DQ541148
 

Information on mRNA DQ541148

Description: Mus musculus piRNA piR-1260, 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: DQ541148
Position: chr12:56960193-56960221

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 |    28  100.0%         12     +  56960193  56960221              DQ541148     1    28    28
browser |    28  100.0%          1     -   4627699   4627728              DQ541148     1    28    28
browser |    28  100.0%          1     +   5819043   5819071              DQ541148     1    28    28
browser |    28  100.0%          1     -   8728934   8728962              DQ541148     1    28    28
browser |    28  100.0%          1     -  11438090  11438118              DQ541148     1    28    28
browser |    28  100.0%          1     -  12017219  12017247              DQ541148     1    28    28
browser |    28  100.0%          1     +  13627513  13627541              DQ541148     1    28    28
browser |    28  100.0%          1     -  17595168  17595196              DQ541148     1    28    28
browser |    28  100.0%          1     -  22065848  22065876              DQ541148     1    28    28
browser |    28  100.0%          1     -  28495689  28495717              DQ541148     1    28    28
browser |    28  100.0%          1     +  28930395  28930423              DQ541148     1    28    28
browser |    28  100.0%          1     +  29697719  29697747              DQ541148     1    28    28
browser |    28  100.0%          1     -  30727230  30727258              DQ541148     1    28    28
browser |    28  100.0%          1     +  31046309  31046337              DQ541148     1    28    28
browser |    28  100.0%          1     +  31512451  31512479              DQ541148     1    28    28
browser |    28  100.0%          1     +  40741220  40741248              DQ541148     1    28    28
browser |    28  100.0%          1     +  41129829  41129857              DQ541148     1    28    28
browser |    28  100.0%          1     +  44334399  44334427              DQ541148     1    28    28
browser |    28  100.0%          1     +  44401711  44401739              DQ541148     1    28    28
browser |    28  100.0%          1     -  47262969  47262997              DQ541148     1    28    28
browser |    28  100.0%          1     -  48710848  48710876              DQ541148     1    28    28
browser |    28  100.0%          1     +  50201251  50201279              DQ541148     1    28    28
browser |    28  100.0%          1     +  53276983  53277011              DQ541148     1    28    28
browser |    28  100.0%          1     +  53547269  53547297              DQ541148     1    28    28
browser |    28  100.0%          1     +  57350071  57350099              DQ541148     1    28    28
browser |    28  100.0%          1     -  57624613  57624641              DQ541148     1    28    28
browser |    28  100.0%          1     -  58789033  58789061              DQ541148     1    28    28
browser |    28  100.0%          1     -  59384760  59384788              DQ541148     1    28    28
browser |    28  100.0%          1     +  65749428  65749456              DQ541148     1    28    28
browser |    28  100.0%          1     +  65856424  65856452              DQ541148     1    28    28
browser |    28  100.0%          1     -  65929115  65929143              DQ541148     1    28    28
browser |    28  100.0%          1     -  72165071  72165099              DQ541148     1    28    28
browser |    28  100.0%          1     +  81962491  81962519              DQ541148     1    28    28
browser |    28  100.0%          1     -  86245848  86245876              DQ541148     1    28    28
browser |    28  100.0%          1     +  89130544  89130573              DQ541148     1    28    28
browser |    28  100.0%          1     +  95626981  95627009              DQ541148     1    28    28
browser |    28  100.0%          1     -  96895070  96895098              DQ541148     1    28    28
browser |    28  100.0%          1     -  98528463  98528491              DQ541148     1    28    28
browser |    28  100.0%          1     + 102079699 102079727              DQ541148     1    28    28
browser |    28  100.0%          1     + 102966099 102966128              DQ541148     1    28    28
browser |    28  100.0%          1     + 103408771 103408799              DQ541148     1    28    28
browser |    28  100.0%          1     + 108067191 108067219              DQ541148     1    28    28
browser |    28  100.0%          1     - 108873360 108873388              DQ541148     1    28    28
browser |    28  100.0%          1     + 108887814 108887842              DQ541148     1    28    28
browser |    28  100.0%          1     - 109056779 109056808              DQ541148     1    28    28
browser |    28  100.0%          1     + 109062870 109062898              DQ541148     1    28    28
browser |    25  100.0%          1     - 112192461 112192486              DQ541148     1    25    28
browser |    28  100.0%          1     - 113608138 113608166              DQ541148     1    28    28
browser |    28  100.0%          1     + 114117819 114117848              DQ541148     1    28    28
browser |    28  100.0%          1     - 117560353 117560381              DQ541148     1    28    28
browser |    28  100.0%          1     - 117630039 117630068              DQ541148     1    28    28
browser |    28  100.0%          1     - 117675326 117675354              DQ541148     1    28    28
browser |    28  100.0%          1     + 117920153 117920181              DQ541148     1    28    28
browser |    28  100.0%          1     - 120498959 120498988              DQ541148     1    28    28
browser |    28  100.0%          1     + 125251294 125251323              DQ541148     1    28    28
browser |    28  100.0%          1     + 128819031 128819059              DQ541148     1    28    28
browser |    28  100.0%          1     + 130466574 130466603              DQ541148     1    28    28
browser |    28  100.0%          1     - 136736146 136736174              DQ541148     1    28    28
browser |    28  100.0%          1     + 140969854 140969883              DQ541148     1    28    28
browser |    28  100.0%          1     - 143723334 143723362              DQ541148     1    28    28
