AB350740
 

Information on mRNA AB350740

Description: Mus musculus non-coding RNA, oocyte_piRNA1556, 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: AB350740
Position: chr12:56797652-56797678

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     -  56797652  56797678              AB350740     3    29    29
browser |    27  100.0%          1     -   5880337   5880363              AB350740     3    29    29
browser |    29  100.0%          1     -  47265786  47265814              AB350740     1    29    29
browser |    27  100.0%          1     -  74698368  74698394              AB350740     3    29    29
browser |    29  100.0%          1     +  76592827  76592855              AB350740     1    29    29
browser |    29  100.0%          1     +  77645675  77645703              AB350740     1    29    29
browser |    29  100.0%          1     + 104293563 104293591              AB350740     1    29    29
browser |    29  100.0%          1     + 166181067 166181095              AB350740     1    29    29
browser |    29  100.0%          1     + 172094627 172094655              AB350740     1    29    29
browser |    29  100.0%         10     +  19674365  19674393              AB350740     1    29    29
browser |    27  100.0%         10     +  31359920  31359946              AB350740     3    29    29
browser |    29  100.0%         10     -  43648706  43648734              AB350740     1    29    29
browser |    29  100.0%         10     +  47547995  47548023              AB350740     1    29    29
browser |    27  100.0%         10     -  66564015  66564041              AB350740     3    29    29
browser |    27  100.0%         10     -  78657564  78657590              AB350740     3    29    29
browser |    26  100.0%         10     -  83253498  83253523              AB350740     4    29    29
browser |    27  100.0%         10     +  85552371  85552397              AB350740     3    29    29
browser |    29  100.0%         10     + 110533442 110533470              AB350740     1    29    29
browser |    27  100.0%         10     + 123696562 123696588              AB350740     3    29    29
browser |    29  100.0%         11     -  23195969  23195997              AB350740     1    29    29
browser |    29  100.0%         11     +  27081722  27081750              AB350740     1    29    29
browser |    29  100.0%         11     +  27085088  27085116              AB350740     1    29    29
browser |    27  100.0%         11     +  28048620  28048646              AB350740     3    29    29
browser |    27  100.0%         11     +  74021085  74021111              AB350740     3    29    29
browser |    29  100.0%         11     -  79635342  79635370              AB350740     1    29    29
browser |    29  100.0%         11     +  79764862  79764890              AB350740     1    29    29
browser |    27  100.0%         11     +  91991210  91991236              AB350740     3    29    29
browser |    27  100.0%         11     + 117392008 117392034              AB350740     3    29    29
browser |    29  100.0%         12     -   3086775   3086803              AB350740     1    29    29
browser |    26  100.0%         12     +  22093296  22093321              AB350740     4    29    29
browser |    26  100.0%         12     +  23252164  23252189              AB350740     4    29    29
browser |    29  100.0%         12     +  24743418  24743446              AB350740     1    29    29
browser |    27  100.0%         12     -  44817703  44817729              AB350740     3    29    29
browser |    29  100.0%         12     +  72686383  72686411              AB350740     1    29    29
browser |    27  100.0%         12     -  85453572  85453598              AB350740     3    29    29
browser |    26  100.0%         13     +   3471772   3471797              AB350740     1    26    29
browser |    29  100.0%         13     -   7328235   7328263              AB350740     1    29    29
browser |    27  100.0%         13     -  31423109  31423135              AB350740     3    29    29
browser |    26  100.0%         13     -  50029249  50029274              AB350740     1    26    29
browser |    29  100.0%         13     -  50888341  50888369              AB350740     1    29    29
browser |    29  100.0%         13     +  51022637  51022665              AB350740     1    29    29
browser |    29  100.0%         13     -  61098102  61098130              AB350740     1    29    29
browser |    29  100.0%         13     +  68144222  68144250              AB350740     1    29    29
browser |    27  100.0%         13     -  77752083  77752109              AB350740     3    29    29
browser |    29  100.0%         13     -  77822021  77822049              AB350740     1    29    29
browser |    29  100.0%         13     - 113701519 113701547              AB350740     1    29    29
browser |    29  100.0%         13     - 114678774 114678802              AB350740     1    29    29
browser |    29  100.0%         14     +  21411917  21411945              AB350740     1    29    29
