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The Release Log contains lists of the published tracks and release dates for the current set of genome assemblies available on our site. It also shows version information for the assemblies of other species used in comparative genomics tracks.
Our internal database representations of coordinates always have a zero-based start and a one-based end. We add 1 to the start before displaying coordinates in the Genome Browser. Therefore, they appear as one-based start, one-based end in the graphical display. The refGene.txt file is a database file, and consequently is based on the internal representation.
We use this particular internal representation because it simplifies coordinate arithmetic, i.e. it eliminates the need to add or subtract 1 at every step. If you use a database dump file but would prefer to see the one-based start coordinates, you will always need to add 1 to each start coordinate.
If you submit data to the browser in position format (chr#:##-##), the browser assumes this information is 1-based. If you submit data in any other format (BED (chr# ## ##) or otherwise), the browser will assume it is 0-based. You can see this both in our liftOver utility and in our search bar, by entering the same numbers in position or BED format and observing the results. Similarly, any data returned by the browser in position format is 1-based, while data returned in BED format is 0-based.
For a detailed explanation, please see our blog entry for the UCSC Genome Browser coordinate counting systems.
The gene search results are obtained from scanning the RefSeq and Known Genes tracks, which are typically based on non-redundant relatively high quality mRNAs. A small fraction of RefSeqs are based on DNA level annotations. In most cases, there is a HUGO Gene Nomenclature Committee symbol or other biological name associated with the gene. In the case of the RefSeq track, the association between these names and the accession is maintained at NCBI and is also present in the refLink table.
The mRNA search results are obtained by scanning data associated with the GenBank record for mRNAs. These are often redundant, but occasionally contain something useful that has not yet made it into RefSeq. The mRNA information is often useful because the people who deposited the mRNA into GenBank are listed in the record. Frequently these same people have written interesting articles on the gene or may serve as a source of information on the gene.
Not always. Sometimes the Genome Browser will return more than one location when there are recent duplication or assembly problems in the human genome. In these cases, usually one of the locations will agree with OMIM. In a few rare instances involving not-quite-so-recent duplications in the genome, UCSC will attempt to assign it uniquely, but OMIM will think it belongs someplace just under our threshold. A Blat search of the cDNA is very informative in these cases. In rare cases, UCSC or NCBI may have made a data processing error. For the vast majority of cases, however, the two sites do match.
Check that you are using the same assembly version that you were using yesterday. Features may change positions within a genome between releases, particularly if they are located in an area of the genome that is still in draft form. See Coordinate changes between assemblies for more information.
It's a very good idea to click into the alignment and check that it looks clean at a detailed level and that the splice sites are reasonable. If you have an alternate exon, it is also good to Blat just that exon. Occasionally you may encounter a recent tandem duplication event that encompasses a single exon, which can masquerade as alternative splicing on the graphical display. If it's an EST, check to see if it is from a RAGE library. If so, alternative promoters are likely to be an artifact of the RAGE process rather than biological. If the alternative splice still looks good after these checks, the next step is to do some RT-PCR in the lab.
If you have a protein sequence, you can use Blat to align your sequence to the desired genome. In the ACTIONS column on the Blat search results page, click the details link to view details of exons blocks. Alternatively, click the browser link to display the search results in the Genome Browser. Look for instances in which a gene from the Blat query track aligns exactly or very similarly to an entry in the Known Genes track. Click on the entry to display details about the gene. The SWISS-PROT link on the details page will lead you to more details about this protein.
Follow a similar procedure with an mRNA sequence. If there is no corresponding entry in the Known Genes or RefSeq track, then congratulations, you may have found an unreported new gene. You may want to doublecheck the results using NCBI BLAST.
One of the copies may be an artifactual duplication resulting from unavoidable compromises in the assembly process. However, there do exist very recent authentic duplication events. Frequently these are pericentromeric or subtelomeric.
There are several checks you can make to determine whether you are viewing an actual duplication or an assembly process artifact. Create a Blat track from the gene's mRNA and examine the details page for a match that is too perfect. Then, open the Genome Browser with the duplication and gap tracks set to dense mode. Look for problems in the flanking sequence in the duplication track. Also look for suspicious placement of the gene, for example inside the intron of another gene. You may also want to follow the OMIM link to look for hand-curated experimental literature summaries. BLASTing the mRNA against a more recent assembly may provide another line of evidence.
The UCSC genome browser uses translated mRNA data exactly as supplied to GenBank by the original sequencing authors. Any errors at GenBank propagate through many other databases and tools. To work effectively in a bioinformatic area subject to errors, it is a good idea to seek supporting data for any unusual finding.
To further investigate this example, you may want to use Blat or BLAST to recover other close members of this gene family. By using comparative alignment, you may discover that the 5' UTR in the mRNA for this protein was likely misinterpreted as coding sequence and that the protein begins with methionine as expected. The error may also be caused by an underlying mRNA in GenBank that stops short of the initiator methionine. In this case, you could use ESTs, other mRNAs, and Blat or BLAST of paralogs against unfinished genome sequence to extend the mRNA to a more plausible full-length sequence.
