[ Japanese ]

4.1 Transcript view

H-InvDB provides annotation items in graphical and text-based table views for each HIT (H-Invitational transcript) in Transcript view. The previous name for the view was cDNA view (mRNA view).


Fig. 4.1.1 Summary view of Transcript view

The text based views for Transcript view can be selected by the pull-down menu at the top of Transcript view within five data format listed below;

The graphical view of Transcript view consists of following sections (tabs) including listed annotation.

No. TAB name SECTION name
1Gene structureGene structure information
2FunctionGene function information
3GOGene ontology information
4CDSPredicted CDS information
5Motif Motif information
6Subcellular loc.Subcellular localization information
7Protein structureProtein structure information (GTOP)
8ExpressionGene expression information
9DiseaseDisease/pathology information
10EvolutionEvolutionary information
11PolymorphismPolymorphism (SNP, indel), microsatellite (Short Tandem Repeat, STR) and repeat information
12Transcript info.Transcript information
Sequence quality information

Annotation items for H-Inv transcripts

1) Gene structure information [Gene structure tab]

Provides annotation items below and related links;


Fig. 4.1.2 H-InvDB Transcript view: Gene structure information


2) Gene function information [Function tab]

Provides annotation items below and related links;


Fig. 4.1.3 H-InvDB Transcript view: Gene function information


H-InvDB Transcript views also provide similarity search tool to view the results of similarity searches such as FASTY and BLASTX against appropriate target databases as illustrated in the figure below.


Fig. 4.1.4 Similarity search tool


3) Gene ontology information (GO) [GO tab]

Provides annotation items below and related links

4) Predicted CDS information [CDS tab]

Provides annotation items below and related links;


Fig. 4.1.5 H-InvDB Transcript view: Predicted CDS information


5) Motif information [Motif tab]

Provides annotation items below and related links;


Fig. 4.1.6 H-InvDB Transcript view: Motif information


6) Subcellular localization information [Subcellular loc. tab]

Provides the summary of subcellular localization prediction below and links to LIFEdb;


4.1.7 H-InvDB Transcript view: Subcellular localization information


7) Protein structure information (GTOP) [Protein structure tab]

Provides assigned PDB and SCOP ID by reverse PSI-BLAST, and summary prediction of 3D structure by GTOP;


Fig. 4.1.8 H-InvDB Transcript view: Protein structure information (GTOP)


8) Gene expression information [Expression tab]

Provides annotation items below and related links;


Fig. 4.1.9 H-InvDB Transcript view: Gene expression information


9) Disease/pathology information [Disease info.]

Provides annotation items below and related links;


Fig. 4.1.10 H-InvDB Transcript view: Disease/pathology information


10) Evolutionary information [Evolutionary info. tab]

Provides annotation items and the links to Evola, database of evolutionary annotation of human genes and phylogenetic trees, phylogenic trees and gene map (G-integra) for the appropriate species;


Fig. 4.1.11 H-InvDB Transcript view: Evolutionary information


In this section, the links to related tools below are provided;

Trees (NJ and NJML+)
Phylogenetic tree data of the Newick format with bootstrap values. The trees were reconstructed by the NJ and NJML+ methods, and can be displayed by a tree viewer program such as TreeView.

Natural selection (dN/dS)
The statistical significance of excess synonymous or nonsynonymous substitutions is examined over a pairwise alignment by window analysis. The alignment is displayed in the lower frame by selecting a species name.

11) Polymorphism (SNP), microsatellite (STR) and repeat information [Polymorphism tab]

Provides annotation items below and related links;


Fig. 4.1.12 H-InvDB Transcript view: Polymorphism (SNP), microsatellite (STR) and repeat information


12) Transcript information/Transcript quality information [Transcript info. Tab]

Provides annotation items below and related links; Transcript information

Transcript quality information


Fig. 4.1.13 H-InvDB Transcript view: Transcript information


Revised: September 5, 2007