Vgf (VGF nerve growth factor inducible) - Rat Genome Database

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Gene: Vgf (VGF nerve growth factor inducible) Rattus norvegicus
Analyze
Symbol: Vgf
Name: VGF nerve growth factor inducible
RGD ID: 69399
Description: Predicted to enable neuropeptide hormone activity. Involved in penile erection; regulation of neuronal synaptic plasticity; and synaptic signaling via neuropeptide. Located in neuron projection; neuronal cell body; and secretory granule membrane. Is active in glutamatergic synapse. Orthologous to human VGF (VGF nerve growth factor inducible); INTERACTS WITH (+)-pilocarpine; 1,3,5-trinitro-1,3,5-triazinane; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC100909521; neurosecretory protein VGF; neurosecretory protein VGF-like; VGF8a protein
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21219,637,313 - 19,645,123 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1219,637,320 - 19,640,341 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1220,774,908 - 20,777,923 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.01221,387,621 - 21,390,636 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.01220,452,159 - 20,455,174 (-)NCBIRnor_WKY
Rnor_6.01222,677,302 - 22,680,630 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1222,677,607 - 22,680,630 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01224,689,881 - 24,692,911 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41220,903,304 - 20,906,327 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11220,892,915 - 20,895,939 (+)NCBI
Celera1221,412,983 - 21,416,003 (-)NCBICelera
Cytogenetic Map12q12NCBI
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
(+)-pilocarpine  (EXP)
1,3,5-trinitro-1,3,5-triazinane  (EXP)
17beta-estradiol  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
3,7-dihydropurine-6-thione  (EXP)
5-fluorouracil  (ISO)
6-propyl-2-thiouracil  (EXP)
8-Br-cAMP  (ISO)
acrylamide  (EXP)
all-trans-retinoic acid  (ISO)
ammonium chloride  (EXP)
antirheumatic drug  (ISO)
benzo[a]pyrene  (ISO)
bisphenol A  (EXP,ISO)
butanal  (ISO)
cadmium atom  (ISO)
carmustine  (ISO)
choline  (ISO)
cisplatin  (ISO)
cocaine  (EXP)
copper atom  (ISO)
copper(0)  (ISO)
copper(II) sulfate  (ISO)
crocidolite asbestos  (ISO)
crocin-1  (EXP)
disulfiram  (ISO)
dorsomorphin  (ISO)
elemental selenium  (ISO)
endosulfan  (EXP)
ethanol  (ISO)
fluoxetine  (ISO)
folic acid  (ISO)
formaldehyde  (ISO)
genistein  (EXP)
gentamycin  (EXP)
graphite  (EXP)
hydrogen chloride  (ISO)
indometacin  (EXP)
L-methionine  (ISO)
lead diacetate  (ISO)
lead(0)  (ISO)
lead(2+)  (ISO)
Licochalcone B  (ISO)
lidocaine  (EXP)
linsidomine  (EXP)
manganese(II) chloride  (ISO)
mercaptopurine  (EXP)
methamphetamine  (EXP)
methylmercury chloride  (ISO)
N-methyl-4-phenylpyridinium  (EXP,ISO)
ozone  (EXP)
p-chloromercuribenzoic acid  (ISO)
paracetamol  (EXP,ISO)
paroxetine  (ISO)
pentanal  (ISO)
propanal  (ISO)
prostaglandin E2  (EXP)
purine-6-thiol  (EXP)
reserpine  (EXP)
rotenone  (ISO)
SB 431542  (ISO)
scopolamine  (EXP)
selenium atom  (ISO)
serpentine asbestos  (ISO)
sodium arsenite  (ISO)
Soman  (EXP)
sotorasib  (ISO)
thapsigargin  (EXP,ISO)
trametinib  (ISO)
trichloroethene  (EXP)
trichostatin A  (ISO)
triclosan  (ISO)
tunicamycin  (ISO)
urethane  (ISO)
valproic acid  (ISO)
vitamin E  (ISO)
zalcitabine  (EXP)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Brain-derived neurotrophic factor-induced gene expression reveals novel actions of VGF in hippocampal synaptic plasticity. Alder J, etal., J Neurosci. 2003 Nov 26;23(34):10800-8.
2. A prohormone convertase cleavage site within a predicted alpha-helix mediates sorting of the neuronal and endocrine polypeptide VGF into the regulated secretory pathway. Garcia AL, etal., J Biol Chem. 2005 Dec 16;280(50):41595-608. Epub 2005 Oct 12.
3. 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.
4. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
5. NGF induces the expression of the VGF gene through a cAMP response element. Hawley RJ, etal., J Neurosci 1992 Jul;12(7):2573-81.
6. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
7. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
8. GOA pipeline RGD automated data pipeline
9. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
10. Structure of the gene encoding VGF, a nervous system-specific mRNA that is rapidly and selectively induced by nerve growth factor in PC12 cells. Salton SR, etal., Mol Cell Biol 1991 May;11(5):2335-49.
11. Pro-VGF-derived peptides induce penile erection in male rats: possible involvement of oxytocin. Succu S, etal., Eur J Neurosci. 2004 Dec;20(11):3035-40.
12. Molecular constituents of the postsynaptic density fraction revealed by proteomic analysis using multidimensional liquid chromatography-tandem mass spectrometry. Yoshimura Y, etal., J Neurochem. 2004 Feb;88(3):759-68.
Additional References at PubMed
PMID:2676516   PMID:10381005   PMID:10433265   PMID:12177191   PMID:15051509   PMID:15706611   PMID:16141392   PMID:16631141   PMID:16983076   PMID:17440014   PMID:18059283   PMID:19077191  
PMID:19466987   PMID:20524965   PMID:20876237   PMID:23485923   PMID:23541636   PMID:24106277   PMID:25002582   PMID:25280008   PMID:25569790   PMID:30371765   PMID:33245952   PMID:35594706  


