DQ569747
 

Information on mRNA DQ569747

Description: Mus musculus piRNA piR-9835, complete sequence.
Gene: n/a
Product: n/a
Author: Girard,A., Sachidanandam,R., Hannon,G.J. and Carmell,M.A.
Organism: Mus musculus
Tissue: n/a
Development stage: n/a
Cell line: n/a
Sex: n/a
Library: n/a
Clone: n/a
CDS: n/a
Date: 2008-11-02
Version: 1
mRNA sequence: DQ569747
Position: chr12:56795158-56795188

mRNA/Genomic Alignments

The alignment you clicked on is first in the table below.
BROWSER | SIZE IDENTITY CHROMOSOME  STRAND    START     END              QUERY      START  END  TOTAL
-----------------------------------------------------------------------------------------------------
browser |    31  100.0%         12     -  56795158  56795188              DQ569747     1    31    31
browser |    31  100.0%          1     -   5635469   5635499              DQ569747     1    31    31
browser |    31  100.0%          1     +   6242474   6242504              DQ569747     1    31    31
browser |    31  100.0%          1     -   6501121   6501151              DQ569747     1    31    31
browser |    31  100.0%          1     -  11957870  11957900              DQ569747     1    31    31
browser |    31  100.0%          1     +  18590875  18590905              DQ569747     1    31    31
browser |    31  100.0%          1     +  19699215  19699245              DQ569747     1    31    31
browser |    31  100.0%          1     +  23344877  23344907              DQ569747     1    31    31
browser |    31  100.0%          1     -  26388783  26388813              DQ569747     1    31    31
browser |    31  100.0%          1     -  26509977  26510007              DQ569747     1    31    31
browser |    31  100.0%          1     +  28930235  28930265              DQ569747     1    31    31
browser |    31  100.0%          1     +  34389888  34389918              DQ569747     1    31    31
browser |    31  100.0%          1     +  35834101  35834131              DQ569747     1    31    31
browser |    31  100.0%          1     +  38747476  38747506              DQ569747     1    31    31
browser |    31  100.0%          1     +  40741060  40741090              DQ569747     1    31    31
browser |    31  100.0%          1     +  45777951  45777981              DQ569747     1    31    31
browser |    31  100.0%          1     -  47995545  47995575              DQ569747     1    31    31
browser |    31  100.0%          1     +  48132886  48132916              DQ569747     1    31    31
browser |    31  100.0%          1     -  48841551  48841581              DQ569747     1    31    31
browser |    31  100.0%          1     +  50201091  50201121              DQ569747     1    31    31
browser |    31  100.0%          1     -  53169315  53169345              DQ569747     1    31    31
browser |    31  100.0%          1     +  55821860  55821890              DQ569747     1    31    31
browser |    31  100.0%          1     +  56817901  56817931              DQ569747     1    31    31
browser |    31  100.0%          1     -  58363054  58363084              DQ569747     1    31    31
browser |    31  100.0%          1     +  58973819  58973849              DQ569747     1    31    31
browser |    31  100.0%          1     -  62573810  62573840              DQ569747     1    31    31
browser |    31  100.0%          1     +  64428802  64428832              DQ569747     1    31    31
browser |    31  100.0%          1     -  65000004  65000034              DQ569747     1    31    31
browser |    31  100.0%          1     -  66057314  66057344              DQ569747     1    31    31
browser |    31  100.0%          1     -  67791121  67791151              DQ569747     1    31    31
browser |    31  100.0%          1     -  69737758  69737788              DQ569747     1    31    31
browser |    31  100.0%          1     -  74693126  74693156              DQ569747     1    31    31
browser |    31  100.0%          1     -  76750525  76750555              DQ569747     1    31    31
browser |    31  100.0%          1     -  81542417  81542447              DQ569747     1    31    31
browser |    31  100.0%          1     -  84974135  84974165              DQ569747     1    31    31
browser |    31  100.0%          1     -  86246006  86246036              DQ569747     1    31    31
browser |    31  100.0%          1     +  87394422  87394452              DQ569747     1    31    31
browser |    31  100.0%          1     +  89130384  89130414              DQ569747     1    31    31
browser |    31  100.0%          1     -  91399474  91399504              DQ569747     1    31    31
browser |    31  100.0%          1     +  93888471  93888501              DQ569747     1    31    31
browser |    31  100.0%          1     + 102965939 102965969              DQ569747     1    31    31
browser |    31  100.0%          1     - 103133442 103133472              DQ569747     1    31    31
browser |    31  100.0%          1     + 103521197 103521227              DQ569747     1    31    31
browser |    31  100.0%          1     - 104217832 104217862              DQ569747     1    31    31
browser |    31  100.0%          1     - 107967064 107967094              DQ569747     1    31    31
browser |    31  100.0%          1     - 108337129 108337159              DQ569747     1    31    31
browser |    31  100.0%          1     - 109056938 109056968              DQ569747     1    31    31
browser |    31  100.0%          1     + 109547671 109547701              DQ569747     1    31    31
browser |    31  100.0%          1     + 110261443 110261473              DQ569747     1    31    31
browser |    31  100.0%          1     - 110865871 110865901              DQ569747     1    31    31
browser |    31  100.0%          1     - 111181896 111181926              DQ569747     1    31    31
browser |    31  100.0%          1     + 112950350 112950380              DQ569747     1    31    31
