DQ561141
 

Information on mRNA DQ561141

Description: Mus musculus piRNA piR-28253, 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: DQ561141
Position: chr12:56958909-56958938

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     -  56958909  56958938              DQ561141     1    29    29
browser |    29  100.0%          1     +   5636735   5636764              DQ561141     1    29    29
browser |    29  100.0%          1     -   5817617   5817646              DQ561141     1    29    29
browser |    29  100.0%          1     -   7679338   7679367              DQ561141     1    29    29
browser |    29  100.0%          1     -   8858076   8858105              DQ561141     1    29    29
browser |    29  100.0%          1     +  11439478  11439507              DQ561141     1    29    29
browser |    29  100.0%          1     +  12020323  12020352              DQ561141     1    29    29
browser |    29  100.0%          1     -  14031877  14031906              DQ561141     1    29    29
browser |    29  100.0%          1     +  17596594  17596623              DQ561141     1    29    29
browser |    29  100.0%          1     +  18324439  18324468              DQ561141     1    29    29
browser |    29  100.0%          1     -  27176476  27176505              DQ561141     1    29    29
browser |    29  100.0%          1     +  28497101  28497130              DQ561141     1    29    29
browser |    29  100.0%          1     -  28929115  28929144              DQ561141     1    29    29
browser |    29  100.0%          1     -  29694603  29694632              DQ561141     1    29    29
browser |    29  100.0%          1     +  30728513  30728542              DQ561141     1    29    29
browser |    29  100.0%          1     -  31045024  31045053              DQ561141     1    29    29
browser |    29  100.0%          1     -  31510006  31510035              DQ561141     1    29    29
browser |    29  100.0%          1     -  41128410  41128439              DQ561141     1    29    29
browser |    29  100.0%          1     -  44400412  44400441              DQ561141     1    29    29
browser |    29  100.0%          1     +  45651606  45651635              DQ561141     1    29    29
browser |    29  100.0%          1     -  47826974  47827003              DQ561141     1    29    29
browser |    29  100.0%          1     +  47996667  47996696              DQ561141     1    29    29
browser |    29  100.0%          1     -  48128955  48128984              DQ561141     1    29    29
browser |    29  100.0%          1     +  48712129  48712158              DQ561141     1    29    29
browser |    29  100.0%          1     -  50199829  50199858              DQ561141     1    29    29
browser |    29  100.0%          1     -  53275711  53275740              DQ561141     1    29    29
browser |    29  100.0%          1     -  57348654  57348683              DQ561141     1    29    29
browser |    29  100.0%          1     +  57627029  57627058              DQ561141     1    29    29
browser |    29  100.0%          1     +  67146585  67146614              DQ561141     1    29    29
browser |    29  100.0%          1     -  81961212  81961241              DQ561141     1    29    29
browser |    29  100.0%          1     +  86247119  86247148              DQ561141     1    29    29
browser |    29  100.0%          1     +  98530565  98530594              DQ561141     1    29    29
browser |    29  100.0%          1     - 102078422 102078451              DQ561141     1    29    29
browser |    29  100.0%          1     - 108065761 108065790              DQ561141     1    29    29
browser |    29  100.0%          1     + 108875776 108875805              DQ561141     1    29    29
browser |    29  100.0%          1     - 109056173 109056202              DQ561141     1    29    29
browser |    29  100.0%          1     + 109063567 109063596              DQ561141     1    29    29
browser |    29  100.0%          1     + 113609428 113609457              DQ561141     1    29    29
browser |    29  100.0%          1     + 117561636 117561665              DQ561141     1    29    29
browser |    29  100.0%          1     + 117676610 117676639              DQ561141     1    29    29
browser |    29  100.0%          1     - 128816588 128816617              DQ561141     1    29    29
browser |    29  100.0%          1     - 129019028 129019057              DQ561141     1    29    29
browser |    29  100.0%          1     + 136737567 136737596              DQ561141     1    29    29
