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VGF Gene

protein-coding   GIFtS: 49

GC07M100592
VGF nerve growth factor inducible
Symbol approved by the HUGO Gene Nomenclature Committee (HGNC) database
Services    
(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc , and/or 7Ensembl, 8miRBase)
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Descriptions
VGF nerve growth factor inducible 2
neuro-endocrine specific protein VGF 2
neurosecretory protein VGF 2
External Ids
HGNC: 126841
Entrez Gene: 74252
UniProtKB: O152403
Ensembl: ENSG000001285647
Search outside databases for aliases for VGF gene

Previous GC identifers: GC07M099289 GC07M100352 GC07M100365 GC07M100401

(According to Entrez Gene, Wikipedia's Gene Wiki,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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EntrezGene summary for VGF:
This gene is specifically expressed in a subpopulation of neuroendocrine cells, and is upregulated
by nerve growth factor. The structural organization of this gene is similar to that of the rat
gene, and both the translated and the untranslated regions show a high degree of sequence
similarity to the rat gene. The encoded secretory protein also shares similarities with the
secretogranin/chromogranin family, however, its exact function is not known. [provided by RefSeq]

UniProtKB/Swiss-Prot: VGF_HUMAN, O15240
Function: May be involved in the regulation of cell-cell interactions or in synatogenesis during
the maturation of the nervous system (By similarity)

(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 36),
and/or miRBase,
Genomic Views according to UCSC and Ensembl, Transcription factor binding sites according to SABiosciences)
About This Section

Genomic View:
UCSC Golden Path with GeneCards custom track

 Transcription factor binding sites upstream to the VGF gene  

Entrez Gene cytogenetic band: 7q22.1   Ensembl cytogenetic band:  7q22.1   HGNC cytogenetic band: 7q22

VGF Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)

GeneLoc gene densities for chromosome 7         GeneLoc Exon Structure

GeneLoc location for GC07M100592:     (about GC identifiers)

Start:
100,592,517 bp from pter
End:
100,595,594 bp from pter
Size:
3,078 bases
Orientation:
minus strand

1 alternative location:
Chr7-,CRA_TCAG 100,164,184-100,167,239     
RefSeq DNA sequence:
NC_000007.12  NT_007933.14  NT_079596.2  
(According to 1UniProtKB, and/or Ensembl, Phosphorylation sites according to 2Phosphosite, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from Invitrogen, Millipore, Sigma-Aldrich, R&D Systems, Enzo Life Sciences, Abnova, OriGene and/or, Abcam,
Biochemical Assays by Invitrogen, Millipore, R&D Systems, Cell Signaling Technology, and/or Enzo Life Sciences, Ontologies according to Gene Ontology Consortium 01 Apr 2009 and Entrez Gene, Antibodies by Invitrogen, Millipore, Sigma-Aldrich, R&D Systems, Cell Signaling Technology, Abcam, Abnova, and/or Novus Biologicals)
About This Section

UniProtKB/Swiss-Prot: VGF_HUMAN, O15240 (See protein sequence)
Recommended Name: Neurosecretory protein VGF precursor  
Size: 615 amino acids; 67258 Da
Subcellular location: Secreted (By similarity). Cytoplasmic vesicle, secretory vesicle (By
similarity). Note=Stored in secretory vesicles and then secreted (By similarity)
Secondary accessions: Q9UDW8

REFSEQ proteins: NP_003369.2  

ENSEMBL proteins: 
ENSP00000249330 


Human Recombinant Proteins 
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Browse recombinant and purified proteins available from Enzo Life Sciences
Recombinant Proteins from Abcam (VGF)
Browse Abnova for Human Recombinant Proteins
                Browse Origene for full length recombinant human proteins expressed in human HEK293 cells 

3 Gene Ontology (GO) cellular component terms (links to tree view):

GO IDQualified GO termEvidencePubMed IDs
GO:0005576 extracellular region IEA--
GO:0005615 extracellular space IDA15706611
GO:0031410 cytoplasmic vesicle IDA17440014
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Antibodies for VGF: 
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Sigma-Aldrich Antibodies for VGF
Browse R&D Systems for Antibodies
Antibodies from Abcam (VGF), each with their AbpromiseSM
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Search Novus for antibodies for VGF

Assays for VGF: 
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Browse Kits and Assays available from Millipore
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Browse biochemical assays available from Enzo Life Sciences

(According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
About This Section

