Cancer protection elicited by a single nucleotide polymorphism close to the adrenomedullin gene.
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):E807-10. doi: 10.1210/jc.. Epub
2013 Feb 28.Cancer protection elicited by a single nucleotide polymorphism close to the adrenomedullin gene.1, .1Oncology Area, Center for Biomedical Research of La Rioja (CIBIR), Logro?o, Spain.AbstractCONTEXT: The risk of developing cancer is regulated by genetic variants, including polymorphisms. Characterizing such variants may help in developing protocols for personalized medicine.OBJECTIVE: Adrenomedullin is a regulatory peptide involved in cancer promotion and progression. Carriers of a single nucleotide polymorphism (SNP) in the proximity of the adrenomedullin gene have lower levels of circulating peptide. The aim of the present work was to investigate whether carriers of this SNP (rs4910118) are protected against cancer.DESIGN: This was a retrospective study. DNA samples were obtained from the Carlos III DNA National Bank (University of Salamanca, Salamanca, Spain).SETTING: Samples represent a variety of donors and patients from Spain.PATIENTS OR OTHER PARTICIPANTS: DNA from patients with breast cancer (n = 238), patients with lung cancer (n = 348), patients with cardiac insufficiency (n = 474), and healthy donors of advanced age (n = 500) was used.INTERVENTIONS: All samples were genotyped using double-mismatch PCR, and confirmation was achieved by direct sequencing.MAIN OUTCOME MEASURES: The minor allele frequency was calculated in all groups. The Pearson χ(2) was used to compare SNP frequencies.RESULTS: Of 1560 samples, 14 had the minor allele, with a minor allele frequency in healthy donors of 0.90%. Patients with cancer had a statistically significantly lower frequency than healthy donors (odds ratio = 0.216, 95% confidence interval = 0.048-0.967, P = .028).CONCLUSIONS: Carriers of the minor allele have a 4.6-fold lower risk of developing cancer than homozygotes for the major allele. Knowledge of the rs4910118 genotype may be useful for stratifying patients in clinical trials and for designing prevention strategies.PMID:
[PubMed - indexed for MEDLINE]
Publication TypesMeSH TermsSubstancesFull Text SourcesOther Literature SourcesMedical
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External link. Please review our .Horizontal gene transfer and nucleotide compositional anomaly in large DNA viruses.
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2007 Dec 10;8:456.Horizontal gene transfer and nucleotide compositional anomaly in large DNA viruses.1, , .1Structural and Genomic Information Laboratory, CNRS - UPR 2589, Institute for Structural Biology and Microbiology, Parc Scientifique de Luminy, 163 avenue de Luminy, FR-13288, Marseille cedex 09, France. Adam.rs-mrs.frAbstractBACKGROUND: DNA viruses have a wide range of genome sizes (5 kb up to 1.2 Mb, compared to 0.16 Mb to 1.5 Mb for obligate parasitic bacteria) that do not correlate with their virulence or the taxonomic distribution of their hosts. The reasons for such large variation are unclear. According to the traditional view of viruses as gifted "gene pickpockets", large viral genome sizes could originate from numerous gene acquisitions from their hosts. We investigated this hypothesis by studying 67 large DNA viruses with genome sizes larger than 150 kb, including the recently characterized giant mimivirus. Given that horizontally transferred DNA often have anomalous nucleotide compositions differing from the rest of the genome, we conducted a detailed analysis of the inter- and intra-genome compositional properties of these viruses. We then interpreted their compositional heterogeneity in terms of possible causes, including strand asymmetry, gene function/expression, and horizontal transfer.RESULTS: We first show that the global nucleotide composition and nucleotide word usage of viral genomes are species-specific and distinct from those of their hosts. Next, we identified compositionally anomalous (cA) genes in viral genomes, using a method based on Bayesian inference. The proportion of cA genes is highly variable across viruses and does not exhibit a significant correlation with genome size. The vast majority of the cA genes were of unknown function, lacking homologs in the databases. For genes with known homologs, we found a substantial