Genomics

Comparative Map Data
Vgf
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21219,637,313 - 19,645,123 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1219,637,320 - 19,640,341 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1220,774,908 - 20,777,923 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.01221,387,621 - 21,390,636 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.01220,452,159 - 20,455,174 (-)NCBIRnor_WKY
Rnor_6.01222,677,302 - 22,680,630 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1222,677,607 - 22,680,630 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01224,689,881 - 24,692,911 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41220,903,304 - 20,906,327 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11220,892,915 - 20,895,939 (+)NCBI
Celera1221,412,983 - 21,416,003 (-)NCBICelera
Cytogenetic Map12q12NCBI
VGF
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh387101,162,509 - 101,169,952 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl7101,162,509 - 101,165,569 (-)EnsemblGRCh38hg38GRCh38
GRCh377100,805,790 - 100,808,850 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 367100,592,517 - 100,595,572 (-)NCBINCBI36Build 36hg18NCBI36
Build 347100,399,231 - 100,402,287NCBI
Celera795,814,146 - 95,817,208 (-)NCBICelera
Cytogenetic Map7q22.1NCBI
HuRef795,398,955 - 95,401,959 (-)NCBIHuRef
CHM1_17100,736,252 - 100,739,314 (-)NCBICHM1_1
T2T-CHM13v2.07102,485,258 - 102,488,318 (-)NCBIT2T-CHM13v2.0
CRA_TCAGchr7v27100,164,177 - 100,167,239 (-)NCBI
Vgf
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm395137,054,156 - 137,062,205 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl5137,055,246 - 137,062,205 (+)EnsemblGRCm39 Ensembl
GRCm385137,025,301 - 137,033,351 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl5137,026,392 - 137,033,351 (+)EnsemblGRCm38mm10GRCm38
MGSCv375137,506,165 - 137,509,221 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv365137,314,922 - 137,317,978 (+)NCBIMGSCv36mm8
Celera5134,047,034 - 134,050,090 (+)NCBICelera
Cytogenetic Map5G2NCBI
cM Map576.13NCBI
Vgf
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495545616,119,073 - 16,126,968 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495545616,119,073 - 16,126,968 (+)NCBIChiLan1.0ChiLan1.0
VGF
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.17106,544,544 - 106,549,329 (-)NCBIpanpan1.1PanPan1.1panPan2
Mhudiblu_PPA_v0793,302,956 - 93,307,892 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
VGF
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.168,701,289 - 8,704,386 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl68,700,667 - 8,704,397 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha610,398,631 - 10,401,711 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.068,520,838 - 8,523,920 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl68,520,536 - 8,523,897 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.168,480,897 - 8,483,981 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.068,451,358 - 8,454,443 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.068,616,024 - 8,619,109 (+)NCBIUU_Cfam_GSD_1.0
Vgf
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024409344132,969,254 - 132,977,238 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365431,059,799 - 1,061,646 (-)EnsemblSpeTri2.0
SpeTri2.0NW_0049365431,059,292 - 1,062,384 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
VGF
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl38,888,506 - 8,891,601 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.138,888,502 - 8,891,399 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
VGF
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12812,016,216 - 12,021,151 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2812,018,800 - 12,020,647 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660704,329,143 - 4,332,216 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Vgf
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462474016,105,227 - 16,109,905 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462474016,105,187 - 16,109,922 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Vgf
30 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:223
Count of miRNA genes:150
Interacting mature miRNAs:163
Transcripts:ENSRNOT00000041808
Prediction methods:Microtar, Miranda, Rnahybrid
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
10755457Coatc14Coat color QTL 140.01759coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)12122591684Rat
6893681Bw109Body weight QTL 1092.30.004body mass (VT:0001259)body weight (CMO:0000012)12123297788Rat
1581516Cm56Cardiac mass QTL 564.20.05heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)12129333307Rat
1598855Bp294Blood pressure QTL 2943.5arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)12134851688Rat
7411660Foco28Food consumption QTL 2810.90.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12142110980Rat
9590086Insglur6Insulin/glucose ratio QTL 618.970.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)12142110980Rat
8694179Bw150Body weight QTL 1502.90.001body mass (VT:0001259)body weight gain (CMO:0000420)12142110980Rat
7411586Foco5Food consumption QTL 55.40.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12142110980Rat
