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;
- Flat file
- XML file
- DDBJ format file
- Nucleotide fasta file
- Protein fasta file
| No. | TAB name | SECTION name |
| 1 | Gene structure | Gene structure information |
| 2 | Function | Gene function information |
| 3 | GO | Gene ontology information |
| 4 | CDS | Predicted CDS information |
| 5 | Motif | Motif information |
| 6 | Subcellular loc. | Subcellular localization information |
| 7 | Protein structure | Protein structure information (GTOP) |
| 8 | Expression | Gene expression information |
| 9 | Disease | Disease/pathology information |
| 10 | Evolution | Evolutionary information |
| 11 | Polymorphism | Polymorphism (SNP, indel), microsatellite (Short Tandem Repeat, STR) and repeat information |
| 12 | Transcript 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;
- H-Inv cluster ID
- Genomic location
- Possible duplicated location(s)
- Gene structure
- Chromosome band
- Related links (Ensembl, RefSeq, EntrezGene, GeneCards, H-GOLD)
Fig. 4.1.2 H-InvDB Transcript view: Gene structure information
2) Gene function information [Function tab]
Provides annotation items below and related links;
- H-Inv ID
- Accession No.
- Gene symbol/name
- Gene family/group
- Definition
- Similarity category
- Coding potential
- Transcript feature
- EC number
- KEGG metabolic pathway
- Protein-protein interaction (PPI)
- PubMed ID
- Curation status
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
- Gene ontology (GO): molecular function
- Gene ontology (GO): biological process
- Gene ontology (GO): cellular component
Provides annotation items below and related links;
- CDS feature (Complete CDS, N-, and C-truncated)
- HIP ID
- Predicted CDS
- Codon Adaptation Index (CAI).
- Related link to UniProt, RefSeq protein, CCDS
Fig. 4.1.5 H-InvDB Transcript view: Predicted CDS information
5) Motif information [Motif tab]
Provides annotation items below and related links;
- InterPro ID
- Location of the predicted motif
- Related links to InterPro
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;
- WoLF PSORT prediction http://wolfpsort.seq.cbrc.jp/
- TargetP prediction http://www.cbs.dtu.dk/services/TargetP/
- SOSUI prediction http://sosui.proteome.bio.tuat.ac.jp/sosuiframe0.html
- TMHMM prediction http://www.cbs.dtu.dk/services/TMHMM-2.0/
- PTS1 prediction http://mendel.imp.ac.at/mendeljsp/sat/pts1/PTS1predictor.jsp
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;
- PDB_ID
- Location (start/end)
- E-value, Identity, coverage
- SCOP_ID
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;
- Tissue-specific expression
- Probe information
Fig. 4.1.9 H-InvDB Transcript view: Gene expression information
9) Disease/pathology information [Disease info.]
Provides annotation items below and related links;
- Disease relation
- Related information in OMIM
- Co-localized orphan diseases
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;
- Orthology
- Phylogenic trees (NJ and NJML+)
- Natural selection (dN/dS)
- Genome map view of orthologs species (G-integra)
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.
Provides annotation items below and related links;
- Polymorphism (SNP)
- microsatellite (STR)
- Microsatellite: Human-Gene diversity Of Life-style related Diseases (H-GOLD)
http://h-invitational.jp/gdbs/viewer/ - Repeat
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
- Accession No.
- Clone No
- Sequence data provider
- Annotation project
- Length of cDNA
- CDS feature
- PolyA
- Vector adapter sequence
- Frame shift
- Remaining intron
- Splice site acceptor (NAGNAG)
- Transcript feature
- NMD predicted
- Reverse orientation revised;
- Predicted readthrough
Fig. 4.1.13 H-InvDB Transcript view: Transcript information