First Genome drafts based the Human-Mouse conserved Synteny Regions/Genes/Alignments
webmaster at softberry.com
webmaster at softberry.com
Fri Apr 5 20:06:00 EST 2002
Human-Mouse Homology chromosome regions and genes
First Genome drafts based the Human-Mouse conserved Synteny
Softberry Inc. developed Human-Mouse Synteny server which provide information
about 18915 Human genes mapped to Mouse genome draft and 18464 Mouse genes
mapped to Human genome draft (among them 14504 ortologous gene pairs).
This is the most comprehensive data about Homology between Human and Mouse
genomic Regions comparing with NCBI homology maps, which contain significantly
less genes and often do not connect directly with draft genomic sequences Human
and Mouse. The data was received by proprietary Softberry programs for gene
prediction, est/RNA mapping and gemomic sequence comparison (some you can test
on line at www.softberry.com).
Genes included in this annotation are from three groups: (m) having 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
(Human and Mouse, respectively): http://genome.cse.ucsc.edu/index.html and in
Genome Explorer Java Browsers at Softberry Inc. servers: Human:
http://www.softberry.com/berry.phtml?topic=genomexp Mouse: http://p69-
The server http://www.softberry.ru/berry.phtml?topic=human-mouse
provides a list of Synteny Regions for each (Human/Mouse) chromosome when you
click on chromosome number (Y chromosome of mouse is absent in draft) and
coordinates of each region on Human (December01 release) and Mouse (November01
release) draft sequences.
For each syntenic region you can click on Genes link and see what orthologous
genes are found in it (some genes in these regions might have no corresponding
It is a good hint that ABSENT mouse/human gene is their, but due to incomplete
and imperfect genome sequence (especially for MOUSE) it is currently do not
mapped/known in genome.
You can GET ALIGNMENT on line by clicking [A] link or ALIGNMENT with
Visualization [AV] (produced instantly by Softberry SCAN2 genomic alignment
tool http://www.softberry.ru/berry.phtml?topic=scanh&prg=SCAN2 ). In DBSCAN
JAVA viewer you can PUSH left mous button AND DRAG MOUSE around any part of
BLOCKS in the top panel and you will see the ALIGNMENT in the middle viewer
Remember that usually longer alignment blocks (> 80 bp) corresponding to coding
exons (with similarity 85-95%) and there are a lot of short similar block
between them often corresponding to short simple sequences.
You can see genes coordinates and their short descriptions by clicking Genes
link for each syntenic region (more info about genes see in mentioned above
Genome Browsers), which will be linked directly with genes shown in syntenic
regions (in the future).
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