AB351929
 

Information on mRNA AB351929

Description: Mus musculus non-coding RNA, oocyte_piRNA2745, 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: AB351929
Position: chr12:56796652-56796678

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 |    27  100.0%         12     -  56796652  56796678              AB351929     1    27    27
browser |    27  100.0%          1     -   5879337   5879363              AB351929     1    27    27
browser |    27  100.0%          1     -   6505366   6505392              AB351929     1    27    27
browser |    27  100.0%          1     +   8066256   8066282              AB351929     1    27    27
browser |    27  100.0%          1     +   8228697   8228723              AB351929     1    27    27
browser |    27  100.0%          1     -   8730377   8730403              AB351929     1    27    27
browser |    27  100.0%          1     -  10804853  10804879              AB351929     1    27    27
browser |    27  100.0%          1     +  13623121  13623147              AB351929     1    27    27
browser |    27  100.0%          1     +  16810767  16810793              AB351929     1    27    27
browser |    27  100.0%          1     +  18029361  18029387              AB351929     1    27    27
browser |    27  100.0%          1     +  18589391  18589417              AB351929     1    27    27
browser |    27  100.0%          1     +  19694975  19695001              AB351929     1    27    27
browser |    27  100.0%          1     -  22070230  22070256              AB351929     1    27    27
browser |    27  100.0%          1     +  26455383  26455409              AB351929     1    27    27
browser |    27  100.0%          1     -  26512942  26512968              AB351929     1    27    27
browser |    27  100.0%          1     +  27221531  27221557              AB351929     1    27    27
browser |    27  100.0%          1     +  34388864  34388890              AB351929     1    27    27
browser |    27  100.0%          1     +  35829860  35829886              AB351929     1    27    27
browser |    27  100.0%          1     -  47264786  47264812              AB351929     1    27    27
browser |    27  100.0%          1     -  48400127  48400153              AB351929     1    27    27
browser |    27  100.0%          1     -  53171617  53171643              AB351929     1    27    27
browser |    27  100.0%          1     +  55819814  55819840              AB351929     1    27    27
browser |    27  100.0%          1     -  58367292  58367318              AB351929     1    27    27
browser |    27  100.0%          1     -  58855600  58855626              AB351929     1    27    27
browser |    27  100.0%          1     -  60768786  60768812              AB351929     1    27    27
browser |    27  100.0%          1     -  67795360  67795386              AB351929     1    27    27
browser |    27  100.0%          1     +  70278549  70278575              AB351929     1    27    27
browser |    27  100.0%          1     -  72169473  72169499              AB351929     1    27    27
browser |    27  100.0%          1     -  74697368  74697394              AB351929     1    27    27
browser |    27  100.0%          1     +  77646676  77646702              AB351929     1    27    27
browser |    27  100.0%          1     +  79917074  79917100              AB351929     1    27    27
browser |    27  100.0%          1     -  81546661  81546687              AB351929     1    27    27
browser |    27  100.0%          1     +  82481110  82481136              AB351929     1    27    27
browser |    27  100.0%          1     -  87066143  87066169              AB351929     1    27    27
browser |    27  100.0%          1     +  87390187  87390213              AB351929     1    27    27
browser |    27  100.0%          1     -  91403716  91403742              AB351929     1    27    27
browser |    27  100.0%          1     +  93886597  93886623              AB351929     1    27    27
browser |    27  100.0%          1     +  95625185  95625211              AB351929     1    27    27
browser |    27  100.0%          1     - 101910651 101910677              AB351929     1    27    27
browser |    27  100.0%          1     + 102961698 102961724              AB351929     1    27    27
browser |    27  100.0%          1     - 103137680 103137706              AB351929     1    27    27
browser |    27  100.0%          1     - 108341368 108341394              AB351929     1    27    27
browser |    27  100.0%          1     + 109543440 109543466              AB351929     1    27    27
browser |    27  100.0%          1     - 111186137 111186163              AB351929     1    27    27
