DQ544761
 

Information on mRNA DQ544761

Description: Mus musculus piRNA piR-12873, 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: DQ544761
Position: chr12:56958601-56958626

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 |    25  100.0%         12     +  56958601  56958626              DQ544761     1    25    26
browser |    25  100.0%          1     +   7678995   7679020              DQ544761     1    25    26
browser |    25  100.0%          1     +   8260831   8260856              DQ544761     1    25    26
browser |    25  100.0%          1     +  14031455  14031480              DQ544761     1    25    26
browser |    25  100.0%          1     +  28928691  28928716              DQ544761     1    25    26
browser |    25  100.0%          1     -  44420186  44420211              DQ544761     1    25    26
browser |    25  100.0%          1     +  47826420  47826445              DQ544761     1    25    26
browser |    25  100.0%          1     +  47826576  47826601              DQ544761     1    25    26
browser |    25  100.0%          1     +  57348155  57348180              DQ544761     1    25    26
browser |    24  100.0%          1     -  81670483  81670507              DQ544761     1    24    26
browser |    25  100.0%          1     -  81670636  81670742              DQ544761     1    25    26
browser |    25  100.0%          1     -  86247616  86247641              DQ544761     1    25    26
browser |    25  100.0%          1     -  96896707  96896732              DQ544761     1    25    26
browser |    24  100.0%          1     - 138733503 138733527              DQ544761     1    24    26
browser |    24  100.0%          1     - 167228212 167228236              DQ544761     1    24    26
browser |    25  100.0%          1     + 167831945 167831970              DQ544761     1    25    26
browser |    25  100.0%          1     + 185036460 185036485              DQ544761     1    25    26
browser |    24  100.0%         10     +   3225635   3225659              DQ544761     1    24    26
browser |    25  100.0%         10     -  65098872  65098897              DQ544761     1    25    26
browser |    25  100.0%         10     -  73386142  73386167              DQ544761     1    25    26
browser |    25  100.0%         10     -  73692611  73692636              DQ544761     1    25    26
browser |    24  100.0%         10     +  78773856  78773880              DQ544761     1    24    26
browser |    25  100.0%         10     +  86978715  86978740              DQ544761     1    25    26
browser |    24  100.0%         10     -  92589448  92589472              DQ544761     1    24    26
browser |    24  100.0%         10     - 103635143 103635167              DQ544761     1    24    26
browser |    25  100.0%         10     + 121189741 121189766              DQ544761     1    25    26
browser |    25  100.0%         10     - 126102266 126102291              DQ544761     1    25    26
browser |    24  100.0%         10     + 128878400 128878424              DQ544761     1    24    26
browser |    25  100.0%         11     +  29230935  29230960              DQ544761     1    25    26
browser |    25  100.0%         11     - 111250791 111250816              DQ544761     1    25    26
browser |    25  100.0%         12     -  18331861  18331886              DQ544761     1    25    26
browser |    25  100.0%         12     -  19867607  19867632              DQ544761     1    25    26
browser |    24  100.0%         12     -  20384792  20384816              DQ544761     1    24    26
browser |    25  100.0%         12     +  20543650  20543675              DQ544761     1    25    26
browser |    25  100.0%         12     +  20917255  20917280              DQ544761     1    25    26
browser |    25  100.0%         12     +  21654775  21654800              DQ544761     1    25    26
browser |    24  100.0%         12     -  26158547  26158571              DQ544761     1    24    26
browser |    25  100.0%         12     +  33797861  33797886              DQ544761     1    25    26
browser |    24  100.0%         12     -  74357013  74357037              DQ544761     1    24    26
browser |    25  100.0%         12     + 114905330 114905355              DQ544761     1    25    26
browser |    25  100.0%         13     -   8319342   8319367              DQ544761     1    25    26
browser |    24  100.0%         13     +  14113056  14113080              DQ544761     1    24    26
browser |    25  100.0%         13     +  50059715  50059740              DQ544761     1    25    26
browser |    25  100.0%         13     -  54570852  54570877              DQ544761     1    25    26
browser |    25  100.0%         13     -  66148321  66148346              DQ544761     1    25    26
browser |    25  100.0%         13     -  81233947  81233972              DQ544761     1    25    26
