--------------------------------------------------------------- calJac4.trackDb.html : Differences exist between hgwbeta and hgw2 (RR fields taken from public MySql server, not individual machine) 111,313d110 < catV2 | html < catV2 |

Description

< catV2 | < catV2 |

< catV2 | This track represents the gene models for the Marmoset assembly, calJac4, generated using Comparative Annotation Toolkit (CAT). < catV2 |

< catV2 |

< catV2 | CAT can be found on GitHub: https://github.com/ComparativeGenomicsToolkit/Comparative-Annotation-Toolkit < catV2 |

< catV2 | < catV2 |

Display Conventions and Configuration

< catV2 | < catV2 |

< catV2 | This track follows the display conventions for gene prediction tracks. The exons for putative non-coding genes and untranslated regions are represented by relatively thin blocks, while those for coding open reading frames are thicker. Gene names are displayed in 'pack' or 'full' mode. More information about each gene can be found by clicking on the specific gene/transcript model. < catV2 |

< catV2 | < catV2 |

< catV2 | The following color key is used: < catV2 |

< catV2 |

Blue: protein coding < catV2 |
Green: non-coding < catV2 |
Purple: novel predictions from augCGP/augPB < catV2 |

< catV2 | < catV2 |

< catV2 | The following metadata is available by clicking on the transcript. < catV2 |

< catV2 |

Gene name: gene symbolic name < catV2 |
Status of CDS start annotation: is the start of the CDS fully annotated < catV2 |
Status of CDS end annotation: is the end of the CDS fully annotated < catV2 |
Exon frame: comma-separate list of per-exon frames, 0,1,2, or -1 if no frame for an exon < catV2 |
Transcript ID: CAT assigned unique transcript id < catV2 |
Transcript type: type of transcript < catV2 |
Gene ID: CAT assigned unique gene id < catV2 |
Gene type: type of gene < catV2 |
Source gene ID: source GENCODE gene id < catV2 |
Source transcript ID: source GENCODE transcript id < catV2 |
Alignment ID: unique alignment id for TransMap based transcripts < catV2 |
Alternative source transcripts: ??? < catV2 |
Paralogous alignment IDs: comma separated list of alignments identified as possible paralogs for this transcript < catV2 |
Unfiltered paralogous alignment IDs: paralogous alignments before filtering < catV2 |
Collapsed Gene IDs: if this gene was a part of a gene family collapse, this field reports the of identifiers of the genes collapsed together < catV2 |
Collapsed Gene Names: common names of the collapsed genes < catV2 |
Frameshifted relative to source?: is the transcript frameshifted relative to source_transcript/ < catV2 |
Exon support in reference annotation: was this exon supported by the reference annotation? < catV2 |
Intron support in reference annotation: was this intron exon supported by the reference annotation? < catV2 |
Transcript class: for projection transcripts, it is maybe ortholog; for de-novo transcripts, will be one of poor_alignment, possible_paralog, putative_novel_isoform, or putative_novel < catV2 |
Transcript mode(s): Comma separated list of transcript modes < catV2 |
Valid start codon: has a valid start-codon < catV2 |
Valid stop codon: has a valid stop-codon < catV2 |
Proper multiple of 3 ORF: is there a full valid st < catV2 |
RNA intron support: RNA-Seq support introns < catV2 |
RNA exon support: RNA-Seq support exons < catV2 |
Is this transcript supported by IsoSeq?: True if the transcript is supported by Iso-Seq < catV2 |

< catV2 | < catV2 | < catV2 |

Methods

< catV2 | < catV2 |

< catV2 | Genome annotation for the calJac4 assembly was performed using Comparative Annotation Toolkit (CAT). CAT leverages whole-genome alignments generated by Cactus to transfer annotations from one source genome to one or more target genomes. CAT also runs AUGUSTUS in both the comparative gene prediction mode and in a single-genome mode that utilizes Iso-Seq data to predict alternative isoforms. CAT then combines all of these annotation methods into a final consensus annotation set that represents orthology relationships as well as species-specific information. < catV2 |

< catV2 | < catV2 |

< catV2 | A Cactus alignment was produced with nine primate assemblies and mouse as an outgroup. < catV2 | The GENCODE v33 annotation for GRCh38 was used as a reference to map onto the calJac4 assembly. 20 IsoSeq libraries were included as evidence for the CAT annotation pipeline. < catV2 |

