G-integra is a genome integrated database, in which one can browse physical maps of Human, Chimpanzee, Mouse and Rat, and other genomes and their gene structures.
The main function of G-integra is summarized as follows.
Top page : http://h-invitational.jp/hinv/g-integra/
H-InvDB has four ways of accessing G-integra.
1. Top page of G-integra
2. Pop-up menu to enter the main view of each chromosome.
3. Search engine window. (ACC#, Locus, transcript ID)
4. Submit search
5. Link to G-integra TOP page
6. Tool bar (Help page, BLAST page, etc.)
7. Pull-down menu for control of nucleotides per thick on main panel. Please click the "submit!" button after choosing the value. This value can be also controlled by the zoom in/out button.
8. Nucleotide coordinates of first site of the current window
9. Checkboxes for selection of tracks. Please click the "submit!" button after checking the corresponding boxes. The results of interspecies mapping etc. will be shown by setting here.
10. This region defines the position in the genome sequence to display with "Sequence Viewer". For details of sequence viewer, please see 20.
11. Zoom in/out button
12. Notification lists of main panel are as follows:
In paticular, for JBIRC gene tracks of human and other species, the color assignment of the exon corresponds to the data source of mapped transcript.
(Light green): H-Inv full-length cDNA
(Dark green): Other mRNA
13. In the default setting, structures of genes etc. are shown.
14. Main panel for gene structures. If a cluster contains too many members, the number of lanes is limited to 200 and some transcript members are omitted from the display. However, the search system has these omitted transcripts' IDs and brings you to the corresponding locus when you submit the omitted IDs to the search system.
15. Contig. If you place your cursor here, a pop-up menu with a link to DDBJ appears.
16. Repetitive region (see 20)
18. EST support bar. If you check the checkbox for EST (sum), zoom in the view and click "submit!" button, the graphic of EST support bar will appears.
EST support graph (sum):
Both color depth and height indicate the number of aligned EST(s) on the site. The five support levels were defined as follows: a site aligned with one EST is defined as level 1, two aligned is level 2, three or four aligned is level 3, five to nine is level 4, and above ten is level 5. For example, if a site is aligned with ten ESTs, it is represented by the deepest and highest bar.
19. Chromosome map. A thin red line or box indicates the location of the current window. If you click somewhere inside of the chromosome figure, you will go to the location selected.
20. "Sequence viewer" provides the genomic sequence and repetitive regions found on the genome. It also provides the name of repeat sequence. The center of the genome sequence to display can be defined by use window 11
21. The pop-up window for the representative transcript contains:
About predicted gene track "JIGSAW"
These genes were predicted on the human genome (build 36.1), including chromosomes from 1 to 22, and X. except for Y chromosome, mitochondrial chromosome, and random sequence (chr*_random). The H-Inv predicted genes are the first report that utilized Cap Analysis Gene Expression (CAGE) tag (http://genomenetwork.nig.ac.jp/public/contents/description.html) for gene prediction. A position on a chromosome where a CAGE tag is mapped indicates that the position is a transcription start site. Therefore, the down stream regions of the mapped CAGE tags are likely to contain novel genes. For such regions, we predicted genes using three predictors first, (FGENESH, GENSCAN, and HMMgene), then integrated them by JIGSAW program.
A pairwise alignment of each transcript with the genome sequence is available as shown in Fig. 4.3.3.
The multiple alignment of all the locus members (transcripts) and the genome sequence are available. If the number of locus members exceeds 150, this viewer is not available. Please see Fig. 4.3.4 for details.