This track shows locations of Sequence Tagged Sites (STS) \ along the rat draft assembly. These markers have been mapped using \ either genetic (Rat FHH x ACI F2 Intercross Genetic Map, Rat SHRSP x BN F2 Intercross Genetic Map) or radiation hybridization (RH Map 2.2) mapping techniques.
\\ Additional data on the individual maps can be found at the following links:\
\ \
By default all genetic map markers are shown as blue; only radiation\ hybrid markers and markers that are neither genetic nor radiation hybrid\ are shown as black; markers that map to more than one position are\ shown in lighter colors. Users can choose a color to highlight a subset\ of markers of interest from the Filter options in STS Markers\ Track Setting page.\ \
The track filter can be used to change the color or include/exclude\ a set of map data within the track. This is helpful when many items\ are shown in the track display, especially when only some are relevant\ to the current task. To use the filter:\
When you have finished configuring the filter, click the\ Submit button.
\ \ \ map 1 gold Assembly bed 3 + Assembly from Fragments 0 10 150 100 30 230 170 40 0 0 0This track shows the draft assembly of the $organism genome.\ Instead of a clone-by-clone assembly, the Rat genome assembly is pieced\ together from Bactig assemblies, which are reassemblies of the reads from\ sets of overlapping skimmed BAC clones, including mapped whole genome\ shotgun reads. The assembly process reworks the contigs (splitting some)\ and selects them under more stringent criteria than are used for the BAC\ submissions.
\In dense display mode, this track depicts the path through the draft and finished\ contigs used to create the assembled sequence. Where gaps\ exist in the path, spaces are shown between the blocks.\
\ map 1 gap Gap bed 3 + Gap Locations 1 11 0 0 0 127 127 127 0 0 0\ This track depicts gaps in the assembly. These gaps - with the\ exception of intractable heterochromatic gaps - will be closed during the\ finishing process. \
\ 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:\
\ Instead of clone-by-clone assemblies, the Rat genome assembly is\ pieced together from Bactig assemblies, which are reassemblies of the\ reads from sets of overlapping skimmed BAC clones, including mapped\ whole genome shotgun (WGS) reads. The assembly process reworks the contigs (splitting some)\ and selects them under more stringent criteria than used for the BAC\ submissions.
\ \\ Thanks to Paul Havlak at the \ \ Baylor College of Medicine Human Genome Sequencing Center \ for providing the data.
\ \ map 1 bacEndPairs BAC End Pairs bed 6 + BAC End Pairs 0 15 0 0 0 80 80 80 0 0 0\ 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 "-".
\\ The scoring scheme used for this annotation assigns 1000 to an alignment \ when the BAC end pair aligns to only one location in the genome (after \ filtering). When a BAC end pair or clone aligns to multiple locations, the \ score is calculated as 1500/(number of alignments).
\ \\ 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\ gcPercent GC Percent bed 4 + Percentage GC in 20,000-Base Windows 0 23 0 0 0 127 127 127 1 0 0\ The GC percent track shows the percentage of G (guanine) and C (cytosine) bases\ in a 20,000 base window. Windows with high GC content are drawn more darkly \ than windows with low GC content. High GC content is typically associated with \ gene-rich areas.\
\\ This track was generated at UCSC.\ map 1 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 \ protein data from SWISS-PROT, TrEMBL, and TrEMBL-NEW and their\ corresponding mRNAs from \ GenBank.
\ \\ This track follows the display conventions for\ gene prediction\ tracks. Black coloring indicates features that have corresponding entries\ in the Protein Databank (PDB). Blue indicates features associated with\ mRNAs from NCBI RefSeq or (dark blue) items having associated proteins in\ the SWISS-PROT database. The variation in blue shading of RefSeq items\ corresponds to the level of review the RefSeq record has undergone:\ predicted (light), provisional (medium), or reviewed (dark).
\\ This track contains an optional codon coloring\ feature that allows users to quickly validate and compare gene predictions.\ To display codon colors, select the genomic codons option from the\ Color track by codons pull-down menu. Click\ here for more\ information about this feature.
\ \\ mRNA sequences were aligned against the $organism genome using blat. When a \ single mRNA aligned in multiple places, only alignments having at least 98% \ base identity with the genomic sequence were kept. This set of mRNA \ alignments was further reduced by keeping only those mRNAs referenced by a \ protein in SWISS-PROT, TrEMBL, or TrEMBL-NEW.