You can accomplish this by using Blat and the Genome Browser Superfamily track. Blat the protein sequence from the NCBI RefSeq record, then choose the choose the Browser display option to view your search results in the Genome Browser window. Set the RefSeq and Superfamily tracks to full display mode. The RefSeq track will contain the entry LIPE, and you will find the corresponding entry ENSP00000244289 in the Superfamily track. Click the Superfamily entry, and then click the Superfamily link on the details page that displays. This will open a browser for the Superfamily site. Click "alpha/beta-Hydrolases" to open the Structural Classification of Proteins (SCOP) page. There you will find multiple families listed under this Superfamily, including the lipase in which you're interested.
These tracks are contributed by institutional programs outside of UCSC. You can access links to their home pages and relevant publications from the description pages associated with the tracks (which can be viewed by clicking on the grey mini-button to the left of the track). You may also obtain supplemental information from the Users Guide and the Credits page. Methods and quality checks are often described in greater detail there. No uniform benchmarking system exists. Finished chromosomes are commonly used, but even here the experimental work continues today on delineating genes.
UCSC does not provide summary statistics for these tracks. However, these may be easily compiled from the appropriate tables in the Table Browser. The number of predicted genes and exons are easily compared. Some quality checks can also easily be run, such as how many of the predicted gene models are incomplete (e.g. the transcription start coordinate is the same as the CDS start).
Looking at almost any coordinate position within the Genome Browser, you can see that there are discrepancies between the predicted gene tracks, as well as further inconsistencies with respect to experimental data tracks such as spliced ESTs. The RefSeq track also contains genes of uncertain status, e.g. lack of initiator methionine. Thus, it is not clear where one can obtain a gold standard for measuring gene prediction quality. A reference set might be hand-curated out of recent journal articles of exceptional thoroughness. UCSC does not currently maintain such a resource.
The varying thickness of features in the Genome Browser gene tracks denotes the various structural features of a gene, such as exons, introns, and untranslated regions (UTRs). The thickest parts of the track indicate the coding exon regions within the gene. The slightly thinner portions at the leading and trailing ends of the gene track show the 5' and 3' UTRs. Introns are depicted as lines with arrows indicating the direction of transcription.
Some aspects of the graphical representation are inevitably lost upon rescaling. For example, coding exons are given preference at coarse scales. For single exon genes, there is no place to put the strand orientation wedges, and therefore the feature's detail page must be consulted.
For more information about annotation track display conventions within the Genome Browser, consult the User's Guide.
The track is defaulting to dense display mode because the size of the track's displayed region is too large. Unfortunately, this particular track doesn't have good visual cues to show you when it's defaulting to dense mode. If you zoom in on the region in which you're having the problem, you should be able to display the details page.
When the second character in the strand is "-", the coordinates of the comma-separated list of tStarts are reverse-complemented relative to tStart, much as qStarts behave when the first letter in the strand is "-".
Your guess is correct. We haven't gotten around to fixing this situation. A while ago, the Twinscan group made a GTF validator. It interpreted the stop codon as not part of the coding region. Prior to that, all GFF and GTF annotations that we received did include the stop codon as part of the coding region; therefore, we didn't have special code in our database to enforce it. In response to the validator, Ensembl, SGP and Geneid switched their handling of stop codons to the way that Twinscan does it, hence the discrepancy.
You can find further information about a specific clone by clicking on the clone name link on the details page for the item. This links to the NCBI Clone Registry website, which lists extensive details about the clone, including distributor information.
This information can be found in the "gap" database table. Use the Table Browser to
extract it. To do this, select your assembly and the gap table, then click the "
filter Create" button. Set the "type" field to centromere telomere
(separated by a space). For help using the Table Browser, visit the
User's Guide.
Each annotation track in the Genome Browser has one or more database tables associated with it. To find the name of the primary table, navigate to the schema page. You will find the schema page by pressing the "mini-button" to the left of the annotation track display, or clicking the hyper-linked track name in the track controls (below the display). From the resulting description page, follow the "View table schema" link. Finally, on the schema page, you will find the name of the database table near the top of the page listed after the "Primary Table" label.
Historically, NCBI RefSeq coordinates were not directly available for building tracks in the UCSC Genome Brower. Instead of using coordinates to map annotations, mappings to the reference assembly were conducted using BLAT (BLAST-like alignment tool) alignment methods. This BLAT alignment method has caused some discrepancies from the NCBI RefSeq database. Most discrepancies arise when the BLAT-generated annotations align to multiple regions where the sequence in the assembly is either identical or nearly identical. In essence, by using BLAT to align the sequence, a single transcript could result in matching to multiple novel places across the genome, or alignments of small exons could differ slightly in final coordinates within the region of a gene rich with repeats. BLAT-generated RefSeq track methods are described in corresponding track description pages (e.g., RefSeq track description for hg19).
In 2017, NCBI RefSeq coordinates for hg38 were used for generating non-discrepant RefSeq tracks in the UCSC Genome Browser. This new NCBI RefSeq track in the UCSC Genome Browser displays identical RNA coordinates to annotations in the NCBI Reference Sequence Database. Please note that when annotations do map to multiple loci, the NCBI RefSeq track displays unique identifiers for each locus, while the UCSC RefSeq track retains the same identifier.
For more information and future plans to integrate coordinate-generated NCBI RefSeq tracks for other assemblies, please see the NCBI RefSeq track blog post.