DQ704676
 

Information on mRNA DQ704676

Description: Mus musculus piRNA piR-119998, complete sequence.
Gene: n/a
Product: n/a
Author: Lau,N.C., Seto,A.G., Kim,J., Kuramochi-Miyagawa,S., Nakano,T., Bartel,D.P. and Kingston,R.E.
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: 2006-06-09
Version: 1
mRNA sequence: DQ704676
Position: chrX:15640716-15640739

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 |    24  100.0%          X     -  15640716  15640739              DQ704676     3    26    26
browser |    26  100.0%          1     -   8864188   8864213              DQ704676     1    26    26
browser |    24  100.0%          1     +  19257676  19257699              DQ704676     3    26    26
browser |    26  100.0%          1     +  27902189  27902214              DQ704676     1    26    26
browser |    26  100.0%          1     +  28194104  28194129              DQ704676     1    26    26
browser |    25  100.0%          1     -  48011256  48011280              DQ704676     1    25    26
browser |    26  100.0%          1     -  50699719  50699744              DQ704676     1    26    26
browser |    26  100.0%          1     -  77551661  77551686              DQ704676     1    26    26
browser |    26  100.0%          1     -  89220688  89220713              DQ704676     1    26    26
browser |    26  100.0%          1     +  96775138  96775163              DQ704676     1    26    26
browser |    26  100.0%          1     - 112300150 112300175              DQ704676     1    26    26
browser |    25  100.0%          1     - 115140303 115140327              DQ704676     2    26    26
browser |    26  100.0%          1     - 140952290 140952315              DQ704676     1    26    26
browser |    26  100.0%          1     + 147012129 147012154              DQ704676     1    26    26
browser |    25  100.0%          1     + 147545148 147545172              DQ704676     1    25    26
browser |    26  100.0%          1     - 147667323 147667348              DQ704676     1    26    26
browser |    26  100.0%          1     - 179707514 179707539              DQ704676     1    26    26
browser |    26  100.0%         10     +   3636971   3636996              DQ704676     1    26    26
browser |    26  100.0%         10     -  20406919  20406944              DQ704676     1    26    26
browser |    26  100.0%         10     -  35707945  35707970              DQ704676     1    26    26
browser |    26  100.0%         10     +  44154589  44154614              DQ704676     1    26    26
browser |    26  100.0%         10     - 112927438 112927463              DQ704676     1    26    26
browser |    26  100.0%         11     -  29070414  29070439              DQ704676     1    26    26
browser |    26  100.0%         11     +  37622267  37622292              DQ704676     1    26    26
browser |    26  100.0%         11     +  44166427  44166452              DQ704676     1    26    26
browser |    26  100.0%         11     -  46872690  46872715              DQ704676     1    26    26
browser |    26  100.0%         11     - 104306949 104306974              DQ704676     1    26    26
browser |    25  100.0%         12     -  10849144  10849168              DQ704676     1    25    26
browser |    25  100.0%         12     -  10975984  10976008              DQ704676     1    25    26
browser |    26  100.0%         12     -  32553726  32553751              DQ704676     1    26    26
browser |    26  100.0%         12     +  45859092  45859117              DQ704676     1    26    26
browser |    26  100.0%         12     -  60500348  60500373              DQ704676     1    26    26
browser |    26  100.0%         12     -  64626794  64626819              DQ704676     1    26    26
browser |    26  100.0%         12     -  64822784  64822809              DQ704676     1    26    26
browser |    26  100.0%         12     +  89124884  89124909              DQ704676     1    26    26
browser |    25  100.0%         12     -  90405476  90405500              DQ704676     1    25    26
browser |    26  100.0%         12     +  97722106  97722131              DQ704676     1    26    26
browser |    26  100.0%         13     +   4374051   4374076              DQ704676     1    26    26
browser |    26  100.0%         13     +  10750141  10750166              DQ704676     1    26    26
browser |    26  100.0%         13     +  12910287  12910312              DQ704676     1    26    26
browser |    26  100.0%         13     +  13070009  13070034              DQ704676     1    26    26
browser |    26  100.0%         13     -  13263204  13263229              DQ704676     1    26    26
browser |    26  100.0%         13     -  28174865  28174890              DQ704676     1    26    26
browser |    26  100.0%         13     -  35459569  35459594              DQ704676     1    26    26
browser |    26  100.0%         13     +  35739844  35739869              DQ704676     1    26    26
browser |    25  100.0%         13     +  75566439  75566463              DQ704676     2    26    26
