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl478,694,447 - 78,715,683 (+)Ensemblrn6Rnor6.0
Rnor_5.04143,383,026 - 143,404,104 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4477,161,352 - 77,182,624 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera472,946,255 - 72,967,354 (+)NCBICelera
RGSC_v3.1477,437,481 - 77,458,752 (+)NCBI
Cytogenetic Map4q24NCBI
JBrowse:




Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(-)-demecolcine  (ISO)
(1->4)-beta-D-glucan  (ISO)
(S)-nicotine  (ISO)
1,1-dichloroethene  (ISO)
1,2-dimethylhydrazine  (EXP)
1-(3-(trifluoromethyl)phenyl)piperazine  (EXP)
1-[(4-chlorophenyl)-phenylmethyl]-4-methylpiperazine  (EXP)
1-benzylpiperazine  (EXP)
1-chloro-2,4-dinitrobenzene  (ISO)
1-naphthyl isothiocyanate  (EXP)
17alpha-ethynylestradiol  (EXP,ISO)
17beta-estradiol  (EXP,ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4-diaminotoluene  (ISO)
2,4-dibromophenyl 2,4,5-tribromophenyl ether  (ISO)
2-palmitoylglycerol  (ISO)
3,3',4,4',5-pentachlorobiphenyl  (EXP)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
3-methylcholanthrene  (ISO)
4,4'-diaminodiphenylmethane  (EXP,ISO)
4,4'-sulfonyldiphenol  (ISO)
5-azacytidine  (ISO)
6-propyl-2-thiouracil  (EXP)
acetamide  (EXP)
acrylamide  (EXP)
aflatoxin B1  (ISO)
aldehydo-D-glucose  (ISO)
all-trans-retinoic acid  (ISO)
amitrole  (EXP)
ammonium chloride  (EXP)
amphetamine  (EXP)
aristolochic acid A  (ISO)
arsane  (EXP,ISO)
arsenic atom  (EXP,ISO)
arsenous acid  (ISO)
atrazine  (EXP)
avobenzone  (ISO)
beauvericin  (ISO)
benzo[a]pyrene  (ISO)
bicalutamide  (ISO)
bisphenol A  (EXP,ISO)
bisphenol AF  (EXP,ISO)
Bisphenol B  (ISO)
bisphenol F  (ISO)
bucladesine  (ISO)
cadmium dichloride  (EXP,ISO)
cadmium sulfate  (ISO)
cannabidiol  (ISO)
carbon nanotube  (EXP,ISO)
carvedilol  (EXP)
cefaloridine  (EXP)
chloroacetaldehyde  (ISO)
chloroquine  (EXP)
chlorpromazine  (EXP)
choline  (ISO)
chromium(6+)  (ISO)
cidofovir anhydrous  (ISO)
cisplatin  (ISO)
clodronic acid  (ISO)
cobalt dichloride  (ISO)
copper atom  (EXP,ISO)
copper(0)  (EXP,ISO)
crocidolite asbestos  (ISO)
Cuprizon  (EXP)
cyclosporin A  (EXP,ISO)
D-glucose  (ISO)
DDT  (EXP)
decabromodiphenyl ether  (EXP)
dexamethasone  (EXP,ISO)
dextran sulfate  (ISO)
diarsenic trioxide  (ISO)
dibenzofurans  (ISO)
dibutyl phthalate  (EXP)
dichloroacetic acid  (ISO)
dioxygen  (EXP,ISO)
diuron  (ISO)
dorsomorphin  (ISO)
doxorubicin  (EXP,ISO)
endosulfan  (EXP)
enniatin  (ISO)
epoxiconazole  (ISO)
etoposide  (ISO)
fenamidone  (ISO)
ferric oxide  (EXP)
flutamide  (EXP)
fluxapyroxad  (ISO)
folic acid  (ISO)
formaldehyde  (ISO)
fructose  (ISO)
furan  (EXP)
genistein  (ISO)
