AB349334
 

Information on mRNA AB349334

Description: Mus musculus non-coding RNA, oocyte_piRNA150, 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: AB349334
Position: chr12:56920517-56920536

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 |    20  100.0%         12     -  56920517  56920536              AB349334     1    20    20
browser |    20  100.0%          1     -   3813807   3813826              AB349334     1    20    20
browser |    20  100.0%          1     +   5714861   5714880              AB349334     1    20    20
browser |    20  100.0%          1     -  13781547  13781566              AB349334     1    20    20
browser |    20  100.0%          1     -  15585017  15585036              AB349334     1    20    20
browser |    20  100.0%          1     +  16453086  16453105              AB349334     1    20    20
browser |    20  100.0%          1     -  17238617  17238636              AB349334     1    20    20
browser |    20  100.0%          1     +  19244486  19244505              AB349334     1    20    20
browser |    20  100.0%          1     +  20860851  20860870              AB349334     1    20    20
browser |    20  100.0%          1     -  22036072  22036091              AB349334     1    20    20
browser |    20  100.0%          1     -  22870157  22870176              AB349334     1    20    20
browser |    20  100.0%          1     +  23359336  23359355              AB349334     1    20    20
browser |    20  100.0%          1     -  24231507  24231526              AB349334     1    20    20
browser |    20  100.0%          1     -  35301732  35301751              AB349334     1    20    20
browser |    20  100.0%          1     -  36258927  36258946              AB349334     1    20    20
browser |    20  100.0%          1     +  38022636  38022655              AB349334     1    20    20
browser |    20  100.0%          1     +  39580681  39580700              AB349334     1    20    20
browser |    20  100.0%          1     +  40034406  40034425              AB349334     1    20    20
browser |    20  100.0%          1     -  43070117  43070136              AB349334     1    20    20
browser |    20  100.0%          1     +  44508636  44508655              AB349334     1    20    20
browser |    20  100.0%          1     -  45700622  45700641              AB349334     1    20    20
browser |    20  100.0%          1     -  54133657  54133676              AB349334     1    20    20
browser |    20  100.0%          1     +  54533416  54533435              AB349334     1    20    20
browser |    20  100.0%          1     +  55297136  55297155              AB349334     1    20    20
browser |    20  100.0%          1     -  55497037  55497056              AB349334     1    20    20
browser |    20  100.0%          1     +  62296021  62296040              AB349334     1    20    20
browser |    20  100.0%          1     +  65675856  65675875              AB349334     1    20    20
browser |    20  100.0%          1     +  65910151  65910170              AB349334     1    20    20
browser |    20  100.0%          1     +  68047996  68048015              AB349334     1    20    20
browser |    20  100.0%          1     -  70490512  70490531              AB349334     1    20    20
browser |    20  100.0%          1     -  71318987  71319006              AB349334     1    20    20
browser |    20  100.0%          1     -  71428217  71428236              AB349334     1    20    20
browser |    20  100.0%          1     +  76675366  76675385              AB349334     1    20    20
browser |    20  100.0%          1     +  87860341  87860360              AB349334     1    20    20
browser |    20  100.0%          1     -  89156947  89156966              AB349334     1    20    20
browser |    20  100.0%          1     -  92280082  92280101              AB349334     1    20    20
browser |    20  100.0%          1     -  97030367  97030386              AB349334     1    20    20
browser |    20  100.0%          1     - 101576137 101576156              AB349334     1    20    20
browser |    20  100.0%          1     - 107017277 107017296              AB349334     1    20    20
browser |    20  100.0%          1     - 112495157 112495176              AB349334     1    20    20
browser |    20  100.0%          1     - 114702827 114702846              AB349334     1    20    20
browser |    20  100.0%          1     - 116659702 116659721              AB349334     1    20    20
browser |    20  100.0%          1     - 117691397 117691416              AB349334     1    20    20
browser |    20  100.0%          1     - 119627262 119627281              AB349334     1    20    20
browser |    20  100.0%          1     - 130358172 130358191              AB349334     1    20    20
browser |    20  100.0%          1     + 141824191 141824210              AB349334     1    20    20
browser |    20  100.0%          1     - 142848427 142848446              AB349334     1    20    20
browser |    20  100.0%          1     + 143920001 143920020              AB349334     1    20    20
browser |    20  100.0%          1     - 145460357 145460376              AB349334     1    20    20
browser |    20  100.0%          1     - 149686407 149686426              AB349334     1    20    20
browser |    20  100.0%          1     - 150909482 150909501              AB349334     1    20    20