7411595Foco9Food consumption QTL 940.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12142110980Rat
7411545Bw128Body weight QTL 1285.20.001body mass (VT:0001259)body weight gain (CMO:0000420)12142110980Rat
9590147Scort7Serum corticosterone level QTL 713.610.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)12142110980Rat
2303575Insul14Insulin level QTL 144blood insulin amount (VT:0001560)blood insulin level (CMO:0000349)12142450532Rat
737979Pia22Pristane induced arthritis QTL 2253.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)12144465750Rat
634351Apr5Acute phase response QTL 56.7blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)12144503507Rat
2302042Pia38Pristane induced arthritis QTL 383.50.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G1 level (CMO:0002115)12144503507Rat
634350Apr4Acute phase response QTL 46orosomucoid 1 amount (VT:0010541)plasma orosomucoid 1 level (CMO:0001467)12117200546172005Rat
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)12556449546669029Rat
7411547Bw129Body weight QTL 1290.001body mass (VT:0001259)body weight gain (CMO:0000420)6556449546669029Rat
7411597Foco10Food consumption QTL 100.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12556449546669029Rat
7411641Foco19Food consumption QTL 1927.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12556449546669029Rat
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)12556449546669029Rat
7411588Foco6Food consumption QTL 60.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12556449546669029Rat
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)12556449846669029Rat
10059594Kidm46Kidney mass QTL 463.790.025kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)12610757946669029Rat
1302792Scl21Serum cholesterol level QTL 213.80.0011blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)12719673046669029Rat
2293086Iddm30Insulin dependent diabetes mellitus QTL 303.82blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)12844949028302290Rat
61331Eau2Experimental allergic uveoretinitis QTL 20.0005uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)12852542328064601Rat
1300157Rf21Renal function QTL 214.4renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)12931821632103380Rat
1549829Scl48Serum cholesterol level QTL 485blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)12960327746669029Rat
2293699Bss49Bone structure and strength QTL 495.610.0001lumbar vertebra size trait (VT:0010518)lumbar vertebra trabecular cross-sectional area (CMO:0001692)121047413746669029Rat
2300186Bmd59Bone mineral density QTL 597.10.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)121047413746669029Rat
1331786Kidm11Kidney mass QTL 113.571kidney mass (VT:0002707)right kidney wet weight (CMO:0000082)121107382524234895Rat
1331755Bp219Blood pressure QTL 2193.041arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)121107382528064557Rat
1331761Bp218Blood pressure QTL 2182.973arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)121107382545055165Rat
61404Bw120Body weight QTL 1205.1body mass (VT:0001259)body mass index (BMI) (CMO:0000105)121235161946669029Rat
1641928Alcrsp5Alcohol response QTL 5response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)121281238546669029Rat
2303569Gluco44Glucose level QTL 442blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)121281238546669029Rat
1549902Bp269Blood pressure QTL 269arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)121318273646669029Rat
1549912Bp268Blood pressure QTL 268arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)101318273646669029Rat
2302060Pia37Pristane induced arthritis QTL 376.10.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G1 level (CMO:0002115)121319815746669029Rat
61416Pia4Pristane induced arthritis QTL 48.4joint integrity trait (VT:0010548)arthritic paw count (CMO:0001460)121363552330827399Rat
61421Cia12Collagen induced arthritis QTL 124.6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)121363552335682913Rat
61443Btemp2Thermal response to stress QTL 23.30.000094body temperature trait (VT:0005535)core body temperature (CMO:0001036)121502518320794014Rat
631543Bp83Blood pressure QTL 835.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)121555082638478808Rat
2293684Bmd26Bone mineral density QTL 264.40.0002femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)121587265332974238Rat
631560Apr1Acute phase response QTL 16.1orosomucoid 1 amount (VT:0010541)plasma orosomucoid 1 level (CMO:0001467)121914436246669029Rat
2306789Ean6Experimental allergic neuritis QTL 64.9nervous system integrity trait (VT:0010566)experimental autoimmune neuritis severity score (CMO:0001528)121961087024139202Rat
737822Alc10Alcohol consumption QTL 102.2consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)121961087040218516Rat
5684888Pia42Pristane induced arthritis QTL 42joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)121961087042828880Rat
61324Eae5Experimental allergic encephalomyelitis QTL 514nervous system integrity trait (VT:0010566)percentage of study population developing relapsing-remitting experimental autoimmune encephalomyelitis during a period of time (CMO:0001402)121961087046669029Rat
1298081Cia25Collagen induced arthritis QTL 254.7joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)121961088935682913Rat