\\ Among multiple mRNAs referenced by a single protein, the best mRNA was \ selected, based on a quality score derived from its length, the level of the\ match between its translation and the protein sequence, and its release date.\ The resulting mRNA and protein pairs were further filtered by removing \ short invalid entries and consolidating entries with identical CDS regions.\
\\ Finally, RefSeq entries derived from DNA sequences instead of \ mRNA sequences were added to produce the final data set shown in this track. \ Disease annotations were obtained from SWISS-PROT.
\ \\ The Known Genes track was produced at UCSC based primarily on cross-references\ between proteins from \ SWISS-PROT \ (including TrEMBL and TrEMBL-NEW) and mRNAs from \ GenBank\ contributed by scientists worldwide. \ NCBI RefSeq \ data were also included in this track.
\ \\ The UniProt data have the following terms of use, UniProt copyright(c) 2002 - \ 2004 UniProt consortium:
\\ For non-commercial use, all databases and documents in the UniProt FTP\ directory may be copied and redistributed freely, without advance\ permission, provided that this copyright statement is reproduced with\ each copy.
\\ For commercial use, all databases and documents in the UniProt FTP\ directory except the files\
\ From January 1, 2005, all databases and documents in the UniProt FTP\ directory may be copied and redistributed freely by all entities,\ without advance permission, provided that this copyright statement is\ reproduced with each copy.
\ \\ Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J,\ Wheeler DL.\ GenBank: update.\ Nucleic Acids Res. 2004 Jan 1;32:D23-6.
\\ Hsu F, Kent WJ, Clawson H, Kuhn RM, Diekhans M, Haussler D.\ The UCSC Known Genes.\ Bioinformatics. 2006 May 1;22(9):1036-46.
\\ Kent WJ.\ BLAT - the BLAST-like alignment tool.\ Genome Res. 2002 Apr;12(4):656-64.
\ genes 1 baseColorDefault genomicCodons\ baseColorUseCds given\ directUrl /cgi-bin/hgGene?hgg_gene=%s&hgg_chrom=%s&hgg_start=%d&hgg_end=%d&hgg_type=%s&db=%s\ hgGene on\ hgsid on\ idXref kgAlias kgID alias\ refGene RefSeq Genes genePred refPep refMrna RefSeq Genes 3 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. \
\ 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 WJ.\ BLAT - the BLAST-like alignment tool.\ Genome Res. 2002 Apr;12(4):656-64.
\ \Pruitt KD, Tatusova T, Maglott DR. \ NCBI Reference Sequence (RefSeq): a curated non-redundant \ sequence database of genomes, transcripts and proteins. Nucleic Acids \ Res. 2005 Jan 1;33(Database issue):D501-4.\
\ genes 1 baseColorUseCds given\ idXref refLink mrnaAcc name\ twinscan Twinscan genePred twinscanPep Twinscan Gene Predictions Using Rat/Human Homology 1 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://mblab.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, Brent MR.\ Integrating genomic homology into gene structure prediction.\ Bioinformatics. 2001 Jun 1;17(90001)S140-8.
\ genes 1 sgpGene SGP Genes genePred sgpPep SGP Gene Predictions Using Rat/Human Homology 1 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 softberryGene Fgenesh++ Genes genePred softberryPep Fgenesh++ Gene Predictions 1 48 0 100 0 127 177 127 0 0 0\ Fgenesh++ predictions are based on Softberry's gene-finding software.
\ \\ Fgenesh++ uses both hidden Markov models (HMMs) and protein similarity to \ find genes in a completely automated manner. For more information, see \ Solovyev, V.V. (2001) in the References section below.
\ \\ The Fgenesh++ gene predictions were produced by \ Softberry Inc. \ Commercial use of these predictions is restricted to viewing in \ this browser. Please contact Softberry Inc. to make arrangements for further \ commercial access.
\ \\ Solovyev, V.V. \ "Statistical approaches in Eukaryotic gene prediction" in the \ Handbook of Statistical Genetics (ed. Balding, D. et al.), \ 83-127. John Wiley & Sons, Ltd. (2001).