browser |    28  100.0%          1     - 148332859 148332888              DQ541148     1    28    28
browser |    28  100.0%          1     - 149382414 149382443              DQ541148     1    28    28
browser |    28  100.0%          1     + 149464019 149464048              DQ541148     1    28    28
browser |    28  100.0%          1     + 161363219 161363247              DQ541148     1    28    28
browser |    28  100.0%          1     + 166183890 166183918              DQ541148     1    28    28
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browser |    28  100.0%          1     - 177954785 177954813              DQ541148     1    28    28
browser |    28  100.0%          1     + 179728268 179728296              DQ541148     1    28    28
browser |    28  100.0%          1     + 183302980 183303008              DQ541148     1    28    28
browser |    27  100.0%          1     + 185038170 185038197              DQ541148     2    28    28
browser |    28  100.0%          1     + 191236203 191236231              DQ541148     1    28    28
browser |    28  100.0%          1     + 191844484 191844513              DQ541148     1    28    28
browser |    28  100.0%          1     + 195009349 195009378              DQ541148     1    28    28
browser |    28  100.0%         10     -   6517151   6517179              DQ541148     1    28    28
browser |    28  100.0%         10     +   7193586   7193614              DQ541148     1    28    28
browser |    28  100.0%         10     +   8513165   8513193              DQ541148     1    28    28
browser |    28  100.0%         10     +   9727124   9727153              DQ541148     1    28    28
browser |    28  100.0%         10     +  11576719  11576748              DQ541148     1    28    28
browser |    28  100.0%         10     -  14485736  14485764              DQ541148     1    28    28
browser |    28  100.0%         10     -  15056126  15056154              DQ541148     1    28    28
browser |    28  100.0%         10     +  18117099  18117127              DQ541148     1    28    28
browser |    28  100.0%         10     +  19676856  19676884              DQ541148     1    28    28
browser |    28  100.0%         10     -  19886753  19886781              DQ541148     1    28    28
browser |    28  100.0%         10     -  22399500  22399528              DQ541148     1    28    28
browser |    28  100.0%         10     +  24567079  24567108              DQ541148     1    28    28
browser |    28  100.0%         10     -  28886788  28886816              DQ541148     1    28    28
browser |    28  100.0%         10     +  30971374  30971403              DQ541148     1    28    28
browser |    28  100.0%         10     +  31365324  31365353              DQ541148     1    28    28
browser |    28  100.0%         10     +  33766639  33766668              DQ541148     1    28    28
browser |    28  100.0%         10     -  34615368  34615396              DQ541148     1    28    28
browser |    28  100.0%         10     -  35599300  35599328              DQ541148     1    28    28
browser |    28  100.0%         10     +  38469443  38469471              DQ541148     1    28    28
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browser |    28  100.0%         10     -  47557155  47557183              DQ541148     1    28    28
browser |    28  100.0%         10     -  48868401  48868430              DQ541148     1    28    28
browser |    28  100.0%         10     +  56603554  56603583              DQ541148     1    28    28
browser |    28  100.0%         10     +  59222464  59222493              DQ541148     1    28    28
browser |    28  100.0%         10     -  73384519  73384547              DQ541148     1    28    28
browser |    28  100.0%         10     -  81506760  81506788              DQ541148     1    28    28
browser |    28  100.0%         10     -  81665888  81665916              DQ541148     1    28    28
browser |    28  100.0%         10     +  81810434  81810463              DQ541148     1    28    28
browser |    28  100.0%         10     -  82407631  82407659              DQ541148     1    28    28
browser |    28  100.0%         10     +  82777351  82777379              DQ541148     1    28    28
browser |    28  100.0%         10     -  83302115  83302143              DQ541148     1    28    28
browser |    28  100.0%         10     -  91650698  91650726              DQ541148     1    28    28
browser |    28  100.0%         10     +  92357011  92357039              DQ541148     1    28    28
browser |    28  100.0%         10     -  92586759  92586787              DQ541148     1    28    28
browser |    28  100.0%         10     -  95993479  95993508              DQ541148     1    28    28
browser |    28  100.0%         10     +  99181694  99181723              DQ541148     1    28    28
browser |    28  100.0%         10     -  99382148  99382176              DQ541148     1    28    28
browser |    28  100.0%         10     + 103911986 103912014              DQ541148     1    28    28
browser |    28  100.0%         10     - 104411335 104411363              DQ541148     1    28    28
browser |    28  100.0%         10     - 109151449 109151478              DQ541148     1    28    28
browser |    28  100.0%         10     + 110536278 110536306              DQ541148     1    28    28
browser |    28  100.0%         10     + 110838394 110838422              DQ541148     1    28    28
browser |    28  100.0%         10     + 122348374 122348402              DQ541148     1    28    28
browser |    28  100.0%         10     + 123702285 123702313              DQ541148     1    28    28
browser |    28  100.0%         10     + 129052439 129052467              DQ541148     1    28    28
browser |    28  100.0%         10     + 129765134 129765163              DQ541148     1    28    28
browser |    28  100.0%         11     +   5312564   5312593              DQ541148     1    28    28
browser |    28  100.0%         11     +   6749740   6749768              DQ541148     1    28    28
browser |    28  100.0%         11     -   9035176   9035204              DQ541148     1    28    28
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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