browser |    27  100.0%          1     + 111633408 111633434              AB351929     1    27    27
browser |    27  100.0%          1     + 112859517 112859543              AB351929     1    27    27
browser |    27  100.0%          1     + 112946115 112946141              AB351929     1    27    27
browser |    27  100.0%          1     - 116580785 116580811              AB351929     1    27    27
browser |    27  100.0%          1     - 117634443 117634469              AB351929     1    27    27
browser |    27  100.0%          1     + 125246903 125246929              AB351929     1    27    27
browser |    27  100.0%          1     - 125275886 125275912              AB351929     1    27    27
browser |    27  100.0%          1     - 127490779 127490805              AB351929     1    27    27
browser |    27  100.0%          1     - 127807578 127807604              AB351929     1    27    27
browser |    27  100.0%          1     - 137203685 137203711              AB351929     1    27    27
browser |    27  100.0%          1     + 140746858 140746884              AB351929     1    27    27
browser |    27  100.0%          1     + 140965456 140965482              AB351929     1    27    27
browser |    27  100.0%          1     + 144262215 144262241              AB351929     1    27    27
browser |    27  100.0%          1     - 144735208 144735234              AB351929     1    27    27
browser |    27  100.0%          1     + 145998982 145999008              AB351929     1    27    27
browser |    27  100.0%          1     - 146162418 146162444              AB351929     1    27    27
browser |    27  100.0%          1     + 149271305 149271331              AB351929     1    27    27
browser |    27  100.0%          1     + 149459615 149459641              AB351929     1    27    27
browser |    27  100.0%          1     - 159802111 159802137              AB351929     1    27    27
browser |    27  100.0%          1     + 162670428 162670454              AB351929     1    27    27
browser |    27  100.0%          1     + 166182066 166182092              AB351929     1    27    27
browser |    27  100.0%          1     - 166594984 166595010              AB351929     1    27    27
browser |    27  100.0%          1     + 169371675 169371701              AB351929     1    27    27
browser |    27  100.0%          1     + 169945662 169945688              AB351929     1    27    27
browser |    27  100.0%          1     - 174873516 174873542              AB351929     1    27    27
browser |    27  100.0%          1     - 176375410 176375436              AB351929     1    27    27
browser |    27  100.0%          1     + 177887927 177887953              AB351929     1    27    27
browser |    27  100.0%          1     + 178003980 178004006              AB351929     1    27    27
browser |    27  100.0%          1     + 179723875 179723901              AB351929     1    27    27
browser |    27  100.0%          1     - 181095867 181095893              AB351929     1    27    27
browser |    27  100.0%          1     + 181322769 181322795              AB351929     1    27    27
browser |    27  100.0%          1     + 183298587 183298613              AB351929     1    27    27
browser |    27  100.0%          1     + 195004964 195004990              AB351929     1    27    27
browser |    27  100.0%         10     -   3555707   3555733              AB351929     1    27    27
browser |    27  100.0%         10     +   8477353   8477379              AB351929     1    27    27
browser |    27  100.0%         10     +  11572332  11572358              AB351929     1    27    27
browser |    27  100.0%         10     -  19419420  19419446              AB351929     1    27    27
browser |    27  100.0%         10     -  19891147  19891173              AB351929     1    27    27
browser |    27  100.0%         10     -  21522993  21523019              AB351929     1    27    27
browser |    27  100.0%         10     -  22403884  22403910              AB351929     1    27    27
browser |    27  100.0%         10     -  22563939  22563965              AB351929     1    27    27
browser |    27  100.0%         10     -  23751994  23752020              AB351929     1    27    27
browser |    27  100.0%         10     -  24980066  24980092              AB351929     1    27    27
browser |    27  100.0%         10     +  25846625  25846651              AB351929     1    27    27
browser |    27  100.0%         10     +  30692293  30692319              AB351929     1    27    27
browser |    27  100.0%         10     +  30966978  30967004              AB351929     1    27    27
browser |    27  100.0%         10     +  31360921  31360947              AB351929     1    27    27
