The chromosome band track represents the approximate \ location of bands seen on Giemsa-stained chromosomes\ under conditions where 400 bands are visible across the entire\ genome.
\Data are derived from the Mouse400.dat file downloaded from the NCBI ftp \ site ftp://ftp.ncbi.nih.gov/genomes/M_musculus/maps/mapview/. Band lengths\ are estimated based on relative sizes as defined by the International System for \ Cytogenetic Nomenclature (ISCN).\ \
We would like to thank NCBI for providing this information.\ map 1 stsMapMouseNew STS Markers bed 5 + STS Markers on Genetic and Radiation Hybrid Maps 1 5 0 0 0 128 128 255 0 0 0
This track shows locations of Sequence Tagged Sites (STS) \ along the mouse draft assembly. These markers have been mapped using \ either genetic mapping (WICGR Mouse Genetic Map, MGD Genetic Map) or radiation hybridization mapping (Whitehead/MRC RH Map) techniques.
\ \ Additional data on the individual maps can be found at the following links:\ \ map 1 ctgPos Map Contigs ctgPos Physical Map Contigs 0 9 150 0 0 202 127 127 0 0 0\ Although this track primarily displays the positions of large clones from the \ mouse reference strain, C57BL/6J, it also shows smaller overlapping contigs from \ alternate strains included in the NCBI data.\ \ map 0 gold Assembly bed 3 + Assembly from Fragments 0 10 150 100 30 230 170 40 0 0 0
\ This track shows the draft assembly of the $organism genome. This\ assembly merges contigs from overlapping clones into longer sequence\ contigs. \
\In dense mode, this track depicts the path through the clones \ (aka the golden path) used to create the assembled sequence. \ Clone boundaries are distinguished by the use of alternating gold and brown \ coloration. Where gaps\ exist in the path, spaces are shown between the gold and brown\ blocks. If the relative order and orientation of the contigs\ between the two blocks is known, a line is drawn to bridge the\ blocks.
\\ All components within this track are of fragment type "W": \ Whole Genome Shotgun contig. \ \ map 1 gap Gap bed 3 + Gap Locations 0 11 0 0 0 127 127 127 0 0 0
\ Gaps are represented as black boxes in this track.\ If the relative order and orientation of the contigs on either side\ of the gap is known, it is a bridged gap and a white line is drawn \ through the black box representing the gap. \
\This assembly contains the following principal types of gaps:\
Bacterial artificial chromosomes (BACs) are a key part of many large\ scale sequencing projects. A BAC typically consists of 50 - 300 kb of\ DNA. During the early phase of a sequencing project, it is common\ to sequence a single read (approximately 500 bases) off each end of\ a large number of BACs. Later on in the project, these BAC end reads\ can be mapped to the genome sequence. \
\This track shows these mappings\ in cases where both ends could be mapped. These BAC end pairs can\ be useful for validating the assembly over relatively long ranges. In some\ cases, the BACs are useful biological reagents. This track can also be\ used for determining which BAC contains a given gene, useful information\ for certain wet lab experiments.\ \
A valid pair of BAC end sequences must be\ at least 50 kb but no more than 600 kb away from each other. \ The orientation of the first BAC end sequence must be "+" and\ the orientation of the second BAC end sequence must be "-".
\ \BAC end sequences are placed on the assembled sequence using\ Jim Kent's \ blat \ program.
\ \Additional information about the clone, including how it\ can be obtained, may be found at the \ NCBI Clone Registry.\ To view the registry entry for a specific clone, open the details page for the clone and click on its name at the top of the page.\
\ map 1 exonArrows off\ gc5Base GC Percent wig 0 100 Percentage GC in 5-Base Windows 0 23.5 0 0 0 128 128 128 0 0 0\ This track may be configured in a variety of ways to highlight different aspects \ of the displayed information. Click the "Graph configuration help" link\ for an explanation of the configuration options.\ \
The data and presentation of this graph were prepared by\ Hiram Clawson (hiram@soe.ucsc.\ edu).\ map 0 autoScaleDefault Off\ defaultViewLimits 30:70\ graphTypeDefault Bar\ gridDefault OFF\ maxHeightPixels 128:36:16\ windowingFunction Mean\ knownGene Known Genes genePred knownGenePep knownGeneMrna Known Genes Based on SWISS-PROT, TrEMBL, mRNA, and RefSeq 3 34 12 12 120 133 133 187 0 0 0
\ The UCSC Known Genes track shows known protein coding genes based on \ proteins from SWISS-PROT, TrEMBL, and TrEMBL-NEW and their\ corresponding mRNAs from \ GenBank.\ Coding exons are displayed as thicker blocks than 5' and 3' \ untranslated regions (UTR). Connecting introns \ are one-pixel lines with hatch marks indicating direction of transcription.\ Entries which have corresponding entries in PDB are colored black.\ Entries which either have corresponding proteins in SWISS-PROT or mRNAs that are \ NCBI Reference Sequences with a "Reviewed" status are colored dark blue.\ Entries which have mRNAs that are \ NCBI Reference Sequences with a "Provisional" status are colored lighter blue.\ Everything else is colored with lightest blue.
\ \\ All mRNAs of a species are aligned against the genome using the blat\ program. When a single mRNA aligns in multiple places, only\ the best alignments are kept. The alignments must also have \ at least 98% sequence identity to be kept. \ This set of mRNA alignments is further reduced by keeping only those mRNAs that \ are referenced by a protein in SWISS-PROT, TrEMBL, or TrEMBL-NEW.
\\ Among multiple mRNAs referenced by a single protein, the best mRNA is chosen based on \ a quality score, which depends on its length, how good its translation matches \ the protein sequence, and its release date.\ The list of mRNA and protein pairs are further cleaned up by removing \ short invalid entries and consolidating entries with identical CDS regions.
\\ Finally, RefSeq entries which are derived from DNA sequences instead of \ mRNA sequences are added. Disease annotations are from SWISS-PROT.
\ \\ The Known Genes track is produced at UCSC based primarily on cross-references \ between proteins from \ SWISS-PROT \ (also including TrEMBL and TrEMBL-NEW) and mRNAs from GenBank\ generated by scientists worldwide. Part of \ NCBI RefSeq \ data are also included in this track.
\ \\ The SWISS-PROT entries in this annotation track are copyrighted. They are \ produced through a collaboration \ between the Swiss Institute of Bioinformatics and the EMBL Outstation - the \ European Bioinformatics Institute. There are no restrictions on their use by \ non-profit institutions as long as their content is in no way modified and this \ statement is not removed. Usage by and for commercial entities requires a \ license agreement (see \ http://www.isb-sib.ch/announce/ or send an email to \ license@isb-sib.ch).
\ \\ Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL. (2004)\ GenBank: update. \ Nucleic Acids Res. 32 Database issue:D23-6.\ genes 1 cdsDrawDefault genomic codons\ hgGene on\ refGene RefSeq Genes genePred refPep refMrna RefSeq Genes 1 35 12 12 120 133 133 187 0 0 0
\ The RefSeq Genes track shows known protein-coding genes taken from \ the NCBI mRNA reference sequences collection (RefSeq). On assemblies in \ which incremental GenBank downloads are supported, the data underlying this \ track are updated nightly.
\ \\ This track follows the display conventions for \ gene prediction \ tracks.\ The color shading indicates the level of review the RefSeq record has \ undergone: predicted (light), provisional (medium), reviewed (dark). \ In some assemblies, non-coding RNA genes are shown in a separate track.