browser |    31  100.0%          1     + 114117659 114117689              DQ569747     1    31    31
browser |    31  100.0%          1     - 115813637 115813667              DQ569747     1    31    31
browser |    31  100.0%          1     - 116576540 116576570              DQ569747     1    31    31
browser |    31  100.0%          1     - 117630198 117630228              DQ569747     1    31    31
browser |    31  100.0%          1     - 117675484 117675514              DQ569747     1    31    31
browser |    31  100.0%          1     - 120499118 120499148              DQ569747     1    31    31
browser |    31  100.0%          1     + 125251134 125251164              DQ569747     1    31    31
browser |    31  100.0%          1     + 126356835 126356865              DQ569747     1    31    31
browser |    31  100.0%          1     + 126871555 126871585              DQ569747     1    31    31
browser |    31  100.0%          1     + 130466414 130466444              DQ569747     1    31    31
browser |    31  100.0%          1     + 139657253 139657283              DQ569747     1    31    31
browser |    31  100.0%          1     + 140751097 140751127              DQ569747     1    31    31
browser |    31  100.0%          1     + 140969694 140969724              DQ569747     1    31    31
browser |    31  100.0%          1     - 159797872 159797902              DQ569747     1    31    31
browser |    31  100.0%          1     - 160643985 160644015              DQ569747     1    31    31
browser |    31  100.0%          1     + 162674663 162674693              DQ569747     1    31    31
browser |    31  100.0%          1     + 171659530 171659560              DQ569747     1    31    31
browser |    31  100.0%          1     - 174870084 174870114              DQ569747     1    31    31
browser |    31  100.0%          1     - 176371166 176371196              DQ569747     1    31    31
browser |    31  100.0%          1     + 177892132 177892162              DQ569747     1    31    31
browser |    31  100.0%          1     + 178008221 178008251              DQ569747     1    31    31
browser |    31  100.0%          1     - 181091622 181091652              DQ569747     1    31    31
browser |    31  100.0%          1     + 185038009 185038039              DQ569747     1    31    31
browser |    31  100.0%          1     + 191236043 191236073              DQ569747     1    31    31
browser |    31  100.0%          1     + 191844324 191844354              DQ569747     1    31    31
browser |    31  100.0%         10     -   3551461   3551491              DQ569747     1    31    31
browser |    31  100.0%         10     -  19415176  19415206              DQ569747     1    31    31
browser |    31  100.0%         10     +  21091895  21091925              DQ569747     1    31    31
browser |    31  100.0%         10     -  21518749  21518779              DQ569747     1    31    31
browser |    31  100.0%         10     -  22559695  22559725              DQ569747     1    31    31
browser |    31  100.0%         10     +  24566919  24566949              DQ569747     1    31    31
browser |    31  100.0%         10     -  24977980  24978010              DQ569747     1    31    31
browser |    31  100.0%         10     +  30696532  30696562              DQ569747     1    31    31
browser |    31  100.0%         10     +  30971214  30971244              DQ569747     1    31    31
browser |    31  100.0%         10     +  31630307  31630337              DQ569747     1    31    31
browser |    31  100.0%         10     +  33766479  33766509              DQ569747     1    31    31
browser |    31  100.0%         10     -  34618353  34618383              DQ569747     1    31    31
browser |    31  100.0%         10     +  41723085  41723115              DQ569747     1    31    31
browser |    31  100.0%         10     -  43646202  43646232              DQ569747     1    31    31
browser |    31  100.0%         10     -  45431531  45431561              DQ569747     1    31    31
browser |    31  100.0%         10     -  47908960  47908990              DQ569747     1    31    31
browser |    31  100.0%         10     +  51763456  51763486              DQ569747     1    31    31
browser |    31  100.0%         10     +  54469043  54469073              DQ569747     1    31    31
browser |    31  100.0%         10     -  55592163  55592193              DQ569747     1    31    31
browser |    31  100.0%         10     +  56603394  56603424              DQ569747     1    31    31
browser |    31  100.0%         10     +  57020313  57020343              DQ569747     1    31    31
browser |    31  100.0%         10     +  59222304  59222334              DQ569747     1    31    31
browser |    31  100.0%         10     -  65787128  65787158              DQ569747     1    31    31
browser |    31  100.0%         10     +  71533798  71533828              DQ569747     1    31    31
browser |    31  100.0%         10     -  73384677  73384707              DQ569747     1    31    31
browser |    31  100.0%         10     -  75216980  75217010              DQ569747     1    31    31
browser |    31  100.0%         10     +  77793158  77793188              DQ569747     1    31    31
browser |    31  100.0%         10     +  77860847  77860877              DQ569747     1    31    31
browser |    31  100.0%         10     +  80816125  80816155              DQ569747     1    31    31
browser |    31  100.0%         10     -  83507316  83507346              DQ569747     1    31    31
browser |    31  100.0%         10     +  83627900  83627930              DQ569747     1    31    31
browser |    31  100.0%         10     +  84585191  84585221              DQ569747     1    31    31
browser |    31  100.0%         10     +  88803494  88803524              DQ569747     1    31    31
browser |    31  100.0%         10     -  90161006  90161036              DQ569747     1    31    31
browser |    31  100.0%         10     -  91650856  91650886              DQ569747     1    31    31
