DQ547087
 

Information on mRNA DQ547087

Description: Mus musculus piRNA piR-15199, 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: DQ547087
Position: chr12:56795579-56795608

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 |    30  100.0%         12     -  56795579  56795608              DQ547087     1    30    30
browser |    30  100.0%          1     -   4628273   4628302              DQ547087     1    30    30
browser |    30  100.0%          1     -   5635890   5635919              DQ547087     1    30    30
browser |    30  100.0%          1     -   5875513   5875542              DQ547087     1    30    30
browser |    30  100.0%          1     +   6242053   6242082              DQ547087     1    30    30
browser |    30  100.0%          1     -   6501543   6501572              DQ547087     1    30    30
browser |    30  100.0%          1     +   8070074   8070103              DQ547087     1    30    30
browser |    30  100.0%          1     -  10801033  10801062              DQ547087     1    30    30
browser |    30  100.0%          1     -  11438663  11438692              DQ547087     1    30    30
browser |    30  100.0%          1     -  11958291  11958320              DQ547087     1    30    30
browser |    30  100.0%          1     -  12017791  12017820              DQ547087     1    30    30
browser |    30  100.0%          1     +  13626938  13626967              DQ547087     1    30    30
browser |    30  100.0%          1     +  16814587  16814616              DQ547087     1    30    30
browser |    30  100.0%          1     +  18033175  18033204              DQ547087     1    30    30
browser |    30  100.0%          1     +  18590461  18590490              DQ547087     1    30    30
browser |    30  100.0%          1     +  19698795  19698824              DQ547087     1    30    30
browser |    30  100.0%          1     +  21654166  21654195              DQ547087     1    30    30
browser |    30  100.0%          1     -  22066422  22066451              DQ547087     1    30    30
browser |    30  100.0%          1     +  23344456  23344485              DQ547087     1    30    30
browser |    30  100.0%          1     +  26459202  26459231              DQ547087     1    30    30
browser |    30  100.0%          1     -  26510398  26510427              DQ547087     1    30    30
browser |    30  100.0%          1     +  27225351  27225380              DQ547087     1    30    30
browser |    30  100.0%          1     -  28496269  28496298              DQ547087     1    30    30
browser |    30  100.0%          1     +  29697145  29697174              DQ547087     1    30    30
browser |    30  100.0%          1     -  29982752  29982781              DQ547087     1    30    30
browser |    30  100.0%          1     +  34389467  34389496              DQ547087     1    30    30
browser |    30  100.0%          1     +  34957300  34957329              DQ547087     1    30    30
browser |    30  100.0%          1     +  35833681  35833710              DQ547087     1    30    30
browser |    30  100.0%          1     -  37318833  37318862              DQ547087     1    30    30
browser |    30  100.0%          1     +  37816722  37816751              DQ547087     1    30    30
browser |    30  100.0%          1     -  47995966  47995995              DQ547087     1    30    30
browser |    30  100.0%          1     -  48394440  48394469              DQ547087     1    30    30
browser |    30  100.0%          1     -  48841972  48842001              DQ547087     1    30    30
browser |    30  100.0%          1     -  81542838  81542867              DQ547087     1    30    30
browser |    30  100.0%          1     +  82482742  82482771              DQ547087     1    30    30
browser |    30  100.0%          1     -  84974556  84974585              DQ547087     1    30    30
browser |    30  100.0%          1     -  87062319  87062348              DQ547087     1    30    30
browser |    30  100.0%          1     +  87394007  87394036              DQ547087     1    30    30
browser |    30  100.0%          1     +  89129964  89129993              DQ547087     1    30    30
browser |    30  100.0%          1     -  91399896  91399925              DQ547087     1    30    30
browser |    30  100.0%          1     -  93036163  93036192              DQ547087     1    30    30
browser |    30  100.0%          1     +  93888050  93888079              DQ547087     1    30    30
browser |    30  100.0%          1     +  97106090  97106119              DQ547087     1    30    30
browser |    30  100.0%          1     - 101906825 101906854              DQ547087     1    30    30
browser |    30  100.0%          1     + 102965518 102965547              DQ547087     1    30    30
browser |    30  100.0%          1     - 103133857 103133886              DQ547087     1    30    30
browser |    30  100.0%          1     + 103520777 103520806              DQ547087     1    30    30
browser |    30  100.0%          1     - 107967486 107967515              DQ547087     1    30    30
browser |    30  100.0%          1     - 108337545 108337574              DQ547087     1    30    30
browser |    30  100.0%          1     + 109547257 109547286              DQ547087     1    30    30
browser |    30  100.0%          1     + 110261028 110261057              DQ547087     1    30    30
browser |    30  100.0%          1     - 110866292 110866321              DQ547087     1    30    30
browser |    30  100.0%          1     - 111182317 111182346              DQ547087     1    30    30