Assemblies used in Cactus alignment
Bonobo	Pan paniscus	Mhudiblu_PPA_v0	GCA_013052645.1
Chimp	Pan troglodytes	Clint_PTRv2	GCF_002880755.1
Gibbon	Nomascus leucogenys	Asia_NLE_v1	GCF_006542625.1
Gorilla	Gorilla gorilla gorilla	Kamilah_GGO_v0	GCF_008122165.1
Human	Homo sapiens	GRCh38	GCA_000001405
Marmoset	Callithrix jacchus	Callithrix_jacchus_cj1700_1.0	GCA_009663435.1
Orangutan	Pongo abelii	Susie_PABv2	GCF_002880775.1
Rhesus	Macaca mulatta	Mmul_10	GCF_003339765.1
Owl_monkey			unsubmitted
Mouse	Mus musculus	GRCm38	GCA_000001635.2

< catV2 | < catV2 |

Data Access

< catV2 | < catV2 |

< catV2 | For automated analysis, the genome annotation is stored in a bigGenePred < catV2 | format file that < catV2 | can be downloaded from the download server at < catV2 | cat-consensus-v2.bb. < catV2 | Annotations can be converted to ASCII text by our tool bigBedToBed < catV2 | which can be compiled from the source code or downloaded as a precompiled < catV2 | binary for your system. Instructions for downloading source code and binaries can be found < catV2 | here. < catV2 | The tool can also be used to obtain only features within a given range, for example: < catV2 |
< catV2 | bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/calJac4/cat/cat-consensus-v2.bb -chrom=chr6 -start=0 -end=1000000 stdout < catV2 |
< catV2 | Please refer to our < catV2 | mailing list archives < catV2 | for questions, or our < catV2 | Data Access FAQ < catV2 | for more information. < catV2 |

< catV2 | < catV2 |

Credits

< catV2 |

< catV2 | The alignments were generated by, Marina Haukness, Mark Diekhans, and Ian Fiddes. < catV2 |

< catV2 | < catV2 |

References

< catV2 | < catV2 |

< catV2 | Armstrong J, Hickey G, Diekhans M, Fiddes IT, Novak AM, Deran A, Fang Q, Xie D, Feng S, Stiller J < catV2 | et al. < catV2 | < catV2 | Progressive Cactus is a multiple-genome aligner for the thousand-genome era. < catV2 | Nature. 2020 Nov;587(7833):246-251. < catV2 | PMID: 33177663; PMC: PMC7673649 < catV2 |

< catV2 | < catV2 |

< catV2 | Fiddes IT, Armstrong J, Diekhans M, Nachtweide S, Kronenberg ZN, Underwood JG, Gordon D, Earl D, < catV2 | Keane T, Eichler EE et al. < catV2 | < catV2 | Comparative Annotation Toolkit (CAT)-simultaneous clade and personal genome annotation. < catV2 | Genome Res. 2018 Jul;28(7):1029-1038. < catV2 | PMID: 29884752; PMC: PMC6028123 < catV2 |

< catV2 | < catV2 |

--- > chainMacFas5 | Lastz (previously known as blastz) was developed at > chainMacFas5 | chainMacFas5 | TARGET=_blank>Pennsylvania State University by > chainMacFas5 | Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from > chainMacFas5 | Ross Hardison.

--- > chainNetHg38 | Lastz (previously known as blastz) was developed at > chainNetHg38 | chainNetHg38 | TARGET=_blank>Pennsylvania State University by > chainNetHg38 | Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from > chainNetHg38 | Ross Hardison.

--- > chainNetMacFas5 | Lastz (previously known as blastz) was developed at > chainNetMacFas5 | chainNetMacFas5 | TARGET=_blank>Pennsylvania State University by > chainNetMacFas5 | Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from > chainNetMacFas5 | Ross Hardison.

--- > chainNetMm10 | Lastz (previously known as blastz) was developed at > chainNetMm10 | chainNetMm10 | TARGET=_blank>Pennsylvania State University by > chainNetMm10 | Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from > chainNetMm10 | Ross Hardison.

--- > chainNetMm39 | Lastz (previously known as blastz) was developed at > chainNetMm39 | chainNetMm39 | TARGET=_blank>Pennsylvania State University by > chainNetMm39 | Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from > chainNetMm39 | Ross Hardison.

--- > netMacFas5 | Lastz (previously known as blastz) was developed at > netMacFas5 | netMacFas5 | TARGET=_blank>Pennsylvania State University by > netMacFas5 | Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from > netMacFas5 | Ross Hardison.