enrichment of cA genes in specific functional classes for some of the viruses. No significant association was found between cA genes and compositional strand asymmetry. A possible exogenous origin for a small fraction of the cA genes could be confirmed by phylogenetic reconstruction.CONCLUSION: At odds with the traditional dogma, our results argue against frequent genetic transfers to large DNA viruses from their modern hosts. The large genome sizes of these viruses are not simply explained by an increased propensity to acquire foreign genes. This study also confirms that the anomalous nucleotide compositions of the cA genes is sometimes linked to particular biological functions or expression patterns, possibly leading to an overestimation of recent horizontal gene transfers.PMID:
[PubMed - indexed for MEDLINE] PMCID: PMC2211322 Difference in genomic signature distance between real and randomized data for all possible pairs of 67 LDVs. The inset figure shows the genomic signature distances between all possible pairs of 67 LDVs for both real and randomized data.BMC Genomics. -456.Comparison of G+C content between LDVs and their hosts.BMC Genomics. -456.Difference in genomic signature distance between real and randomized data for LDV-host pairs. The inset figure shows the genomic signature distances between the LDV-host pairs for both real and randomized data.BMC Genomics. -456.Proportions of the cA genes detected in the 67 LDV genomes, compared with the genome sizes.BMC Genomics. -456.Gene organization and the locations of the cA genes for herpesviruses. The phylogenetic reconstruction (on the left) is based on the DNA polymerase catalytic subunit sequences. Red and pink dots (on the right) correspond to the cA genes and the remaining genes, respectively. Green lines show orthologous gene relationships defined by BLAST reciprocal best hit.BMC Genomics. -456.Functional categories of the cA genes detected in the 67 LDV genomes.BMC Genomics. -456.Publication TypesMeSH TermsFull Text SourcesOther Literature Sources
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External link. Please review our .Gna12 guanine nucleotide binding protein, alpha 12 [Mus musculus (house mouse)] - Gene - NCBI
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CategoriesSequence contentStatus(1)Chromosome locationsFromToApply
FormatFull ReportFull Report (text)Gene TableGene Table (text)GeneRIFSummarySummary (text)TabularTabular (text)ASN.1XMLUI ListChoose DestinationFileClipboardCollectionsFormatFull Report (text)Gene Table (text)Summary (text)Tabular (text)ASN.1XMLUI ListCreate FileAdd to ClipboardAdd to Collections
Gna12provided by
guanine nucleotide binding protein, alpha 12provided by
Primary source
protein coding
RefSeq status
PROVISIONAL
E M C C V E M E E G R S M M M M Mus
Also known as
AI414047; AI504261; Galpha12
See Gna12 in ,
Annotation release
GRCm38.p3 ()
NC_ (.., complement)
Build 37.2
previous assembly
MGSCv37 ()
NC_ (.., complement)
Chromosome 5 - NC_
Genomic Sequence:
NC_ Chromosome 5 Reference GRCm38.p3 C57BL/6J
AC_ Chromosome 5 Alternate Mm_Celera
NC_ Chromosome 5 Reference MGSCv37 C57BL/6J
Go to nucleotide:
Related articles in PubMed
GeneRIFs: Gene References Into Functions
Title: Polycystin-1 and Gα12 regulate the cleavage of E-cadherin in kidney epithelial cells.
Title: G protein-dependent basal and evoked endothelial cell vWF secretion.
Title: Distinct role of Pyk2 in mediating thromboxane generation downstream of both G12/13 and integrin αIIbβ3 in platelets.
Title: PRR5L degradation promotes mTORC2-mediated PKC-δ phosphorylation and cell migration downstream of Gα12.
Title: 5-HT7R/G12 signaling regulates neuronal morphology and function in an age-dependent manner.
Title: Gαi2 signaling promotes skeletal muscle hypertrophy, myoblast differentiation, and muscle regeneration.
Title: Negative regulation of Gq-mediated pathways in platelets by G(12/13) pathways through Fyn kinase.
Title: G(alpha)12/13 induction of CYR61 in association with arteriosclerotic intimal hyperplasia: effect of sphingosine-1-phosphate.
Title: Galpha12 is critical for TCR-induced IL-2 production and differentiation of T helper 2 and T helper 17 cells.
Title: Constitutive Gs-mediated, but not G12-mediated, activity of the 5-hydroxytryptamine 5-HT7(a) receptor is modulated by the palmitoylation of its C-terminal domain.
