This list shows all tables associated with the track specified in the track list. Some tables may be unavailable due to the data provider's restrictions on sharing. Select genome to apply the query to the entire genome not available for certain tracks with restrictions on data sharing.
To limit the query to a specific position, type a chromosome name, e. You can select multiple genomic regions by clicking the "define regions" button and entering up to 1, regions in a 3- or 4-field BED file format. If no identifiers are entered, all table data within the specified region will be displayed. Click the Create button to add a filter, the Edit button to modify an existing filter, or the Clear button to remove an existing filter.
The intersection can be configured to retain the existing alignment structure of the table with a specified amount of overlap, or discard the structure in favor of a simple list of position ranges using a base-pair intersection or union of the two data sets.
The button functionalities are similar to those of the filter option. Formats include: all fields from selected table - data from the selected table displayed in a tab-separated format suitable for import into spreadsheets and relational databases. BED - positions of data items in a standard UCSC Browser format with the name column containing exon information separated by underscores. Output sequence can be in either nucleotide-space or translated to protein-space. Multiple alignments of 8 vertebrate genomes with Marmoset Conservation scores for alignments of 8 vertebrate genomes with Marmoset.
Multiple alignments of 4 vertebrate genomes with Medaka Conservation scores for alignments of 4 vertebrate genomes with Medaka. Multiple alignments of 6 vertebrate genomes with the Medium ground finch Conservation scores for alignments of 6 vertebrate genomes with the Medium ground finch Basewise conservation scores phyloP of 6 vertebrate genomes with the Medium ground finch. Multiple alignments of 59 vertebrate genomes with Mouse Conservation scores for alignments of 59 vertebrate genomes with Mouse Basewise conservation scores phyloP of 59 vertebrate genomes with Mouse FASTA alignments of 59 vertebrate genomes with Mouse for CDS regions.
GRCm38 Patch 6 - Sequence files. Multiple alignments of 29 vertebrate genomes with Mouse Conservation scores for alignments of 29 vertebrate genomes with Mouse Basewise conservation scores phyloP of 29 vertebrate genomes with Mouse FASTA alignments of 29 vertebrate genomes with Mouse for CDS regions.
Multiple alignments of 16 vertebrate genomes with Mouse Conservation scores for alignments of 16 vertebrate genomes with Mouse. Multiple alignments of 9 vertebrate genomes with Mouse Conservation scores for alignments of 9 vertebrate genomes with Mouse.
Multiple alignments of 4 vertebrate genomes with Mouse Conservation scores for alignments of 4 vertebrate genomes with Mouse. Multiple alignments of 8 vertebrate genomes with Opossum Conservation scores for alignments of 8 vertebrate genomes with Opossum.
Multiple alignments of 6 vertebrate genomes with Opossum Conservation scores for alignments of 6 vertebrate genomes with Opossum. Multiple alignments of 7 vertebrate genomes with Orangutan Conservation scores for alignments of 7 vertebrate genomes with Orangutan.
Multiple alignments of 5 vertebrate genomes with Platypus Conservation scores for alignments of 5 vertebrate genomes with Platypus. Multiple alignments of 19 vertebrate genomes with Rat Conservation scores for alignments of 19 vertebrate genomes with Rat Basewise conservation scores phyloP of 19 vertebrate genomes with Rat FASTA alignments of 19 vertebrate genomes with Rat. Multiple alignments of 12 vertebrate genomes with Rat Conservation scores for alignments of 12 vertebrate genomes with Rat Basewise conservation scores phyloP of 12 vertebrate genomes with Rat.
Multiple alignments of 8 vertebrate genomes with Rat Conservation scores for alignments of 8 vertebrate genomes with Rat. Multiple alignments of 8 vertebrate genomes with Stickleback Conservation scores for alignments of 8 vertebrate genomes with Stickleback.
Multiple alignments of 19 mammalian 16 primate genomes with Tariser Conservation scores for alignments of 19 mammalian 16 primate genomes with Tarsier Basewise conservation scores phyloP of 19 mammalian 16 primate genomes with Tarsier FASTA alignments of 19 mammalian 16 primate genomes with Tarsier for CDS regions. Multiple alignments of 10 vertebrate genomes with X. Multiple alignments of 8 vertebrate genomes with X. Multiple alignments of 6 vertebrate genomes with X.
Multiple alignments of 4 vertebrate genomes with X. Multiple alignments of 7 genomes with Zebrafish Conservation scores for alignments of 7 genomes with Zebrafish Basewise conservation scores phyloP of 7 genomes with Zebrafish. Tropicalis xenTro2. Multiple alignments of 5 vertebrate genomes with Zebrafish Conservation scores for alignments of 5 vertebrate genomes with Zebrafish.