browser |    27  100.0%         10     -  34622597  34622623              AB351929     1    27    27
browser |    27  100.0%         10     +  41718847  41718873              AB351929     1    27    27
browser |    27  100.0%         10     +  51761405  51761431              AB351929     1    27    27
browser |    27  100.0%         10     +  56599153  56599179              AB351929     1    27    27
browser |    27  100.0%         10     +  57016073  57016099              AB351929     1    27    27
browser |    27  100.0%         10     +  62942075  62942101              AB351929     1    27    27
browser |    27  100.0%         10     -  65478400  65478426              AB351929     1    27    27
browser |    27  100.0%         10     -  66563015  66563041              AB351929     1    27    27
browser |    27  100.0%         10     +  70629566  70629592              AB351929     1    27    27
browser |    27  100.0%         10     +  71529559  71529585              AB351929     1    27    27
browser |    27  100.0%         10     +  77788917  77788943              AB351929     1    27    27
browser |    27  100.0%         10     -  78656564  78656590              AB351929     1    27    27
browser |    27  100.0%         10     -  81511149  81511175              AB351929     1    27    27
browser |    27  100.0%         10     -  81670277  81670303              AB351929     1    27    27
browser |    27  100.0%         10     +  81806037  81806063              AB351929     1    27    27
browser |    27  100.0%         10     -  83306505  83306531              AB351929     1    27    27
browser |    27  100.0%         10     -  83511560  83511586              AB351929     1    27    27
browser |    27  100.0%         10     +  85553371  85553397              AB351929     1    27    27
browser |    27  100.0%         10     +  88489158  88489184              AB351929     1    27    27
browser |    27  100.0%         10     -  94202708  94202734              AB351929     1    27    27
browser |    27  100.0%         10     -  96033168  96033194              AB351929     1    27    27
browser |    27  100.0%         10     -  97163087  97163113              AB351929     1    27    27
browser |    27  100.0%         10     +  99177297  99177323              AB351929     1    27    27
browser |    27  100.0%         10     + 104393524 104393550              AB351929     1    27    27
browser |    27  100.0%         10     + 104673741 104673767              AB351929     1    27    27
browser |    27  100.0%         10     + 105015260 105015286              AB351929     1    27    27
browser |    27  100.0%         10     + 107837670 107837696              AB351929     1    27    27
browser |    27  100.0%         10     - 109155854 109155880              AB351929     1    27    27
browser |    27  100.0%         10     + 110534441 110534467              AB351929     1    27    27
browser |    27  100.0%         10     - 113563380 113563406              AB351929     1    27    27
browser |    27  100.0%         10     - 116446941 116446967              AB351929     1    27    27
browser |    27  100.0%         10     + 117908864 117908890              AB351929     1    27    27
browser |    27  100.0%         10     + 121002949 121002975              AB351929     1    27    27
browser |    27  100.0%         10     - 122204550 122204576              AB351929     1    27    27
browser |    27  100.0%         10     - 122673427 122673453              AB351929     1    27    27
browser |    27  100.0%         10     + 123697561 123697587              AB351929     1    27    27
browser |    27  100.0%         10     + 124414536 124414562              AB351929     1    27    27
browser |    27  100.0%         10     - 124519621 124519647              AB351929     1    27    27
browser |    27  100.0%         10     - 129229466 129229492              AB351929     1    27    27
browser |    27  100.0%         10     + 129763484 129763510              AB351929     1    27    27
browser |    27  100.0%         10     - 130399675 130399701              AB351929     1    27    27
browser |    27  100.0%         11     -   6096268   6096294              AB351929     1    27    27
browser |    27  100.0%         11     -   7530460   7530486              AB351929     1    27    27
browser |    27  100.0%         11     -   9662759   9662785              AB351929     1    27    27
browser |    27  100.0%         11     +  10712637  10712663              AB351929     1    27    27
browser |    27  100.0%         11     +  12514247  12514273              AB351929     1    27    27
browser |    27  100.0%         11     +  12747919  12747945              AB351929     1    27    27