Markers in Region
D12Rat70  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21219,642,166 - 19,642,312 (+)MAPPERmRatBN7.2
Rnor_6.01222,682,228 - 22,682,373NCBIRnor6.0
Rnor_5.01224,694,509 - 24,694,654UniSTSRnor5.0
RGSC_v3.41220,901,332 - 20,901,478RGDRGSC3.4
RGSC_v3.41220,901,333 - 20,901,478UniSTSRGSC3.4
RGSC_v3.11220,890,916 - 20,891,241RGD
Celera1221,417,829 - 21,417,974UniSTS
SHRSP x BN Map1222.74UniSTS
SHRSP x BN Map1222.74RGD
Cytogenetic Map12q12UniSTS


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 hemolymphoid system nervous system reproductive system respiratory system
High
Medium 27
Low 1 33 5
Below cutoff 3 6 9 4 12 19 2

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000041808   ⟹   ENSRNOP00000050024
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1219,637,320 - 19,640,341 (-)Ensembl
Rnor_6.0 Ensembl1222,677,607 - 22,680,630 (-)Ensembl
RefSeq Acc Id: NM_030997   ⟹   NP_112259
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21219,637,320 - 19,640,341 (-)NCBI
Rnor_6.01222,677,607 - 22,680,630 (-)NCBI
Rnor_5.01224,689,881 - 24,692,911 (-)NCBI
RGSC_v3.41220,903,304 - 20,906,327 (+)RGD
Celera1221,412,983 - 21,416,003 (-)RGD
Sequence:
RefSeq Acc Id: XM_039089290   ⟹   XP_038945218
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21219,637,313 - 19,645,123 (-)NCBI
RefSeq Acc Id: XM_039089291   ⟹   XP_038945219
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21219,637,313 - 19,644,985 (-)NCBI
RefSeq Acc Id: XM_039089292   ⟹   XP_038945220
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21219,637,313 - 19,645,123 (-)NCBI
RefSeq Acc Id: XM_039089293   ⟹   XP_038945221
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21219,637,313 - 19,645,123 (-)NCBI
RefSeq Acc Id: XM_039089294   ⟹   XP_038945222
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21219,637,313 - 19,645,123 (-)NCBI
RefSeq Acc Id: XM_039089296   ⟹   XP_038945224
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21219,637,313 - 19,645,120 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_112259   ⟸   NM_030997
- Peptide Label: precursor
- UniProtKB: P20156 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000050024   ⟸   ENSRNOT00000041808
RefSeq Acc Id: XP_038945222   ⟸   XM_039089294
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038945220   ⟸   XM_039089292
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038945221   ⟸   XM_039089293
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038945218   ⟸   XM_039089290
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038945224   ⟸   XM_039089296
- Peptide Label: isoform X2
- UniProtKB: P20156 (UniProtKB/Swiss-Prot)
RefSeq Acc Id: XP_038945219   ⟸   XM_039089291
- Peptide Label: isoform X1

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-P20156-F1-model_v2 AlphaFold P20156 1-617 view protein structure

Transcriptome

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

Promoters
RGD ID:13698527
Promoter ID:EPDNEW_R9051
Type:single initiation site
Name:Vgf_1
Description:VGF nerve growth factor inducible
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_6.01222,680,629 - 22,680,689EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:69399 AgrOrtholog
BioCyc Gene G2FUF-19676 BioCyc
Ensembl Genes ENSRNOG00000001416 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000050024 ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000041808 ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro VGF UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:29461 UniProtKB/Swiss-Prot
NCBI Gene 29461 ENTREZGENE
PANTHER PTHR15159 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Vgf PhenoGen
UniProt F1LP80_RAT UniProtKB/TrEMBL
  P20156 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2021-03-09 Vgf  VGF nerve growth factor inducible  LOC100909521  neurosecretory protein VGF-like  Data Merged 737654 PROVISIONAL
2012-07-05 LOC100909521  neurosecretory protein VGF-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2002-06-10 Vgf  VGF nerve growth factor inducible       Name updated 70584 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_domains contains TATAA and CCAAT elements, several GC boxes, and a consensus cAMP response element binding protein (CREB) binding site 69396
gene_expression mRNA expressed in central and peripheral nervous system tissue 69396
gene_regulation gene induction regulated by neuronal growth factor (NGF) and cAMP-mediated agents 730082