\\ The item labels and display colors of features within this track can be\ configured through the controls at the top of the track description page. \ This page is accessed via the small button to the left of the track's \ graphical display or through the link on the track's control menu. \
\ After you have made your selections, click the Submit button to \ return to the tracks display page.
\ \\ RefSeq mRNAs were aligned against the $organism genome using blat; those\ with an alignment of less than 15% were discarded. When a single mRNA \ aligned in multiple places, the alignment having the highest base identity \ was identified. Only alignments having a base identity level within 0.1% of \ the best and at least 96% base identity with the genomic sequence were kept.\
\ \ \\ This track was produced at UCSC from mRNA sequence data\ generated by scientists worldwide and curated by the \ NCBI RefSeq project.
\ \\ Kent, W.J.\ BLAT - the BLAST-like alignment tool.\ Genome Res. 12(4), 656-664 (2002).
\ genes 1 mgcGenes MGC Genes genePred Mammalian Gene Collection Full ORF mRNAs 0 36 34 139 34 144 197 144 0 0 0\ This track shows alignments of $organism mRNAs from the\ Mammalian Gene Collection (MGC)\ having full-length open reading frames (ORFs) to the genome. \ Coding exons are represented by \ blocks connected by horizontal lines representing introns. The 5' and 3' \ untranslated regions (UTRs) are displayed as thinner blocks on the leading \ and trailing ends of the aligning regions. In full display mode, arrowheads \ on the connecting intron lines indicate the direction of transcription.\
\\ GenBank $organism MGC mRNAs identified as having full-length ORFs are\ aligned against the genome using the blat program. When a single mRNA aligns\ in multiple places, the alignment having the highest base identity is found. \ Only alignments that have a base identity level within 1% of\ the best and also have at least 95% base identity with the genomic sequence \ are kept.
\ \\ The $organism MGC full-length mRNA track is produced at UCSC from mRNA \ sequence data submitted to \ GenBank by the \ Mammalian Gene Collection project.
\ \\ Kent, W.J.\ BLAT - the BLAST-like alignment tool.\ Genome Res. 12(4), 656-664 (2002).
\ \ genes 1 ensGene Ensembl Genes genePred ensPep Ensembl Gene Predictions 1 40 150 0 0 202 127 127 0 0 0 http://www.ensembl.org/Mus_musculus/transview?transcript=$$\ This track shows gene predictions from Project Ensembl.
\ \\ For a description of the methods used in Ensembl gene prediction, see\ Hubbard, T. et al. (2002) in the References section below.
\ \\ Thanks to the Project Ensembl for providing this annotation.
\ \\ Hubbard, T. et al.. \ The Ensembl genome database project.\ Nucleic Acids Research 30(1), 38-41 (2002).
\ \ genes 1 twinscan Twinscan genePred twinscanPep Twinscan Gene Predictions Using Mouse/Human Homology 0 45 0 100 100 0 50 50 0 0 0\ The Twinscan program predicts genes in a manner similar to Genscan, except \ that Twinscan takes advantage of genome comparisons to improve gene prediction\ accuracy. More information and a web server can be found at\ http://genes.cs.wustl.edu/.
\ \\ This track follows the display conventions for \ gene prediction \ tracks.
\\ The track description page offers the following filter and configuration\ options:\
\ The Twinscan algorithm is described in Korf, I. et al. (2001) in the\ References section below.
\ \\ Thanks to Michael Brent's Computational Genomics Group at Washington \ University St. Louis for providing these data.
\ \\ Korf, I., Flicek, P., Duan, D. and Brent, M.R. \ Integrating genomic homology into gene structure prediction.\ Bioinformatics 17, S140-148 (2001).
\ genes 1 sgpGene SGP Genes genePred sgpPep SGP Gene Predictions Using Mouse/Human Homology 0 47 0 90 100 127 172 177 0 0 0\ This track shows gene predictions from the SGP program, which is being developed at \ the Grup de Recerca en\ Informàtica Biomèdica (GRIB) at Institut Municipal d'Investigació Mèdica (IMIM) in \ Barcelona. To predict genes in a genomic\ query, SGP combines geneid predictions with tblastx comparisons of the genomic query against other genomic sequences.\
\\ Thanks to GRIB for providing these gene predictions.\
\ \ \ \ genes 1 geneid Geneid Genes genePred geneidPep Geneid Gene Predictions 0 49 0 90 100 127 172 177 0 0 0\ This track shows gene predictions from the geneid program developed at the \ Grup de Recerca en\ Informàtica Biomèdica (GRIB) at Institut Municipal d'Investigació Mèdica (IMIM) in \ Barcelona. \
\\ Geneid is a program to predict genes in anonymous genomic sequences designed \ with a hierarchical structure. In the first step, splice sites, start and stop \ codons are predicted and scored along the sequence using Position Weight Arrays \ (PWAs). Next, exons are built from the sites. Exons are scored as the sum of the \ scores of the defining sites, plus the the log-likelihood ratio of a \ Markov Model for coding DNA. Finally, from the set of predicted exons, the gene \ structure is assembled, maximizing the sum of the scores of the assembled exons. \
\\ Thanks to GRIB for providing these data.\
\ genes 1 genscan Genscan Genes genePred genscanPep Genscan Gene Predictions 0 50 170 100 0 212 177 127 0 0 0\ This track shows predictions from the \ Genscan program \ written by Chris Burge. The predictions are based on transcriptional, \ translational, and donor/acceptor splicing signals, as well as the length \ and compositional distributions of exons, introns and intergenic regions.
\ \\ This track follows the display conventions for \ gene prediction \ tracks. \
\ The track description page offers the following filter and configuration\ options:\
\ For a description of the Genscan program and the model that underlies it, \ refer to Burge, C. and Karlin, S. (1997) in the References section below. \ The splice site models used are described in more detail in Burge, C. (1998)\ below.
\ \\ Burge, C. \ Modeling Dependencies in Pre-mRNA Splicing Signals. \ In Salzberg, S., Searls, D., and Kasif, S., eds. \ Computational Methods in Molecular Biology, \ Elsevier Science, Amsterdam, 127-163 (1998).
\\ Burge, C. and Karlin, S. \ Prediction of Complete Gene Structures in Human Genomic DNA.\ J. Mol. Biol. 268(1), 78-94 (1998).
\ genes 1 superfamily Superfamily bed 4 + Superfamily/SCOP: Proteins Having Homologs with Known Structure/Function 0 53 150 0 0 202 127 127 0 0 0 http://supfam.mrc-lmb.cam.ac.uk/SUPERFAMILY/cgi-bin/gene.cgi?genome=\ The \ Superfamily \ track shows proteins having homologs with known structures or functions.
\\ Each entry on the track shows the coding region of a gene (based on Ensembl gene predictions).\ In full display mode, the label for an entry consists of the names of \ all known protein domains encoded by this gene. This \ usually contains structural and/or functional descriptions that provide valuable \ information to help users get a quick grasp of the biological significance of the \ gene.
\ \\ Data are downloaded from the Superfamily server.\ Using the cross-reference between Superfamily entries and Ensembl gene prediction \ entries and their alignment to the appropriate genome, the associated data are \ processed to generate a simple BED format track.
\\ Superfamily was developed by\ Julian\ Gough at the MRC Laboratory\ of Molecular Biology, Cambridge.
\\ Gough, J., Karplus, K., Hughey, R. and\ Chothia, C. (2001). "Assignment of Homology to Genome Sequences using a\ Library of Hidden Markov Models that Represent all Proteins of Known Structure". \ J. Mol. Biol., 313(4), 903-919.
\ \ genes 1 mrna $Organism mRNAs psl . $Organism mRNAs from GenBank 3 54 0 0 0 127 127 127 1 0 0\ The mRNA track shows alignments between $organism mRNAs\ in GenBank and the genome.
