Locus Not Found
Sorry, but we could not find any gene matching --LOC55871 -- in the AceView system. Some possible problems and run-arounds are:
- Did you choose the correct species?
The human, worm and arabidopsis genes are in separate databases: select from the second pull down menu, to the left of the main AceView page.
- We did not recognize what you asked for, please try another identifier.
There are many alias names, names may change, we may know this gene under another name, and despite our efforts to track gene names (see the FAQ), a gene name from the previous build may not be recognized. But AceView should recognize a number of other NCBI identifiers that point to the gene: LocusLink/GeneID, GenBank mRNA or EST accession, RefSeq accession, OMIM accession, or Unigene cluster name Hs.#. You might also try a cDNA clone name, or a functional or descriptive name. If you are interested by function, try the “Pfam query”. But please do NOT look for a gi number, a protein or NP accession, an STS marker name (go to LocusLink then back to us), an older AceView name (e.g. Hs11_34081_29_1_661, only archived on our ftp site), a WormPep accession, an NT contig or a genomic sequence accession since these queries are not supported in AceView. We do not yet support either queries by chromosome or by region. If you are interested in IGH@, IGK@, IGL@, TRB@ or TRG@, call for one gene in the region, click on the graphic "Full page" and zoom out from there (left icon) to see the whole area.
- Please remain concise in your queries: we do not search for partial matches and do not ignore spelling mistakes, like Google does. All you typed had to be found in the same gene entry. So, type the minimal number of words or word roots that translate your thought.
- Are you sure you spelt your word(s) correctly?
The character case does not matter (BRCA1 == brca1 == BrCa1) but we do not look for approximate matches: spelling mistakes are deadly. We extend what you typed (with any character) until we find a match (see the help on query), so, for best results, avoid useless constraints: type only the roots of meaningful words that undoubtedly should be found in your gene. If you are unsure of the spelling, type only what you are sure of: prefer lecit choleste to lecitin cholestelol and phosphor (hardly ambiguous in fact) to phosphorilation. When in doubt, prefer a space or a question mark to an uncertain character. Prefer singular to plural (e.g. use claudin rather than claudins) and avoid using dashes or dots in names unless strictly necessary. For example, NF kappa b, NFkappaB or NF-KB will not give the same answers: in human build 33, you get 205 genes for the first query, 13 for the second and 11 for the third. Keep spaces between words as usual: RNA pol III is more frequently used than RNApolIII, ubiquitin1 will not be recognized.
- If you come directly from LocusLink/Gene, or were interested in a gene associated to a disease
it is possible that we did not succeed yet in mapping the sequence(s) associated to the locus unambiguously, or that this locus has no associated sequence because it has not been cloned yet. In this case, OMIM or LocusLink would be more informative: AceView is only a complementary sequence oriented view. In the top ‘Query’ box, search “All databases” at NCBI, or “OMIM”, or “LocusLink/Gene”.
- If you found nothing with a short query
and no spelling mistake, we apologize, and suggest that you try one of the two other ways to query AceView: through PFAM or through Blast. Some words, such as actin (also found in acting and interacting) or transcription factor, are so frequent in the literature that our indexing system gets saturated, and you get no answer.
If you are interested by homologs of a gene from another species (like for example NF Kappa B), you will get your answer, complete and quantified, by entering the sequence from your favorite gene in the "query AceView via Blast" that we provide (thanks to S. Altschul and the Blast team).
If you asked for a DNA sequence, such as an oligonucleotide, directly in the query box, this will unfortunately not bring an answer. Sorry, we do not yet provide a direct AceView align service. Please try the “Blast” query in the left margin, it will align your DNA or protein against all the AceView transcripts in the selected species
If you are interested by genes belonging to a well known family, or that have a known function
your best chances are to use the "query Pfam" on the left. Here again you will benefit from the work of the Pfam and InterPro teams, world experts in defining, recognizing, and describing conserved families of proteins. We have just run their programs (slow and heavy) on all the AceView transcripts and have compiled the data for you, so that you get complete answers over the entire genome fast.
- If you requested a particular mRNA variant by name and suffix (a, b or c)
from a previous build and got no answer, this is expected. From the December 03 release on, mRNA variants have a unique identifier, to avoid confusion of having objects with different sequences named the same in successive versions of AceView. And we do not have room to maintain more than the last two builds on our server. Archives may be available from Jim Kent, at UCSC.
You are welcome to report problems or ask for help. We would be happy to try to fix any reproducible bug as well as to add desirable features.