browser |    20  100.0%          1     + 151620266 151620285              AB349334     1    20    20
browser |    20  100.0%          1     + 153271186 153271205              AB349334     1    20    20
browser |    20  100.0%          1     - 158033152 158033171              AB349334     1    20    20
browser |    20  100.0%          1     - 160365967 160365986              AB349334     1    20    20
browser |    20  100.0%          1     + 164828341 164828360              AB349334     1    20    20
browser |    20  100.0%          1     - 168340962 168340981              AB349334     1    20    20
browser |    20  100.0%          1     + 174342861 174342880              AB349334     1    20    20
browser |    20  100.0%          1     - 174968982 174969001              AB349334     1    20    20
browser |    20  100.0%          1     + 176174601 176174620              AB349334     1    20    20
browser |    20  100.0%          1     + 178117341 178117360              AB349334     1    20    20
browser |    20  100.0%          1     - 178209237 178209256              AB349334     1    20    20
browser |    20  100.0%          1     - 181777002 181777021              AB349334     1    20    20
browser |    20  100.0%          1     + 183665321 183665340              AB349334     1    20    20
browser |    20  100.0%          1     + 183934431 183934450              AB349334     1    20    20
browser |    20  100.0%          1     - 195009767 195009786              AB349334     1    20    20
browser |    20  100.0%         10     -   3379142   3379161              AB349334     1    20    20
browser |    20  100.0%         10     +   3420561   3420580              AB349334     1    20    20
browser |    20  100.0%         10     +   3702886   3702905              AB349334     1    20    20
browser |    20  100.0%         10     +   7060511   7060530              AB349334     1    20    20
browser |    20  100.0%         10     -   8909112   8909131              AB349334     1    20    20
browser |    20  100.0%         10     -  10354217  10354236              AB349334     1    20    20
browser |    20  100.0%         10     +  11387091  11387110              AB349334     1    20    20
browser |    20  100.0%         10     -  16183692  16183711              AB349334     1    20    20
browser |    20  100.0%         10     -  16450987  16451006              AB349334     1    20    20
browser |    20  100.0%         10     -  18104432  18104451              AB349334     1    20    20
browser |    20  100.0%         10     -  18106712  18106731              AB349334     1    20    20
browser |    20  100.0%         10     -  19281547  19281566              AB349334     1    20    20
browser |    20  100.0%         10     -  20178912  20178931              AB349334     1    20    20
browser |    20  100.0%         10     +  22104531  22104550              AB349334     1    20    20
browser |    20  100.0%         10     -  23783612  23783631              AB349334     1    20    20
browser |    20  100.0%         10     +  24985331  24985350              AB349334     1    20    20
browser |    20  100.0%         10     -  27586752  27586771              AB349334     1    20    20
browser |    20  100.0%         10     +  28131721  28131740              AB349334     1    20    20
browser |    20  100.0%         10     -  37172207  37172226              AB349334     1    20    20
browser |    20  100.0%         10     -  40588347  40588366              AB349334     1    20    20
browser |    20  100.0%         10     -  43022677  43022696              AB349334     1    20    20
browser |    20  100.0%         10     -  44091367  44091386              AB349334     1    20    20
browser |    20  100.0%         10     -  45624187  45624206              AB349334     1    20    20
browser |    20  100.0%         10     +  46475701  46475720              AB349334     1    20    20
browser |    20  100.0%         10     +  52318236  52318255              AB349334     1    20    20
browser |    20  100.0%         10     +  61544121  61544140              AB349334     1    20    20
browser |    20  100.0%         10     +  62567386  62567405              AB349334     1    20    20
browser |    20  100.0%         10     +  66397026  66397045              AB349334     1    20    20
browser |    20  100.0%         10     -  80278542  80278561              AB349334     1    20    20
browser |    20  100.0%         10     -  82353347  82353366              AB349334     1    20    20
browser |    20  100.0%         10     +  84309321  84309340              AB349334     1    20    20
browser |    20  100.0%         10     -  90625862  90625881              AB349334     1    20    20
browser |    20  100.0%         10     +  93223051  93223070              AB349334     1    20    20
browser |    20  100.0%         10     -  94341777  94341796              AB349334     1    20    20
browser |    20  100.0%         10     - 110808332 110808351              AB349334     1    20    20
browser |    20  100.0%         10     + 110974256 110974275              AB349334     1    20    20
browser |    20  100.0%         10     - 112330272 112330291              AB349334     1    20    20
browser |    20  100.0%         10     - 118215092 118215111              AB349334     1    20    20