browser |    31  100.0%         10     +  92356851  92356881              DQ569747     1    31    31
browser |    31  100.0%         10     -  94198967  94198997              DQ569747     1    31    31
browser |    31  100.0%         10     -  95993638  95993668              DQ569747     1    31    31
browser |    31  100.0%         10     -  98934589  98934619              DQ569747     1    31    31
browser |    31  100.0%         10     +  99181534  99181564              DQ569747     1    31    31
browser |    31  100.0%         10     - 104655882 104655912              DQ569747     1    31    31
browser |    31  100.0%         10     + 104677983 104678013              DQ569747     1    31    31
browser |    31  100.0%         10     + 105017108 105017138              DQ569747     1    31    31
browser |    31  100.0%         10     - 105509047 105509077              DQ569747     1    31    31
browser |    31  100.0%         10     + 107841910 107841940              DQ569747     1    31    31
browser |    31  100.0%         10     - 109151608 109151638              DQ569747     1    31    31
browser |    31  100.0%         10     + 110838234 110838264              DQ569747     1    31    31
browser |    31  100.0%         10     + 111893706 111893736              DQ569747     1    31    31
browser |    31  100.0%         10     - 113559145 113559175              DQ569747     1    31    31
browser |    31  100.0%         10     + 117911826 117911856              DQ569747     1    31    31
browser |    31  100.0%         10     + 121004617 121004647              DQ569747     1    31    31
browser |    31  100.0%         10     - 122202500 122202530              DQ569747     1    31    31
browser |    31  100.0%         10     + 124418778 124418808              DQ569747     1    31    31
browser |    31  100.0%         10     + 124446278 124446308              DQ569747     1    31    31
browser |    31  100.0%         10     - 124516884 124516914              DQ569747     1    31    31
browser |    31  100.0%         10     - 129225228 129225258              DQ569747     1    31    31
browser |    31  100.0%         10     + 129764974 129765004              DQ569747     1    31    31
browser |    31  100.0%         11     -   6092028   6092058              DQ569747     1    31    31
browser |    31  100.0%         11     +   6485231   6485261              DQ569747     1    31    31
browser |    31  100.0%         11     -  12457826  12457856              DQ569747     1    31    31
browser |    31  100.0%         11     +  12518482  12518512              DQ569747     1    31    31
browser |    31  100.0%         11     -  12904553  12904583              DQ569747     1    31    31
browser |    31  100.0%         11     +  15812137  15812167              DQ569747     1    31    31
browser |    31  100.0%         11     -  19516713  19516743              DQ569747     1    31    31
browser |    31  100.0%         11     +  20470597  20470627              DQ569747     1    31    31
browser |    31  100.0%         11     -  22285790  22285820              DQ569747     1    31    31
browser |    31  100.0%         11     +  22532442  22532472              DQ569747     1    31    31
browser |    31  100.0%         11     -  23169114  23169144              DQ569747     1    31    31
browser |    31  100.0%         11     +  26510191  26510221              DQ569747     1    31    31
browser |    31  100.0%         11     -  27901616  27901646              DQ569747     1    31    31
browser |    31  100.0%         11     +  28053857  28053887              DQ569747     1    31    31
browser |    31  100.0%         11     +  29079230  29079260              DQ569747     1    31    31
browser |    31  100.0%         11     +  31726435  31726465              DQ569747     1    31    31
browser |    31  100.0%         11     +  38377606  38377636              DQ569747     1    31    31
browser |    31  100.0%         11     -  39955089  39955119              DQ569747     1    31    31
browser |    31  100.0%         11     +  44277194  44277224              DQ569747     1    31    31
browser |    31  100.0%         11     +  51332320  51332350              DQ569747     1    31    31
browser |    31  100.0%         11     -  51556390  51556420              DQ569747     1    31    31
browser |    31  100.0%         11     -  55132300  55132330              DQ569747     1    31    31
browser |    31  100.0%         11     +  61317828  61317858              DQ569747     1    31    31
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browser |    31  100.0%         11     +  64687640  64687670              DQ569747     1    31    31
browser |    31  100.0%         11     -  66839187  66839217              DQ569747     1    31    31
browser |    31  100.0%         11     -  73627329  73627359              DQ569747     1    31    31
browser |    31  100.0%         11     -  74111051  74111081              DQ569747     1    31    31
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browser |    31  100.0%         11     -  90851532  90851562              DQ569747     1    31    31
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browser |    31  100.0%         11     - 115646257 115646287              DQ569747     1    31    31
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browser |    31  100.0%         12     +  81634060  81634090              DQ569747     1    31    31
browser |    31  100.0%         12     -  82508394  82508424              DQ569747     1    31    31
browser |    29  100.0%         12     -  94003817  94003845              DQ569747     1    29    31
browser |    31  100.0%         12     -  96197494  96197524              DQ569747     1    31    31
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View details of parts of alignment within browser window
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View table schema