ProtoNet protein and cluster: O15240

(According to MGI Jun 06 2009, UniProtKB, IUBMB,and/or Genatlas,
shRNA from OriGene, Sigma-Aldrich, RNAi from Sigma-Aldrich,
RNAi Products, Clones, and Q-PCR Products from Invitrogen, Millipore, OriGene, and/or Abnova, siRNAs from Applied Biosystems, SYBR primers from OriGene, Cell-based Assays from Millipore, Ontologies according to Gene Ontology Consortium 01 Apr 2009 via Entrez Gene.)
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Inhib.
RNA:
Invitrogen RNAi Products for gene knock-down (VGF)
Browse for Gene Knock-down Tools from Millipore
Browse Abnova for Chimera RNAi Products
              OriGene 29mer shRNA kit in GFP-retroviral vector: NM_003378

              Applied Biosystems Silencer® siRNAs for VGF

              Sigma-Aldrich siRNA for VGF  
                     Sigma-Aldrich shRNA for VGF  
                     Explore Sigma-Aldrich super-pooled esiRNAs  

Clones:Browse Clone Ranger at Invitrogen for clones
Browse Clones for the Expression of Recombinant Proteins Available from Millipore
              OriGene GFP tagged cDNA clone in CMV expression vector: NM_003378
                                 Myc/DDK tagged cDNA clone in CMV expression vector: NM_003378
                                 untagged cDNA clone in CMV expression vector: NM_003378 

Primers: Browse Quantitative PCR Central at Invitrogen for Q-PCR LUX™ Primers
              OriGene genome-wide validated SYBR primer pairs: NM_003378

UniProtKB/Swiss-Prot: VGF_HUMAN, O15240
Function: May be involved in the regulation of cell-cell interactions or in synatogenesis during
the maturation of the nervous system (By similarity)

Genatlas biochemistry entry for VGF:
neurotrophin responsive factor,70kDa,expressed in the brain,with a C terminal region encoding
posttranslationaly processed peptides

8 MGI mutant phenotypes (inferred from 2 alleles(MGI details for Vgf):

adipose tissuebehavior/neurologicalendocrine/exocrine glandgrowth/sizehomeostasis/metabolism
lethality-postnatalnervous systemreproductive system

3 Gene Ontology (GO) molecular function terms (links to tree view):

GO IDQualified GO termEvidencePubMed IDs
GO:0003674 molecular_function ND--
GO:0005184 neuropeptide hormone activity IEA--
GO:0008083 growth factor activity IEA--
About this table

(Pathways according to Invitrogen (maps by GeneGo), Millipore, Cell Signaling Technology, Sigma-Aldrich, KEGG and/or UniProtKB,
Sets of similar genes according to GeneDecks, Proteins Network according to SABiosciences, Interactions according to 1UniProtKB, 2MINT, and/or 3STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2009 via Entrez Gene.)
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 Gene Network CentralTM Interacting Genes and Proteins Network for  VGF 


5/15 Interacting proteins for VGF (ENSP000002493303) via UniProtKB, MINT, and/or STRING (see all 15 )
InteractantInteraction Details
GeneCardExternal ID(s)
NGFENSP000003585253STRING (score=.969)
BDNFENSP000003200023STRING (score=.968)
NTF3ENSP000003287383STRING (score=.938)
CREB1ENSP000002369963STRING (score=.92)
RASD1ENSP000002256883STRING (score=.888)
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5/9 Gene Ontology (GO) biological process terms (links to tree view) (see all 9 ):

GO IDQualified GO termEvidencePubMed IDs
GO:0001541 ovarian follicle development IEA--
GO:0002021 response to dietary excess IEA--
GO:0006091 generation of precursor metabolites and energy IEA--
GO:0009409 response to cold IEA--
GO:0019953 sexual reproduction IEA--
About this table
(Chemical Compounds according to UniProtKB, Enzo Life Sciences, Sigma-Aldrich, Tocris Bioscience, and/or Novoseek and Drugs according to Enzo Life Sciences and/or PharmGKB)
About This Section

Browse drugs & compounds from Enzo Life Sciences
Browse Small Molecules at Sigma-Aldrich

Browse Tocris compounds for VGF
4 Novoseek chemical compound relationships for VGF gene
Compound   Score   Articles   PubMed IDs for Articles with Shared Sentences (# sentences)
forskolin 27.88 3 8395923 (1), 7476021 (1)
cyclic amp 25.43 1 9084409 (1)
tyrosine 18.90 4 8525617 (3), 7875312 (1)
thymidine 16.38 2 12522439 (1), 12603984 (1)
About this table


(GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 219 Homo sapiens; Jun 2 2009) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView,
non coding RNAs according to RNAdb,
ESTs according to GeneTide,
exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
RNAi Products from Invitrogen, Millipore, and/or Abnova,
siRNAs from Applied Biosystems, Sigma-Aldrich,
shRNA from Sigma-Aldrich, OriGene,
Tagged/untagged cDNA clones from OriGene,
Expression Assays from Applied Biosystems)
About This Section