browser |    26  100.0%         13     +  81393971  81393996              DQ704676     1    26    26
browser |    26  100.0%         13     -  87832266  87832291              DQ704676     1    26    26
browser |    26  100.0%         13     +  95097484  95097509              DQ704676     1    26    26
browser |    26  100.0%         13     - 111237886 111237911              DQ704676     1    26    26
browser |    26  100.0%         13     + 114520522 114520547              DQ704676     1    26    26
browser |    26  100.0%         14     +   8851734   8851759              DQ704676     1    26    26
browser |    26  100.0%         14     -  12160229  12160254              DQ704676     1    26    26
browser |    26  100.0%         14     +  35324657  35324682              DQ704676     1    26    26
browser |    26  100.0%         14     +  53364709  53364734              DQ704676     1    26    26
browser |    26  100.0%         14     -  53789218  53789243              DQ704676     1    26    26
browser |    26  100.0%         14     + 107338731 107338756              DQ704676     1    26    26
browser |    26  100.0%         14     + 108813428 108813453              DQ704676     1    26    26
browser |    26  100.0%         14     + 116460333 116460358              DQ704676     1    26    26
browser |    26  100.0%         15     -   3344043   3344068              DQ704676     1    26    26
browser |    26  100.0%         15     -   8888371   8888396              DQ704676     1    26    26
browser |    26  100.0%         15     -  10033735  10033760              DQ704676     1    26    26
browser |    26  100.0%         15     -  14020283  14020308              DQ704676     1    26    26
browser |    26  100.0%         15     +  15703016  15703041              DQ704676     1    26    26
browser |    26  100.0%         15     +  16452827  16452852              DQ704676     1    26    26
browser |    26  100.0%         15     +  18204207  18204232              DQ704676     1    26    26
browser |    25  100.0%         15     -  20595556  20595580              DQ704676     1    25    26
browser |    25  100.0%         15     -  34973446  34973470              DQ704676     1    25    26
browser |    26  100.0%         15     +  35890332  35890357              DQ704676     1    26    26
browser |    26  100.0%         15     +  56969697  56969722              DQ704676     1    26    26
browser |    26  100.0%         15     -  68620950  68620975              DQ704676     1    26    26
browser |    26  100.0%         15     +  90757683  90757708              DQ704676     1    26    26
browser |    26  100.0%         16     +  16480397  16480422              DQ704676     1    26    26
browser |    26  100.0%         16     -  19461950  19461975              DQ704676     1    26    26
browser |    26  100.0%         16     +  24814902  24814927              DQ704676     1    26    26
browser |    26  100.0%         16     +  27660854  27660879              DQ704676     1    26    26
browser |    26  100.0%         16     +  82952526  82952551              DQ704676     1    26    26
browser |    26  100.0%         17     -  18856603  18856628              DQ704676     1    26    26
browser |    26  100.0%         17     +  19867577  19867602              DQ704676     1    26    26
browser |    26  100.0%         17     -  22223644  22223669              DQ704676     1    26    26
browser |    26  100.0%         17     -  22890075  22890100              DQ704676     1    26    26
browser |    25  100.0%         17     -  40025544  40025568              DQ704676     1    25    26
browser |    25  100.0%         17     -  58772403  58772427              DQ704676     2    26    26
browser |    24  100.0%         17     -  71758629  71758652              DQ704676     3    26    26
browser |    26  100.0%         17     +  92818109  92818134              DQ704676     1    26    26
browser |    26  100.0%         18     -  11356908  11356933              DQ704676     1    26    26
browser |    24  100.0%         18     +  11490303  11490326              DQ704676     3    26    26
browser |    26  100.0%         18     -  23319938  23319963              DQ704676     1    26    26
browser |    26  100.0%         18     +  47357042  47357067              DQ704676     1    26    26
browser |    25  100.0%         18     +  77175978  77176002              DQ704676     1    25    26
browser |    26  100.0%         19     -   9213163   9213188              DQ704676     1    26    26
browser |    26  100.0%         19     -  13268970  13268995              DQ704676     1    26    26
browser |    26  100.0%          2     -   7297295   7297320              DQ704676     1    26    26
browser |    26  100.0%          2     -   7679661   7679686              DQ704676     1    26    26
browser |    26  100.0%          2     -  12731171  12731196              DQ704676     1    26    26
browser |    25  100.0%          2     -  40318449  40318473              DQ704676     1    25    26
browser |    26  100.0%          2     -  41090013  41090038              DQ704676     1    26    26