browser |    20  100.0%         10     + 123453936 123453955              AB349334     1    20    20
browser |    20  100.0%         11     +   5321036   5321055              AB349334     1    20    20
browser |    20  100.0%         11     -   8563452   8563471              AB349334     1    20    20
browser |    20  100.0%         11     +   8931736   8931755              AB349334     1    20    20
browser |    20  100.0%         11     -   9723257   9723276              AB349334     1    20    20
browser |    20  100.0%         11     +  11741171  11741190              AB349334     1    20    20
browser |    20  100.0%         11     +  14582591  14582610              AB349334     1    20    20
browser |    20  100.0%         11     -  21372997  21373016              AB349334     1    20    20
browser |    20  100.0%         11     +  21542666  21542685              AB349334     1    20    20
browser |    20  100.0%         11     -  23009927  23009946              AB349334     1    20    20
browser |    20  100.0%         11     -  23079532  23079551              AB349334     1    20    20
browser |    20  100.0%         11     +  24718796  24718815              AB349334     1    20    20
browser |    20  100.0%         11     +  25035376  25035395              AB349334     1    20    20
browser |    20  100.0%         11     +  27849706  27849725              AB349334     1    20    20
browser |    20  100.0%         11     +  31139316  31139335              AB349334     1    20    20
browser |    20  100.0%         11     -  33896332  33896351              AB349334     1    20    20
browser |    20  100.0%         11     +  37483751  37483770              AB349334     1    20    20
browser |    20  100.0%         11     +  42339291  42339310              AB349334     1    20    20
browser |    20  100.0%         11     +  46630021  46630040              AB349334     1    20    20
browser |    20  100.0%         11     +  58099111  58099130              AB349334     1    20    20
browser |    20  100.0%         11     +  59262141  59262160              AB349334     1    20    20
browser |    20  100.0%         11     +  63225111  63225130              AB349334     1    20    20
browser |    20  100.0%         11     -  63342182  63342201              AB349334     1    20    20
browser |    20  100.0%         11     -  68472157  68472176              AB349334     1    20    20
browser |    20  100.0%         11     +  92716576  92716595              AB349334     1    20    20
browser |    20  100.0%         11     -  96135902  96135921              AB349334     1    20    20
browser |    20  100.0%         11     - 101282987 101283006              AB349334     1    20    20
browser |    20  100.0%         11     + 111932441 111932460              AB349334     1    20    20
browser |    20  100.0%         11     + 112249051 112249070              AB349334     1    20    20
browser |    20  100.0%         11     + 116276376 116276395              AB349334     1    20    20
browser |    20  100.0%         12     +   3168601   3168620              AB349334     1    20    20
browser |    20  100.0%         12     -   6709262   6709281              AB349334     1    20    20
browser |    20  100.0%         12     -   8486077   8486096              AB349334     1    20    20
browser |    20  100.0%         12     +   9154591   9154610              AB349334     1    20    20
browser |    20  100.0%         12     -  13742657  13742676              AB349334     1    20    20
browser |    20  100.0%         12     -  13853132  13853151              AB349334     1    20    20
browser |    20  100.0%         12     +  15133941  15133960              AB349334     1    20    20
browser |    20  100.0%         12     +  15135426  15135445              AB349334     1    20    20
browser |    20  100.0%         12     -  17946397  17946416              AB349334     1    20    20
browser |    20  100.0%         12     -  24866297  24866316              AB349334     1    20    20
browser |    20  100.0%         12     -  27852897  27852916              AB349334     1    20    20
browser |    20  100.0%         12     -  32269327  32269346              AB349334     1    20    20
browser |    20  100.0%         12     -  32942857  32942876              AB349334     1    20    20
browser |    20  100.0%         12     +  43643776  43643795              AB349334     1    20    20
browser |    20  100.0%         12     +  46669796  46669815              AB349334     1    20    20
browser |    20  100.0%         12     +  47361691  47361710              AB349334     1    20    20
browser |    20  100.0%         12     -  67925892  67925911              AB349334     1    20    20
browser |    20  100.0%         12     -  71960112  71960131              AB349334     1    20    20
browser |    20  100.0%         12     -  78373042  78373061              AB349334     1    20    20
browser |    20  100.0%         12     +  78675391  78675410              AB349334     1    20    20
browser |    20  100.0%         12     +  78754641  78754660              AB349334     1    20    20
browser |    20  100.0%         12     -  79169272  79169291              AB349334     1    20    20
browser |    20  100.0%         12     -  81873037  81873056              AB349334     1    20    20