gentamycin  (EXP)
glucose  (ISO)
Hexachloro-1,3-butadiene  (EXP)
hydrogen peroxide  (ISO)
indometacin  (ISO)
iron dichloride  (ISO)
isoprenaline  (ISO)
L-methionine  (ISO)
lead(0)  (ISO)
lead(II) chloride  (ISO)
lidocaine  (EXP)
lipopolysaccharide  (EXP)
lithium atom  (ISO)
lithium hydride  (ISO)
lucanthone  (ISO)
manganese(II) chloride  (EXP)
medroxyprogesterone acetate  (ISO)
melamine  (EXP)
mercury dibromide  (ISO)
mercury dichloride  (EXP)
metformin  (EXP)
methamphetamine  (ISO)
methylmercury chloride  (ISO)
milrinone  (EXP)
N-methyl-4-phenylpyridinium  (EXP)
N-nitrosodiethylamine  (EXP)
N-nitrosodimethylamine  (EXP)
naled  (ISO)
nickel atom  (ISO)
nickel sulfate  (ISO)
nicotine  (ISO)
nitrofen  (EXP)
okadaic acid  (ISO)
oxaliplatin  (EXP)
ozone  (ISO)
p-chloromercuribenzoic acid  (ISO)
paclitaxel  (EXP)
paracetamol  (ISO)
paraquat  (EXP)
perfluorohexanesulfonic acid  (ISO)
perfluorooctane-1-sulfonic acid  (ISO)
phenacetin  (EXP)
phenformin  (EXP)
phenylhydrazine  (EXP)
phenylmercury acetate  (ISO)
polymyxin B2  (ISO)
propiconazole  (ISO)
quercetin  (ISO)
raloxifene  (ISO)
resorcinol  (ISO)
rotenone  (EXP)
Rutecarpine  (ISO)
Salinomycin  (ISO)
SB 431542  (ISO)
silicon dioxide  (EXP,ISO)
sirolimus  (EXP)
sodium arsenate  (ISO)
sodium arsenite  (ISO)
sodium dichromate  (EXP)
sotorasib  (ISO)
sunitinib  (ISO)
tacrolimus hydrate  (EXP)
tamoxifen  (ISO)
temozolomide  (ISO)
tert-butyl hydroperoxide  (ISO)
testosterone  (EXP)
tetrachloroethene  (ISO)
tetrachloromethane  (EXP,ISO)
thioacetamide  (EXP)
titanium dioxide  (ISO)
topotecan  (EXP)
trametinib  (ISO)
tremolite asbestos  (ISO)
tributylstannane  (ISO)
trichloroethene  (EXP)
trichostatin A  (ISO)
triclosan  (ISO)
triptonide  (ISO)
triticonazole  (EXP)
troglitazone  (EXP,ISO)
urethane  (ISO)
ursodeoxycholic acid  (EXP)
valproic acid  (ISO)
vinclozolin  (EXP)
vincristine  (ISO)
zoledronic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Identification of new therapeutic targets by genome-wide analysis of gene expression in the ipsilateral cortex of aged rats after stroke. Buga AM, etal., PLoS One. 2012;7(12):e50985. doi: 10.1371/journal.pone.0050985. Epub 2012 Dec 12.
2. 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.
3. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
4. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
5. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
6. GOA pipeline RGD automated data pipeline
7. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
8. Cloning and characterization of osteoactivin, a novel cDNA expressed in osteoblasts. Safadi FF, etal., J Cell Biochem 2001;84(1):12-26.
9. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
Additional References at PubMed
PMID:11114299   PMID:12609765   PMID:12638126   PMID:14568261   PMID:15489334   PMID:15763343   PMID:17034042   PMID:17382907   PMID:17475886   PMID:17588730   PMID:18036345   PMID:19179976  
PMID:19350579   PMID:20709912   PMID:20711474   PMID:21389974   PMID:21503878   PMID:21946207   PMID:22891158   PMID:23221696   PMID:25010402   PMID:25054912   PMID:26581806   PMID:26781840  
PMID:28148779   PMID:28426701   PMID:32236569   PMID:38400732   PMID:38782114  


Genomics

Comparative Map Data
Gpnmb
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8479,341,128 - 79,362,366 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl479,341,021 - 79,380,240 (+)EnsemblGRCr8
mRatBN7.2478,010,247 - 78,031,491 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl478,010,197 - 78,049,367 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx483,217,702 - 83,238,961 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0478,993,176 - 79,014,437 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0477,433,480 - 77,454,739 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0478,694,447 - 78,715,685 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl478,694,447 - 78,715,683 (+)Ensemblrn6Rnor6.0
Rnor_5.04143,383,026 - 143,404,104 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4477,161,352 - 77,182,624 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera472,946,255 - 72,967,354 (+)NCBICelera
RGSC_v3.1477,437,481 - 77,458,752 (+)NCBI
Cytogenetic Map4q24NCBI
GPNMB
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38723,246,775 - 23,275,108 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl723,235,967 - 23,275,108 (+)Ensemblhg38GRCh38
GRCh37723,286,394 - 23,314,727 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36723,252,841 - 23,281,254 (+)NCBIBuild 36Build 36hg18NCBI36
Build 34723,059,555 - 23,087,968NCBI
Celera723,272,604 - 23,301,017 (+)NCBICelera
Cytogenetic Map7p15.3NCBI
HuRef723,168,651 - 23,197,066 (+)NCBIHuRef
CHM1_1723,286,943 - 23,315,354 (+)NCBICHM1_1
T2T-CHM13v2.0723,383,213 - 23,411,546 (+)NCBIT2T-CHM13v2.0
CRA_TCAGchr7v2723,338,195 - 23,366,606 (+)NCBI
Gpnmb
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39649,013,449 - 49,044,413 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl649,013,480 - 49,047,863 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm38649,036,518 - 49,058,182 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl649,036,546 - 49,070,929 (+)Ensemblmm10GRCm38
MGSCv37648,986,517 - 49,008,181 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv36648,966,211 - 48,987,694 (+)NCBIMGSCv36mm8
Celera649,546,153 - 49,567,869 (+)NCBICelera
Cytogenetic Map6B2.3NCBI
cM Map623.82NCBI
Gpnmb
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541025,553,973 - 25,582,500 (+)Ensembl
ChiLan1.0NW_00495541025,554,279 - 25,583,368 (+)NCBIChiLan1.0ChiLan1.0
GPNMB
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2628,079,304 - 28,141,376 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1776,404,030 - 76,466,104 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0723,931,220 - 23,959,687 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1723,540,451 - 23,568,624 (+)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl723,539,928 - 23,568,624 (+)EnsemblpanPan2panpan1.1
GPNMB
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11436,919,184 - 36,947,023 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1436,919,296 - 36,946,643 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha1436,460,144 - 36,487,696 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.01436,845,151 - 36,877,705 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
UMICH_Zoey_3.11436,964,735 - 36,992,553 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01436,662,258 - 36,689,076 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01436,998,735 - 37,025,688 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Gpnmb
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440511881,185,446 - 81,214,079 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936478397,145 - 424,801 (+)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_004936478397,200 - 425,663 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