browser |    29  100.0%         14     -  23024973  23025001              AB350740     1    29    29
browser |    29  100.0%         14     -  37225640  37225668              AB350740     1    29    29
browser |    29  100.0%         14     +  39454760  39454788              AB350740     1    29    29
browser |    29  100.0%         14     -  60805972  60806000              AB350740     1    29    29
browser |    27  100.0%         14     -  80035933  80035959              AB350740     3    29    29
browser |    29  100.0%         14     -  85418230  85418258              AB350740     1    29    29
browser |    27  100.0%         14     + 111618672 111618698              AB350740     3    29    29
browser |    29  100.0%         14     - 117319581 117319609              AB350740     1    29    29
browser |    27  100.0%         14     - 119719605 119719631              AB350740     3    29    29
browser |    29  100.0%         15     +   3196749   3196777              AB350740     1    29    29
browser |    29  100.0%         15     -  17576805  17576833              AB350740     1    29    29
browser |    29  100.0%         15     +  24322643  24322671              AB350740     1    29    29
browser |    27  100.0%         15     -  26908642  26908668              AB350740     3    29    29
browser |    29  100.0%         15     +  39578690  39578718              AB350740     1    29    29
browser |    29  100.0%         15     +  46367014  46367042              AB350740     1    29    29
browser |    26  100.0%         15     -  92514677  92514702              AB350740     4    29    29
browser |    27  100.0%         15     + 103811773 103811799              AB350740     3    29    29
browser |    29  100.0%         16     -  19411118  19411146              AB350740     1    29    29
browser |    29  100.0%         16     -  61135768  61135796              AB350740     1    29    29
browser |    29  100.0%         16     +  64787656  64787684              AB350740     1    29    29
browser |    27  100.0%         16     +  67428094  67428120              AB350740     3    29    29
browser |    29  100.0%         16     -  71819324  71819352              AB350740     1    29    29
browser |    27  100.0%         16     -  80562536  80562562              AB350740     3    29    29
browser |    29  100.0%         16     -  87086859  87086887              AB350740     1    29    29
browser |    29  100.0%         16     +  88943450  88943478              AB350740     1    29    29
browser |    29  100.0%         17     -  66837277  66837305              AB350740     1    29    29
browser |    29  100.0%         17     -  72885050  72885078              AB350740     1    29    29
browser |    29  100.0%         17     -  94102096  94102124              AB350740     1    29    29
browser |    29  100.0%         18     +   3041588   3041616              AB350740     1    29    29
browser |    29  100.0%         18     -   4482403   4482431              AB350740     1    29    29
browser |    27  100.0%         18     -   4700485   4700511              AB350740     3    29    29
browser |    27  100.0%         18     -   8775102   8775128              AB350740     3    29    29
browser |    29  100.0%         18     -  37023937  37023965              AB350740     1    29    29
browser |    29  100.0%         18     -  58420663  58420691              AB350740     1    29    29
browser |    27  100.0%         18     +  71215926  71215952              AB350740     3    29    29
browser |    29  100.0%         19     +  30942369  30942397              AB350740     1    29    29
browser |    27  100.0%          2     +   5690160   5690186              AB350740     3    29    29
browser |    29  100.0%          2     -  19361800  19361828              AB350740     1    29    29
browser |    27  100.0%          2     -  36254083  36254109              AB350740     1    27    29
browser |    29  100.0%          2     -  70713699  70713727              AB350740     1    29    29
browser |    29  100.0%          2     -  81624804  81624832              AB350740     1    29    29
browser |    27  100.0%          2     - 124671513 124671539              AB350740     3    29    29
browser |    29  100.0%          2     + 148459574 148459602              AB350740     1    29    29
browser |    29  100.0%          2     - 157465427 157465455              AB350740     1    29    29
browser |    27  100.0%          2     + 167125954 167125980              AB350740     3    29    29
browser |    29  100.0%          2     + 180813066 180813094              AB350740     1    29    29
browser |    29  100.0%          3     -  21070910  21070938              AB350740     1    29    29
browser |    27  100.0%          3     -  40817227  40817253              AB350740     3    29    29
browser |    29  100.0%          3     +  49115913  49115941              AB350740     1    29    29