3680c3487 < netMm39 | RepeatMasker --- > netMm39 | RepeatMasker 3853c3660 < refSeqComposite | hide. Note: Not all subtracks are available on all assemblies.

--- > refSeqComposite | hide. Note: Not all subtracts are available on all assemblies.

3907,3927d3713 < refSeqComposite |

< refSeqComposite | NCBI Orthologs – Orthologous genes were identified by < refSeqComposite | < refSeqComposite | NCBI's Eukaryotic Genome Annotation Pipeline < refSeqComposite | for the NCBI Gene dataset using a combination of protein sequence similarity < refSeqComposite | and local synteny analysis. Orthology is determined between the genome being annotated and a < refSeqComposite | reference genome, such as human or zebrafish, and pairs of orthologs are grouped together. < refSeqComposite | Transitive relationships are inferred within each group, for example, zebrafish <-> < refSeqComposite | human <-> mouse. For more information on how NCBI calculates orthologs, see the details < refSeqComposite | provided < refSeqComposite | < refSeqComposite | here. This track is available for the following assemblies: < refSeqComposite | hg38, < refSeqComposite | mm39, < refSeqComposite | danRer11, < refSeqComposite | canFam6, and < refSeqComposite | bosTau9. < refSeqComposite |

4039,4050d3824 < refSeqComposite |

< refSeqComposite | The NCBI Orthologs track was generated using the latest < refSeqComposite | NCBI files (gene2accession and < refSeqComposite | gene_orthologs). NCBI chromosome identifiers were mapped to UCSC-compatible IDs using < refSeqComposite | species-specific chromosome alias files, and genes were filtered to include only those located on < refSeqComposite | valid NCBI chromosomes. A custom Python script processed the ortholog relationships and created bed files for < refSeqComposite | each species. The bed files were then converted to BigBed format, with indexing for search < refSeqComposite | functionality. The procedure is documented in the makeDoc from our GitHub repository.

4068c3842 < refSeqComposite | The data in the RefSeq Other, RefSeq Diffs, and NCBI Orthologs tracks are organized in --- > refSeqComposite | The data in the RefSeq Other and RefSeq Diffs tracks are organized in 4091c3865 < refSeqComposite | The annotations in the RefSeqOther, RefSeqDiffs, and NCBI Orthologs tracks are stored in bigBed --- > refSeqComposite | The annotations in the RefSeqOther and RefSeqDiffs tracks are stored in bigBed 4094,4098c3868,3870 < refSeqComposite | target="_blank">ncbiRefSeqOther.bb, < refSeqComposite | ncbiRefSeqDiffs.bb, and < refSeqComposite | ncbiOrtho.bb. --- > refSeqComposite | target="_blank">ncbiRefSeqOther.bb and > refSeqComposite | refSeqComposite | target="_blank">ncbiRefSeqDiffs.bb. 4168c3940 < rmsk | RepeatMasker --- > rmsk | RepeatMasker 4187,4199d3958 < rmsk |

< rmsk | When analyzing the data tables of this track, keep in mind that Repbase is not the same < rmsk | as the Repeatmasker sequence database and that the repeat names in the < rmsk | Repeatmasker output are not the same as the sequence names in the Repeatmasker < rmsk | database. Concretely, you can find a name such as "L1PA4" in the Repeatmasker < rmsk | output and this track, but there is not necessarily a single sequence "L1PA4" < rmsk | in the Repeatmasker database. This is because Repeatmasker creates annotations < rmsk | by joining matches to partial pieces of the database together so there is no < rmsk | 1:1 relationship between its sequence database and the annotations. To learn < rmsk | more, you can read the Repeatmasker paper, its source code or reach out to the < rmsk | Repeatmasker authors, your local expert on transposable elements or us. < rmsk |

Description

< uniprot | < uniprot |

< uniprot | This track shows protein sequences and annotations on them from the UniProt/SwissProt database, < uniprot | mapped to genomic coordinates. < uniprot |

< uniprot |

< uniprot | UniProt/SwissProt data has been curated from scientific publications by the UniProt staff, < uniprot | UniProt/TrEMBL data has been predicted by various computational algorithms. < uniprot | The annotations are divided into multiple subtracks, based on their "feature type" in UniProt. < uniprot | The first two subtracks below - one for SwissProt, one for TrEMBL - show the < uniprot | alignments of protein sequences to the genome, all other tracks below are the protein annotations < uniprot | mapped through these alignments to the genome. < uniprot |