\ \\ This track follows the display conventions for \ PSL alignment tracks. In dense display mode, the items that\ are more darkly shaded indicate matches of better quality.
\\ The description page for this track has a filter that can be used to change \ the display mode, alter the color, and include/exclude a subset of items \ within the track. This may be helpful when many items are shown in the track \ display, especially when only some are relevant to the current task.
\\ To use the filter:\
\ This track may also be configured to display codon coloring, a feature that\ allows the user to quickly validate and compare mRNA. For more \ information about this option, click \ here.\
\ \\ GenBank $organism mRNAs were aligned against the genome using the \ blat program. When a single mRNA aligned in multiple places, \ the alignment having the highest base identity was found. \ Only alignments having a base identity level within 0.5% of\ the best and at least 96% base identity with the genomic sequence were kept.\
\ \\ The mRNA track was produced at UCSC from mRNA sequence data\ submitted to the international public sequence databases by \ scientists worldwide.
\ \\ Benson, D.A., Karsch-Mizrachi, I., Lipman, D.J., Ostell, J., and \ Wheeler, D.L. \ GenBank: update. Nucleic Acids Res. 32,\ D23-6 (2004).
\\ Kent, W.J.\ BLAT - the BLAST-like alignment tool.\ Genome Res. 12(4), 656-664 (2002).
\ \ rna 1 cdsDrawOptions enabled\ NIAGene NIA Gene Index psl . NIA Mouse Gene Index Version 3 0 54 0 60 120 200 220 255 1 0 0 http://lgsun.grc.nia.nih.gov/geneindex3/bin/giT.cgi?genename=$$\ This track displays alignments of the National Institute on Aging (NIA) \ Mouse Gene Index (Version 3) against the mouse genome. \ \
\ The index was assembled from Blat alignments of the following to the mouse\ genome ($db/$date):\
\ See the NIA/NIH Mouse Genomics home page for more information.\ \
\ Sharov et al. (2003).\ Transcriptome Analysis of Mouse Stem Cells and Early Embryos.\ PLoS Biology 1: 410-419.\
\ Sharov, A.A., Dudekula, D.B. and Ko, M.S.H. "Genome-Wide Analysis of Alternative \ Transcription in Mouse". Submitted.\ genes 1 intronEst Spliced ESTs psl est $Organism ESTs That Have Been Spliced 1 56 0 0 0 127 127 127 1 0 0
\ This track shows alignments between $organism expressed sequence tags \ (ESTs) in GenBank and the genome that show signs of splicing when\ aligned against the genome. ESTs are single-read sequences, typically about \ 500 bases in length, that usually represent fragments of transcribed genes.\
\\ To be considered spliced, an EST must show \ evidence of at least one cannonical intron, i.e. one that is at least\ 32 bases in length and has GT/AG ends. By requiring splicing, the level \ of contamination in the EST databases is drastically reduced\ at the expense of eliminating many genuine 3' ESTs.\ For a display of all ESTs (including unspliced), see the \ $organism EST track.
\ \\ This track follows the display conventions for \ PSL alignment tracks. In dense display mode, the items that\ are more darkly shaded indicate matches of better quality.
\\ The strand information (+/-) indicates the\ direction of the match between the EST and the matching\ genomic sequence. It bears no relationship to the direction\ of transcription of the RNA with which it might be associated.
\\ The description page for this track has a filter that can be used to change \ the display mode, alter the color, and include/exclude a subset of items \ within the track. This may be helpful when many items are shown in the track \ display, especially when only some are relevant to the current task.
\\ To use the filter:\
\ This track may also be configured to display base labeling, a feature that\ allows the user to display all bases in the aligning sequence or only those \ that differ from the genomic sequence. For more information about this option,\ click \ here.\
\ \\ To make an EST, RNA is isolated from cells and reverse\ transcribed into cDNA. Typically, the cDNA is cloned\ into a plasmid vector and a read is taken from the 5'\ and/or 3' primer. For most -- but not all -- ESTs, the\ reverse transcription is primed by an oligo-dT, which\ hybridizes with the poly-A tail of mature mRNA. The\ reverse transcriptase may or may not make it to the 5'\ end of the mRNA, which may or may not be degraded.
\\ In general, the 3' ESTs mark the end of transcription\ reasonably well, but the 5' ESTs may end at any point\ within the transcript. Some of the newer cap-selected\ libraries cover transcription start reasonably well. Before the \ cap-selection techniques\ emerged, some projects used random rather than poly-A\ priming in an attempt to retrieve sequence distant from the\ 3' end. These projects were successful at this, but as\ a side effect also deposited sequences from unprocessed\ mRNA and perhaps even genomic sequences into the EST databases.\ Even outside of the random-primed projects, there is a\ degree of non-mRNA contamination. Because of this, a\ single unspliced EST should be viewed with considerable\ skepticism.
\\ To generate this track, $organism ESTs from GenBank were aligned \ against the genome using blat. Note that the maximum intron length\ allowed by blat is 500,000 bases, which may eliminate some ESTs with very \ long introns that might otherwise align. When a single \ EST aligned in multiple places, the alignment having the \ highest base identity was identified. Only alignments having\ a base identity level within 0.5% of the best and at least 96% base identity \ with the genomic sequence are displayed in this track.
\ \\ This track was produced at UCSC from EST sequence data\ submitted to the international public sequence databases by \ scientists worldwide.
\ \\ Benson, D.A., Karsch-Mizrachi, I., Lipman, D.J., Ostell, J., and \ Wheeler, D.L. \ GenBank: update. Nucleic Acids Res. 32,\ D23-6 (2004).
\\ Kent, W.J.\ BLAT - the BLAST-like alignment tool.\ Genome Res. 12(4), 656-664 (2002).
\ \ rna 1 intronGap 30\ pslSequenceBases no\ est $Organism ESTs psl est $Organism ESTs Including Unspliced 0 57 0 0 0 127 127 127 1 0 0\ This track shows alignments between $organism expressed sequence tags \ (ESTs) in GenBank and the genome. ESTs are single-read sequences, \ typically about 500 bases in length, that usually represent fragments of \ transcribed genes.
\ \\ This track follows the display conventions for \ PSL alignment tracks. In dense display mode, the items that\ are more darkly shaded indicate matches of better quality.
\\ The strand information (+/-) indicates the\ direction of the match between the EST and the matching\ genomic sequence. It bears no relationship to the direction\ of transcription of the RNA with which it might be associated.
\\ The description page for this track has a filter that can be used to change \ the display mode, alter the color, and include/exclude a subset of items \ within the track. This may be helpful when many items are shown in the track \ display, especially when only some are relevant to the current task.
\\ To use the filter:\
\ This track may also be configured to display base labeling, a feature that\ allows the user to display all bases in the aligning sequence or only those \ that differ from the genomic sequence. For more information about this option,\ click \ here.\
\ \\ To make an EST, RNA is isolated from cells and reverse\ transcribed into cDNA. Typically, the cDNA is cloned\ into a plasmid vector and a read is taken from the 5'\ and/or 3' primer. For most -- but not all -- ESTs, the\ reverse transcription is primed by an oligo-dT, which\ hybridizes with the poly-A tail of mature mRNA. The\ reverse transcriptase may or may not make it to the 5'\ end of the mRNA, which may or may not be degraded.