browser |    20  100.0%         12     -  81874527  81874546              AB349334     1    20    20
browser |    20  100.0%         12     +  82230936  82230955              AB349334     1    20    20
browser |    20  100.0%         12     +  82406241  82406260              AB349334     1    20    20
browser |    20  100.0%         12     -  84525262  84525281              AB349334     1    20    20
browser |    20  100.0%         12     -  91688582  91688601              AB349334     1    20    20
browser |    20  100.0%         12     +  96908986  96909005              AB349334     1    20    20
browser |    20  100.0%         12     - 101837282 101837301              AB349334     1    20    20
browser |    20  100.0%         12     + 101962311 101962330              AB349334     1    20    20
browser |    20  100.0%         12     + 102282426 102282445              AB349334     1    20    20
browser |    20  100.0%         12     - 105683657 105683676              AB349334     1    20    20
browser |    20  100.0%         12     - 107809542 107809561              AB349334     1    20    20
browser |    20  100.0%         12     - 108815027 108815046              AB349334     1    20    20
browser |    20  100.0%         12     - 109121267 109121286              AB349334     1    20    20
browser |    20  100.0%         12     - 109723607 109723626              AB349334     1    20    20
browser |    20  100.0%         12     + 113262816 113262835              AB349334     1    20    20
browser |    20  100.0%         12     - 119680317 119680336              AB349334     1    20    20
browser |    20  100.0%         13     -   3990187   3990206              AB349334     1    20    20
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browser |    20  100.0%         13     -  11203757  11203776              AB349334     1    20    20
browser |    20  100.0%         13     -  12358177  12358196              AB349334     1    20    20
browser |    20  100.0%         13     +  13489151  13489170              AB349334     1    20    20
browser |    20  100.0%         13     -  27087542  27087561              AB349334     1    20    20
browser |    20  100.0%         13     -  27319697  27319716              AB349334     1    20    20
browser |    20  100.0%         13     -  34111352  34111371              AB349334     1    20    20
browser |    20  100.0%         13     -  48670052  48670071              AB349334     1    20    20
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browser |    20  100.0%         13     - 102668017 102668036              AB349334     1    20    20
browser |    20  100.0%         13     - 107268022 107268041              AB349334     1    20    20
browser |    20  100.0%         13     - 108165987 108166006              AB349334     1    20    20
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browser |    20  100.0%         14     -   4233027   4233046              AB349334     1    20    20
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browser |    20  100.0%         14     -   8869757   8869776              AB349334     1    20    20
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browser |    20  100.0%         14     -  29848812  29848831              AB349334     1    20    20
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browser |    20  100.0%         14     +  33131686  33131705              AB349334     1    20    20
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browser |    20  100.0%         14     -  48166312  48166331              AB349334     1    20    20
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browser |    20  100.0%         14     +  50298426  50298445              AB349334     1    20    20
browser |    20  100.0%         14     +  58824421  58824440              AB349334     1    20    20
browser |    20  100.0%         14     -  60484512  60484531              AB349334     1    20    20
browser |    20  100.0%         14     +  61978531  61978550              AB349334     1    20    20
browser |    20  100.0%         14     +  63550021  63550040              AB349334     1    20    20
browser |    20  100.0%         14     +  65993991  65994010              AB349334     1    20    20
browser |    20  100.0%         14     +  71682521  71682540              AB349334     1    20    20
browser |    20  100.0%         14     +  71683981  71684000              AB349334     1    20    20
browser |    20  100.0%         14     -  83685117  83685136              AB349334     1    20    20
browser |    20  100.0%         14     +  85359916  85359935              AB349334     1    20    20
browser |    20  100.0%         14     -  91726042  91726061              AB349334     1    20    20
browser |    20  100.0%         14     -  97392032  97392051              AB349334     1    20    20
browser |    20  100.0%         14     +  97968501  97968520              AB349334     1    20    20
browser |    20  100.0%         14     - 105430012 105430031              AB349334     1    20    20
browser |    20  100.0%         14     - 106401962 106401981              AB349334     1    20    20
browser |    20  100.0%         14     - 106477557 106477576              AB349334     1    20    20
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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