browser |    25  100.0%         13     -  86562752  86562777              DQ544761     1    25    26
browser |    25  100.0%         13     - 108594811 108594836              DQ544761     1    25    26
browser |    25  100.0%         14     +   6629036   6629061              DQ544761     1    25    26
browser |    24  100.0%         14     +  29264941  29264965              DQ544761     1    24    26
browser |    25  100.0%         14     +  29492971  29492996              DQ544761     1    25    26
browser |    24  100.0%         14     +  33370455  33370479              DQ544761     1    24    26
browser |    25  100.0%         14     +  39780456  39780481              DQ544761     1    25    26
browser |    24  100.0%         14     +  52975830  52975854              DQ544761     1    24    26
browser |    25  100.0%         14     +  72039235  72039260              DQ544761     1    25    26
browser |    25  100.0%         14     -  84080482  84080507              DQ544761     1    25    26
browser |    25  100.0%         14     +  92287391  92287416              DQ544761     1    25    26
browser |    25  100.0%         14     + 109432115 109432140              DQ544761     1    25    26
browser |    25  100.0%         14     - 110733392 110733417              DQ544761     1    25    26
browser |    25  100.0%         15     +  15995265  15995290              DQ544761     1    25    26
browser |    25  100.0%         15     +  16612736  16612761              DQ544761     1    25    26
browser |    26  100.0%         15     +  23958956  23958982              DQ544761     1    26    26
browser |    25  100.0%         15     -  32786092  32786117              DQ544761     1    25    26
browser |    25  100.0%         15     -  49600676  49600701              DQ544761     1    25    26
browser |    24  100.0%         15     +  57764061  57764085              DQ544761     1    24    26
browser |    25  100.0%         15     +  91304326  91304351              DQ544761     1    25    26
browser |    25  100.0%         15     -  97384476  97384501              DQ544761     1    25    26
browser |    24  100.0%         15     + 103859581 103859605              DQ544761     1    24    26
browser |    25  100.0%         16     +  20924265  20924290              DQ544761     1    25    26
browser |    25  100.0%         16     +  70179396  70179421              DQ544761     1    25    26
browser |    25  100.0%         17     +  29156956  29156981              DQ544761     1    25    26
browser |    24  100.0%         17     +  31771851  31771875              DQ544761     1    24    26
browser |    25  100.0%         17     +  37946656  37946681              DQ544761     1    25    26
browser |    25  100.0%         17     -  40047651  40047676              DQ544761     1    25    26
browser |    25  100.0%         18     -   6802901   6802926              DQ544761     1    25    26
browser |    25  100.0%         18     +  70975841  70975866              DQ544761     1    25    26
browser |    25  100.0%         19     +   9480071   9480096              DQ544761     1    25    26
browser |    24  100.0%         19     -  11402223  11402247              DQ544761     1    24    26
browser |    25  100.0%         19     -  13246927  13246952              DQ544761     1    25    26
browser |    25  100.0%         19     +  13587290  13587315              DQ544761     1    25    26
browser |    24  100.0%         19     +  13587371  13587395              DQ544761     1    24    26
browser |    25  100.0%          2     -   8203086   8203111              DQ544761     1    25    26
browser |    24  100.0%          2     -   9031658   9031682              DQ544761     1    24    26
browser |    25  100.0%          2     -  24057892  24057917              DQ544761     1    25    26
browser |    25  100.0%          2     +  32007705  32007730              DQ544761     1    25    26
browser |    24  100.0%          2     +  32007786  32007810              DQ544761     1    24    26
browser |    25  100.0%          2     +  40475051  40475076              DQ544761     1    25    26
browser |    25  100.0%          2     +  78147850  78147875              DQ544761     1    25    26
browser |    25  100.0%          2     -  87426341  87426366              DQ544761     1    25    26
browser |    24  100.0%          2     +  99266931  99266955              DQ544761     1    24    26
browser |    25  100.0%          2     - 110858012 110858037              DQ544761     1    25    26
browser |    25  100.0%          2     - 124194721 124194746              DQ544761     1    25    26
browser |    24  100.0%          2     - 129366438 129366462              DQ544761     1    24    26
browser |    25  100.0%          2     - 131489516 131489541              DQ544761     1    25    26
browser |    25  100.0%          2     - 138777076 138777101              DQ544761     1    25    26