\\ In general, the 3' ESTs mark the end of transcription\ reasonably well, but the 5' ESTs may end at any point\ within the transcript. Some of the newer cap-selected\ libraries cover transcription start reasonably well. Before the \ cap-selection techniques\ emerged, some projects used random rather than poly-A\ priming in an attempt to retrieve sequence distant from the\ 3' end. These projects were successful at this, but as\ a side effect also deposited sequences from unprocessed\ mRNA and perhaps even genomic sequences into the EST databases.\ Even outside of the random-primed projects, there is a\ degree of non-mRNA contamination. Because of this, a\ single unspliced EST should be viewed with considerable\ skepticism.
\\ To generate this track, $organism ESTs from GenBank were aligned \ against the genome using blat. Note that the maximum intron length\ allowed by blat is 500,000 bases, which may eliminate some ESTs with very \ long introns that might otherwise align. When a single \ EST aligned in multiple places, the alignment having the \ highest base identity was identified. Only alignments having\ a base identity level within 0.5% of the best and at least 96% base identity \ with the genomic sequence were kept.
\ \\ This track was produced at UCSC from EST sequence data\ submitted to the international public sequence databases by \ scientists worldwide.
\ \\ Benson, D.A., Karsch-Mizrachi, I., Lipman, D.J., Ostell, J., and \ Wheeler, D.L. \ GenBank: update. Nucleic Acids Res. 32,\ D23-6 (2004).
\\ Kent, W.J.\ BLAT - the BLAST-like alignment tool.\ Genome Res. 12(4), 656-664 (2002).
\ \ rna 1 intronGap 30\ pslSequenceBases no\ xenoMrna Non-$Organism mRNAs psl xeno Non-$Organism mRNAs from GenBank 0 63 0 0 0 127 127 127 1 0 0\ This track displays translated blat alignments of vertebrate and\ invertebrate mRNA in \ GenBank from organisms other than $organism.\ Better alignments are indicated by darker coloration in the display.
\\ The strand information (+/-) for this track is in two parts. The\ first + indicates the orientation of the query sequence whose\ translated protein produced the match (here always 5' to 3', hence +).\ The second + or - indicates the orientation of the matching \ translated genomic sequence. Because the two orientations of a DNA \ sequence give different predicted protein sequences, there are four \ combinations. ++ is not the same as --; nor is +- the same as -+.
\ \\ The mRNAs were aligned against the $organism genome using translated blat. \ When a single mRNA aligned in multiple places, the alignment having the \ highest base identity was found. Only those alignments having a base \ identity level within 1% of the best and at least 25% base identity with the \ genomic sequence were kept.
\ \\ This track has a filter that can be used to change the display mode, \ change the color, and include/exclude a subset of items within the track.\ This may be helpful when many items are shown in the track display, \ especially when only some are relevant to the current task. \ The filter is located at the top of the track description page, which is \ accessed via the small button to the left of the track's graphical \ display or through the link on the track's control menu. \ To use the filter:\
\ When you have finished configuring the filter, click the Submit \ button.
\ \\ The mRNA track was produced at UCSC from mRNA sequence data\ submitted to the international public sequence databases by \ scientists worldwide.
\ \\ Benson, D.A., Karsch-Mizrachi, I., Lipman, D.J., Ostell, J., and \ Wheeler, D.L. \ GenBank: update. Nucleic Acids Res. 32,\ D23-6 (2004).
\\ Kent, W.J.\ BLAT - the BLAST-like alignment tool.\ Genome Res. 12(4), 656-664 (2002).
\ rna 1 cdsDrawOptions enabled\ miRNA miRNA bed 8 . MicroRNAs from the miRNA Registry 0 63 255 64 64 255 159 159 1 0 0 http://www.sanger.ac.uk/cgi-bin/Rfam/mirna/mirna_entry.pl?id=$$\ The miRNA track shows microRNAs from the\ \ miRNA Registry at The \ Wellcome Trust Sanger Institute. Mature miRNAs (miRs) are represented by \ thick lines; the predicted stem-loop portions of the primary transcripts\ are indicated by thinner lines. miRNAs in the sense orientation are shown in\ black; those in the reverse orientation are colored grey. When a single \ precursor produces two mature miRs from its 5' and 3' parts, it is displayed \ twice with the two different positions of the mature miR.\
\ \\ Mature and precursor miRNAs from the miRNA Registry are\ aligned against the genome using blat.\ The extents of the precursor sequences are not generally known, and are\ predicted based on base-paired hairpin structure. The miRNA Registry is\ described in Griffiths-Jones, S. (2004) in the References section below.
\ \\ This track was created by Michel Weber of \ Laboratoire de Biologie \ Moléculaire Eucaryote, CNRS Université Paul Sabatier (Toulouse, France) \ and Sam Griffiths-Jones of The Wellcome Trust Sanger Institute (Cambridge, UK).
\ \\ When making use of these data, please cite: \ Griffiths-Jones, S. \ The microRNA Registry,\ Nucl. Acids Res. 32, D109-D111 (2004).
\\ You may also want to cite The Wellcome Trust Sanger Institute \ miRNA Registry.
\\ The following publication provides guidelines on miRNA annotation:\ Ambros, V. et al., \ A uniform system for microRNA annotation. \ RNA 9(3), 277-279 (2003).
\\ For more information on blat, see this publication:\ Kent, W.J.\ BLAT - the BLAST-like alignment tool.\ Genome Res. 12(4), 656-664 (2002).
\ \ genes 1 urlLabel miRNA Registry:\ xenoEst Non-$Organism ESTs psl xeno Non-$Organism ESTs from GenBank 0 65 0 0 0 127 127 127 1 0 0 http://www.ncbi.nlm.nih.gov/htbin-post/Entrez/query?form=4&db=n&term=$$\ This track displays translated blat alignments of expressed sequence tags \ (ESTs) in GenBank from organisms other than $organism.
\\ The strand information (+/-) for this track is in two parts. The\ first + or - indicates the orientation of the query sequence whose\ translated protein produced the match. The second + or - indicates the\ orientation of the matching translated genomic sequence. Because the two\ orientations of a DNA sequence give different predicted protein sequences,\ there are four combinations. ++ is not the same as --; nor is +- the same\ as -+.
\ \\ To generate this track, the ESTs were aligned against the genome using \ the blat program. When a single EST aligned in multiple places, the \ alignment having the highest base identity was identified. Only alignments \ having a base identity level within 1% of the best and at least 10% base \ identity with the genomic sequence were kept.
\ \\ This track has a filter that can be used to change the display mode, \ change the color, and include/exclude a subset of items within the track.\ This may be helpful when many items are shown in the track display, \ especially when only some are relevant to the current task. \ The filter is located at the top of the track description page, which is \ accessed via the small button to the left of the track's graphical \ display or through the link on the track's control menu. \ To use the filter:\
\ When you have finished configuring the filter, click the Submit \ button.
\ \\ This track was produced at UCSC from EST sequence data submitted to the \ international public sequence databases by scientists worldwide.
\ \\ Benson, D.A., Karsch-Mizrachi, I., Lipman, D.J., Ostell, J., and \ Wheeler, D.L. \ GenBank: update. Nucleic Acids Res. 32,\ D23-6 (2004).
\\ Kent, W.J.\ BLAT - the BLAST-like alignment tool.\ Genome Res. 12(4), 656-664 (2002).
\ \ rna 1 pslSequenceBases no\ tigrGeneIndex TIGR Gene Index genePred Alignment of TIGR Gene Index TCs Against the $Organism Genome 0 68 100 0 0 177 127 127 0 0 0 http://www.tigr.org/tigr-scripts/tgi/tc_report.pl?$$This track displays alignments of the TIGR Gene Index (TGI)\ against the $organism genome. The TIGR Gene Index is based\ largely on assemblies of EST sequences in the public databases.\ See \ www.tigr.org for more information about TIGR and the Gene Index.
