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4.3 G-integra

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.

  1. Graphically displaying the gene locations of the primates and the rodents etc. with their exon-intron structure and protein-coding regions.
  2. Comparing results of EST mapping, inter-species mapping, and predicted genes.
  3. Some genome annotation is available. For example, annotation of repetitive elements on the genome is provided from "sequence viewer". DDBJ accession numbers (and external hyperlinks to DDBJ) of genomic contigs are also available in their pop-up menu.
  4. A popup menu will appear if you mouse on an object alongside of genomic sequence. The pop-up menu provides much detailed information, such as mapping results (%ID and %Cov). This menu also provides internal ( H-InvDB ) and external links to other web sites (DDBJ etc.).
  5. The "Alignment viewer" provides sequence alignments of cDNA and genome. The link to the viewer can be found on some pop-up menus.
  6. ID search using locus IDs or transcript IDs is also available.

Access to G-integra

Top page : http://h-invitational.jp/hinv/g-integra/

H-InvDB has four ways of accessing G-integra.

Fig. 4.3.1 Four entrances to G-integra.
  1. Clickable chromosome map
  2. G-integra icon on common frame on Transcript/Locus view.
  3. G-integra icon. This icon can be seen elsewhere.
  4. Mini G-integra.

    G-integra icon g_inte_button.gif

4.3.1 Main parts and functions of G-integra

Fig.4.3.2 Summary of 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
(Blue): RefSeq
(Orange): Ensembl

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)
17. SNPs
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:

  1. Cluster ID (HIX)
  2. Transcript ID (HIT), ACC#
  3. "Representative transcript"
  4. Definition
  5. Aligned region of genome (Length of aligned region).
  6. Aligned region of transcript.
  7. Number of exon
  8. %ID of transcript-genome alignment
  9. %ID of each exon
  10. %Coverage
  11. Link to Transcript view in H-InvDB
  12. Link to Locus view in H-InvDB
  13. Link to DDBJ or RefSeq, Ensembl
  14. Link to H-ANGEL
  15. Link to H-GOLD
  16. Link to cDNA-genome pairwise alignment
  17. Link to cDNA-genome multiple alignment
  18. Link to Evola
  19. Ortholog candidate and ACC# with link to physical map
22. The pop-up menu for a non-representative transcript contains:
  1. Cluster ID (HIX)
  2. Transcript ID (HIT) , ACC#
  3. Aligned region of genome (Length of aligned region).
  4. Aligned region of transcript.
  5. Number of exon
  6. %ID of transcript-genome alignment
  7. %ID of each exon
  8. %Coverage
  9. Link to transcript view in H-InvDB
  10. Link to locus view in H-InvDB
  11. Link to DDBJ or RefSeq, Ensembl
  12. Link to cDNA-genome pairwise alignment
  13. Link to transcript-genome multiple alignment
23. The cDNA-genome pairwise alignment. Details of this viewer are described in section 4.3.2
24. The cDNA-genome multiple alignment. Details are shown in section 4.3.3.

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.

4.3.2 cDNA-genome pairwise alignment

A pairwise alignment of each transcript with the genome sequence is available as shown in Fig. 4.3.3.

Fig. 4.3.3 The cDNA-genome pairwise alignment

4.3.3 cDNA-genome multiple alignment

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.

Fig. 4.3.4 cDNA-genome multiple alignment
Revised: December 26, 2007