browser |    26  100.0%          3     -  49389182  49389207              AB350740     1    26    29
browser |    29  100.0%          3     +  51838898  51838926              AB350740     1    29    29
browser |    27  100.0%          3     -  61620257  61620283              AB350740     3    29    29
browser |    29  100.0%          3     -  63958989  63959017              AB350740     1    29    29
browser |    27  100.0%          3     +  88575014  88575040              AB350740     3    29    29
browser |    29  100.0%          3     - 115164413 115164441              AB350740     1    29    29
browser |    29  100.0%          3     + 136988648 136988676              AB350740     1    29    29
browser |    29  100.0%          3     + 150043890 150043918              AB350740     1    29    29
browser |    29  100.0%          3     + 155884976 155885004              AB350740     1    29    29
browser |    29  100.0%          4     -   5146035   5146063              AB350740     1    29    29
browser |    27  100.0%          4     -   7100784   7100810              AB350740     3    29    29
browser |    29  100.0%          4     +  14639634  14639662              AB350740     1    29    29
browser |    26  100.0%          4     -  19295745  19295770              AB350740     4    29    29
browser |    29  100.0%          4     -  23083074  23083102              AB350740     1    29    29
browser |    29  100.0%          4     -  31635361  31635389              AB350740     1    29    29
browser |    29  100.0%          4     -  52190048  52190076              AB350740     1    29    29
browser |    26  100.0%          4     +  71211081  71211106              AB350740     4    29    29
browser |    29  100.0%          4     +  71882724  71882752              AB350740     1    29    29
browser |    27  100.0%          4     +  73121778  73121804              AB350740     3    29    29
browser |    27  100.0%          4     +  79480466  79480492              AB350740     3    29    29
browser |    29  100.0%          4     - 118533489 118533517              AB350740     1    29    29
browser |    26  100.0%          4     - 147556560 147556585              AB350740     1    26    29
browser |    29  100.0%          5     +   6613441   6613469              AB350740     1    29    29
browser |    29  100.0%          5     -  38631994  38632022              AB350740     1    29    29
browser |    27  100.0%          5     +  59598251  59598277              AB350740     3    29    29
browser |    29  100.0%          5     -  60915019  60915047              AB350740     1    29    29
browser |    29  100.0%          5     +  76425118  76425146              AB350740     1    29    29
browser |    29  100.0%          5     +  83698198  83698226              AB350740     1    29    29
browser |    26  100.0%          5     - 110083747 110083772              AB350740     4    29    29
browser |    29  100.0%          5     + 136185854 136185882              AB350740     1    29    29
browser |    27  100.0%          6     +   3250922   3250948              AB350740     3    29    29
browser |    29  100.0%          6     -  26070532  26070560              AB350740     1    29    29
browser |    29  100.0%          6     +  31885804  31885832              AB350740     1    29    29
browser |    29  100.0%          6     -  37525645  37525673              AB350740     1    29    29
browser |    26  100.0%          6     +  68971659  68971684              AB350740     4    29    29
browser |    29  100.0%          6     +  97883079  97883107              AB350740     1    29    29
browser |    29  100.0%          6     - 105468488 105468516              AB350740     1    29    29
browser |    29  100.0%          6     - 111649101 111649129              AB350740     1    29    29
browser |    29  100.0%          7     -   4282977   4283005              AB350740     1    29    29
browser |    26  100.0%          7     -   6009511   6009536              AB350740     1    26    29
browser |    29  100.0%          7     +  14034536  14034564              AB350740     1    29    29
browser |    29  100.0%          7     +  15438475  15438503              AB350740     1    29    29
browser |    29  100.0%          7     +  33105465  33105493              AB350740     1    29    29
browser |    27  100.0%          7     -  33214389  33214415              AB350740     3    29    29
browser |    27  100.0%          7     -  48021323  48021349              AB350740     3    29    29
browser |    29  100.0%          7     -  53474617  53474645              AB350740     1    29    29
browser |    29  100.0%          7     +  55987486  55987514              AB350740     1    29    29
browser |    29  100.0%          7     +  56766095  56766123              AB350740     1    29    29
browser |    29  100.0%          7     -  84749458  84749486              AB350740     1    29    29
browser |    29  100.0%          7     -  89302401  89302429              AB350740     1    29    29