\ \Thanks to Foo Cheung and Razvan Sultana of the The Institute for Genomic Research, for converting these data into a track for the browser.
\ rna 1 autoTranslate 0\ gnfAtlas2 GNF Atlas 2 expRatio GNF Expression Atlas 2 0 81 0 0 0 127 127 127 0 0 0This track shows expression data from the GNF Gene Expression\ Atlas 2. This contains two replicates each of 61 mouse tissues and 79 human\ tissues run over Affymetrix microarrays. In full mode all tissues are\ displayed. In packed or dense mode averages of related tissues are shown.\ As is standard with microarray data red indicates overexpression in the \ tissue, and green indicates underexpression. You may want to view gene\ expression with the Gene Sorter as \ well as the Genome Browser.
\ \\ This track shows gene expression differences between adult male \ and female tissues, as described in Rinn, J.L. et al. (2004) \ in the References section below.
\ \\ In full display mode, the medians of all replicates (technical and biological)\ for each sex's tissue are shown. To view the individual replicates, use the \ UCSC Gene Sorter. In packed and squished \ display modes, the average over all tissues is shown for each sex. Dense \ display mode shows the placement of the Affy MOE430A target sequences \ colored by overall expression level in both sexes, with darker colors \ representing higher levels of expression.
\ \\ Five adult mouse tissues (liver, kidney, hypothalamus, ovary and testis) \ were studied. For each somatic tissue, triple selected poly-A mRNA was \ prepared from six independent pools (biological replicates), three male and \ three female. Likewise, three pools were prepared from the ovary and three \ pools from the testis. Each pool of RNA was derived from ten individuals. \ For each biological replicate, two cDNAs (technical replicates) \ were prepared and independently hybridized to Affymetrix MOE430A chips.
\ \Thanks to John Rinn for providing these data.
\ \\ Rinn, J.L. et al. \ Major molecular differences between mammalian sexes are involved\ in drug metabolism and renal function, Developmental Cell \ 6, 791-800 (2004).
\ regulation 1 chip MOE430A\ expScale 8.0\ expStep 1.0\ expTable mouseRinnSexMedianExps\ affyGnfU74A GNF U74A expRatio GNF Expression Atlas on Mouse Affymetrix U74A Chip 0 82 0 0 0 127 127 127 0 0 0\ This track shows expression data from GNF (The Genomics Institute of the Novartis Research \ Foundation) using the Affymetrix U74A chip.
\ \\ For detailed information about the experiments, see Su et al. (2002)\ in the References section below. Alignments displayed on the track correspond \ to the consensus sequences used by Affymetrix to choose probes.
\\ In dense mode, the track color denotes the average signal over all\ experiments on a log base 2 scale. Lighter colors correspond to lower signals;\ darker colors correspond to higher signals. In full\ mode, the color of each item represents the log base 2 ratio of the signal of\ that particular experiment to the median signal of all experiments for that \ probe.
\\ More information about individual probes and probe sets is available at\ Affymetrix's netaffx.com website.
\ \\ Thanks to GNF for providing these data.
\ \\ Su, A.I., Cooke, M.P., Ching, K.A., Hakak, Y., Walker, J.R., Wiltshire, T., \ Orth, A.P., Vega, R.G., Sapinoso, L.M., Moqrich, A. et al. \ Large-scale analysis of the human and mouse transcriptomes. \ Proc Natl Acad Sci USA 99(7), 4465-70 (2002).
\ regulation 0 chip U74\ expScale 4.0\ expStep 0.5\ expTable gnfMouseU74aAllExps\ affyGnfU74B GNF U74B expRatio GNF Expression Atlas on Mouse Affymetrix U74B Chip 0 82.1 0 0 0 127 127 127 0 0 0\ This track shows expression data from GNF (The Genomics Institute of the Novartis Research \ Foundation) using the Affymetrix U74B chip.
\ \\ For detailed information about the experiments, see Su et al. (2002)\ in the References section below. Alignments displayed on the track\ correspond to the consensus sequences used by Affymetrix to choose probes.
\ \\ In dense mode, the track color denotes the average signal over all\ experiments on a log base 2 scale. Lighter colors correspond to lower signals;\ darker colors correspond to higher signals. In full\ mode, the color of each item represents the log base 2 ratio of the signal of\ that particular experiment to the median signal of all experiments for that \ probe.
\\ More information about individual probes and probe sets is available at\ Affymetrix's netaffx.com website.
\ \\ Thanks to GNF for providing these data.
\ \\ Su, A.I., Cooke, M.P., Ching, K.A., Hakak, Y., Walker, J.R., Wiltshire, T., \ Orth, A.P., Vega, R.G., Sapinoso, L.M., Moqrich, A. et al. \ Large-scale analysis of the human and mouse transcriptomes. \ Proc Natl Acad Sci USA 99(7), 4465-70 (2002).
\ regulation 0 chip U74\ expScale 4.0\ expStep 0.5\ expTable gnfMouseU74bAllExps\ affyGnfU74C GNF U74C expRatio GNF Expression Atlas on Mouse Affymetrix U74C Chip 0 82.2 0 0 0 127 127 127 0 0 0\ This track shows expression data from GNF (The Genomics Institute of the Novartis Research \ Foundation) using the Affymetrix U74C chip.
\ \\ For detailed information about the experiments, see Su et al. (2002)\ in the References section below. Alignments displayed on the track correspond \ to the consensus sequences used by Affymetrix to choose probes.
\\ In dense mode, the track color denotes the average signal over all\ experiments on a log base 2 scale. Lighter colors correspond to lower signals \ and darker colors correspond to higher signals. In full\ mode, the color of each item represents the log base 2 ratio of the signal of\ that particular experiment to the median signal of all experiments for that \ probe.
\\ More information about individual probes and probe sets is available at\ Affymetrix's netaffx.com website.
\ \\ Thanks to GNF for providing these data.
\ \\ Su, A.I., Cooke, M.P., Ching, K.A., Hakak, Y., Walker, J.R., Wiltshire, T., \ Orth, A.P., Vega, R.G., Sapinoso, L.M., Moqrich, A. et al. \ Large-scale analysis of the human and mouse transcriptomes. \ Proc Natl Acad Sci USA 99(7), 4465-70 (2002).
\ regulation 0 chip U74\ expScale 4.0\ expStep 0.5\ expTable gnfMouseU74cAllExps\ affyGnf1m Affy GNF1M psl . Alignments of Probes from Affymetrix GNF1M Chip 0 85 0 0 0 127 127 127 0 0 0\ This track shows the location of the sequences used for the selection of \ probes on the Affymetrix GNF1M chips. The annotation contains 31,000 \ non-overlapping mouse genes and gene predictions.
\ \\ The sequences were mapped to the genome with blat followed by pslReps \ using the parameters -minCover=0.3, -minAli=0.95 and \ -nearTop=0.005.
\ \\ Thanks to the \ Genomics Institute of the Novartis\ Research Foundation (GNF) for the data underlying this track.
\ regulation 1 affyU74 Affy U74 psl . Alignments of Affymetrix Consensus Sequences from MG-U74 v2 (A,B, and C) 0 86 0 0 0 127 127 127 0 0 0\ This track shows the location of the consensus sequences used for the \ selection of probes on the Affymetrix MG-U74v2 set (A,B and C) of chips.
\ \\ Consensus sequences were downloaded from the\ Affymetrix Product Support\ and mapped to the genome with blat followed by pslReps using the parameters\ -minCover=0.3, -minAli=0.95 and -nearTop=0.005.