Track Name	Description
UCSC Alignment, SwissProt = curated protein sequences	Protein sequences from SwissProt mapped to the genome. All other < uniprot \| tracks are (start,end) SwissProt annotations on these sequences mapped < uniprot \| through this alignment. Even protein sequences without a single curated < uniprot \| annotation (splice isoforms) are visible in this track. Each UniProt protein < uniprot \| has one main isoform, which is colored in dark. Alternative isoforms are < uniprot \| sequences that do not have annotations on them and are colored in light-blue. < uniprot \| They can be hidden with the TrEMBL/Isoform filter (see below).
UCSC Alignment, TrEMBL = predicted protein sequences	Protein sequences from TrEMBL mapped to the genome. All other tracks < uniprot \| below are (start,end) TrEMBL annotations mapped to the genome using < uniprot \| this track. This track is hidden by default. To show it, click its < uniprot \| checkbox on the track configuration page.
UniProt Signal Peptides	Regions found in proteins destined to be secreted, generally cleaved from mature protein.
UniProt Extracellular Domains	Protein domains with the comment "Extracellular".
UniProt Transmembrane Domains	Protein domains of the type "Transmembrane".
UniProt Cytoplasmic Domains	Protein domains with the comment "Cytoplasmic".
UniProt Polypeptide Chains	Polypeptide chain in mature protein after post-processing.
UniProt Regions of Interest	Regions that have been experimentally defined, such as the role of a region in mediating protein-protein interactions or some other biological process.
UniProt Domains	Protein domains, zinc finger regions and topological domains.
UniProt Disulfide Bonds	Disulfide bonds.
UniProt Amino Acid Modifications	Glycosylation sites, modified residues and lipid moiety-binding regions.
UniProt Amino Acid Mutations	Mutagenesis sites and sequence variants.
UniProt Protein Primary/Secondary Structure Annotations	Beta strands, helices, coiled-coil regions and turns.
UniProt Sequence Conflicts	Differences between Genbank sequences and the UniProt sequence.
UniProt Repeats	Regions of repeated sequence motifs or repeated domains.
UniProt Other Annotations	All other annotations, e.g. compositional bias

< uniprot |

< uniprot | For consistency and convenience for users of mutation-related tracks, < uniprot | the subtrack "UniProt/SwissProt Variants" is a copy of the track < uniprot | "UniProt Variants" in the track group "Phenotype and Literature", or < uniprot | "Variation and Repeats", depending on the assembly. < uniprot |

< uniprot | < uniprot |

Display Conventions and Configuration

< uniprot | < uniprot |

< uniprot | Genomic locations of UniProt/SwissProt annotations are labeled with a short name for < uniprot | the type of annotation (e.g. "glyco", "disulf bond", "Signal peptide" < uniprot | etc.). A click on them shows the full annotation and provides a link to the UniProt/SwissProt < uniprot | record for more details. TrEMBL annotations are always shown in < uniprot | light blue, except in the Signal Peptides, < uniprot | Extracellular Domains, Transmembrane Domains, and Cytoplamsic domains subtracks.

< uniprot | < uniprot |

< uniprot | Mouse over a feature to see the full UniProt annotation comment. For variants, the mouse over will < uniprot | show the full name of the UniProt disease acronym. < uniprot |

< uniprot | < uniprot |

< uniprot | The subtracks for domains related to subcellular location are sorted from outside to inside of < uniprot | the cell: Signal peptide, < uniprot | extracellular, < uniprot | transmembrane, and cytoplasmic. < uniprot |

< uniprot | < uniprot |

< uniprot | Features in the "UniProt Modifications" (modified residues) track are drawn in < uniprot | light green. Disulfide bonds are shown in < uniprot | dark grey. Topological domains < uniprot | in maroon and zinc finger regions in < uniprot | olive green. < uniprot |

< uniprot | < uniprot |

< uniprot | Duplicate annotations are removed as far as possible: if a TrEMBL annotation < uniprot | has the same genome position and same feature type, comment, disease and < uniprot | mutated amino acids as a SwissProt annotation, it is not shown again. Two < uniprot | annotations mapped through different protein sequence alignments but with the same genome < uniprot | coordinates are only shown once.