browser |    29  100.0%          1     + 142288260 142288289              DQ561141     1    29    29
browser |    29  100.0%          1     - 150106722 150106751              DQ561141     1    29    29
browser |    29  100.0%          1     - 171658406 171658435              DQ561141     1    29    29
browser |    29  100.0%          1     + 177956200 177956229              DQ561141     1    29    29
browser |    29  100.0%          1     - 185036884 185036913              DQ561141     1    29    29
browser |    29  100.0%          1     - 191234919 191234948              DQ561141     1    29    29
browser |    29  100.0%         10     -   7192165   7192194              DQ561141     1    29    29
browser |    29  100.0%         10     -   7315889   7315918              DQ561141     1    29    29
browser |    29  100.0%         10     -   8511880   8511909              DQ561141     1    29    29
browser |    29  100.0%         10     +  11778363  11778392              DQ561141     1    29    29
browser |    29  100.0%         10     +  14488426  14488455              DQ561141     1    29    29
browser |    29  100.0%         10     -  18115697  18115726              DQ561141     1    29    29
browser |    28  100.0%         10     -  30358082  30358110              DQ561141     1    28    29
browser |    29  100.0%         10     -  30965377  30965406              DQ561141     1    29    29
browser |    29  100.0%         10     +  34617458  34617487              DQ561141     1    29    29
browser |    29  100.0%         10     +  35600563  35600592              DQ561141     1    29    29
browser |    29  100.0%         10     +  37729183  37729212              DQ561141     1    29    29
browser |    29  100.0%         10     -  38467027  38467056              DQ561141     1    29    29
browser |    29  100.0%         10     +  47513812  47513841              DQ561141     1    29    29
browser |    29  100.0%         10     +  47910079  47910108              DQ561141     1    29    29
browser |    29  100.0%         10     +  48871090  48871119              DQ561141     1    29    29
browser |    29  100.0%         10     +  73385796  73385825              DQ561141     1    29    29
browser |    29  100.0%         10     +  73692264  73692293              DQ561141     1    29    29
browser |    29  100.0%         10     -  74712420  74712449              DQ561141     1    29    29
browser |    29  100.0%         10     +  81512794  81512823              DQ561141     1    29    29
browser |    29  100.0%         10     +  81671922  81671951              DQ561141     1    29    29
browser |    29  100.0%         10     +  82410073  82410102              DQ561141     1    29    29
browser |    29  100.0%         10     -  82775928  82775957              DQ561141     1    29    29
browser |    29  100.0%         10     +  83254144  83254173              DQ561141     1    29    29
browser |    29  100.0%         10     -  86979136  86979165              DQ561141     1    29    29
browser |    29  100.0%         10     +  91651987  91652016              DQ561141     1    29    29
browser |    29  100.0%         10     -  92355721  92355750              DQ561141     1    29    29
browser |    29  100.0%         10     +  92589175  92589204              DQ561141     1    29    29
browser |    29  100.0%         10     - 103910564 103910593              DQ561141     1    29    29
browser |    29  100.0%         10     + 104412626 104412655              DQ561141     1    29    29
browser |    29  100.0%         10     - 110836952 110836981              DQ561141     1    29    29
browser |    29  100.0%         10     - 121977678 121977707              DQ561141     1    29    29
browser |    29  100.0%         10     - 122342352 122342381              DQ561141     1    29    29
browser |    29  100.0%         10     - 123695946 123695975              DQ561141     1    29    29
browser |    29  100.0%         10     + 124303940 124303969              DQ561141     1    29    29
browser |    29  100.0%         11     -   6748312   6748341              DQ561141     1    29    29
browser |    29  100.0%         11     +   9036597   9036626              DQ561141     1    29    29
browser |    29  100.0%         11     -  13823877  13823906              DQ561141     1    29    29
browser |    29  100.0%         11     +  14849115  14849144              DQ561141     1    29    29
browser |    29  100.0%         11     -  15811025  15811054              DQ561141     1    29    29