browser |    24  100.0%          3     +   4069770   4069794              DQ544761     1    24    26
browser |    25  100.0%          3     +   5146355   5146380              DQ544761     1    25    26
browser |    25  100.0%          3     +   6126796   6126821              DQ544761     1    25    26
browser |    25  100.0%          3     -   8641267   8641292              DQ544761     1    25    26
browser |    25  100.0%          3     -  17046497  17046522              DQ544761     1    25    26
browser |    25  100.0%          3     -  23741782  23741807              DQ544761     1    25    26
browser |    25  100.0%          3     +  25330755  25330780              DQ544761     1    25    26
browser |    25  100.0%          3     -  33482546  33482571              DQ544761     1    25    26
browser |    25  100.0%          3     +  36470131  36470156              DQ544761     1    25    26
browser |    25  100.0%          3     -  49688222  49688247              DQ544761     1    25    26
browser |    25  100.0%          3     +  67682865  67682890              DQ544761     1    25    26
browser |    24  100.0%          3     -  85214708  85214732              DQ544761     1    24    26
browser |    25  100.0%          3     -  96227277  96227302              DQ544761     1    25    26
browser |    25  100.0%          3     + 108599381 108599406              DQ544761     1    25    26
browser |    24  100.0%          3     + 114658226 114658250              DQ544761     1    24    26
browser |    25  100.0%          3     - 116997961 116997986              DQ544761     1    25    26
browser |    24  100.0%          3     + 122448466 122448490              DQ544761     1    24    26
browser |    25  100.0%          3     - 147824817 147824842              DQ544761     1    25    26
browser |    24  100.0%          4     +  15747651  15747675              DQ544761     2    25    26
browser |    25  100.0%          4     -  73188197  73188222              DQ544761     1    25    26
browser |    25  100.0%          4     -  73312247  73312272              DQ544761     1    25    26
browser |    24  100.0%          4     -  88650358  88650382              DQ544761     1    24    26
browser |    25  100.0%          4     -  96830827  96830852              DQ544761     1    25    26
browser |    25  100.0%          4     + 130265366 130265391              DQ544761     1    25    26
browser |    25  100.0%          4     - 147133532 147133557              DQ544761     1    25    26
browser |    25  100.0%          4     - 153029622 153029647              DQ544761     1    25    26
browser |    24  100.0%          5     -   4512812   4512836              DQ544761     1    24    26
browser |    25  100.0%          5     -  25787096  25787121              DQ544761     1    25    26
browser |    25  100.0%          5     +  40718741  40718766              DQ544761     1    25    26
browser |    25  100.0%          5     -  50739961  50739986              DQ544761     1    25    26
browser |    24  100.0%          5     +  57807221  57807245              DQ544761     1    24    26
browser |    25  100.0%          5     -  83020856  83020881              DQ544761     1    25    26
browser |    25  100.0%          5     - 100140877 100140902              DQ544761     1    25    26
browser |    24  100.0%          5     + 124410046 124410070              DQ544761     1    24    26
browser |    25  100.0%          5     + 137843171 137843196              DQ544761     1    25    26
browser |    25  100.0%          6     -  14304451  14304557              DQ544761     1    25    26
browser |    25  100.0%          6     +  50589410  50589435              DQ544761     1    25    26
browser |    25  100.0%          6     -  68637762  68637787              DQ544761     1    25    26
browser |    25  100.0%          6     + 123925816 123925841              DQ544761     1    25    26
browser |    24  100.0%          6     + 128667040 128667064              DQ544761     1    24    26
browser |    25  100.0%          7     -   7017277   7017302              DQ544761     1    25    26
browser |    25  100.0%          7     -   7167986   7168011              DQ544761     1    25    26
browser |    25  100.0%          7     -   8582936   8582961              DQ544761     1    25    26
browser |    25  100.0%          7     +  11308351  11308376              DQ544761     1    25    26
browser |    25  100.0%          7     +  20032225  20032250              DQ544761     1    25    26
browser |    25  100.0%          7     +  31287960  31287985              DQ544761     1    25    26
browser |    25  100.0%          7     +  33329090  33329115              DQ544761     1    25    26
browser |    24  100.0%          7     +  33329245  33329269              DQ544761     1    24    26