Gna12 (e-PCR), detects polymorphism
M63659 (e-PCR)
D5Mit247 (e-PCR), detects polymorphism
Gna12 (e-PCR), detects polymorphism
D5Mit327 (e-PCR), detects polymorphism
NoName (e-PCR)
Gna12 (e-PCR), detects polymorphism
RH144209 (e-PCR)
Inferred from Sequence Orthology
Inferred from Biological aspect of Ancestor
Inferred from Electronic Annotation
Inferred from Electronic Annotation
Inferred from Sequence Alignment
Traceable Author Statement
Inferred from Electronic Annotation
Inferred from Electronic Annotation
Inferred from Electronic Annotation
Inferred from Biological aspect of Ancestor
Evidence Code
Inferred from Sequence Alignment
Traceable Author Statement
Inferred from Direct Assay
Inferred from Biological aspect of Ancestor
Inferred from Direct Assay
Inferred from Genetic Interaction
Inferred from Genetic Interaction
Inferred from Direct Assay
Inferred from Mutant Phenotype
Inferred from Sequence Orthology
Inferred from Direct Assay
Inferred from Mutant Phenotype
Inferred from Mutant Phenotype
Inferred from Sequence Orthology
Inferred from Electronic Annotation
Inferred from Electronic Annotation
Evidence Code
Inferred from Biological aspect of Ancestor
Inferred from Sequence Orthology
Inferred from Sequence Orthology
Traceable Author Statement
Inferred from Electronic Annotation
Preferred Names
guanine nucleotide-binding protein subunit alpha-12
G-protein subunit alpha-12
g alpha-12
These reference sequences exist independently of genome builds.
These reference sequences are curated independently of the genome
annotation cycle, so their versions may not match the RefSeq versions in the current
genome build. Identify version mismatches by comparing the version of the RefSeq in
this section to the one reported in
mRNA and Protein(s)
guanine nucleotide-binding protein subunit alpha-12
Status: PROVISIONAL
Source sequence(s)
Consensus CDS
UniProtKB/Swiss-Prot
Conserved Domains (2)
Location:56 → 373
G- Alpha subunit of G proteins (guanine nucleotide binding)
Location:40 → 377
G_ G protein alpha subunit
The following sections contain reference sequences that belong to a
specific genome build.
Reference GRCm38.p3 C57BL/6J
NC_ Reference GRCm38.p3 C57BL/6J
.. complement
Alternate Mm_Celera
AC_ Alternate Mm_Celera
.. complement
Protein Accession
GenPept Link
UniProtKB Link
Gene Expression Database (GXD) at MGI
The following
resources are supplied by external providers. These providers are responsible for maintaining the links.
Interologous Interaction Database
Allen Brain Atlas
CREB Target Gene Database
GenScript:ORF Clones in your selected vector
GeneNetwork
Genevisible
Immunological Genome Project
Ingenuity Pathways Analysis
KOMP Repository
Kyoto Encyclopedia of Genes and Genomes
NIA Mouse Gene Index
Nuclear Receptor Signaling Atlas (NURSA)
OrthoDB: The Hierarchical Catalog of Eukaryotic Orthologs
PhosphoSitePlus
Protein Ontology Consortium
SeekQuence Research Antibodies
iHOP - Information Hyperlinked over Proteins
iRefWeb - iRefIndex release 9.0 - Consolidated Interactome
Addgene Non-profit plasmid repository
ExactAntigen/Labome
GeneCopoeia Inc.
GeneWeaver
InterologFinder.org
QIAGEN GeneGlobe
Supplemental Content
Order cDNA clone
3D structure of a gene
Related PubChem BioAssays
BioAssays related to the gene by protein target or RNAi target
Summarized PubChem Data on the gene, showing the active data by default
PubChem BioAssays done on the Gene target
BioAssays that contain the gene as the target of a RNAi reagent
BioProjects related to a gene
BioSystems
Links from Gene to CCDS are established if a gene encodes a protein sequence that is a member of a Consensus CDS (CCDS).
Conserved Domain Database
Links between Entrez Gene and Conserved Domain Database (CDD) are calculated from the domains annotated by the CDD group on Reference Sequence proteins.
Link from Gene to dbVar
Full text in PubMedCentral identified from shared sequence links
Overlapping genes and two nearest non-overlapping genes on either side
Genome records having the gene annotated on corresponding genomic reference sequence.
