DQ547088
 

Information on mRNA DQ547088

Description: Mus musculus piRNA piR-15200, 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: DQ547088
Position: chr12:56795580-56795608

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 |    29  100.0%         12     -  56795580  56795608              DQ547088     1    29    30
browser |    29  100.0%          1     -   4628274   4628302              DQ547088     1    29    30
browser |    29  100.0%          1     -   5635891   5635919              DQ547088     1    29    30
browser |    29  100.0%          1     -   5875514   5875542              DQ547088     1    29    30
browser |    29  100.0%          1     +   6242053   6242081              DQ547088     1    29    30
browser |    29  100.0%          1     -   6501544   6501572              DQ547088     1    29    30
browser |    29  100.0%          1     +   8070074   8070102              DQ547088     1    29    30
browser |    29  100.0%          1     -  10801034  10801062              DQ547088     1    29    30
browser |    29  100.0%          1     -  11438664  11438692              DQ547088     1    29    30
browser |    29  100.0%          1     -  11958292  11958320              DQ547088     1    29    30
browser |    29  100.0%          1     -  12017792  12017820              DQ547088     1    29    30
browser |    29  100.0%          1     +  13626938  13626966              DQ547088     1    29    30
browser |    29  100.0%          1     +  16814587  16814615              DQ547088     1    29    30
browser |    29  100.0%          1     +  18033175  18033203              DQ547088     1    29    30
browser |    29  100.0%          1     +  18590461  18590489              DQ547088     1    29    30
browser |    29  100.0%          1     +  19698795  19698823              DQ547088     1    29    30
browser |    29  100.0%          1     +  21654166  21654194              DQ547088     1    29    30
browser |    29  100.0%          1     -  22066423  22066451              DQ547088     1    29    30
browser |    29  100.0%          1     +  23344456  23344484              DQ547088     1    29    30
browser |    29  100.0%          1     +  26459202  26459230              DQ547088     1    29    30
browser |    29  100.0%          1     -  26510399  26510427              DQ547088     1    29    30
browser |    29  100.0%          1     +  27225351  27225379              DQ547088     1    29    30
browser |    29  100.0%          1     -  28496270  28496298              DQ547088     1    29    30
browser |    29  100.0%          1     +  29697145  29697173              DQ547088     1    29    30
browser |    29  100.0%          1     -  29982753  29982781              DQ547088     1    29    30
browser |    29  100.0%          1     +  34389467  34389495              DQ547088     1    29    30
browser |    29  100.0%          1     +  34957300  34957328              DQ547088     1    29    30
browser |    29  100.0%          1     +  35833681  35833709              DQ547088     1    29    30
browser |    29  100.0%          1     -  37318834  37318862              DQ547088     1    29    30
browser |    29  100.0%          1     +  37816722  37816750              DQ547088     1    29    30
browser |    29  100.0%          1     -  47995967  47995995              DQ547088     1    29    30
browser |    29  100.0%          1     -  48394441  48394469              DQ547088     1    29    30
browser |    29  100.0%          1     -  48841973  48842001              DQ547088     1    29    30
browser |    29  100.0%          1     -  81542839  81542867              DQ547088     1    29    30
browser |    29  100.0%          1     +  82482742  82482770              DQ547088     1    29    30
browser |    29  100.0%          1     -  84974557  84974585              DQ547088     1    29    30
browser |    29  100.0%          1     -  87062320  87062348              DQ547088     1    29    30
browser |    29  100.0%          1     +  87394007  87394035              DQ547088     1    29    30
browser |    29  100.0%          1     +  89129964  89129992              DQ547088     1    29    30
browser |    29  100.0%          1     -  91399897  91399925              DQ547088     1    29    30
browser |    29  100.0%          1     -  93036164  93036192              DQ547088     1    29    30
browser |    29  100.0%          1     +  93888050  93888078              DQ547088     1    29    30
browser |    29  100.0%          1     +  97106090  97106118              DQ547088     1    29    30
browser |    29  100.0%          1     - 101906826 101906854              DQ547088     1    29    30
browser |    29  100.0%          1     + 102965518 102965546              DQ547088     1    29    30
browser |    29  100.0%          1     - 103133858 103133886              DQ547088     1    29    30
browser |    29  100.0%          1     + 103520777 103520805              DQ547088     1    29    30
browser |    29  100.0%          1     - 107967487 107967515              DQ547088     1    29    30
browser |    29  100.0%          1     - 108337546 108337574              DQ547088     1    29    30
browser |    29  100.0%          1     + 109547257 109547285              DQ547088     1    29    30
browser |    29  100.0%          1     + 110261028 110261056              DQ547088     1    29    30
browser |    29  100.0%          1     - 110866293 110866321              DQ547088     1    29    30
browser |    29  100.0%          1     - 111182318 111182346              DQ547088     1    29    30
browser |    29  100.0%          1     + 111637227 111637255              DQ547088     1    29    30