GPNMB
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl992,037,509 - 92,071,499 (+)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1992,037,428 - 92,071,501 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
GPNMB
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12135,037,197 - 35,066,143 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2135,037,001 - 35,066,171 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366604269,541,048 - 69,570,412 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Gpnmb
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247397,359,741 - 7,387,279 (-)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046247397,358,824 - 7,386,852 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Gpnmb
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v1691,921,395 - 91,944,738 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Gpnmb
261 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:49
Count of miRNA genes:43
Interacting mature miRNAs:47
Transcripts:ENSRNOT00000011945
Prediction methods: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
1358352Srcrt3Stress Responsive Cort QTL 32.29blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)439431983123203361Rat
1549843Bw53Body weight QTL 530.0001body mass (VT:0001259)body weight gain (CMO:0000420)459753119104753119Rat
61445Strs3Sensitivity to stroke QTL 33cerebrum integrity trait (VT:0010549)post-insult time to onset of cerebrovascular lesion (CMO:0002343)44140057786400577Rat
6893678Bw108Body weight QTL 1082.60.006body mass (VT:0001259)body weight (CMO:0000012)44442502489425024Rat
10755501Bp390Blood pressure QTL 3902.5arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)427730518170099664Rat
1357342Bw40Body weight QTL 400.001body mass (VT:0001259)body weight (CMO:0000012)474233320119233320Rat
1358363Sradr3Stress Responsive Adrenal Weight QTL 36.19adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)458817672103817672Rat
61330Eau1Experimental allergic uveoretinitis QTL 10.0003uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)426234499134199155Rat
70167Bw22Body weight QTL 223.1body mass (VT:0001259)body weight (CMO:0000012)474233320119233320Rat
61336Bp21Blood pressure QTL 214.6arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)45808014680212111Rat
1549839Bw52Body weight QTL 520.0001body mass (VT:0001259)body weight gain (CMO:0000420)471647492116647492Rat
6909128Pancm4Pancreatic morphology QTL 411.35pancreas mass (VT:0010144)pancreas wet weight (CMO:0000626)427862204126119996Rat
8694439Bw168Body weight QTL 1689.570.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)44140060386400603Rat
61476Aia3Adjuvant induced arthritis QTL 33.9joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)475939858140508796Rat
8655906Rf60Renal function QTL 603.8blood creatinine amount (VT:0005328)creatinine clearance (CMO:0000765)43044896182336920Rat
1641919Alc22Alcohol consumption QTL 220.0005drinking behavior trait (VT:0001422)ethanol drink intake rate (CMO:0001407)465060960127749483Rat
1354660Salc1Saline consumption QTL 111.26drinking behavior trait (VT:0001422)saline drink intake rate (CMO:0001627)445429897149763204Rat
1298082Stresp4Stress response QTL 4blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)451085655113588029Rat
2317588Eae27Experimental allergic encephalomyelitis QTL 27nervous system integrity trait (VT:0010566)percentage of study population developing experimental autoimmune encephalomyelitis during a period of time (CMO:0001047)469036742114036742Rat
1300139Hrtrt6Heart rate QTL 62.85heart pumping trait (VT:2000009)heart rate (CMO:0000002)440490442117737312Rat
70200Alc18Alcohol consumption QTL 189.2drinking behavior trait (VT:0001422)ethanol intake volume to total fluid intake volume ratio (CMO:0001591)457613339151163960Rat
4889969Bss96Bone structure and strength QTL 964.9tibia size trait (VT:0100001)tibia cortical bone volume (CMO:0001725)457613242102613242Rat
2316958Gluco58Glucose level QTL 5810blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)412212457182430611Rat
4889972Bss97Bone structure and strength QTL 975.6tibia size trait (VT:0100001)tibia total bone volume (CMO:0001724)457613242102613242Rat
6478684Anxrr30Anxiety related response QTL 300.00087defecation behavior trait (VT:0010462)defecation rate (CMO:0000998)464084079109084079Rat