\ \\ Thanks to Affymetrix \ for the data underlying this track.
\ regulation 1 affyMOE430 Affy MOE430 psl . Alignments of Affymetrix Consensus Sequences from Mouse MOE430 (A and B) 0 87 0 0 0 127 127 127 0 0 0\ This track shows the location of the consensus sequences used for the \ selection of probes on the Affymetrix Mouse MOE430 set (A and B) of chips.
\ \\ Consensus sequences were downloaded from the\ Affymetrix Product Support\ and mapped to the genome with blat followed by pslReps using the parameters\ -minCover=0.3, -minAli=0.95 and -nearTop=0.005.
\ \\ Thanks to Affymetrix \ for the data underlying this track.
\ \ regulation 1 cpgIsland CpG Islands bed 4 + CpG Islands (Islands < 300 Bases are Light Green) 0 90 0 100 0 128 228 128 0 0 0\ CpG islands are associated with genes, particularly housekeeping\ genes, in vertebrates. CpG islands are typically common near\ transcription start sites, and may be associated with promoter\ regions. Normally a C (cytosine) base followed immediately by a \ G (guanine) base (a CpG) is rare in\ vertebrate DNA because the Cs in such an arrangement tend to be\ methylated. This methylation helps distinguish the newly synthesized\ DNA strand from the parent strand, which aids in the final stages of\ DNA proofreading after duplication. However, over evolutionary time\ methylated Cs tend to turn into Ts because of spontaneous\ deamination. The result is that CpGs are relatively rare unless\ there is selective pressure to keep them or a region is not methylated\ for some reason, perhaps having to do with the regulation of gene\ expression. CpG islands are regions where CpGs are present at\ significantly higher levels than is typical for the genome as a whole.\
\ \\ CpG islands are predicted by searching the sequence one base at a\ time, scoring each dinucleotide (+17 for CG and -1 for others) and\ identifying maximally scoring segments. Each segment is then\ evaluated for the following criteria:\
\ The CpG count is the number of CG dinucleotides in the island. \ The Percentage CpG is the ratio of CpG nucleotide bases\ (twice the CpG count) to the length.
\ \\ This track was generated using a modification of a program developed by \ G. Miklem and L. Hillier.
\ \ regulation 1 chainHg16 Human Chain chain hg16 $o_Organism ($o_date/$o_db) Chained Blastz Alignments 0 115 100 50 0 255 240 200 1 0 0\ This track shows alignments of $o_organism ($o_db, $o_date) to the\ $organism genome using a gap scoring system that allows longer gaps \ than traditional affine gap scoring systems. It can also tolerate gaps in both\ $o_organism and $organism simultaneously. These \ "double-sided" gaps can be caused by local inversions and \ overlapping deletions in both species. \
\ The chain track displays boxes joined together by either single or\ double lines. The boxes represent aligning regions.\ Single lines indicate gaps that are largely due to a deletion in the\ $o_organism assembly or an insertion in the $organism \ assembly. Double lines represent more complex gaps that involve substantial\ sequence in both species. This may result from inversions, overlapping\ deletions, an abundance of local mutation, or an unsequenced gap in one\ species. In cases where multiple chains align over a particular region of\ the $organism genome, the chains with single-lined gaps are often \ due to processed pseudogenes, while chains with double-lined gaps are more \ often due to paralogs and unprocessed pseudogenes.
\\ In the "pack" and "full" display\ modes, the individual feature names indicate the chromosome, strand, and\ location (in thousands) of the match for each matching alignment.
\ \\ Transposons that have been inserted since the $o_organism/$organism\ split were removed from the assemblies. The abbreviated genomes were\ aligned with blastz, and the transposons were then added back in.\ The resulting alignments were converted into axt format using the lavToAxt\ program. The axt alignments were fed into axtChain, which organizes all\ alignments between a single $o_organism chromosome and a single\ $organism chromosome into a group and creates a kd-tree out\ of the gapless subsections (blocks) of the alignments. A dynamic program\ was then run over the kd-trees to find the maximally scoring chains of these\ blocks. Chains scoring below a threshold were discarded; the remaining\ chains are displayed in this track.
\ \\ Blastz was developed at Pennsylvania State University by \ Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\ Ross Hardison.
\\ Lineage-specific repeats were identified by Arian Smit and his \ RepeatMasker\ program.
\\ The axtChain program was developed at the University of California at \ Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler.
\\ The browser display and database storage of the chains were generated\ by Robert Baertsch and Jim Kent.
\ \\ Chiaromonte, F., Yap, V.B., Miller, W. \ Scoring pairwise genomic sequence alignments. \ Pac Symp Biocomput 2002, 115-26 (2002).
\\ Kent, W.J., Baertsch, R., Hinrichs, A., Miller, W., and Haussler, D.\ Evolution's cauldron: Duplication, deletion, and rearrangement\ in the mouse and human genomes.\ Proc Natl Acad Sci USA 100(20), 11484-11489 (2003).
\\ Schwartz, S., Kent, W.J., Smit, A., Zhang, Z., Baertsch, R., Hardison, R., \ Haussler, D., and Miller, W.\ Human-Mouse Alignments with BLASTZ. \ Genome Res. 13(1), 103-7 (2003).
\ \ compGeno 1 otherDb hg16\ netHg16 Human Net netAlign hg16 chainHg16 $o_Organism ($o_date/$o_db) Alignment Net 0 116 0 0 0 127 127 127 1 0 0\ This track shows the best $o_organism/$organism chain for \ every part of the $organism genome. It is useful for\ finding orthologous regions and for studying genome\ rearrangement. The $o_organism sequence used in this annotation is from\ the $o_date ($o_db) assembly.
\ \\ In full display mode, the top-level (level 1)\ chains are the largest, highest-scoring chains that\ span this region. In many cases gaps exist in the\ top-level chain. When possible, these are filled in by\ other chains that are displayed at level 2. The gaps in \ level 2 chains may be filled by level 3 chains and so\ forth.
\\ In the graphical display, the boxes represent ungapped \ alignments; the lines represent gaps. Click\ on a box to view detailed information about the chain\ as a whole; click on a line to display information\ about the gap. The detailed information is useful in determining\ the cause of the gap or, for lower level chains, the genomic\ rearrangement.
\\ Individual items in the display are categorized as one of four types\ (other than gap):
\\ Chains were derived from blastz alignments, using the methods\ described on the chain tracks description pages, and sorted with the \ highest-scoring chains in the genome ranked first. The program\ chainNet was then used to place the chains one at a time, trimming them as \ necessary to fit into sections not already covered by a higher-scoring chain. \ During this process, a natural hierarchy emerged in which a chain that filled \ a gap in a higher-scoring chain was placed underneath that chain. The program \ netSyntenic was used to fill in information about the relationship between \ higher- and lower-level chains, such as whether a lower-level\ chain was syntenic or inverted relative to the higher-level chain. \ The program netClass was then used to fill in how much of the gaps and chains \ contained Ns (sequencing gaps) in one or both species and how much\ was filled with transposons inserted before and after the two organisms \ diverged.
\ \\ The chainNet, netSyntenic, and netClass programs were\ developed at the University of California\ Santa Cruz by Jim Kent.
\\ Blastz was developed at Pennsylvania State University by\ Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\ Ross Hardison.
\\ Lineage-specific repeats were identified by Arian Smit and his program \ RepeatMasker.
\\ The browser display and database storage of the nets were made\ by Robert Baertsch and Jim Kent.
