The
AceView genes
last updated October 16, 2012
March 6, 2008: we added
downloadable files mapping microarray probes from commercial microarrays to
AceView, RefSeq and Ensembl transcripts as well as to the genome.
June 30th, 2007: New and enhanced releases of the Human,
Mouse Arabidopsis and C. elegans genes, with more in depth biological and
molecular annotation, using GenBank/dbEST/Trace cDNA data from March 26th, 2007
for human and June 22, 2007 for mouse have been made public…
AceView provides a curated,
comprehensive and non-redundant sequence representation of all public mRNA
sequences (mRNAs from GenBank or RefSeq, and single pass cDNA sequences from
dbEST and Trace). These experimental cDNA sequences
are first co-aligned on the genome then clustered into a minimal number of alternative transcript variants and grouped into genes. Using exhaustively and with high
quality standards the available cDNA sequences evidences the beauty and
complexity of mammals’ transcriptome, and the relative simplicity of the
nematode and plant transcriptomes. Genes are classified according to their
inferred coding potential; many presumably non-coding genes are discovered.
Genes are named by Entrez Gene names when available, else by AceView gene names,
stable from release to release.
Alternative features (promoters,
introns and exons, polyadenylation signals) and coding potential, including motifs,
domains, and homologies are annotated in depth; tissues where expression has
been observed are listed in order of representation; diseases,
phenotypes, pathways, functions, localization or interactions are annotated by
mining selected sources, in particular PubMed, GAD and Entrez Gene, and also by
performing manual annotation, especially in the worm.
In this way, both the anatomy and
physiology of the experimentally cDNA supported human, mouse and nematode genes
are thoroughly annotated.
Our goals are to offer an
up-to-date resource on the genes, in the hope to stimulate further experiments
at the bench, or to help medical research.
AceView
can be queried by
meaningful words or groups of words as well
as by most standard identifiers, such as gene names, Entrez Gene ID, UniGene ID,
GenBank accessions.
This work is in continuous
development, please send us your wishes,
comments, and bug reports.
If you wish to receive an
announcement when we update the data on the site, please mail us.
To
learn more about AceView, you may enjoy these documents:
·
Danielle Thierry-Mieg and Jean Thierry-Mieg, AceView: a comprehensive
cDNA-supported gene and transcripts annotation, Genome Biology 2006, 7(Suppl
1):S12
·
About AceView: Overview
, News and recent
improvements; release statistics; special notes on Worm, Development corner, About history of Acembly/AceView, acknowledgements
To
get help, please see these:
·
Frequently asked questions (updated Sept 13, 2005)
·
Help on the three ways to query
AceView
·
Help with texts, tables, displays:
o the “Gene on Genome” page
(updated July, 2007)
o the“Annotated mRNA” page
(updated May 2006)
To
link to AceView, cite us , Download sequence data, Register on the AceView list