browser |    27  100.0%         11     +  15180017  15180043              AB351929     1    27    27
browser |    27  100.0%         11     -  18761232  18761258              AB351929     1    27    27
browser |    27  100.0%         11     -  19518201  19518227              AB351929     1    27    27
browser |    27  100.0%         11     +  20468703  20468729              AB351929     1    27    27
browser |    27  100.0%         11     -  23173359  23173385              AB351929     1    27    27
browser |    27  100.0%         11     -  23194972  23194998              AB351929     1    27    27
browser |    27  100.0%         11     -  27904745  27904771              AB351929     1    27    27
browser |    27  100.0%         11     +  28049620  28049646              AB351929     1    27    27
browser |    27  100.0%         11     -  31402339  31402365              AB351929     1    27    27
browser |    27  100.0%         11     -  39959328  39959354              AB351929     1    27    27
browser |    27  100.0%         11     +  51330835  51330861              AB351929     1    27    27
browser |    27  100.0%         11     -  54472176  54472202              AB351929     1    27    27
browser |    27  100.0%         11     -  55136539  55136565              AB351929     1    27    27
browser |    27  100.0%         11     +  61313588  61313614              AB351929     1    27    27
browser |    27  100.0%         11     +  63360877  63360903              AB351929     1    27    27
browser |    27  100.0%         11     -  65347386  65347412              AB351929     1    27    27
browser |    27  100.0%         11     -  66842845  66842871              AB351929     1    27    27
browser |    27  100.0%         11     +  74022085  74022111              AB351929     1    27    27
browser |    27  100.0%         11     -  74115255  74115281              AB351929     1    27    27
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browser |    27  100.0%         11     +  81438691  81438717              AB351929     1    27    27
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browser |    27  100.0%         11     -  90855776  90855802              AB351929     1    27    27
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browser |    27  100.0%         11     - 106186103 106186129              AB351929     1    27    27
browser |    27  100.0%         11     + 111075656 111075682              AB351929     1    27    27
browser |    27  100.0%         11     - 111111248 111111274              AB351929     1    27    27
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browser |    27  100.0%         11     - 115650502 115650528              AB351929     1    27    27
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browser |    27  100.0%         11     + 120214307 120214333              AB351929     1    27    27
browser |    27  100.0%         11     + 120963059 120963085              AB351929     1    27    27
browser |    27  100.0%         12     +   3054694   3054720              AB351929     1    27    27
browser |    27  100.0%         12     -   3385585   3385611              AB351929     1    27    27
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browser |    27  100.0%         12     -  18329864  18329890              AB351929     1    27    27
browser |    27  100.0%         12     -  19313016  19313042              AB351929     1    27    27
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browser |    27  100.0%         12     - 105271258 105271284              AB351929     1    27    27
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browser |    27  100.0%         12     + 114599364 114599390              AB351929     1    27    27
browser |    27  100.0%         12     + 115524172 115524198              AB351929     1    27    27
browser |    27  100.0%         12     + 118320427 118320453              AB351929     1    27    27
browser |    27  100.0%         12     + 119556846 119556872              AB351929     1    27    27
browser |    27  100.0%         13     +   3666671   3666697              AB351929     1    27    27
browser |    27  100.0%         13     +   4390771   4390797              AB351929     1    27    27
browser |    27  100.0%         13     +   5330350   5330376              AB351929     1    27    27
browser |    27  100.0%         13     -   7327238   7327264              AB351929     1    27    27
browser |    27  100.0%         13     -   8003953   8003979              AB351929     1    27    27
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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