On the configuration page of this track, you can choose to hide any TrEMBL annotations. < uniprot | This filter will also hide the UniProt alternative isoform protein sequences because < uniprot | both types of information are less relevant to most users. Please contact us if you < uniprot | want more detailed filtering features.
< uniprot | < uniprot |Note that for the human hg38 assembly and SwissProt annotations, there --- > uniprot |
Note that only for the human hg38 assembly and SwissProt annotations, there 1242c1234 < uniprot | href="hgTracks?db=hg38&hubUrl=https://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/genome_annotation_tracks/UP000005640_9606_hub/hub.txt" target=_blank>public --- > uniprot | href="hgTracks?db=hg38&hubUrl=ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/genome_annotation_tracks/UP000005640_9606_hub/hub.txt">public 1246,1248c1238 < uniprot | for a given protein. For proteins that differ from the genome, UniProt's mapping method < uniprot | will, in most cases, map a protein and its annotations to an unexpected location < uniprot | (see below for details on UCSC's mapping method).
--- > uniprot | for a given protein. 1253,1311c1243,1245 < uniprot | Briefly, UniProt protein sequences were aligned to the transcripts associated < uniprot | with the protein, the top-scoring alignments were retained, and the result was < uniprot | projected to the genome through a transcript-to-genome alignment. < uniprot | Depending on the genome, the transcript-genome alignments was either < uniprot | provided by the source database (NBCI RefSeq), created at UCSC (UCSC RefSeq) or < uniprot | derived from the transcripts (Ensembl/Augustus). The transcript set is NCBI < uniprot | RefSeq for hg38, UCSC RefSeq for hg19 (due to alt/fix haplotype misplacements < uniprot | in the NCBI RefSeq set on hg19). For other genomes, RefSeq, Ensembl and Augustus < uniprot | are tried, in this order. The resulting protein-genome alignments of this process < uniprot | are available in the file formats for liftOver or pslMap from our data archive < uniprot | (see "Data Access" section below). < uniprot | < uniprot | < uniprot |An important step of the mapping process is filtering the alignment from < uniprot | protein to transcript. Due to differences between the UniProt proteins and the < uniprot | transcripts and the genome, the best matching transcript is not always the < uniprot | correct transcript. Therefore, only for organisms that have a RefSeq transcript track, < uniprot | proteins are only aligned to the RefSeq transcripts that are annotated < uniprot | by UniProt for this protein. If no transcripts are annotated on the protein, or < uniprot | the annotated ones do not exist anymore, but a NCBI Gene ID is annotated, < uniprot | the RefSeq transcripts for the gene are used. If no NCBI Gene is annotated, < uniprot | then the best matching alignment is used. Only a handful of edge cases < uniprot | (pseudogenes, very recently added proteins) on hg38 remain where the < uniprot | global transcriptome-wide matches have to be used. The details page of the < uniprot | protein alignments shows the transcripts used for the mapping and how < uniprot | these transcripts were found. There can be multiple transcripts for one < uniprot | protein, as their coding sequences can be identical or several of them do < uniprot | not differ by more than 1% in alignment score. < uniprot |
< uniprot | < uniprot |In other words, when an NCBI or UCSC RefSeq track is used for the mapping and to align a < uniprot | protein sequence to the correct transcript, we use a three stage process: < uniprot |
This system was designed to resolve the problem of incorrect mappings of < uniprot | proteins, mostly on hg38, due to differences between the SwissProt < uniprot | sequences and the genome reference sequence, which has changed since the < uniprot | proteins were defined. The problem is most pronounced for gene families < uniprot | composed of either very repetitive or very similar proteins. To make sure that < uniprot | the alignments always go to the best chromosome location, all _alt and _fix < uniprot | reference patch sequences are ignored for the alignment, so the patches are < uniprot | entirely free of UniProt annotations. Please contact us if you have feedback on < uniprot | this process or example edge cases. We are not aware of a way to evaluate the < uniprot | results completely and in an automated manner.
< uniprot |< uniprot | Proteins were aligned to transcripts with TBLASTN, converted to PSL, filtered < uniprot | with pslReps (93% query coverage, keep alignments within top 1% score), lifted to genome < uniprot | positions with pslMap and filtered again with pslReps. UniProt annotations were --- > uniprot | UniProt sequences were aligned to one of UCSC, Gencode, Ensembl or Augustus transcript sequences, first with > uniprot | BLAT, filtered with pslReps (93% query coverage, within top 1% score), lifted > uniprot | to genome positions with pslMap and filtered again. UniProt annotations were 1313c1247 < uniprot | genome through the alignment described above using the pslMap program. This approach --- > uniprot | genome through the alignment using the pslMap program. This mapping approach 1315,1318c1249,1253 < uniprot | TARGET="_BLANK">LS-SNP pipeline by Mark Diekhans. < uniprot | Like all Genome Browser source code, the main script used to build this track < uniprot | can be found on Github. --- > uniprot | TARGET="_BLANK">LS-SNP pipeline by Mark Diekhans. For human and mouse, the > uniprot | alignments were filtered by retaining only proteins annotated with > uniprot | a given transcript in the Genome Browser table kgXref. Like all Genome Browser > uniprot | source code, the main script used to build this track can be found on > uniprot | github. 1321,1344d1255 < uniprot |
< uniprot | This track is automatically updated on an ongoing basis, every 2-3 months. < uniprot | The current version is always shown on the track details page, it includes the < uniprot | release of UniProt, the version of the transcript set and a unique MD5 that is < uniprot | based on the protein sequences, the transcript sequences, the mapping file < uniprot | between both and the transcript-genome alignment. The exact transcript < uniprot | that was used for the alignment is shown when clicking a protein alignment < uniprot | in one of the two alignment tracks. < uniprot |
< uniprot | < uniprot |< uniprot | For reproducibility of older analysis results, previous versions of this track < uniprot | are available for browsing in the form of the UCSC UniProt Archive Track Hub. The underlying data of < uniprot | all releases of this track (past and current) can be obtained from our downloads server, including the UniProt < uniprot | protein-to-genome alignment. The file formats available are in the < uniprot | command line programs liftOver or pslMap, which can be used to map < uniprot | coordinates on protein sequences to genome coordinates. The filenames are < uniprot | unipToGenome.over.chain.gz (liftOver) and unipToGenomeLift.psl.gz (pslMap).
< uniprot | 1348c1259 < uniprot | The raw data of the current track can be explored interactively with the --- > uniprot | The raw data can be explored interactively with the 1355c1266 < uniprot | track configuration file. --- > uniprot | track configuration file. 1361c1272 < uniprot |
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< uniprot | 1376,1378c1290,1292 < uniprot | This track was created by Maximilian Haeussler at UCSC, with a lot of input from Chris < uniprot | Lee, Mark Diekhans and Brian Raney, feedback from the UniProt staff, Alejo < uniprot | Mujica, Regeneron Pharmaceuticals and Pia Riestra, GeneDx. Thanks to UniProt for making all data --- > uniprot | This track was created by Maximilian Haeussler at UCSC, with help from Chris > uniprot | Lee, Mark Diekhans and Brian Raney, feedback from the UniProt staff and Alejo > uniprot | Mujica, Regeneron Pharmaceuticals. Thanks to UniProt for making all data