< uniprot | < uniprot |

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 | also is a public < uniprot | track hub prepared by UniProt itself, with < uniprot | genome annotations maintained by UniProt using their own mapping < uniprot | method based on those Gencode/Ensembl gene models that are annotated in UniProt < 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 | < uniprot |

Methods

< uniprot | < uniprot |

< 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 protein -> transcript -> < uniprot | genome is filtering the alignment from protein to transcript. Due to < uniprot | differences between the UniProt proteins and the transcripts (proteins were < uniprot | made many years before the transcripts were made, and human genomes have < uniprot | variants), the transcript with the highest BLAST score when aligning the < uniprot | protein to all transcripts is not always the correct transcript for a protein < uniprot | sequence. Therefore, the protein sequence is aligned to only a very short list < uniprot | of one or sometimes more transcripts, selected by a three-step procedure: < uniprot |

Use transcripts directly annotated by UniProt: for organisms that have a RefSeq transcript track, < uniprot | proteins are aligned to the RefSeq transcripts that are annotated < uniprot | by UniProt for this particular protein. < uniprot |
Use transcripts for NCBI Gene ID annotated by UniProt: If no transcripts are annotated on the < uniprot | protein, or the annotated ones have been deprecated by NCBI, but a NCBI Gene ID is < uniprot | annotated, the RefSeq transcripts for this Gene ID are used. This can result in multiple matching transcripts for a protein. < uniprot |
Use best matching transcript: If no NCBI Gene is < uniprot | annotated, then BLAST scores are used to pick the transcripts. There can be multiple transcripts for one < uniprot | protein, as their coding sequences can be identical. All transcripts within 1% of the highest observed BLAST score are used. < uniprot |

< uniprot |

< uniprot | < uniprot |

< uniprot | For strategy 2 and 3, many of the transcripts found do not differ in coding < uniprot | sequence, so the resulting alignments on the genome will be identical. < uniprot | Therefore, any identical alignments are removed in a final filtering step. The < uniprot | details page of these alignments will contain a list of all transcripts that < uniprot | result in the same protein-genome alignment. On hg38, only a handful of edge < uniprot | cases (pseudogenes, very recently added proteins) remain in 2023 where strategy < uniprot | 3 has to be used.

< 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 |

If UniProt has annotated a given RefSeq transcript for a given protein < uniprot | sequence, the protein is aligned to this transcript. Any difference in the < uniprot | version suffix is tolerated in this comparison. < uniprot |
If no transcript is annotated or the transcript cannot be found in the < uniprot | NCBI/UCSC RefSeq track, the UniProt-annotated NCBI Gene ID is resolved to a < uniprot | set of NCBI RefSeq transcript IDs via the most current version of NCBI < uniprot | genes tables. Only the top match of the resulting alignments and all < uniprot | others within 1% of its score are used for the mapping. < uniprot |
If no transcript can be found after step (2), the protein is aligned to all transcripts, < uniprot | the top match, and all others within 1% of its score are used. < uniprot |

< uniprot | < 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 | obtained from the UniProt XML file. The UniProt annotations were then mapped to the < uniprot | genome through the alignment described above using the pslMap program. This approach < uniprot | draws heavily on the 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 |

< uniprot | < uniprot |

Older releases

< uniprot |

< uniprot | This track is automatically updated on an ongoing basis, every 2-3 months. < uniprot | The current version name 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 and for manual inspection, previous versions of this track < uniprot | are available for browsing in the form of the UCSC UniProt Archive Track Hub (click this link to connect the hub now). 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.

< uniprot | < uniprot |

Data Access

< uniprot | < uniprot |

< uniprot | The raw data of the current track can be explored interactively with the < uniprot | Table Browser, or the < uniprot | Data Integrator. < uniprot | For automated analysis, the genome annotation is stored in a bigBed file that < uniprot | can be downloaded from the < uniprot | download server. < uniprot | The exact filenames can be found in the < uniprot | track configuration file. < uniprot | Annotations can be converted to ASCII text by our tool bigBedToBed < uniprot | which can be compiled from the source code or downloaded as a precompiled < uniprot | binary for your system. Instructions for downloading source code and binaries can be found < uniprot | here. < uniprot | The tool can also be used to obtain only features within a given range, for example: < uniprot |

< uniprot | bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/calJac4/uniprot/unipStruct.bb -chrom=chr6 -start=0 -end=1000000 stdout < uniprot |

< uniprot | < uniprot |

Lifting from UniProt to genome coordinates in pipelines

< uniprot |

To facilitate mapping protein coordinates to the genome, we provide the < uniprot | alignment files in formats that are suitable for our command line tools. Our < uniprot | command line programs liftOver or pslMap 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 | < uniprot |