browser |    24  100.0%          7     -  33496702  33496726              DQ544761     1    24    26
browser |    25  100.0%          7     +  42538800  42538825              DQ544761     1    25    26
browser |    24  100.0%          7     +  55059610  55059634              DQ544761     1    24    26
browser |    25  100.0%          7     +  74811545  74811570              DQ544761     1    25    26
browser |    24  100.0%          7     +  88922890  88922914              DQ544761     1    24    26
browser |    25  100.0%          7     + 124583615 124583640              DQ544761     1    25    26
browser |    24  100.0%          8     -  15790502  15790526              DQ544761     1    24    26
browser |    25  100.0%          8     +  30648450  30648475              DQ544761     1    25    26
browser |    24  100.0%          8     -  43410152  43410176              DQ544761     1    24    26
browser |    25  100.0%          8     +  45896770  45896795              DQ544761     1    25    26
browser |    24  100.0%          8     -  47907188  47907212              DQ544761     1    24    26
browser |    25  100.0%          8     +  55901716  55901741              DQ544761     1    25    26
browser |    25  100.0%          8     -  55981617  55981642              DQ544761     1    25    26
browser |    24  100.0%          8     +  78028046  78028070              DQ544761     1    24    26
browser |    25  100.0%          8     +  81916845  81916870              DQ544761     1    25    26
browser |    25  100.0%          8     +  91109321  91109346              DQ544761     1    25    26
browser |    24  100.0%          8     -  92469503  92469527              DQ544761     1    24    26
browser |    24  100.0%          8     - 100423297 100423321              DQ544761     1    24    26
browser |    25  100.0%          8     - 101718681 101718706              DQ544761     1    25    26
browser |    25  100.0%          8     - 102692716 102692741              DQ544761     1    25    26
browser |    24  100.0%          9     -   8399018   8399042              DQ544761     1    24    26
browser |    25  100.0%          9     -  33130837  33130862              DQ544761     1    25    26
browser |    24  100.0%          9     +  78973921  78973945              DQ544761     1    24    26
browser |    25  100.0%          9     -  81137954  81137979              DQ544761     1    25    26
browser |    25  100.0%          9     -  85800846  85800871              DQ544761     1    25    26
browser |    25  100.0%          X     -  16562906  16562931              DQ544761     1    25    26
browser |    24  100.0%          X     -  24352527  24352551              DQ544761     1    24    26
browser |    24  100.0%          X     +  42468545  42468569              DQ544761     1    24    26
browser |    25  100.0%          X     -  57597277  57597302              DQ544761     1    25    26
browser |    25  100.0%          X     +  73851346  73851371              DQ544761     1    25    26
browser |    25  100.0%          X     -  77391541  77391566              DQ544761     1    25    26
browser |    24  100.0%          X     +  88144676  88144700              DQ544761     1    24    26
browser |    25  100.0%          X     -  91282247  91282272              DQ544761     1    25    26
browser |    24  100.0%          X     -  96803677  96803701              DQ544761     1    24    26
browser |    25  100.0%          X     - 102094847 102094872              DQ544761     1    25    26
browser |    25  100.0%          X     - 104696501 104696526              DQ544761     1    25    26
browser |    25  100.0%          X     + 112867731 112867756              DQ544761     1    25    26
browser |    25  100.0%          X     + 115420000 115420025              DQ544761     1    25    26
browser |    25  100.0%          X     + 116386946 116386971              DQ544761     1    25    26
browser |    25  100.0%          X     - 117619651 117619676              DQ544761     1    25    26
browser |    25  100.0%          Y     +   2361400   2361425              DQ544761     1    25    26
browser |    25  100.0%          Y     -   5521171   5521196              DQ544761     1    25    26
browser |    25  100.0%          Y     -   6779621   6779646              DQ544761     1    25    26
browser |    25  100.0%          Y     +  15093046  15093071              DQ544761     1    25    26
browser |    25  100.0%          Y     -  40172056  40172081              DQ544761     1    25    26
browser |    25  100.0%          Y     -  41500461  41500486              DQ544761     1    25    26
browser |    25  100.0%          Y     +  42313945  42313970              DQ544761     1    25    26
browser |    25  100.0%          Y     -  46203451  46203476              DQ544761     1    25    26

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