browser |    26  100.0%          2     +  47361004  47361029              DQ704676     1    26    26
browser |    25  100.0%          2     +  54290899  54290923              DQ704676     1    25    26
browser |    26  100.0%          2     +  64093994  64094019              DQ704676     1    26    26
browser |    24  100.0%          2     +  77964181  77964204              DQ704676     3    26    26
browser |    26  100.0%          2     -  86812404  86812429              DQ704676     1    26    26
browser |    25  100.0%          2     +  87617978  87618002              DQ704676     1    25    26
browser |    26  100.0%          2     + 107720891 107720916              DQ704676     1    26    26
browser |    26  100.0%          2     - 129508211 129508236              DQ704676     1    26    26
browser |    24  100.0%          3     +   8426650   8426673              DQ704676     3    26    26
browser |    26  100.0%          3     -   9998498   9998523              DQ704676     1    26    26
browser |    25  100.0%          3     +  14253143  14253167              DQ704676     2    26    26
browser |    26  100.0%          3     +  22561433  22561458              DQ704676     1    26    26
browser |    24  100.0%          3     +  33514308  33514331              DQ704676     3    26    26
browser |    25  100.0%          3     +  44906267  44906291              DQ704676     1    25    26
browser |    25  100.0%          3     +  45199539  45199563              DQ704676     1    25    26
browser |    26  100.0%          3     +  50178062  50178087              DQ704676     1    26    26
browser |    26  100.0%          3     +  81783172  81783197              DQ704676     1    26    26
browser |    26  100.0%          3     -  82105181  82105206              DQ704676     1    26    26
browser |    26  100.0%          3     + 110435867 110435892              DQ704676     1    26    26
browser |    26  100.0%          3     - 156830546 156830571              DQ704676     1    26    26
browser |    26  100.0%          4     -  16026543  16026568              DQ704676     1    26    26
browser |    26  100.0%          4     -  21491684  21491709              DQ704676     1    26    26
browser |    25  100.0%          4     -  25701831  25701855              DQ704676     1    25    26
browser |    26  100.0%          4     -  26969570  26969595              DQ704676     1    26    26
browser |    26  100.0%          4     -  28573710  28573735              DQ704676     1    26    26
browser |    26  100.0%          4     +  30042934  30042959              DQ704676     1    26    26
browser |    25  100.0%          4     -  37906531  37906555              DQ704676     1    25    26
browser |    26  100.0%          4     -  64734124  64734149              DQ704676     1    26    26
browser |    26  100.0%          4     -  76814125  76814150              DQ704676     1    26    26
browser |    25  100.0%          4     -  77055229  77055253              DQ704676     1    25    26
browser |    26  100.0%          4     +  93619473  93619498              DQ704676     1    26    26
browser |    26  100.0%          4     -  95004354  95004379              DQ704676     1    26    26
browser |    26  100.0%          4     - 121131919 121131944              DQ704676     1    26    26
browser |    26  100.0%          5     +  19782732  19782757              DQ704676     1    26    26
browser |    26  100.0%          5     -  42856960  42856985              DQ704676     1    26    26
browser |    25  100.0%          5     -  63531216  63531240              DQ704676     1    25    26
browser |    26  100.0%          5     +  80483326  80483351              DQ704676     1    26    26
browser |    26  100.0%          5     -  86428244  86428269              DQ704676     1    26    26
browser |    26  100.0%          5     -  88596276  88596301              DQ704676     1    26    26
browser |    24  100.0%          5     -  91672518  91672541              DQ704676     3    26    26
browser |    26  100.0%          5     +  95639921  95639946              DQ704676     1    26    26
browser |    26  100.0%          5     + 109345408 109345433              DQ704676     1    26    26
browser |    26  100.0%          6     -   7115866   7115891              DQ704676     1    26    26
browser |    26  100.0%          6     -  14376846  14376871              DQ704676     1    26    26
browser |    26  100.0%          6     +  35692809  35692834              DQ704676     1    26    26
browser |    26  100.0%          6     -  41673246  41673271              DQ704676     1    26    26
browser |    26  100.0%          6     -  56917316  56917341              DQ704676     1    26    26
browser |    26  100.0%          6     +  67820153  67820178              DQ704676     1    26    26
browser |    26  100.0%          6     -  69672709  69672734              DQ704676     1    26    26
browser |    26  100.0%          6     -  76584163  76584188              DQ704676     1    26    26