Multiple alignments of 6 vertebrate genomes with Zebrafish Conservation scores for alignments of 6 vertebrate genomes with Zebrafish. Multiple alignments of 4 vertebrate genomes with Zebrafish Conservation scores for alignments of 4 vertebrate genomes with Zebrafish. Multiple alignments of 26 insects with D.
The Convert utility, which is accessed from the View menu on the Genome Browser annotation tracks page, supports forward, reverse, and cross-species conversions, but does not accept batch input.
The LiftOver tool, accessed via the Tools link on the Genome Browser home page, also supports forward, reverse, and cross-species conversions, as well as batch conversions. If you wish to update a large number of coordinates to a different assembly and have access to a Linux platform, you may find it useful to try the command-line version of the LiftOver tool.
The executable file for this utility can be downloaded here. LiftOver requires a pre-generated over. If the desired file is not available, send a request to the genome mailing list and we may be able to provide you with one.
For the Known Genes, use the kgAlias table. To obtain a complete copy of the entire Known Genes data set for an organism, open the Genome Browser Downloads page , jump to the section specific to the organism, click the Annotation database link in that section, then click the link for the knownGene.
Set the position to the region of interest, then click the "get output" button. UCSC uses the latest versions of RepeatMasker and repeat libraries available on the date when the assembly data is processed.
Masking is done using the RepeatMasker -s flag. For mouse repeats, we also use -m. In addition to RepeatMasker, we use the Tandem Repeat Finder trf program, masking out repeats of period 12 or less. The repeats are just "soft" masked. Alignments are allowed to extend through repeats, but not initiate in them. Yes, you can obtain the repeat-masked files via the Table Browser or from the organism's annotation database downloads directory.
UCSC occasionally uses updated versions of the RepeatMasker software and repeat libraries that are not yet available on the RepeatMasker website see Repeat-masking data for more information. The Genome Browser downloads site provides prepackaged downloads of bp, bp, and bp upstream sequence for RefSeq genes that have a coding portion and annotated 5' and 3' UTRs.
You can obtain these from the bigZips downloads directory for the assembly of interest. To fetch the upstream sequence for a specific gene, use the Table Browser. Enter the genome, assembly, and select the knownGene table. Paste the gene name or accession number in the identifier field. Choose sequence for the output format type, then click the get output button. On the next page, select genomic. On the final page, you will have the opportunity to configure the amount of upstream promoter sequence to fetch, along with several other options.
Click Get Sequence when you've finished configuring the output. You can also use the Genome Browser to obtain sequence for a specific gene. Open the Genome Browser window to display the gene in which you're interested. Alternatively, you can click the DNA link in the top menu bar of the Genome Browser tracks window to access options for displaying the sequence. The conservation score data are stored in a group of tables in the annotation database downloads directory.
The naming conventions of the tables vary among releases. Is this alignment on the minus strand? Minus strand coordinates in axt files are handled differently from how they are handled in the Genome Browser. To convert axt minus strand coordinates to Genome Browser coordinates, use:. See an explanation of coordinate transforms in the genomeWiki. To determine the location of a specific marker, look up the marker's name in the stsAlias table to determine the UCSC ID assigned to the marker, and then use this ID to look it up in the stsMap table where the marker is located.
You can obtain this information from the combination of a couple of tables. This file also contains information about the position on the genome-wide maps, including the deCODE map. A second file, stsInfo2, contains additional information about each marker, including aliases, primer sequence information, etc.
This table is related to the first table by an ID the identNo field in both files. The fourth column of the BED output contains a lot of information separated by underscores.
For example:. The raw data underlying a track can be explored interactively with the Table Browser , Data Integrator , or Variant Annotation Integrator. Instructions for downloading source code and binaries can be found here. The tool can also be used to obtain only features within a given range using one of the hgdownload servers, example:. Read more in our blog about Accessing the Genome Browser Programmatically to acquire data.
How do I download dbSNP data? For versions dbSNP and above, the data is formatted in bigBed files. Previous versions are MySQL tables. For automated analysis, the track data files can be downloaded from the downloads server for hg19 and hg Below are specific examples for dbSNP , however, the same methods and directories will work by substituting a more recent dbSNP release.
Several utilities for working with bigBed-formatted binary files can be downloaded here. Run a utility with no arguments in order to see a brief description of the utility and its options.
With the -as option, the output includes an autoSql definition of data columns, useful for interpreting the column values. Output can be restricted to a particular region by using the -chrom, -start and -end options.
See our searchable mailing list archives for more information and example queries. We also have information on our blog about Accessing the Genome Browser Programmatically to acquire data. When using the SNP tracks, some records may contain information about one or more alleles instead of the usual two alleles for the SNP.
The following information should explain how this is possible. For simplicity, GTF files have been generated using the genePredToGtf method described above and are available on our download server for the main gene transcript sets. For example, the hg38 GTF files.
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