browser |    30  100.0%          1     + 111637227 111637256              DQ547087     1    30    30
browser |    30  100.0%          1     - 112193030 112193059              DQ547087     1    30    30
browser |    30  100.0%          1     - 112492982 112493011              DQ547087     1    30    30
browser |    30  100.0%          1     + 112862220 112862249              DQ547087     1    30    30
browser |    30  100.0%          1     + 112949935 112949964              DQ547087     1    30    30
browser |    30  100.0%          1     + 114117245 114117274              DQ547087     1    30    30
browser |    30  100.0%          1     - 115814052 115814081              DQ547087     1    30    30
browser |    30  100.0%          1     - 116576962 116576991              DQ547087     1    30    30
browser |    30  100.0%          1     - 117630619 117630648              DQ547087     1    30    30
browser |    30  100.0%          1     + 125250720 125250749              DQ547087     1    30    30
browser |    30  100.0%          1     + 126356414 126356443              DQ547087     1    30    30
browser |    30  100.0%          1     + 126871140 126871169              DQ547087     1    30    30
browser |    30  100.0%          1     - 159798287 159798316              DQ547087     1    30    30
browser |    30  100.0%          1     + 162674248 162674277              DQ547087     1    30    30
browser |    30  100.0%          1     - 163297017 163297046              DQ547087     1    30    30
browser |    30  100.0%          1     - 166591660 166591689              DQ547087     1    30    30
browser |    30  100.0%          1     + 169375492 169375521              DQ547087     1    30    30
browser |    30  100.0%          1     + 172096322 172096351              DQ547087     1    30    30
browser |    30  100.0%          1     - 174870505 174870534              DQ547087     1    30    30
browser |    30  100.0%          1     - 176371587 176371616              DQ547087     1    30    30
browser |    30  100.0%          1     + 177891717 177891746              DQ547087     1    30    30
browser |    30  100.0%          1     + 178007801 178007830              DQ547087     1    30    30
browser |    30  100.0%          1     + 180442987 180443016              DQ547087     1    30    30
browser |    30  100.0%          1     - 181092043 181092072              DQ547087     1    30    30
browser |    30  100.0%          1     + 181326086 181326115              DQ547087     1    30    30
browser |    30  100.0%          1     + 183302405 183302434              DQ547087     1    30    30
browser |    30  100.0%          1     + 195008781 195008810              DQ547087     1    30    30
browser |    30  100.0%         10     -   3267290   3267319              DQ547087     1    30    30
browser |    30  100.0%         10     -   3551882   3551911              DQ547087     1    30    30
browser |    30  100.0%         10     -   6517725   6517754              DQ547087     1    30    30
browser |    30  100.0%         10     +   7365493   7365522              DQ547087     1    30    30
browser |    30  100.0%         10     +   8481173   8481202              DQ547087     1    30    30
browser |    30  100.0%         10     +   9726556   9726585              DQ547087     1    30    30
browser |    30  100.0%         10     +  11576151  11576180              DQ547087     1    30    30
browser |    30  100.0%         10     -  15056700  15056729              DQ547087     1    30    30
browser |    30  100.0%         10     +  18116531  18116560              DQ547087     1    30    30
browser |    30  100.0%         10     -  19415597  19415626              DQ547087     1    30    30
browser |    30  100.0%         10     -  19887327  19887356              DQ547087     1    30    30
browser |    30  100.0%         10     +  21091475  21091504              DQ547087     1    30    30
browser |    30  100.0%         10     -  21519170  21519199              DQ547087     1    30    30
browser |    30  100.0%         10     -  22560116  22560145              DQ547087     1    30    30
browser |    30  100.0%         10     -  23748171  23748200              DQ547087     1    30    30
browser |    30  100.0%         10     -  24978395  24978424              DQ547087     1    30    30
browser |    30  100.0%         10     +  25848216  25848245              DQ547087     1    30    30
browser |    30  100.0%         10     +  30360581  30360610              DQ547087     1    30    30
browser |    30  100.0%         10     +  30696113  30696142              DQ547087     1    30    30
browser |    30  100.0%         10     +  31364743  31364772              DQ547087     1    30    30
browser |    30  100.0%         10     +  31629887  31629916              DQ547087     1    30    30
browser |    30  100.0%         10     +  32814188  32814217              DQ547087     1    30    30
browser |    30  100.0%         10     +  33766059  33766088              DQ547087     1    30    30
browser |    30  100.0%         10     -  34618774  34618803              DQ547087     1    30    30
browser |    30  100.0%         10     -  35599874  35599903              DQ547087     1    30    30
browser |    30  100.0%         10     -  39637861  39637890              DQ547087     1    30    30
browser |    30  100.0%         10     +  41722665  41722694              DQ547087     1    30    30
browser |    30  100.0%         10     -  45431952  45431981              DQ547087     1    30    30
browser |    30  100.0%         10     +  50370592  50370621              DQ547087     1    30    30