browser |    29  100.0%          7     - 125131861 125131889              AB350740     1    29    29
browser |    29  100.0%          8     +  63318339  63318367              AB350740     1    29    29
browser |    29  100.0%          8     -  63371243  63371271              AB350740     1    29    29
browser |    27  100.0%          8     + 100976730 100976756              AB350740     3    29    29
browser |    29  100.0%          8     - 102856851 102856879              AB350740     1    29    29
browser |    29  100.0%          8     - 129356559 129356587              AB350740     1    29    29
browser |    29  100.0%          9     +   3080732   3080760              AB350740     1    29    29
browser |    29  100.0%          9     +   4242201   4242229              AB350740     1    29    29
browser |    29  100.0%          9     -   7374177   7374205              AB350740     1    29    29
browser |    29  100.0%          9     +   9888870   9888898              AB350740     1    29    29
browser |    29  100.0%          9     +   9922843   9922871              AB350740     1    29    29
browser |    29  100.0%          9     -  12471976  12472004              AB350740     1    29    29
browser |    27  100.0%          9     -  16997774  16997800              AB350740     3    29    29
browser |    29  100.0%          9     -  17301585  17301613              AB350740     1    29    29
browser |    29  100.0%          9     -  18054808  18054836              AB350740     1    29    29
browser |    26  100.0%          9     -  19877643  19877668              AB350740     4    29    29
browser |    29  100.0%          9     +  24484091  24484119              AB350740     1    29    29
browser |    29  100.0%          9     -  31993471  31993499              AB350740     1    29    29
browser |    27  100.0%          9     -  85950573  85950599              AB350740     3    29    29
browser |    29  100.0%          9     + 114800474 114800502              AB350740     1    29    29
browser |    29  100.0%  Un_GL456396v1     -     20044     20072              AB350740     1    29    29
browser |    27  100.0%          X     -  29427888  29427914              AB350740     3    29    29
browser |    29  100.0%          X     -  35181858  35181886              AB350740     1    29    29
browser |    29  100.0%          X     -  49505990  49506018              AB350740     1    29    29
browser |    29  100.0%          X     -  51086161  51086189              AB350740     1    29    29
browser |    29  100.0%          X     +  65803255  65803283              AB350740     1    29    29
browser |    29  100.0%          X     +  66092702  66092730              AB350740     1    29    29
browser |    29  100.0%          X     +  70729046  70729074              AB350740     1    29    29
browser |    29  100.0%          X     -  70926411  70926439              AB350740     1    29    29
browser |    29  100.0%          X     -  80886060  80886088              AB350740     1    29    29
browser |    29  100.0%          X     -  83555414  83555442              AB350740     1    29    29
browser |    29  100.0%          X     -  88567227  88567255              AB350740     1    29    29
browser |    29  100.0%          X     +  88722517  88722545              AB350740     1    29    29
browser |    29  100.0%          X     +  96227894  96227922              AB350740     1    29    29
browser |    29  100.0%          X     - 105737236 105737264              AB350740     1    29    29
browser |    27  100.0%          X     - 111657534 111657560              AB350740     3    29    29
browser |    29  100.0%          X     - 113802886 113802914              AB350740     1    29    29
browser |    29  100.0%          X     + 115562760 115562788              AB350740     1    29    29
browser |    29  100.0%          X     + 122907412 122907440              AB350740     1    29    29
browser |    27  100.0%          X     + 124960951 124960977              AB350740     3    29    29
browser |    29  100.0%          X     - 125261587 125261615              AB350740     1    29    29
browser |    27  100.0%          X     + 126859406 126859432              AB350740     3    29    29
browser |    27  100.0%          X     + 127628156 127628182              AB350740     3    29    29
browser |    29  100.0%          X     - 130245145 130245173              AB350740     1    29    29
browser |    29  100.0%          X     - 139797257 139797285              AB350740     1    29    29
browser |    26  100.0%          X     - 146458524 146458549              AB350740     1    26    29
browser |    29  100.0%          X     - 151355289 151355317              AB350740     1    29    29
browser |    29  100.0%          X     - 151979532 151979560              AB350740     1    29    29
browser |    29  100.0%  X_GL456233v2_random     +    495862    495890              AB350740     1    29    29

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