GeneView: Francci3_4056

Summary section of Francci3_4056 gene.

ID indicates the ORF ID.

Type indicates the type of the gene: Protein Coding or RNA.

Gene Symbol indicates the symbols of the gene which are released under the genome project quality.

Curated Gene Symbol indicates the gene symbols which are curated by biologists.

GeneIndexing gname indicates the gene symbols which are released by GeneIndexing project effort. These symbols are assigned by curators with various evidences.

Definition is transfered from the gene definition in the original GenBank file..

Function category is assigned by a COG bases method or transfered from the category of the original genome project.

Genes and Mutants indicates mutant information submitted by biologists directly via CyanoGenes/Mutants system. You can see more details for each record at the Mutants section.

Genomic context section of the Francci3_4056 gene.

Location indicates the genomic location including the chromosome name, the start position and the stop position.

Strand indicates the orientation of the gene on the choromosome: direct or complement

Genomic context indicates the visual display of the gene and the surrounding genes. It contains the navigation links among the genes.

GenomeView icon indicates the link of the Kazusa Genome Browser.

MapView icon indicates the link of the chromosome map.

Transcript section of the Francci3_4056 gene.

FNA icon indicates the link of the nucleotide sequence of the gene in fasta format.

Length indicates the length of the nucleotide sequence of the gene.

Sequence retrieving allows you to retrieve the genomic nucleotide sequence specified by a genomic range form the initial position to the terminal position. For example you can retrieve the upstream/internal/downstream sequence of the gene.

Peptide section of the Francci3_4056 gene.

FAA icon indicates the link of the protein sequence of the gene in fasta format.

Length indicates the length of the protein sequence of the gene.

Protein Domains section of the Francci3_4056 gene.

Graphical view by InterProScan indicates a graphical display of the arrangment of the predicted domains by InterProScan.

show/hide icon is a toggle switch to show or hide the graphical display.

PNG icon indicates the link of the PNG file of the graphical display.

Table view by InterProScan indicates the summary table of the InterProScan prediction. Each InterPro ID indicates the link to the InterPro entry. [S] links to the list of genes which predicted the InterPro ID (FRANCCI3 species-wise prediction). [D] links to the list of genes which predicted the InterPro ID (rhizobase dataset-wise prediction). GO terms indicate the link to the GO entry.

show/hide icon is a toggle switchto show or hide the table..

TableView icon indicates the link of the table page..

GFF3 icon indicates the link of the GFF file of the InterProScan prediction.

Transmembrane regions predicted by SOSUI indicates the SOSUI predicted regions.

Go SOSUI bottun link to the SOSUI prediction.

Mutants section of the Francci3_4056 gene.

Genes and Mutants is a social mutants information repository. It allows biologist to submit a mutant information directly. This is a manual curated resource. You can contact the submitter by the e-mail address indicated.

MutantName indicates the mutant name.

GeneName indicates the gene name.

ProductName indicates the gene product name.

GeneticBackground indicates the genetic background: GT, Kazusa, PCC and etc...

DNA indicates the availability of the DNA material: yes or no.

DrugDirection indicates the direction of the drug marker: Fw (forward) or Rv (reverse).

DrugMarker indicates the construction of the drug maker.

AdditionalInformation indicates a free text of the mutant.

Post new mutant information of the Francci3_4056 gene ... links to the submition form.

Gene annotations section of the Francci3_4056 gene.

TogoAnnotation is a social genome annotation system. It allows us to fetch annotations of the gene, search annotations by the ORF ID and submit new annotation of the gene via TogoAnnotation system.

Gene Ontology [IEA] ipr2go indicates an automated GO gene associations assigned by the InterProSacn prediction. GO IDs link to the GO term entry.

References section of the Francci3_4056 gene.

This section contains the reference list of the Francci3_4056 gene. It is a part of the GeneIndexing effort. Each article mentions the Francci3_4056 gene at the sections indicated by tags (colored boxes). Title links to the PMID page at TogoAnnotaion system. PMID: indicates the link to the PubMed entry. Abstract is a toggle switch to show/hide the abstract text. MeSH is a toggle switch to show/hide the MeSH terms. Gene Index links to the GeneIndexView of the PMID page at TogoAnnotation. The view contains the genes mentioned by the article.

Homology search result by blast2 programs section of the Francci3_4056 gene. This section contains pre-computed blast search results against varous sequence databases.

show/hide icon is a toggle switch to show/hide the table.

TableView icon indicates the link to the TableView page. TableView allows us to sorting records by a column.

GFF3 icon indicates the GFF3 file of the search result.

Target Database is the sequence database name of the homology search: sprot is SwissProtKB protein sequences, nr is the NCBI non-redundant nucleotide sequences, TAIR_pep is the peptide sequences of TAIR and pln_est is a plant EST nucleotide sequences. It indicates the link to the homology search result page.

Accession is the accession which links to the original entry.

Score is the blast score.

Identity (%) is the blast hit identity value.

Positive (%) is the blast hit positive value.

Definition is the definition of the target entry.

PNG icon indicates the link to the graphical display of the blast hits.

Putative ortholog table section of the Francci3_4056 gene.

This putative ortholog table contains a reciprocal best hit paris by blast2 between Francci3_4056 and a species in rhizobase.

show/hide icon is a toggle switch to show/hide the table.

TableView icon indicates the link to the TableView page. It allows us to sorting the hit by column.

GFF3 icon indicates the link to the GFF3 file of the search result.

Genome indicates the species name of the hit gene. It links to the SpeciesView page.

Hit id indicates the hit gene id. It links to the GeneView page.

Score indicates the blast score.

Identity(%) indicates the blast hit identity value.

BLAST icon indicates the link to the pre-computed blast search resuilt against the sequences of the species.

Description is the description of the hit gene.

External links section of the Francci3_4056 gene.

API section of the Francci3_4056 gene.

API provides a REST style application programming interfaces (APIs) to access the data of the Francci3_4056 gene in various formats.