browser |    29  100.0%         11     +  16156040  16156069              DQ561141     1    29    29
browser |    29  100.0%         11     +  20460861  20460890              DQ561141     1    29    29
browser |    29  100.0%         11     +  27366761  27366790              DQ561141     1    29    29
browser |    29  100.0%         11     +  29115705  29115734              DQ561141     1    29    29
browser |    29  100.0%         11     -  29231203  29231232              DQ561141     1    29    29
browser |    29  100.0%         11     -  31163686  31163715              DQ561141     1    29    29
browser |    29  100.0%         11     -  44276070  44276099              DQ561141     1    29    29
browser |    29  100.0%         11     -  64683711  64683740              DQ561141     1    29    29
browser |    29  100.0%         11     -  67021534  67021563              DQ561141     1    29    29
browser |    29  100.0%         11     +  70959403  70959432              DQ561141     1    29    29
browser |    29  100.0%         11     +  73839878  73839907              DQ561141     1    29    29
browser |    29  100.0%         11     +  85332148  85332177              DQ561141     1    29    29
browser |    29  100.0%         11     -  90399400  90399429              DQ561141     1    29    29
browser |    29  100.0%         11     + 108715982 108716011              DQ561141     1    29    29
browser |    29  100.0%         12     -   4838735   4838764              DQ561141     1    29    29
browser |    29  100.0%         12     +  14650570  14650599              DQ561141     1    29    29
browser |    29  100.0%         12     -  17979506  17979535              DQ561141     1    29    29
browser |    29  100.0%         12     -  18180925  18180954              DQ561141     1    29    29
browser |    29  100.0%         12     -  24396565  24396594              DQ561141     1    29    29
browser |    29  100.0%         12     -  33798205  33798234              DQ561141     1    29    29
browser |    29  100.0%         12     -  36666844  36666873              DQ561141     1    29    29
browser |    29  100.0%         12     -  40232602  40232631              DQ561141     1    29    29
browser |    29  100.0%         12     -  42920790  42920819              DQ561141     1    29    29
browser |    29  100.0%         12     +  54918055  54918084              DQ561141     1    29    29
browser |    29  100.0%         12     -  60824329  60824358              DQ561141     1    29    29
browser |    29  100.0%         12     -  63337405  63337434              DQ561141     1    29    29
browser |    29  100.0%         12     -  65730964  65730993              DQ561141     1    29    29
browser |    29  100.0%         12     +  65833016  65833045              DQ561141     1    29    29
browser |    29  100.0%         12     -  65880326  65880355              DQ561141     1    29    29
browser |    29  100.0%         12     +  70971158  70971187              DQ561141     1    29    29
browser |    29  100.0%         12     -  76700792  76700821              DQ561141     1    29    29
browser |    29  100.0%         12     -  79162017  79162046              DQ561141     1    29    29
browser |    29  100.0%         12     -  91195144  91195173              DQ561141     1    29    29
browser |    29  100.0%         12     -  96904316  96904345              DQ561141     1    29    29
browser |    29  100.0%         12     + 101335781 101335810              DQ561141     1    29    29
browser |    29  100.0%         12     - 105595245 105595274              DQ561141     1    29    29
browser |    29  100.0%         12     + 109788721 109788750              DQ561141     1    29    29
browser |    29  100.0%         12     - 112852060 112852089              DQ561141     1    29    29
browser |    29  100.0%         12     - 114489023 114489052              DQ561141     1    29    29
browser |    29  100.0%         12     - 114905823 114905852              DQ561141     1    29    29
browser |    29  100.0%         12     - 115522520 115522549              DQ561141     1    29    29
browser |    29  100.0%         12     - 118759341 118759370              DQ561141     1    29    29
browser |    29  100.0%         13     +   3067312   3067341              DQ561141     1    29    29
browser |    29  100.0%         13     -   3665917   3665946              DQ561141     1    29    29
browser |    29  100.0%         13     +   6318656   6318685              DQ561141     1    29    29
