AB349628
 

Information on mRNA AB349628

Description: Mus musculus non-coding RNA, oocyte_piRNA444, complete sequence.
Gene: n/a
Product: n/a
Author: Watanabe,T., Totoki,Y., Toyoda,A., Kaneda,M., Kuramochi-Miyagawa,S., Obata,Y., Chiba,H., Kohara,Y., Kono,T., Nakano,T., Surani,M.A., Sakaki,Y. and Sasaki,H.
Organism: Mus musculus
Tissue: ovary
Development stage: p8
Cell line: n/a
Sex: n/a
Library: n/a
Clone: n/a
CDS: n/a
Date: 2008-04-24
Version: 1
mRNA sequence: AB349628
Position: chr12:56796463-56796488

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 |    26  100.0%         12     -  56796463  56796488              AB349628     1    26    26
browser |    26  100.0%          1     -   5879148   5879173              AB349628     1    26    26
browser |    26  100.0%          1     -   6505177   6505202              AB349628     1    26    26
browser |    26  100.0%          1     +   8066446   8066471              AB349628     1    26    26
browser |    26  100.0%          1     +   8228887   8228912              AB349628     1    26    26
browser |    26  100.0%          1     -  10804664  10804689              AB349628     1    26    26
browser |    26  100.0%          1     -  11101415  11101440              AB349628     1    26    26
browser |    26  100.0%          1     +  13623311  13623336              AB349628     1    26    26
browser |    26  100.0%          1     +  16810957  16810982              AB349628     1    26    26
browser |    26  100.0%          1     +  18029551  18029576              AB349628     1    26    26
browser |    26  100.0%          1     +  18589581  18589606              AB349628     1    26    26
browser |    26  100.0%          1     +  19695165  19695190              AB349628     1    26    26
browser |    26  100.0%          1     -  22070041  22070066              AB349628     1    26    26
browser |    26  100.0%          1     +  26455573  26455598              AB349628     1    26    26
browser |    26  100.0%          1     -  26512753  26512778              AB349628     1    26    26
browser |    26  100.0%          1     +  27221721  27221746              AB349628     1    26    26
browser |    26  100.0%          1     +  29696345  29696370              AB349628     1    26    26
browser |    26  100.0%          1     -  29985883  29985908              AB349628     1    26    26
browser |    26  100.0%          1     +  34389054  34389079              AB349628     1    26    26
browser |    26  100.0%          1     -  47264597  47264622              AB349628     1    26    26
browser |    26  100.0%          1     -  48399938  48399963              AB349628     1    26    26
browser |    26  100.0%          1     -  53171428  53171453              AB349628     1    26    26
browser |    26  100.0%          1     +  56813857  56813882              AB349628     1    26    26
browser |    26  100.0%          1     -  58367103  58367128              AB349628     1    26    26
browser |    26  100.0%          1     -  58855411  58855436              AB349628     1    26    26
browser |    26  100.0%          1     +  64424757  64424782              AB349628     1    26    26
browser |    26  100.0%          1     -  67795171  67795196              AB349628     1    26    26
browser |    26  100.0%          1     +  70278739  70278764              AB349628     1    26    26
browser |    26  100.0%          1     -  72169283  72169308              AB349628     1    26    26
browser |    26  100.0%          1     -  74697179  74697204              AB349628     1    26    26
browser |    26  100.0%          1     +  79917264  79917289              AB349628     1    26    26
browser |    26  100.0%          1     -  81546472  81546497              AB349628     1    26    26
browser |    26  100.0%          1     +  82481300  82481325              AB349628     1    26    26
browser |    26  100.0%          1     -  87065954  87065979              AB349628     1    26    26
browser |    26  100.0%          1     +  87390377  87390402              AB349628     1    26    26
browser |    26  100.0%          1     -  91403527  91403552              AB349628     1    26    26
browser |    26  100.0%          1     +  93886787  93886812              AB349628     1    26    26
browser |    26  100.0%          1     +  95625375  95625400              AB349628     1    26    26
browser |    26  100.0%          1     +  97102986  97103011              AB349628     1    26    26
browser |    26  100.0%          1     - 101910462 101910487              AB349628     1    26    26
browser |    26  100.0%          1     + 102961888 102961913              AB349628     1    26    26
browser |    26  100.0%          1     - 103137491 103137516              AB349628     1    26    26
browser |    26  100.0%          1     - 108341179 108341204              AB349628     1    26    26
browser |    26  100.0%          1     + 109543630 109543655              AB349628     1    26    26
browser |    26  100.0%          1     + 111633598 111633623              AB349628     1    26    26
browser |    26  100.0%          1     - 112196657 112196682              AB349628     1    26    26
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browser |    26  100.0%          1     - 116580596 116580621              AB349628     1    26    26
browser |    26  100.0%          1     - 117634254 117634279              AB349628     1    26    26
browser |    26  100.0%          1     - 125275697 125275722              AB349628     1    26    26
browser |    26  100.0%          1     - 127490590 127490615              AB349628     1    26    26
browser |    26  100.0%          1     - 127807389 127807414              AB349628     1    26    26
browser |    26  100.0%          1     + 130464552 130464577              AB349628     1    26    26
browser |    26  100.0%          1     - 137203496 137203521              AB349628     1    26    26
browser |    26  100.0%          1     + 140747048 140747073              AB349628     1    26    26
browser |    26  100.0%          1     + 140965646 140965671              AB349628     1    26    26
browser |    26  100.0%          1     + 144262405 144262430              AB349628     1    26    26
browser |    26  100.0%          1     + 145999172 145999197              AB349628     1    26    26
browser |    26  100.0%          1     + 149271495 149271520              AB349628     1    26    26
browser |    26  100.0%          1     - 149394628 149394653              AB349628     1    26    26
browser |    26  100.0%          1     + 149459806 149459831              AB349628     1    26    26
browser |    26  100.0%          1     - 154779289 154779314              AB349628     1    26    26