Example commands: < uniprot |

< uniprot | wget -q https://hgdownload.soe.ucsc.edu/goldenPath/archive/hg38/uniprot/2022_03/unipToGenome.over.chain.gz
< uniprot | wget -q https://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/liftOver
< uniprot | chmod a+x liftOver
< uniprot | echo 'Q99697 1 10 annotationOnProtein' > prot.bed
< uniprot | liftOver prot.bed unipToGenome.over.chain.gz genome.bed
< uniprot | cat genome.bed
< uniprot |

< uniprot |

< uniprot | < uniprot |

Credits

< uniprot | < uniprot |

< 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 | available for download. < uniprot |

< uniprot | < uniprot |

References

< uniprot | < uniprot |

< uniprot | < uniprot |

< uniprot | Yip YL, Scheib H, Diemand AV, Gattiker A, Famiglietti LM, Gasteiger E, Bairoch A. < uniprot | < uniprot | The Swiss-Prot variant page and the ModSNP database: a resource for sequence and structure < uniprot | information on human protein variants. < uniprot | Hum Mutat. 2004 May;23(5):464-70. < uniprot | PMID: 15108278 < uniprot |

Description

< uwIsoSeq | < uwIsoSeq |

< uwIsoSeq | These tracks show the Iso-Seq long read alignments of marmoset cDNAs to the < uwIsoSeq | genome. The data set consists eleven tissue samples from two individuals. < uwIsoSeq |

< uwIsoSeq | < uwIsoSeq |

Display Conventions and Configuration

< uwIsoSeq |

< uwIsoSeq | These track use the BAM Display Conventions and Configuration. < uwIsoSeq |

< uwIsoSeq | < uwIsoSeq |

Methods

< uwIsoSeq |

Generation of Full Length cDNA and Library Preparation for Sequencing < uwIsoSeq |
< uwIsoSeq | Full-length cDNA was prepared and sequenced from total RNA isolated from various tissues of both a two year old male and a two year old female Callithrix jacchus. Iso-Seq library production was performed as per the Iso-Seq Express protocol (https://www.pacb.com/wp-content/uploads/Procedure-Checklist-IsoSeq-Express-Template-Preparation-for-Sequel-and-Sequel-II-Systems.pdf) and barcoded using barcoded adapters. One library was generated for each tissue. < uwIsoSeq |
< uwIsoSeq |
Sequencing with the PacBio Sequel II Platform < uwIsoSeq |
< uwIsoSeq | Libraries were pooled equimolar and sequenced on 3 SMRT Cell 8M on the Sequel II platform with chemistry version 2EA. < uwIsoSeq |
< uwIsoSeq |
Data Processing < uwIsoSeq |
< uwIsoSeq | Collected data was demultiplexed with lima (demultiplex barcoding), then analyzed with CCS with a requirement of 1 minimum pass and at least 0.9 identity (--minPasses 1 --min-rq 0.9). The Iso-Seq analysis pipeline was used to generate FLNC reads ensuring each has a poly-A tail, plus a single 3' and 5' primer signal for downstream analysis. < uwIsoSeq |
< uwIsoSeq |
Mapping < uwIsoSeq |
Resulting reads were aligned to the marmoset genome with < uwIsoSeq | minimap2 2.17-r941 using the options < uwIsoSeq | -t 12 -ax splice:hq -u. < uwIsoSeq |
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< uwIsoSeq | < uwIsoSeq |

Data Access

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< uwIsoSeq | The genomic alignments are stored in a BAM file that can be obtained from the < uwIsoSeq | download server. < uwIsoSeq |

< uwIsoSeq | < uwIsoSeq |

Credits

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< uwIsoSeq | Samples were provided from the New England Primate Research Center < uwIsoSeq | by Ricardo del Rosario and Anna Newman of the Broad Institute. < uwIsoSeq |

< uwIsoSeq |

< uwIsoSeq | Iso-Seq sequencing & FLNC analysis performed by: Evan Eichler, Alexandra < uwIsoSeq | Lewis, Shwetha Murali, and Katherine Munson of the University of Washington. < uwIsoSeq |

< uwIsoSeq | < uwIsoSeq |

References

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< uwIsoSeq | Warren WC, Harris RA, Haukness M, Fiddes IT, Murali SC, Fernandes J, Dishuck PC, Storer JM, < uwIsoSeq | Raveendran M, Hillier LW et al. < uwIsoSeq | < uwIsoSeq | Sequence diversity analyses of an improved rhesus macaque genome enhance its biomedical utility. < uwIsoSeq | Science. 2020 Dec 18;370(6523). < uwIsoSeq | PMID: 33335035; PMC: PMC7818670 < uwIsoSeq |