Go to Mouse mRNAs track controls

Data last updated at UCSC: 2020-08-18

Description

The mRNA track shows alignments between mouse mRNAs in GenBank and the genome.

Display Conventions and Configuration

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:

  1. Type a term in one or more of the text boxes to filter the mRNA display. For example, to apply the filter to all mRNAs expressed in a specific organ, type the name of the organ in the tissue box. To view the list of valid terms for each text box, consult the table in the Table Browser that corresponds to the factor on which you wish to filter. For example, the "tissue" table contains all the types of tissues that can be entered into the tissue text box. Multiple terms may be entered at once, separated by a space. Wildcards may also be used in the filter.
  2. If filtering on more than one value, choose the desired combination logic. If "and" is selected, only mRNAs that match all filter criteria will be highlighted. If "or" is selected, mRNAs that match any one of the filter criteria will be highlighted.
  3. Choose the color or display characteristic that should be used to highlight or include/exclude the filtered items. If "exclude" is chosen, the browser will not display mRNAs that match the filter criteria. If "include" is selected, the browser will display only those mRNAs that match the filter criteria.

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, go to the Codon and Base Coloring for Alignment Tracks page. Several types of alignment gap may also be colored; for more information, go to the Alignment Insertion/Deletion Display Options page.

Methods

GenBank mouse 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.

Credits

The mRNA track was produced at UCSC from mRNA sequence data submitted to the international public sequence databases by scientists worldwide.

References

Benson DA, Cavanaugh M, Clark K, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW. GenBank. Nucleic Acids Res. 2013 Jan;41(Database issue):D36-42. PMID: 23193287; PMC: PMC3531190

Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL. GenBank: update. Nucleic Acids Res. 2004 Jan 1;32(Database issue):D23-6. PMID: 14681350; PMC: PMC308779

Kent WJ. BLAT - the BLAST-like alignment tool. Genome Res. 2002 Apr;12(4):656-64. PMID: 11932250; PMC: PMC187518