browser |    26  100.0%          1     - 159801922 159801947              AB349628     1    26    26
browser |    26  100.0%          1     + 162670618 162670643              AB349628     1    26    26
browser |    26  100.0%          1     - 166594795 166594820              AB349628     1    26    26
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browser |    26  100.0%          1     - 174873327 174873352              AB349628     1    26    26
browser |    26  100.0%          1     - 176375221 176375246              AB349628     1    26    26
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browser |    26  100.0%          1     + 178004170 178004195              AB349628     1    26    26
browser |    26  100.0%          1     + 179724065 179724090              AB349628     1    26    26
browser |    26  100.0%          1     - 181095678 181095703              AB349628     1    26    26
browser |    26  100.0%          1     + 183298777 183298802              AB349628     1    26    26
browser |    26  100.0%          1     + 195005154 195005179              AB349628     1    26    26
browser |    26  100.0%         10     -   3555518   3555543              AB349628     1    26    26
browser |    26  100.0%         10     +   8477543   8477568              AB349628     1    26    26
browser |    26  100.0%         10     +  11572522  11572547              AB349628     1    26    26
browser |    26  100.0%         10     -  19419231  19419256              AB349628     1    26    26
browser |    26  100.0%         10     +  19675394  19675419              AB349628     1    26    26
browser |    26  100.0%         10     -  19890958  19890983              AB349628     1    26    26
browser |    26  100.0%         10     -  21522804  21522829              AB349628     1    26    26
browser |    26  100.0%         10     -  22403695  22403720              AB349628     1    26    26
browser |    26  100.0%         10     -  22563750  22563775              AB349628     1    26    26
browser |    26  100.0%         10     -  23751805  23751830              AB349628     1    26    26
browser |    26  100.0%         10     -  24979877  24979902              AB349628     1    26    26
browser |    26  100.0%         10     +  25846815  25846840              AB349628     1    26    26
browser |    26  100.0%         10     +  30692483  30692508              AB349628     1    26    26
browser |    26  100.0%         10     +  30967168  30967193              AB349628     1    26    26
browser |    26  100.0%         10     +  31361111  31361136              AB349628     1    26    26
browser |    26  100.0%         10     +  41719037  41719062              AB349628     1    26    26
browser |    26  100.0%         10     -  43647680  43647705              AB349628     1    26    26
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browser |    26  100.0%         10     +  62942265  62942290              AB349628     1    26    26
browser |    26  100.0%         10     -  65478211  65478236              AB349628     1    26    26
browser |    26  100.0%         10     -  66562826  66562851              AB349628     1    26    26
browser |    26  100.0%         10     +  70629756  70629781              AB349628     1    26    26
browser |    26  100.0%         10     +  71529749  71529774              AB349628     1    26    26
browser |    26  100.0%         10     +  77789107  77789132              AB349628     1    26    26
browser |    26  100.0%         10     -  78656375  78656400              AB349628     1    26    26
browser |    26  100.0%         10     -  81510960  81510985              AB349628     1    26    26
browser |    26  100.0%         10     -  81670088  81670113              AB349628     1    26    26
browser |    26  100.0%         10     +  81806227  81806252              AB349628     1    26    26
browser |    26  100.0%         10     -  83306316  83306341              AB349628     1    26    26
browser |    26  100.0%         10     -  83511371  83511396              AB349628     1    26    26
browser |    26  100.0%         10     +  85553561  85553586              AB349628     1    26    26
browser |    26  100.0%         10     +  88489348  88489373              AB349628     1    26    26
browser |    26  100.0%         10     -  94202519  94202544              AB349628     1    26    26
browser |    26  100.0%         10     -  96032979  96033004              AB349628     1    26    26
browser |    26  100.0%         10     -  97162898  97162923              AB349628     1    26    26
browser |    26  100.0%         10     +  99177487  99177512              AB349628     1    26    26
browser |    26  100.0%         10     + 104393714 104393739              AB349628     1    26    26
browser |    26  100.0%         10     + 104673931 104673956              AB349628     1    26    26
browser |    26  100.0%         10     + 105015450 105015475              AB349628     1    26    26
browser |    26  100.0%         10     + 107837860 107837885              AB349628     1    26    26
browser |    26  100.0%         10     - 109155665 109155690              AB349628     1    26    26
browser |    26  100.0%         10     + 110534631 110534656              AB349628     1    26    26
browser |    26  100.0%         10     - 113563191 113563216              AB349628     1    26    26
browser |    26  100.0%         10     - 116446752 116446777              AB349628     1    26    26
browser |    26  100.0%         10     + 117909054 117909079              AB349628     1    26    26
browser |    26  100.0%         10     + 121003139 121003164              AB349628     1    26    26
browser |    26  100.0%         10     - 122204361 122204386              AB349628     1    26    26
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browser |    26  100.0%         10     - 124519432 124519457              AB349628     1    26    26
browser |    26  100.0%         10     - 129229277 129229302              AB349628     1    26    26
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browser |    26  100.0%         11     -   6096079   6096104              AB349628     1    26    26
browser |    26  100.0%         11     -   7530271   7530296              AB349628     1    26    26
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browser |    26  100.0%         11     -  19518012  19518037              AB349628     1    26    26
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View details of parts of alignment within browser window
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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