5685012Bmd87Bone mineral density QTL 875.1tibia mineral mass (VT:1000283)bone mineral content (CMO:0001554)43511329080113290Rat
5685009Bmd86Bone mineral density QTL 863.7tibia mineral mass (VT:1000283)bone mineral density (CMO:0001226)457613242102613242Rat
634311Sach7Saccharin preference QTL 7taste sensitivity trait (VT:0001986)saccharin intake volume to total fluid intake volume ratio (CMO:0001601)45807987582597589Rat
2306547Iddm38Insulin dependent diabetes mellitus QTL 38blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)468353567113353567Rat
738009Sach4Saccharine consumption QTL 44.90.000016consumption behavior trait (VT:0002069)saccharin intake volume to total fluid intake volume ratio (CMO:0001601)460916264184426481Rat
2306545Iddm39Insulin dependent diabetes mellitus QTL 39blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)478687630123687630Rat
631261Tcas3Tongue tumor susceptibility QTL 36.88tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)41170660492690519Rat
6478772Anxrr49Anxiety related response QTL 490.15488defecation behavior trait (VT:0010462)defecation rate (CMO:0000998)464084079109084079Rat
631646Stl4Serum triglyceride level QTL 46.50.0001blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)474169813134199155Rat
2312569Pur19Proteinuria QTL 193.40.001urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)459836842104836842Rat
8655961Kidm43Kidney mass QTL 4318kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)43726957782269577Rat
61406Scwia1Streptococcal cell wall induced arthritis QTL 12.3joint integrity trait (VT:0010548)experimental arthritis severity measurement (CMO:0001459)475939858140508796Rat
1354612Foco1Food consumption QTL 18.87eating behavior trait (VT:0001431)food intake rate (CMO:0000427)445429897149763204Rat
634344Hcar7Hepatocarcinoma resistance QTL 77.8liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)46104105794638356Rat
2303168Bp330Blood pressure QTL 3304.250.017arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)45889999148002343Rat
738031Alc14Alcohol consumption QTL 147.60.00003consumption behavior trait (VT:0002069)ethanol drink intake rate to body weight ratio (CMO:0001616)460916264174095838Rat
1576305Emca6Estrogen-induced mammary cancer QTL 65.8mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)445429709157555683Rat
61418Pia5Pristane induced arthritis QTL 54.5joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)463245026129846354Rat
631651Bp124Blood pressure QTL 1243arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)464209744109209744Rat
738016Alc16Alcohol consumption QTL 163.60.00015consumption behavior trait (VT:0002069)ethanol drink intake rate to body weight ratio (CMO:0001616)460916264184426481Rat
1558651Swd3Spike wave discharge measurement QTL 34.620.000024brain electrophysiology trait (VT:0010557)brain spike-and-wave discharge frequency (CMO:0001742)44140057786400577Rat
1641833Alc21Alcohol consumption QTL 218.60.0001drinking behavior trait (VT:0001422)ethanol drink intake rate (CMO:0001407)457664252127749483Rat
631546Bp86Blood pressure QTL 863.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)45807987592690793Rat
631674Iddm14Insulin dependent diabetes mellitus QTL 14blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)465495851159259805Rat
6478743Anxrr40Anxiety related response QTL 400.83076defecation behavior trait (VT:0010462)defecation rate (CMO:0000998)464084079109084079Rat
61434Cia3Collagen induced arthritis QTL 34.8joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)463224393108224393Rat
7394826Bw126Body weight QTL 1260.002body mass (VT:0001259)body weight gain (CMO:0000420)46390045888813920Rat
12798520Anxrr55Anxiety related response QTL 554.450.01locomotor behavior trait (VT:0001392)number of rearing movements with lid-pushing in an experimental apparatus (CMO:0002715)433538597116185060Rat
631671Iddm11Insulin dependent diabetes mellitus QTL 113.60.0012blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)45960331980216952Rat

Markers in Region
D4Rhw16  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2478,029,319 - 78,029,567 (+)MAPPERmRatBN7.2
Rnor_6.0478,713,514 - 78,713,761NCBIRnor6.0
Rnor_5.04143,401,933 - 143,402,180UniSTSRnor5.0
RGSC_v3.4477,180,453 - 77,180,700UniSTSRGSC3.4