\ \\ Kent, W.J., Baertsch, R., Hinrichs, A., Miller, W., and Haussler, D.\ Evolution's cauldron: Duplication, deletion, and rearrangement\ in the mouse and human genomes.\ Proc Natl Acad Sci USA 100(20), 11484-11489 (2003).
\\ Schwartz, S., Kent, W.J., Smit, A., Zhang, Z., Baertsch, R., Hardison, R.,\ Haussler, D., and Miller, W.\ Human-Mouse Alignments with BLASTZ.\ Genome Res. 13(1), 103-7 (2003).
\ \ \ compGeno 0 otherDb hg16\ blastzTightHg16 Human Tight psl xeno hg16 $o_Organism ($o_date/$o_db) Blastz Tight Subset of Best Alignments 0 117.5 0 100 0 255 240 200 1 0 0\ This track displays blastz alignments of the $o_organism assembly\ ($o_db, $o_date) to the $organism genome, filtered by axtBest and\ subsetAxt with very stringent constraints as described below.\ The track has an optional feature that color codes alignments to indicate\ the chromosomes from which they are derived in the aligning assembly. To\ activate the color feature, click the on button next to\ "Color track based on chromosome" on the track description page.
\\ Each item in the display is identified by the chromosome, strand, and\ location of the match (in thousands).
\ \\ For blastz, 12 of 19 seeds were used and then scored using:\
\
A C G T\
A 91 -114 -31 -123\
C -114 100 -125 -31\
G -31 -125 100 -114\
T -123 -31 -114 91\
\
O = 400, E = 30, K = 3000, L = 3000, M = 50\
\
\ A second pass was made at reduced stringency (7mer seeds and\ MSP threshold of K=2200) to attempt to fill in gaps of up to about 10K bp.\ Lineage-specific repeats were abridged during this alignment.
\ AxtBest was used to select only the best alignment for any given region\ of the genome. SubsetAxt was then run on axtBest-filtered alignments\ with this matrix:\\
A C G T\
A 100 -200 -100 -200\
C -200 100 -200 -100\
G -100 -200 100 -200\
T -200 -100 -200 100\
\
with a gap open penalty of 2000 and a gap extension penalty of 50.\
The minimum score threshold was 3400.\
\
\ This track has a filter that can be used to change the display mode,\ turn on the chromosome color track, or filter the display output by\ chromosome. The filter is located at the top of the track description page,\ which is accessed via the small button to the left of the track's graphical\ display or through the link on the track's control menu.\
\ When you have finished configuring the filter, click the Submit\ button.
\ \\ These alignments were contributed by Scott Schwartz of the\ Penn State Bioinformatics\ Group. The best-in-genome filtering was done using UCSC's\ axtBest program.
\ \\ Chiaromonte, F., Yap, V.B., Miller, W.\ Scoring pairwise genomic sequence alignments.\ Pac Symp Biocomput 2002, 115-26 (2002).
\\ Schwartz, S., Kent, W.J., Smit, A., Zhang, Z., Baertsch, R., Hardison, R.,\ Haussler, D., and Miller, W.\ Human-mouse alignments with BLASTZ.\ Genome Res. 13(1), 103-107 (2003).
\ \ \ compGeno 1 otherDb hg16\ snpMap SNPs bed 4 . Simple Nucleotide Polymorphisms (SNPs) 0 144 0 0 0 127 127 127 0 0 0\ This track consolidates all the Simple Nucleotide Polymorphisms \ into a single track.
\ \\ The SNPs in this track include all known polymorphisms that\ can be mapped against the current assembly. These include known point\ mutations (Single Nucleotide Polymorphisms), insertions, deletions,\ and segmental mutations from the current build of \ dbSnp, \ which is shown in the Genome Browser \ release log.\
\\ There are three major cases that are not mapped and/or annotated:\
The heuristics for the non-SNP variations (i.e. named elements and\ STRs) are quite conservative; therefore, some of these are probably lost. This\ approach was chosen to avoid false annotation of variation in\ inappropriate locations.
\ \\ Positional information can be found in the annotations section\ of the Genome Browser \ downloads page, \ which is organized by species and assembly. Non-positional information\ displayed on this page can be found in the \ shared\ data section of the same page, where it is split into tables by\ organism: \ dbSnpRsHg for Human, \ dbSnpRsMm for Mouse, and \ dbSnpRsRn for Rat.\ \
\ Thanks to NIH's dbSNP for providing the public data, which \ are available from dbSnp at the NCBI.
\ \ varRep 1 rmsk RepeatMasker rmsk Repeating Elements by RepeatMasker 1 147 0 0 0 127 127 127 1 0 0\
This track was created by using Arian Smit's
\ The RepBase version used on this mouse assembly was\ RepBase Update 8.4, RM database version 20030619 \ and RepeatMasker script version 20030623.
\ \\ In full display mode, this track displays nine different classes of repeats:\
\ The level of color shading in the graphical display reflects the amount of \ base mismatch, base deletion, and base insertion associated with a repeat \ element. The higher the combined number of these, the lighter the shading.
\ \\ UCSC has used the most current versions of the RepeatMasker software \ and repeat libraries available to generate these data. Note that these \ versions may be newer than those that are publicly available on the Internet. \
\\ Data are generated using the RepeatMasker -s flag. Additional flags\ may be used for certain organisms. Repeats are soft-masked. Alignments may \ extend through repeats, but are not permitted to initiate in them. \ See the \ FAQ for \ more information.
\ \\ Thanks to Arian Smit and GIRI\ for providing the tools and repeat libraries used to generate this track.
\ \\ RepBase is described in \ Jurka, J. \ Repbase Update: a database and an electronic journal of \ repetitive elements. \ Trends Genet. 9, 418-420 (2000).
\\ For a discussion of repeats in mammalian genomes, see: \
\ Smit, A.F. Interspersed repeats and other mementos of transposable \ elements in mammalian genomes. Curr Opin Genet Dev 9(6),\ 657-63 (1999).
\\ Smit, A.F. The origin of interspersed repeats in the human genome. \ Curr Opin Genet Dev. 6(6), 743-8 (1996).\
\ varRep 0 simpleRepeat Simple Repeats bed 4 + Simple Tandem Repeats by TRF 0 149.3 0 0 0 127 127 127 0 0 0\ This track displays simple tandem repeats (possibly imperfect) located\ by Tandem Repeats\ Finder (TRF), which is specialized for this purpose. These repeats can\ occur within coding regions of genes and may be quite\ polymorphic. Repeat expansions are sometimes associated with specific\ diseases.
\ \\ For more information about the Tandem Repeats Finder, see Benson, G. \ Tandem repeats finder: a program to analyze DNA sequences.\ Nucleic Acids Research 27(2), 573-580 (1999).
\ \\ Tandem Repeats Finder was written by \ Gary Benson.
\ \ varRep 1 blastzTightRn3 Rat Tight psl xeno rn3 $o_Organism ($o_date/$o_db) Blastz Tight Subset of Best Alignments 0 259.96 100 50 0 255 240 200 1 0 0\ This track displays blastz alignments of the $o_organism assembly\ ($o_db, $o_date) to the $organism genome, filtered by axtBest and\ subsetAxt with very stringent constraints as described below.\ The track has an optional feature that color codes alignments to indicate\ the chromosomes from which they are derived in the aligning assembly. To\ activate the color feature, click the on button next to\ "Color track based on chromosome" on the track description page.
\\ Each item in the display is identified by the chromosome, strand, and\ location of the match (in thousands).