Inhib.
RNA:
Invitrogen RNAi Products for gene knock-down (VGF)
Browse for Gene Knock-down Tools from Millipore
Browse Abnova for Chimera RNAi Products
              OriGene 29mer shRNA kit in GFP-retroviral vector: NM_003378

              Sigma-Aldrich siRNA for VGF  
                     Sigma-Aldrich shRNA for VGF  
                     Explore Sigma-Aldrich super-pooled esiRNAs  

Applied Biosystems Silencer® siRNAs: 

NM_003378  

REFSEQ mRNAs for VGF gene: 

NM_003378.3   

Applied Biosystems TaqMan ® Gene Expression Assays: 

NM_003378  

              OriGene GFP tagged cDNA clone in CMV expression vector: NM_003378
                                 Myc/DDK tagged cDNA clone in CMV expression vector: NM_003378
                                 untagged cDNA clone in CMV expression vector: NM_003378 

Additional cDNA sequence: 

AK225839.1 BC006217.2 BC036537.1 BC044212.1 BC063835.1 

5 DOTS entries:

DT.91892495  DT.97794502  DT.101984471  DT.300806  DT.75102021 

24/86 AceView cDNA sequences (see all 86 ):

CK820236 CK904657 BM142488 BQ637569 BQ639541 NM_003378 BC063835 BU166517 
BM126861 BM911486 BC006217 BM068821 BM263198 BM718178 BG236881 CD108874 
BM726762 BE855486 BC044212 AW245132 BM142297 BI963104 CK904961 BU784525 

highest scoring ESTs for VGF:

BC036537 BC063835 BI712777 AA224159 AI811072 AI951596 AL523909 AW248251 BI552988 BM023247 

Unigene Cluster for VGF:

VGF nerve growth factor inducible
Hs.718797  [show with all ESTs]
Unigene Representative Sequence: BC063835


GeneLoc Exon Structure

1 Ensembl transcript including schematic representation:
ENST00000249330  
(Experimental results according to 1GeneNote and GNF BioGPS,
probe sets-to-genes annotations according to 2GeneAnnot , 3GeneTide , Sets of similar genes according to GeneDecks, Electronic Northern calculations according to data from UniGene (Build 219 Homo sapiens), SAGE tags according to CGAP, plus additional links to SOURCE, and/or GNF BioGPS, and/or EXPOLDB, and/or UniProtKB,
Expression Assays from Applied Biosystems )
About This Section

VGF expression in normal and diseased human tissues

 Applied Biosystems TaqMan ® Gene Expression Assays for VGF

1 / 2 / 3

4 probe-sets matching VGF gene


Affymetrix
probe-set
Array  GeneAnnot data GeneNote data GeneTide data
# genes Sensitivity Specificity Correlation Length Gb_Accession Consensus Uniqueness Score Rank
59503_at2, 3 U95-B 1 1.00 1.00 0.98 1.01 AI811072 0.60 1.00 0.82 1
32969_r_at2, 3 U95-A 1 0.94 1.00 0.97 1.00 Y12661 0.20 1.00 0.72 1

205586_x_at2, 3 U133-A 7 0.73 0.82 -- -- NM_003378 0.60 1.00 0.82 1

205586_x_at2 U133Plus2 7 0.73 0.82 -- -- -- -- -- -- --
GeneDecks  VGF for binary patterns associated with the probe-sets selected above  
About GeneDecksing
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Data from (Publications) and GNF BioGPS
    About these images
About these images

CGAP SAGE TAG: CGCCCCGGCC

SOURCE GeneReport for Unigene cluster: Hs.718797

Expression variation in blood from EXPOLDB for VGF

UniProtKB/Swiss-Prot: VGF_HUMAN, O15240
Tissue specificity: Expressed in brain

(Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD and/or 5MGI Jun 06 2009, with possible further links to Flybase and/or WormBase, Gene Trees according to Ensembl)
About This Section


Orthologs for VGF gene from 5 species
Organism Gene Locus Description Human
Similarity
NCBI accessions
chimpanzee
(Pan troglodytes)
VGF1   -- VGF nerve growth factor inducible 98.36(n)
98.3(a)
463616  XM_519275.2  XP_519275.2 
rat
(Rattus norvegicus)
Vgf1   -- VGF nerve growth factor inducible 86.08(n)
86.79(a)
29461  NM_030997.1  NP_112259.1 
mouse
(Mus musculus)
Vgf1, 5 5 (79.00 cM)5
VGF nerve growth factor inducible1, 5 85.48(n)1
86.3(a)1
3816771  NM_001039385.11  NP_001034474.11 
 BC0851345  BC1385535  (see all 8)
zebrafish
(Danio rerio)
wu:fj49c031   -- wu:fj49c03 46.77(n)
34.88(a)
793455  XM_001333183.1  XP_001333219.1 
rice
(Oryza sativa)
Os.467622   -- Oryza sativa (japonica cultivar-group) cDNA cloneJ more 74.39(n)  AK120364.1 
About this table        Species with no ortholog for VGF