Related GEO
Links between HomoloGene and Gene are provided by the HomoloGene group when a gene is included in a HomoloGene record.
These links are maintained by the Map Viewer group and are provided when a GeneID is annotated on a map for the same species.
Link to related Nucleotide entry
Related Probe entry
Link to related protein entry
PubChem Compounds
PubChem Substances
Links between Gene and PubMed are the result of the following:
1. Manual curation within NCBI. Part of the process of generating a REVIEWED RefSeq is an analysis of the current literature. Papers that are seminal in defining the gene, its sequence, and its function are added to the record at that time. Alert users point out gaps or errors in papers associated with a Gene record. These messages are reviewed and implemented as required.
2. Integration of information from other public databases. Gene integrates gene-citation from resources external to NCBI such as model organism-specific databases, Gene Ontology (GO), groups curating interactions, and sequence databases. The assumption in using these source is that they report citations specific to a gene in a known species. Gene does not process citations from OMIM automatically, because many of citations in OMIM refer to studies of genes in species other than human.
GeneRIF -- Gene Reference Into Function
Staff of the Index Section in the National Library of Medicine review the current literature. When they find articles focused on the structure and function of a gene, they write a brief summary of the impact of the paper and make the connection between the citation (PubMed) and Gene. An interface exists for interested users to submit such data as well.
http://www.ncbi.nlm.nih.gov/projects/GeneRIF/GeneRIFhelp.html
Citations in PubMed identified from shared sequence and PMC links.
Link to Protein RefSeqs
Link to Nucleotide RefSeq RNAs
Related SNP records
SNPs linked from GeneView
Link to related taxonomy entry
Links are provided between Gene and UniGene when both databases calculate links to the same mRNA record (gi).
Gna12 guanine nucleotide binding protein, alpha 12 [Mus musculus]Gene ID:14673
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请教如在NCBI上批量下载GeneBank注释格式的nucleotide 文件
请教如在NCBI上批量下载GeneBank注释格式的nucleotide 文件
分享到哪里？
这个帖子发布于7年零145天前，其中的信息可能已发生改变或有所发展。
手中有一批NCBI nucleotide 的gi 号和gb号，因为很多，所以不宜手工一条条下载。有什么办法可以在NCBI上批量下载GeneBank注释格式的nucleotide 文件？我将所有gi号输入 search (nucleotide) for (***,***,***[gi]) %***表示gi号，后可以把哪些序列的ID link都列出来，全部选中这些序列ID后，选Display [GeneBank]---& sort by [file]出来的文件，只有这些序列ID的信息，而不是真正的genebank 格式文件。求助中。。。谢谢
回复：请教如在NCBI上批量下载GeneBank注释格式的nucleotide 文件
分享到哪里？
我这里可以出现下载后的gb文件呀，里面有内容
回复：请教如在NCBI上批量下载GeneBank注释格式的nucleotide 文件
分享到哪里？
Downlaod id1_fetch fromAnd Run the Win32 program:id1_fetch -qf YOUR_GI_FILE -fmt genbank -db Nucleotide -out YOUR_GBK_FILEYOUR_GI_FILE: your input, write all GIs in that txt file, 1 GI per lineYOUR_GBK_FILE: your outputHave fun.
回复：请教如在NCBI上批量下载GeneBank注释格式的nucleotide 文件
分享到哪里？
我有一个perl写的脚本，可以连到NCBI上下载，需要的话可以联系我免费送给你， QQ:----------------上海敏芯信息科技有限公司
回复：请教如在NCBI上批量下载GeneBank注释格式的nucleotide 文件
分享到哪里？
id1_fetch 在 dos命令行里很容易就实现了。。支持
回复：请教如在NCBI上批量下载GeneBank注释格式的nucleotide 文件
分享到哪里？
id1_fetch 在有没有图形支持的？dos命令行很容易看花。
回复：请教如在NCBI上批量下载GeneBank注释格式的nucleotide 文件
分享到哪里？
yili_528 id1_fetch 在有没有图形支持的？dos命令行很容易看花。正在开发GUI,希望有编程经验的朋友助上一臂之力。没有编程经验的朋友请给点电击鼓励。
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