\ \\ For blastz, 12 of 19 seeds were used and then scored using:\
\
A C G T\
A 91 -114 -31 -123\
C -114 100 -125 -31\
G -31 -125 100 -114\
T -123 -31 -114 91\
\
O = 400, E = 30, K = 3000, L = 3000, M = 50\
\
\ A second pass was made at reduced stringency (7mer seeds and\ MSP threshold of K=2200) to attempt to fill in gaps of up to about 10K bp.\ Lineage-specific repeats were abridged during this alignment.
\ AxtBest was used to select only the best alignment for any given region\ of the genome. SubsetAxt was then run on axtBest-filtered alignments\ with this matrix:\\
A C G T\
A 100 -200 -100 -200\
C -200 100 -200 -100\
G -100 -200 100 -200\
T -200 -100 -200 100\
\
with a gap open penalty of 2000 and a gap extension penalty of 50.\
The minimum score threshold was 3400.\
\
\ This track has a filter that can be used to change the display mode,\ turn on the chromosome color track, or filter the display output by\ chromosome. The filter is located at the top of the track description page,\ which is accessed via the small button to the left of the track's graphical\ display or through the link on the track's control menu.\
\ When you have finished configuring the filter, click the Submit\ button.
\ \\ These alignments were contributed by Scott Schwartz of the\ Penn State Bioinformatics\ Group. The best-in-genome filtering was done using UCSC's\ axtBest program.
\ \\ Chiaromonte, F., Yap, V.B., Miller, W.\ Scoring pairwise genomic sequence alignments.\ Pac Symp Biocomput 2002, 115-26 (2002).
\\ Schwartz, S., Kent, W.J., Smit, A., Zhang, Z., Baertsch, R., Hardison, R.,\ Haussler, D., and Miller, W.\ Human-mouse alignments with BLASTZ.\ Genome Res. 13(1), 103-107 (2003).
\ \ \ compGeno 1 otherDb rn3\ chainRn3 Rat Chain chain rn3 $o_Organism ($o_date/$o_db) Chained Blastz Alignments 0 260 100 50 0 255 240 200 1 0 0\ This track shows alignments of $o_organism ($o_db, $o_date) to the\ $organism genome using a gap scoring system that allows longer gaps \ than traditional affine gap scoring systems. It can also tolerate gaps in both\ $o_organism and $organism simultaneously. These \ "double-sided" gaps can be caused by local inversions and \ overlapping deletions in both species. \
\ The chain track displays boxes joined together by either single or\ double lines. The boxes represent aligning regions.\ Single lines indicate gaps that are largely due to a deletion in the\ $o_organism assembly or an insertion in the $organism \ assembly. Double lines represent more complex gaps that involve substantial\ sequence in both species. This may result from inversions, overlapping\ deletions, an abundance of local mutation, or an unsequenced gap in one\ species. In cases where multiple chains align over a particular region of\ the $organism genome, the chains with single-lined gaps are often \ due to processed pseudogenes, while chains with double-lined gaps are more \ often due to paralogs and unprocessed pseudogenes.
\\ In the "pack" and "full" display\ modes, the individual feature names indicate the chromosome, strand, and\ location (in thousands) of the match for each matching alignment.
\ \\ Transposons that have been inserted since the $o_organism/$organism\ split were removed from the assemblies. The abbreviated genomes were\ aligned with blastz, and the transposons were then added back in.\ The resulting alignments were converted into axt format using the lavToAxt\ program. The axt alignments were fed into axtChain, which organizes all\ alignments between a single $o_organism chromosome and a single\ $organism chromosome into a group and creates a kd-tree out\ of the gapless subsections (blocks) of the alignments. A dynamic program\ was then run over the kd-trees to find the maximally scoring chains of these\ blocks. Chains scoring below a threshold were discarded; the remaining\ chains are displayed in this track.
\ \\ Blastz was developed at Pennsylvania State University by \ Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\ Ross Hardison.
\\ Lineage-specific repeats were identified by Arian Smit and his \ RepeatMasker\ program.
\\ The axtChain program was developed at the University of California at \ Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler.
\\ The browser display and database storage of the chains were generated\ by Robert Baertsch and Jim Kent.
\ \\ Chiaromonte, F., Yap, V.B., Miller, W. \ Scoring pairwise genomic sequence alignments. \ Pac Symp Biocomput 2002, 115-26 (2002).
\\ Kent, W.J., Baertsch, R., Hinrichs, A., Miller, W., and Haussler, D.\ Evolution's cauldron: Duplication, deletion, and rearrangement\ in the mouse and human genomes.\ Proc Natl Acad Sci USA 100(20), 11484-11489 (2003).
\\ Schwartz, S., Kent, W.J., Smit, A., Zhang, Z., Baertsch, R., Hardison, R., \ Haussler, D., and Miller, W.\ Human-Mouse Alignments with BLASTZ. \ Genome Res. 13(1), 103-7 (2003).
\ \ compGeno 1 otherDb rn3\ netRn3 Rat Net netAlign rn3 chainRn3 $o_Organism ($o_date/$o_db) Alignment Net 1 260.1 0 0 0 127 127 127 1 0 0\ This track shows the best $o_organism/$organism chain for \ every part of the $organism genome. It is useful for\ finding orthologous regions and for studying genome\ rearrangement. The $o_organism sequence used in this annotation is from\ the $o_date ($o_db) assembly.
\ \\ In full display mode, the top-level (level 1)\ chains are the largest, highest-scoring chains that\ span this region. In many cases gaps exist in the\ top-level chain. When possible, these are filled in by\ other chains that are displayed at level 2. The gaps in \ level 2 chains may be filled by level 3 chains and so\ forth.
\\ In the graphical display, the boxes represent ungapped \ alignments; the lines represent gaps. Click\ on a box to view detailed information about the chain\ as a whole; click on a line to display information\ about the gap. The detailed information is useful in determining\ the cause of the gap or, for lower level chains, the genomic\ rearrangement.
\\ Individual items in the display are categorized as one of four types\ (other than gap):
\\ Chains were derived from blastz alignments, using the methods\ described on the chain tracks description pages, and sorted with the \ highest-scoring chains in the genome ranked first. The program\ chainNet was then used to place the chains one at a time, trimming them as \ necessary to fit into sections not already covered by a higher-scoring chain. \ During this process, a natural hierarchy emerged in which a chain that filled \ a gap in a higher-scoring chain was placed underneath that chain. The program \ netSyntenic was used to fill in information about the relationship between \ higher- and lower-level chains, such as whether a lower-level\ chain was syntenic or inverted relative to the higher-level chain. \ The program netClass was then used to fill in how much of the gaps and chains \ contained Ns (sequencing gaps) in one or both species and how much\ was filled with transposons inserted before and after the two organisms \ diverged.
\ \\ The chainNet, netSyntenic, and netClass programs were\ developed at the University of California\ Santa Cruz by Jim Kent.
\\ Blastz was developed at Pennsylvania State University by\ Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\ Ross Hardison.
\\ Lineage-specific repeats were identified by Arian Smit and his\ program RepeatMasker.\
\\ The browser display and database storage of the nets were made\ by Robert Baertsch and Jim Kent.
\ \\ Kent, W.J., Baertsch, R., Hinrichs, A., Miller, W., and Haussler, D.\ Evolution's cauldron: Duplication, deletion, and rearrangement\ in the mouse and human genomes.\ Proc Natl Acad Sci USA 100(20), 11484-11489 (2003).
\\ Schwartz, S., Kent, W.J., Smit, A., Zhang, Z., Baertsch, R., Hardison, R.,\ Haussler, D., and Miller, W.\ Human-Mouse Alignments with BLASTZ.\ Genome Res. 13(1), 103-7 (2003).
\ \ \ compGeno 0 otherDb rn3\