browser |    29  100.0%          1     - 112193031 112193059              DQ547088     1    29    30
browser |    29  100.0%          1     - 112492983 112493011              DQ547088     1    29    30
browser |    29  100.0%          1     + 112862220 112862248              DQ547088     1    29    30
browser |    29  100.0%          1     + 112949935 112949963              DQ547088     1    29    30
browser |    29  100.0%          1     + 114117245 114117273              DQ547088     1    29    30
browser |    29  100.0%          1     - 115814053 115814081              DQ547088     1    29    30
browser |    29  100.0%          1     - 116576963 116576991              DQ547088     1    29    30
browser |    29  100.0%          1     - 117630620 117630648              DQ547088     1    29    30
browser |    29  100.0%          1     + 125250720 125250748              DQ547088     1    29    30
browser |    29  100.0%          1     + 126356414 126356442              DQ547088     1    29    30
browser |    29  100.0%          1     + 126871140 126871168              DQ547088     1    29    30
browser |    29  100.0%          1     - 159798288 159798316              DQ547088     1    29    30
browser |    29  100.0%          1     + 162674248 162674276              DQ547088     1    29    30
browser |    29  100.0%          1     - 163297018 163297046              DQ547088     1    29    30
browser |    29  100.0%          1     - 166591661 166591689              DQ547088     1    29    30
browser |    29  100.0%          1     + 169375492 169375520              DQ547088     1    29    30
browser |    29  100.0%          1     + 172096322 172096350              DQ547088     1    29    30
browser |    29  100.0%          1     - 174870506 174870534              DQ547088     1    29    30
browser |    29  100.0%          1     - 176371588 176371616              DQ547088     1    29    30
browser |    29  100.0%          1     + 177891717 177891745              DQ547088     1    29    30
browser |    29  100.0%          1     + 178007801 178007829              DQ547088     1    29    30
browser |    29  100.0%          1     + 180442987 180443015              DQ547088     1    29    30
browser |    29  100.0%          1     - 181092044 181092072              DQ547088     1    29    30
browser |    29  100.0%          1     + 181326086 181326114              DQ547088     1    29    30
browser |    29  100.0%          1     + 183302405 183302433              DQ547088     1    29    30
browser |    29  100.0%          1     + 195008781 195008809              DQ547088     1    29    30
browser |    29  100.0%         10     -   3267291   3267319              DQ547088     1    29    30
browser |    29  100.0%         10     -   3551883   3551911              DQ547088     1    29    30
browser |    29  100.0%         10     -   6517726   6517754              DQ547088     1    29    30
browser |    29  100.0%         10     +   7365493   7365521              DQ547088     1    29    30
browser |    29  100.0%         10     +   8481173   8481201              DQ547088     1    29    30
browser |    29  100.0%         10     +   9726556   9726584              DQ547088     1    29    30
browser |    29  100.0%         10     +  11576151  11576179              DQ547088     1    29    30
browser |    29  100.0%         10     -  15056701  15056729              DQ547088     1    29    30
browser |    29  100.0%         10     +  18116531  18116559              DQ547088     1    29    30
browser |    29  100.0%         10     -  19415598  19415626              DQ547088     1    29    30
browser |    29  100.0%         10     -  19887328  19887356              DQ547088     1    29    30
browser |    29  100.0%         10     +  21091475  21091503              DQ547088     1    29    30
browser |    29  100.0%         10     -  21519171  21519199              DQ547088     1    29    30
browser |    29  100.0%         10     -  22560117  22560145              DQ547088     1    29    30
browser |    29  100.0%         10     -  23748172  23748200              DQ547088     1    29    30
browser |    29  100.0%         10     -  24978396  24978424              DQ547088     1    29    30
browser |    29  100.0%         10     +  25848216  25848244              DQ547088     1    29    30
browser |    29  100.0%         10     +  30360581  30360609              DQ547088     1    29    30
browser |    29  100.0%         10     +  30696113  30696141              DQ547088     1    29    30
browser |    29  100.0%         10     +  31364743  31364771              DQ547088     1    29    30
browser |    29  100.0%         10     +  31629887  31629915              DQ547088     1    29    30
browser |    29  100.0%         10     +  32814188  32814216              DQ547088     1    29    30
browser |    29  100.0%         10     +  33766059  33766087              DQ547088     1    29    30
browser |    29  100.0%         10     -  34618775  34618803              DQ547088     1    29    30
browser |    29  100.0%         10     -  35599875  35599903              DQ547088     1    29    30
browser |    29  100.0%         10     -  39637862  39637890              DQ547088     1    29    30
browser |    29  100.0%         10     +  41722665  41722693              DQ547088     1    29    30
browser |    29  100.0%         10     -  45431953  45431981              DQ547088     1    29    30
browser |    29  100.0%         10     +  50370592  50370620              DQ547088     1    29    30
browser |    29  100.0%         10     +  54468622  54468650              DQ547088     1    29    30
browser |    29  100.0%         10     -  55592580  55592608              DQ547088     1    29    30