browser |    30  100.0%         10     +  54468622  54468651              DQ547087     1    30    30
browser |    30  100.0%         10     -  55592579  55592608              DQ547087     1    30    30
browser |    30  100.0%         10     -  66559195  66559224              DQ547087     1    30    30
browser |    30  100.0%         10     +  80815704  80815733              DQ547087     1    30    30
browser |    30  100.0%         10     -  81507332  81507361              DQ547087     1    30    30
browser |    30  100.0%         10     -  81666460  81666489              DQ547087     1    30    30
browser |    30  100.0%         10     +  81809853  81809882              DQ547087     1    30    30
browser |    30  100.0%         10     -  83302687  83302716              DQ547087     1    30    30
browser |    30  100.0%         10     -  83507737  83507766              DQ547087     1    30    30
browser |    30  100.0%         10     +  85555578  85555607              DQ547087     1    30    30
browser |    30  100.0%         10     -  85605243  85605272              DQ547087     1    30    30
browser |    30  100.0%         10     +  88492959  88492988              DQ547087     1    30    30
browser |    30  100.0%         10     +  88803080  88803109              DQ547087     1    30    30
browser |    30  100.0%         10     -  92587333  92587362              DQ547087     1    30    30
browser |    30  100.0%         10     -  94199389  94199418              DQ547087     1    30    30
browser |    30  100.0%         10     -  95994060  95994089              DQ547087     1    30    30
browser |    30  100.0%         10     -  96029345  96029374              DQ547087     1    30    30
browser |    30  100.0%         10     -  97157373  97157402              DQ547087     1    30    30
browser |    30  100.0%         10     -  98935010  98935039              DQ547087     1    30    30
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browser |    30  100.0%         10     -  99382720  99382749              DQ547087     1    30    30
browser |    30  100.0%         10     + 100418650 100418679              DQ547087     1    30    30
browser |    30  100.0%         10     + 104397341 104397370              DQ547087     1    30    30
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browser |    30  100.0%         10     + 105016687 105016716              DQ547087     1    30    30
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browser |    30  100.0%         10     - 109152030 109152059              DQ547087     1    30    30
browser |    30  100.0%         10     + 111893286 111893315              DQ547087     1    30    30
browser |    30  100.0%         10     - 113559560 113559589              DQ547087     1    30    30
browser |    30  100.0%         10     - 116443118 116443147              DQ547087     1    30    30
browser |    30  100.0%         10     + 117911406 117911435              DQ547087     1    30    30
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browser |    30  100.0%         11     -   6092444   6092473              DQ547087     1    30    30
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browser |    30  100.0%          Y     -  15105959  15105988              DQ547087     1    30    30
browser |    30  100.0%          Y     -  15896125  15896154              DQ547087     1    30    30
browser |    30  100.0%          Y     +  17256248  17256277              DQ547087     1    30    30
browser |    30  100.0%          Y     -  19818562  19818591              DQ547087     1    30    30
browser |    30  100.0%          Y     +  21229146  21229175              DQ547087     1    30    30
browser |    30  100.0%          Y     -  21874271  21874300              DQ547087     1    30    30
browser |    30  100.0%          Y     -  23481763  23481792              DQ547087     1    30    30
browser |    30  100.0%          Y     +  35056501  35056530              DQ547087     1    30    30
browser |    30  100.0%          Y     -  35704348  35704377              DQ547087     1    30    30
browser |    30  100.0%          Y     -  39960283  39960312              DQ547087     1    30    30
browser |    30  100.0%          Y     -  42189406  42189435              DQ547087     1    30    30
browser |    30  100.0%          Y     -  42326885  42326914              DQ547087     1    30    30
browser |    30  100.0%          Y     -  42464949  42464978              DQ547087     1    30    30
browser |    30  100.0%          Y     +  43177878  43177907              DQ547087     1    30    30
browser |    30  100.0%          Y     -  43724587  43724616              DQ547087     1    30    30
browser |    30  100.0%          Y     +  68895073  68895102              DQ547087     1    30    30
browser |    30  100.0%          Y     +  81110296  81110325              DQ547087     1    30    30
browser |    30  100.0%          Y     -  82267191  82267220              DQ547087     1    30    30
browser |    30  100.0%          Y     +  84726407  84726436              DQ547087     1    30    30
browser |    30  100.0%          Y     -  85100916  85100945              DQ547087     1    30    30
browser |    30  100.0%          Y     +  87791250  87791279              DQ547087     1    30    30
browser |    30  100.0%          Y     +  88475941  88475970              DQ547087     1    30    30
browser |    30  100.0%          Y     +  89142453  89142482              DQ547087     1    30    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