Human-Mouse-Rat Synteny: Homology chromosome regions alignments and genes

Softberry Team softberry at softberry.com
Thu Jan 23 04:11:48 EST 2003


Human-Mouse-Rat Synteny: Homology chromosome regions, alignments and genes

We present Human-Mouse, Human-Rat and Rat-Mouse synteny alignments based on
annotated genes in their draft genomic
sequences:
http://www.softberry.com/berry.phtml?topic=human-mouse&prg=none
http://www.softberry.com/berry.phtml?topic=human-rat&prg=none
http://www.softberry.com/berry.phtml?topic=rat-mouse&prg=none

This server provides information about ~4000 syntenic chromosome regions
between each genome pairs.
These regions contain ~19000 human genes mapped to Mouse genome, ~17000
Human
genes mapped to Rat genome, and
~19000 genes of Mouse mapped to Rat genome and vice versa.

So far, this is the most comprehensive collection of information about
homology between human, mouse and rat genomic
regions. Compared to NCBI homology maps, Softberry map contains
significantly
more genes and is directly linked
to genomic sequences. The data were generated by Softberry programs for gene
prediction, EST/RNA mapping
and genomic sequence comparison - some of them can be tested at this site.

Genes included in this annotation can be divided into three groups: (m) have
known mRNA from Refseq database,
(h) predicted and supported by protein homolog from NR database, and (a) ab
initio predicted. All these genes
(Fgenesh++ gene sets) are presented in the UCSC Genome Browser
(http://genome.ucsc.edu/) - and in Genome Explorer
Java Browsers at Softberry (http://www.softberry.com/berry.phtml) for Human,
Mouse and Rat.

Softberry synteny server  shows a list of synteny regions for each
(human/mouse/rat) chromosome and coordinates of
each region on Human (November 02 release), Mouse (February 02 release) and
Rat (November 02) draft sequences
when chromosome number is clicked (mouse and rat Y chromosome is currently
absent in genome draft).

For each syntenic region, you can click on Genes link and see which
orthologous genes are found for it. Some genes
in these regions might have no corresponding pair known. It is a good hint
that ABSENT mouse/human/rat gene is there,
but due to incomplete and imperfect genome sequences, especially for mouse,
it
is currently not mapped/known in genome.

You can GET ALIGNMENT on-line by clicking [A] link or ALIGNMENT with
Visualization by clicking [AV] link.
Alignment is produced instantly by Softberry SCAN2 genomic alignment tools.
In
a viewer, you can use left mouse
button to drag around any part of blocks in the top panel to see sequence
alignment in the middle viewer panel.
You can increase resolution of a particular region by reducing/increasing
size
of coordinates bar and moving it
along the sequence coordinates.

Remember that usually longer alignment blocks (>80 bp) correspond to coding
exons with similarity 85-95%,
and there are a lot of short similarity block between them, which often
correspond to short simple sequences.

You can see coordinates of genes, and genes' short descriptions, by clicking
Genes link for each syntenic region.
More info about genes can be obtained in Genome Explorer Browser, which is
linked directly to genes
shown in syntenic regions (click [GE]).

If you have your protein/mRNA sequence and want to see what synteny region
it
belong, then you can BLAST your sequence
against Fgenesh++ annotated genes for Human, Mouse and Rat genomes at

http://www.softberry.com/berry.phtml?topic=scanh&prg=BLAST

After that you can check the synteny region for proteins found
similar/identical with your sequence.
The Blast results have chromosome coordinates and gene names that can be
used
to search
corresponding synteny page and see syntenic regions.

Example of Blast search:

Sequences producing significant alignments:                        (bits)
Value

C2001912 chr2 3 exon (s) 131715145 - 131691265 ORF: 261 - 686 o...   300
5e-82
C8001597 chr8 3 exon (s) 143995318 - 143996938 ORF: 18 - 389 or...    44
9e-05

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