Celera472,965,183 - 72,965,430UniSTS
Cytogenetic Map4q24RGD


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
16 12 67 164 91 90 59 92 59 6 356 192 11 143 81 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000011945   ⟹   ENSRNOP00000011945
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl479,341,128 - 79,362,363 (+)Ensembl
mRatBN7.2 Ensembl478,010,287 - 78,031,491 (+)Ensembl
Rnor_6.0 Ensembl478,694,447 - 78,715,683 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000103594   ⟹   ENSRNOP00000088304
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl479,341,162 - 79,362,364 (+)Ensembl
mRatBN7.2 Ensembl478,010,247 - 78,032,673 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000104789   ⟹   ENSRNOP00000076498
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl479,341,021 - 79,362,364 (+)Ensembl
mRatBN7.2 Ensembl478,010,247 - 78,032,673 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000105809   ⟹   ENSRNOP00000096210
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl479,341,021 - 79,380,240 (+)Ensembl
mRatBN7.2 Ensembl478,010,197 - 78,049,367 (+)Ensembl
RefSeq Acc Id: NM_133298   ⟹   NP_579832
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8479,341,128 - 79,362,366 (+)NCBI
mRatBN7.2478,010,247 - 78,031,491 (+)NCBI
Rnor_6.0478,694,447 - 78,715,685 (+)NCBI
Rnor_5.04143,383,026 - 143,404,104 (+)NCBI
RGSC_v3.4477,161,352 - 77,182,624 (+)RGD
Celera472,946,255 - 72,967,354 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_579832 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAF03400 (Get FASTA)   NCBI Sequence Viewer  
  AAH61725 (Get FASTA)   NCBI Sequence Viewer  
  EDL88216 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000076498
  ENSRNOP00000076498.1
GenBank Protein Q6P7C7 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_579832   ⟸   NM_133298
- Peptide Label: precursor
- UniProtKB: Q6P7C7 (UniProtKB/Swiss-Prot),   Q9QZF6 (UniProtKB/TrEMBL),   A6K0K2 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000011945   ⟸   ENSRNOT00000011945
Ensembl Acc Id: ENSRNOP00000076498   ⟸   ENSRNOT00000104789
Ensembl Acc Id: ENSRNOP00000096210   ⟸   ENSRNOT00000105809
Ensembl Acc Id: ENSRNOP00000088304   ⟸   ENSRNOT00000103594
Protein Domains
PKD

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q6P7C7-F1-model_v2 AlphaFold Q6P7C7 1-572 view protein structure

Transcriptome

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

Promoters
RGD ID:13693035
Promoter ID:EPDNEW_R3558
Type:initiation region
Name:Gpnmb_1
Description:glycoprotein nmb
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_6.0478,694,484 - 78,694,544EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:71008 AgrOrtholog
BioCyc Gene G2FUF-44925 BioCyc
Ensembl Genes ENSRNOG00000008816 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000104789 ENTREZGENE
  ENSRNOT00000104789.1 UniProtKB/Swiss-Prot
Gene3D-CATH 2.60.40.10 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:5598392 IMAGE-MGC_LOAD
InterPro Ig-like_fold UniProtKB/Swiss-Prot
  PKAT UniProtKB/Swiss-Prot
  PKAT_KLD UniProtKB/Swiss-Prot
  PKD/Chitinase_dom UniProtKB/Swiss-Prot
  PKD_dom UniProtKB/Swiss-Prot
  PKD_dom_sf UniProtKB/Swiss-Prot
MGC_CLONE MGC:72320 IMAGE-MGC_LOAD
NCBI Gene 113955 ENTREZGENE
PANTHER PTHR11861 UniProtKB/Swiss-Prot
  TRANSMEMBRANE GLYCOPROTEIN NMB UniProtKB/Swiss-Prot
Pfam PKAT_KLD UniProtKB/Swiss-Prot
  PKD_4 UniProtKB/Swiss-Prot
PhenoGen Gpnmb PhenoGen
PROSITE PKD UniProtKB/Swiss-Prot
RatGTEx ENSRNOG00000008816 RatGTEx
SMART PKD UniProtKB/Swiss-Prot
Superfamily-SCOP SSF49299 UniProtKB/Swiss-Prot
UniProt A0A8I6AAJ2_RAT UniProtKB/TrEMBL
  A0A8I6GLH9_RAT UniProtKB/TrEMBL
  A0A8L2Q5B8_RAT UniProtKB/TrEMBL
  A6K0K2 ENTREZGENE, UniProtKB/TrEMBL
  GPNMB_RAT UniProtKB/Swiss-Prot, ENTREZGENE
  Q9QZF6 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-02-11 Gpnmb  glycoprotein nmb  Gpnmb  glycoprotein (transmembrane) nmb  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2002-07-09 Gpnmb  glycoprotein (transmembrane) nmb      Symbol and Name updated to reflect Human and Mouse nomenclature 70877 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_domains contains thirteen predicted N-linked glycosylation sites and a potential RGD integrin recognition site 632991
gene_expression expressed in osteoblasts 632991