browser |    29  100.0%         13     +   7654608   7654637              DQ561141     1    29    29
browser |    29  100.0%         13     +   8073672   8073701              DQ561141     1    29    29
browser |    29  100.0%         13     +   8319070   8319099              DQ561141     1    29    29
browser |    29  100.0%         13     +   9909408   9909437              DQ561141     1    29    29
browser |    29  100.0%         13     -  10828127  10828156              DQ561141     1    29    29
browser |    29  100.0%         13     -  11142775  11142804              DQ561141     1    29    29
browser |    29  100.0%         13     -  14113399  14113428              DQ561141     1    29    29
browser |    29  100.0%         13     -  24411460  24411489              DQ561141     1    29    29
browser |    29  100.0%         13     -  27472889  27472918              DQ561141     1    29    29
browser |    29  100.0%         13     +  28384165  28384194              DQ561141     1    29    29
browser |    29  100.0%         13     +  33960344  33960373              DQ561141     1    29    29
browser |    29  100.0%         13     -  39863336  39863365              DQ561141     1    29    29
browser |    29  100.0%         13     -  50060064  50060093              DQ561141     1    29    29
browser |    29  100.0%         13     +  50658407  50658436              DQ561141     1    29    29
browser |    29  100.0%         13     +  50712795  50712824              DQ561141     1    29    29
browser |    29  100.0%         13     -  51187308  51187337              DQ561141     1    29    29
browser |    29  100.0%         13     -  52205278  52205307              DQ561141     1    29    29
browser |    29  100.0%         13     -  62697213  62697242              DQ561141     1    29    29
browser |    29  100.0%         13     +  64648210  64648239              DQ561141     1    29    29
browser |    29  100.0%         13     -  65667420  65667449              DQ561141     1    29    29
browser |    29  100.0%         13     +  75358479  75358508              DQ561141     1    29    29
browser |    29  100.0%         13     -  76181749  76181778              DQ561141     1    29    29
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browser |    29  100.0%         13     - 106275858 106275887              DQ561141     1    29    29
browser |    29  100.0%         13     - 106922896 106922925              DQ561141     1    29    29
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browser |    29  100.0%         13     - 118286768 118286797              DQ561141     1    29    29
browser |    29  100.0%         14     +   4399248   4399277              DQ561141     1    29    29
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browser |    29  100.0%         15     +  32785820  32785849              DQ561141     1    29    29
browser |    29  100.0%         15     +  33660877  33660906              DQ561141     1    29    29
browser |    29  100.0%         15     +  38464398  38464427              DQ561141     1    29    29
browser |    29  100.0%         15     +  45059624  45059653              DQ561141     1    29    29
browser |    29  100.0%         15     +  49600418  49600447              DQ561141     1    29    29
browser |    29  100.0%         15     -  51946246  51946275              DQ561141     1    29    29
browser |    29  100.0%         15     -  56323271  56323300              DQ561141     1    29    29
browser |    29  100.0%         15     +  56668122  56668151              DQ561141     1    29    29
browser |    29  100.0%         15     -  57764329  57764358              DQ561141     1    29    29
browser |    29  100.0%         15     -  65917941  65917970              DQ561141     1    29    29
browser |    29  100.0%         15     -  65920226  65920255              DQ561141     1    29    29
browser |    29  100.0%         15     -  71083188  71083217              DQ561141     1    29    29
browser |    29  100.0%         15     -  77454457  77454486              DQ561141     1    29    29
browser |    29  100.0%         15     +  82492187  82492216              DQ561141     1    29    29
browser |    26  100.0%         15     +  84032615  84032641              DQ561141     4    29    29
browser |    29  100.0%         15     +  87400472  87400501              DQ561141     1    29    29
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View details of parts of alignment within browser window
.
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