\ 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 \ Genome Bionformatics \ Laboratory (GBL), which is part of the \ Grup de Recerca\ en Informàtica Biomèdica (GRIB) at the Institut Municipal d'Investigació \ Mèdica (IMIM) / Centre de Regulació Genòmica (CRG) 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 GBL 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 and Karlin (1997) in the References section below. \ The splice site models used are described in more detail in Burge (1998)\ below.
\ \\ Burge C. \ Modeling Dependencies in Pre-mRNA Splicing Signals. \ In Salzberg S, Searls D, Kasif S, eds. \ Computational Methods in Molecular Biology, \ Elsevier Science, Amsterdam. 1998;127-163.
\\ Burge C, Karlin S. \ Prediction of Complete Gene Structures in Human Genomic DNA.\ J. Mol. Biol. 1997 Apr 25;268(1):78-94.
\ genes 1 mrna $Organism mRNAs psl . $Organism mRNAs from GenBank 3 54 0 0 0 127 127 127 0 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 compare mRNAs against the genomic sequence. For more \ information about this option, click \ here.\ Several types of alignment gap may also be colored; \ for more information, 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 DA, Karsch-Mizrachi I, Lipman DJ, Ostell J,\ Wheeler DL.\ GenBank: update. Nucleic Acids Res.\ 2004 Jan 1;32(Database issue):D23-6.
\\ Kent WJ.\ BLAT - the BLAST-like alignment tool.\ Genome Res. 2002 Apr;12(4):656-64.
\ rna 1 baseColorDefault diffCodons\ baseColorUseCds genbank\ baseColorUseSequence genbank\ indelDoubleInsert on\ indelPolyA on\ indelQueryInsert on\ showDiffBasesAllScales .\ 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 canonical intron, i.e. the genomic \ sequence between EST alignment blocks must be at least 32 bases in \ length and have 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, darker shading\ indicates a larger number of aligned ESTs.
\\ 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.\ Several types of alignment gap may also be colored; \ for more information, 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 750,000 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 DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, \ Wheeler DL. \ GenBank: update. Nucleic Acids Res.\ 2004 Jan 1;32(Database issue):D23-6.
\\ Kent WJ.\ BLAT - the BLAST-like alignment tool.\ Genome Res. 2002 Apr;12(4):656-64.
\ rna 1 baseColorUseSequence genbank\ indelDoubleInsert on\ indelQueryInsert on\ intronGap 30\ maxItems 300\ showDiffBasesAllScales .\ 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.\ Several types of alignment gap may also be colored; \ for more information, 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, $organism ESTs from GenBank were aligned \ against the genome using blat. Note that the maximum intron length\ allowed by blat is 750,000 bases, which may eliminate some ESTs with very \ long introns that might otherwise align. When a single \ EST aligned in multiple places, the alignment having the \ highest base identity was identified. Only alignments having\ a base identity level within 0.5% of the best and at least 96% base identity \ with the genomic sequence were kept.
\ \\ This track was produced at UCSC from EST sequence data\ submitted to the international public sequence databases by \ scientists worldwide.
\ \\ Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J,\ Wheeler DL.\ GenBank: update. Nucleic Acids Res.\ 2004 Jan 1;32(Database issue):D23-6.
\\ Kent WJ.\ BLAT - the BLAST-like alignment tool.\ Genome Res. 2002 Apr;12(4):656-64.
\ rna 1 baseColorUseSequence genbank\ indelDoubleInsert on\ indelQueryInsert on\ intronGap 30\ maxItems 300\ xenoMrna Other mRNAs psl xeno Non-$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.\ \
\ 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 (+/-) 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 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 compare mRNAs against the genomic sequence. For more \ information about this option, click \ here.\ Several types of alignment gap may also be colored; \ for more information, click \ here.\
\ \\ 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.
\ \\ The mRNA track was produced at UCSC from mRNA sequence data\ submitted to the international public sequence databases by \ scientists worldwide.
\ \\ Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, \ Wheeler DL. \ GenBank: update. Nucleic Acids Res.\ 2004 Jan 1;32(Database issue):D23-6.
\\ Kent WJ.\ BLAT - the BLAST-like alignment tool.\ Genome Res. 2002 Apr;12(4):656-64.