ENSEMBL Gene Tree for VGF
(Paralogs according to 1HomoloGene
and 2Ensembl, Pseudogenes according to 3Pseudogene.org)
About This Section

  --
(According to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, and UniProtKB, Linkage Disequilibrium by HapMap, Genotyping Reagents from Applied Biosystems)
About This Section


10/24 NCBI SNPs in VGF are shown (see all 24 )
(Click for Applied Biosystems TaqMan ® Genotyping Assay)  (see all 48)
ABGenomic DataTranscription DataAllele Frequencies
SNP IDValidChr 7 posSequenceRecsAA
Chg
TypeMoreRecsAllele
freq
PopTotal
sample
More
------------
rs109533251,2
A,C,F,H100592228(+) AATTGG/ACTCTT 1 -- ng5110Minor allele frequency- A:0.47EU EA WA NA 1020
rs99186351,2
A,C,F,H100592424(+) GGAGAT/CGGGGA 1 -- ng518Minor allele frequency- C:0.37EU EA WA 836
rs107558661,2
A,C,F,H100592180(+) GGGTCA/GCCTTT 1 -- ng518Minor allele frequency- G:0.37EU EA WA 838
rs39194821,2
A,C100597420(+) GAGGCA/GATGCC 1 -- ng310--------
rs21078041,2
C100592391(+) CCCCTC/TGCCTT 1 -- ng510--------
rs359077661,2
F100594032(+) GCCACG/CCCTTG 1 G/G syn11Minor allele frequency- C:0.04NA 44
--
rs616570491,2
--100596526(+) GGGGG-/GGTGACT 1 -- ng310--------
--
rs737121001,2
--100592655(+) GAGACA/GGACAC 1 -- ut310--------
--
rs718656651,2
--100596517(+) AGGTG-/GGGGGGG 1 -- ng310--------
--
rs125354451,2
--100595470(+) CGGTGC/GCCGGG 1 -- ut51 ese30--------
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HapMap Linkage Disequilibrium images for VGF (up to first 250kb)

(in which this Gene is Involved, According to OMIM, UniProtKB, Novoseek, PharmGKB, Genatlas, GeneTests, Blood group antigen gene mutations by BGMUT, HGMD, GAD, HuGE Navigator, BCGD, and/or TGDB.)
About This Section

OMIM: 602186

2 Novoseek disease relationships for VGF gene

Disease   Score   Articles   PubMed IDs for Articles with Shared Sentences (# sentences)
pheochromocytoma 41.13 3 9478934 (1), 1469059 (1), 9084409 (1)
tumors 0.00 2 18328103 (1)
About this table

Human Genome Epidemiology Navigator: VGF (2 documents)

(Possibly Related Articles in Doctor's Guide)
About This Section

  --

(in PubMed. Associations of this gene to articles via 1Novoseek, 2HGNC, 3Entrez Gene, 4UniProtKB/Swiss-Prot, 5UniProtKB/TrEMBL, 6GAD, and/or 7PharmGKB)
About This Section

10/61 PubMed articles for VGF gene (see all 61 ):
(in PubMed, OMIM, and NCBI Bookshelf)
About This Section

 ANDOR
Aliases
Free Text  

  Query String
PubMed
OMIM
NCBI Bookshelf
  (Note: In FireFox, select the above section and copy using Ctrl-C)
(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, and/or H-InvDB)
About This Section

Entrez Gene: 7425 HGNC: 12684 AceView: VGF Ensembl:ENSG00000128564 euGenes: HUgn7425
ECgene: VGF H-InvDB: VGF
(According to HUGE)
About This Section

  --
(According to ATLAS, HORDE, IMGT, MTDB, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
About This Section

  --
(Available from WIS Yeda, Salk, Tufts)
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  --
(Reagents available from Applied Biosystems, Antibodies and assays by Cell Signaling Technology, Abcam, Novus Biologicals,
Sigma-Aldrich, R&D Systems, Millipore, Abnova, and/or Invitrogen, Clones available from OriGene,and/or Invitrogen, Drugs and/or compounds by Sigma-Aldrich,
Enzo Life Sciences, and/or Tocris Bioscience)
About This Section



Products for VGF:
 TaqMan ® Gene Expression Assays
 TaqMan ® Genotyping Assays
  Free SNP selection tool



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 Predesigned and custom siRNAs for VGF Antibodies for VGF
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 Search Novus for antibodies for VGF

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