browser |    26  100.0%          6     -  79966353  79966378              DQ704676     1    26    26
browser |    26  100.0%          6     +  93405343  93405368              DQ704676     1    26    26
browser |    26  100.0%          6     - 103243954 103243979              DQ704676     1    26    26
browser |    26  100.0%          6     - 124963236 124963261              DQ704676     1    26    26
browser |    26  100.0%          6     + 141243803 141243828              DQ704676     1    26    26
browser |    24  100.0%          7     -   5637566   5637589              DQ704676     3    26    26
browser |    26  100.0%          7     -  48073806  48073831              DQ704676     1    26    26
browser |    26  100.0%          7     -  58413770  58413795              DQ704676     1    26    26
browser |    25  100.0%          7     +  87639074  87639098              DQ704676     1    25    26
browser |    26  100.0%          7     -  91529785  91529810              DQ704676     1    26    26
browser |    26  100.0%          7     - 103334033 103334058              DQ704676     1    26    26
browser |    26  100.0%          7     - 104663078 104663103              DQ704676     1    26    26
browser |    26  100.0%          7     + 128513718 128513743              DQ704676     1    26    26
browser |    26  100.0%          7     - 136350648 136350673              DQ704676     1    26    26
browser |    26  100.0%          8     +  25949194  25949219              DQ704676     1    26    26
browser |    26  100.0%          8     -  35714559  35714584              DQ704676     1    26    26
browser |    26  100.0%          8     -  40358349  40358374              DQ704676     1    26    26
browser |    26  100.0%          8     -  51394634  51394659              DQ704676     1    26    26
browser |    26  100.0%          8     -  54720671  54720696              DQ704676     1    26    26
browser |    26  100.0%          8     +  58593726  58593751              DQ704676     1    26    26
browser |    25  100.0%          8     -  67494366  67494390              DQ704676     1    25    26
browser |    24  100.0%          8     - 129565130 129565153              DQ704676     3    26    26
browser |    25  100.0%          8     + 129845388 129845412              DQ704676     1    25    26
browser |    26  100.0%          9     +   7213691   7213716              DQ704676     1    26    26
browser |    25  100.0%          9     +  11109648  11109672              DQ704676     1    25    26
browser |    26  100.0%          9     -  12178185  12178210              DQ704676     1    26    26
browser |    26  100.0%          9     -  17532058  17532083              DQ704676     1    26    26
browser |    26  100.0%          9     -  23518151  23518176              DQ704676     1    26    26
browser |    26  100.0%          9     +  36061661  36061686              DQ704676     1    26    26
browser |    26  100.0%          9     -  80897213  80897238              DQ704676     1    26    26
browser |    26  100.0%          X     +  13759052  13759077              DQ704676     1    26    26
browser |    26  100.0%          X     +  16261998  16262023              DQ704676     1    26    26
browser |    26  100.0%          X     +  42692722  42692747              DQ704676     1    26    26
browser |    25  100.0%          X     -  43513129  43513153              DQ704676     2    26    26
browser |    26  100.0%          X     +  51824114  51824139              DQ704676     1    26    26
browser |    26  100.0%          X     -  54945435  54945460              DQ704676     1    26    26
browser |    26  100.0%          X     -  63185965  63185990              DQ704676     1    26    26
browser |    26  100.0%          X     -  79404545  79404570              DQ704676     1    26    26
browser |    25  100.0%          X     -  88428371  88428395              DQ704676     1    25    26
browser |    25  100.0%          X     -  88679430  88679454              DQ704676     1    25    26
browser |    25  100.0%          X     -  96540621  96540645              DQ704676     1    25    26
browser |    26  100.0%          X     + 102896876 102896901              DQ704676     1    26    26
browser |    26  100.0%          X     - 105410979 105411004              DQ704676     1    26    26
browser |    25  100.0%          X     + 108371690 108371714              DQ704676     2    26    26
browser |    25  100.0%          X     + 117478747 117478771              DQ704676     1    25    26
browser |    26  100.0%          X     + 131772813 131772838              DQ704676     1    26    26
browser |    26  100.0%          X     + 135373974 135373999              DQ704676     1    26    26
browser |    25  100.0%          X     + 142102919 142102943              DQ704676     1    25    26
browser |    26  100.0%          X     - 146718583 146718608              DQ704676     1    26    26
browser |    26  100.0%          X     - 164529836 164529861              DQ704676     1    26    26

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