\ rna 1 baseColorUseCds genbank\ baseColorUseSequence genbank\ indelDoubleInsert on\ indelQueryInsert on\ showDiffBasesAllScales .\ rnaCluster Gene Bounds bed 12 . Gene Boundaries as Defined by RNA and Spliced EST Clusters 0 71 200 0 50 227 127 152 0 0 0\ This track shows the boundaries of genes and the direction of\ transcription as deduced from clustering spliced ESTs and mRNAs\ against the genome. When many spliced variants of the same gene exist, \ this track shows the variant that spans the greatest distance in the \ genome.
\ \\ ESTs and mRNAs from \ GenBank were aligned against the genome using blat.\ Alignments with less than 97.5% base identity within the aligning blocks \ were filtered out. When multiple alignments occurred, only those\ alignments with a percentage identity within 0.2% of the\ best alignment were kept. The following alignments were also discarded: \ ESTs that aligned without any introns, blocks smaller than 10 bases, and \ blocks smaller than 130 bases that were not located next to an intron. \ The orientations of the ESTs and mRNAs were deduced from the GT/AG splice \ sites at the introns; ESTs and mRNAs with overlapping blocks\ on the same strand were merged into clusters. Only the\ extent and orientation of the clusters are shown in this track.
\\ Scores for individual gene boundaries were assigned based on the number of \ cDNA alignments used:\
\ This track, which was originally developed by Jim Kent,\ was generated at UCSC and uses data submitted to GenBank by \ scientists worldwide.
\ \\ Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL. \ GenBank: update. Nucleic Acids Res. \ 2004 Jan 1;32:D23-6.
\\ Kent WJ.\ BLAT - the BLAST-like alignment tool.\ Genome Res. 2002 Apr;12(4):656-64.
\ rna 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 blatFugu Fugu Blat psl xeno Takifugu rubripes Translated Blat Alignments 1 113 0 60 120 200 220 255 1 0 0\ The Fugu v.3.0 whole genome shotgun assembly was provided by the\ US DOE Joint \ Genome Institute (JGI). The assembly was constructed with the JGI\ assembler, JAZZ, from paired end sequencing reads produced at JGI, Myriad \ Genetics, and Celera Genomics, resulting in a sequence coverage of 5.7X. All \ reads are plasmid, cosmid, or BAC end-sequences, with the predominant coverage\ derived from 2 Kb insert plasmids. This assembly contains 20,379\ scaffolds totaling 319 million base pairs. The largest 679 scaffolds\ total 160 million base pairs.
\\ 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 -+.
\ \\ The alignments were made with blat in translated protein mode requiring two\ nearby 4-mer matches to trigger a detailed alignment. The $organism\ genome was masked with RepeatMasker and Tandem Repeat Finder before \ running blat.
\ \\ The 3.0 draft from the\ \ JGI Fugu rubripes website was used in the\ UCSC Genome Browser Fugu blat alignments. These data were freely provided \ by the JGI for use in this publication only.
\ \\ Kent, W.J.\ BLAT - the BLAST-like alignment tool.\ Genome Res. 12(4), 656-664 (2002).
\ \ compGeno 1 rmsk RepeatMasker rmsk Repeating Elements by RepeatMasker 1 149.1 0 0 0 127 127 127 1 0 0\
This track was created by using Arian Smit's
\ In full display mode, this track displays up to ten 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.
\ \\ Smit, AFA, Hubley, R and Green, P. RepeatMasker Open-3.0.\ http://www.repeatmasker.org. 1996-2007.\
\\ RepBase is described in \ Jurka J. \ Repbase update: a database and an electronic journal of \ repetitive elements. \ Trends Genet. 2000 Sep;16(9):418-420.
\\ For a discussion of repeats in mammalian genomes, see: \
\ Smit AF. Interspersed repeats and other mementos of transposable \ elements in mammalian genomes. Curr Opin Genet Dev. 1999 Dec;9(6):\ 657-63.
\\ Smit AF. The origin of interspersed repeats in the human genome. \ Curr Opin Genet Dev. 1996 Dec;6(6):743-8.\
\ 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 TRF program, see Benson (1999).\
\ \\ TRF was written by \ Gary Benson.
\ \\ Benson G. \ Tandem repeats finder: a program to analyze DNA sequences.\ Nucleic Acids Res. 1999 Jan 15;27(2):573-80.
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