browser |    29  100.0%         10     -  66559196  66559224              DQ547088     1    29    30
browser |    29  100.0%         10     +  80815704  80815732              DQ547088     1    29    30
browser |    29  100.0%         10     -  81507333  81507361              DQ547088     1    29    30
browser |    29  100.0%         10     -  81666461  81666489              DQ547088     1    29    30
browser |    29  100.0%         10     +  81809853  81809881              DQ547088     1    29    30
browser |    29  100.0%         10     -  83302688  83302716              DQ547088     1    29    30
browser |    29  100.0%         10     -  83507738  83507766              DQ547088     1    29    30
browser |    29  100.0%         10     +  85555578  85555606              DQ547088     1    29    30
browser |    29  100.0%         10     -  85605244  85605272              DQ547088     1    29    30
browser |    29  100.0%         10     +  88492959  88492987              DQ547088     1    29    30
browser |    29  100.0%         10     +  88803080  88803108              DQ547088     1    29    30
browser |    29  100.0%         10     -  92587334  92587362              DQ547088     1    29    30
browser |    29  100.0%         10     -  94199390  94199418              DQ547088     1    29    30
browser |    29  100.0%         10     -  95994061  95994089              DQ547088     1    29    30
browser |    29  100.0%         10     -  96029346  96029374              DQ547088     1    29    30
browser |    29  100.0%         10     -  97157374  97157402              DQ547088     1    29    30
browser |    29  100.0%         10     -  98935011  98935039              DQ547088     1    29    30
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browser |    29  100.0%         10     -  99382721  99382749              DQ547088     1    29    30
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browser |    29  100.0%         10     + 104397341 104397369              DQ547088     1    29    30
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browser |    29  100.0%         10     + 105016687 105016715              DQ547088     1    29    30
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browser |    29  100.0%         10     - 109152031 109152059              DQ547088     1    29    30
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browser |    29  100.0%         10     - 113559561 113559589              DQ547088     1    29    30
browser |    29  100.0%         10     - 116443119 116443147              DQ547088     1    29    30
browser |    29  100.0%         10     + 117911406 117911434              DQ547088     1    29    30
browser |    29  100.0%         10     + 121004203 121004231              DQ547088     1    29    30
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browser |    29  100.0%         11     -   6092445   6092473              DQ547088     1    29    30
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browser |    29  100.0%         11     +  10716456  10716484              DQ547088     1    29    30
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browser |    29  100.0%          Y     +  12544374  12544402              DQ547088     1    29    30
browser |    29  100.0%          Y     -  15105960  15105988              DQ547088     1    29    30
browser |    29  100.0%          Y     -  15896126  15896154              DQ547088     1    29    30
browser |    29  100.0%          Y     +  17256248  17256276              DQ547088     1    29    30
browser |    29  100.0%          Y     -  19818563  19818591              DQ547088     1    29    30
browser |    29  100.0%          Y     +  21229146  21229174              DQ547088     1    29    30
browser |    29  100.0%          Y     -  21874272  21874300              DQ547088     1    29    30
browser |    29  100.0%          Y     -  23481764  23481792              DQ547088     1    29    30
browser |    29  100.0%          Y     +  35056501  35056529              DQ547088     1    29    30
browser |    29  100.0%          Y     -  35704349  35704377              DQ547088     1    29    30
browser |    29  100.0%          Y     -  39960284  39960312              DQ547088     1    29    30
browser |    29  100.0%          Y     -  42189407  42189435              DQ547088     1    29    30
browser |    29  100.0%          Y     -  42326886  42326914              DQ547088     1    29    30
browser |    29  100.0%          Y     -  42464950  42464978              DQ547088     1    29    30
browser |    29  100.0%          Y     +  43177878  43177906              DQ547088     1    29    30
browser |    29  100.0%          Y     -  43724588  43724616              DQ547088     1    29    30
browser |    29  100.0%          Y     +  68895073  68895101              DQ547088     1    29    30
browser |    29  100.0%          Y     +  81110296  81110324              DQ547088     1    29    30
browser |    29  100.0%          Y     -  82267192  82267220              DQ547088     1    29    30
browser |    29  100.0%          Y     +  84726407  84726435              DQ547088     1    29    30
browser |    29  100.0%          Y     -  85100917  85100945              DQ547088     1    29    30
browser |    29  100.0%          Y     +  87791250  87791278              DQ547088     1    29    30
browser |    29  100.0%          Y     +  88475941  88475969              DQ547088     1    29    30
browser |    29  100.0%          Y     +  89142453  89142481              DQ547088     1    29    30

View details of parts of alignment within browser window
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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