AB338368
 

Information on mRNA AB338368

Description: Mus musculus non-coding RNA, oocyte_clustered_small_RNA3569, 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: n/a
Development stage: growing stage
Cell line: n/a
Sex: n/a
Library: n/a
Clone: n/a
CDS: n/a
Date: 2008-04-24
Version: 1
mRNA sequence: AB338368
Position: chr12:56958397-56958422

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 |    25  100.0%         12     -  56958397  56958422              AB338368     1    25    25
browser |    23  100.0%          1     -   7678801   7678823              AB338368     1    23    25
browser |    23  100.0%          1     -   8857313   8857335              AB338368     1    23    25
browser |    25  100.0%          1     -  13621162  13621187              AB338368     1    25    25
browser |    25  100.0%          1     +  18324828  18324853              AB338368     1    25    25
browser |    25  100.0%          1     +  22072271  22072296              AB338368     1    25    25
browser |    25  100.0%          1     -  44330371  44330396              AB338368     1    25    25
browser |    23  100.0%          1     +  65930862  65930884              AB338368     1    23    25
browser |    25  100.0%          1     +  72171475  72171500              AB338368     1    25    25
browser |    25  100.0%          1     -  76565606  76565631              AB338368     1    25    25
browser |    25  100.0%          1     +  86247898  86247923              AB338368     1    25    25
browser |    25  100.0%          1     - 179721916 179721941              AB338368     1    25    25
browser |    25  100.0%          1     - 183297107 183297132              AB338368     1    25    25
browser |    25  100.0%         10     -   7191699   7191724              AB338368     1    25    25
browser |    25  100.0%         10     -  30357772  30357797              AB338368     1    25    25
browser |    25  100.0%         10     +  35600951  35600976              AB338368     1    25    25
browser |    25  100.0%         10     -  74711957  74711982              AB338368     1    25    25
browser |    25  100.0%         10     +  81513183  81513208              AB338368     1    25    25
browser |    25  100.0%         10     +  81672311  81672336              AB338368     1    25    25
browser |    25  100.0%         10     +  83254524  83254548              AB338368     1    25    25
browser |    25  100.0%         10     +  83308470  83308495              AB338368     1    25    25
browser |    25  100.0%         10     +  92589569  92589594              AB338368     1    25    25
browser |    25  100.0%         10     - 110836481 110836506              AB338368     1    25    25
browser |    25  100.0%         11     -   6741542   6741566              AB338368     1    25    25
browser |    25  100.0%         11     +   7987110   7987135              AB338368     1    25    25
browser |    25  100.0%         11     -  12745909  12745934              AB338368     1    25    25
browser |    25  100.0%         11     +  29116168  29116193              AB338368     1    25    25
browser |    25  100.0%         11     - 116650748 116650773              AB338368     1    25    25
browser |    25  100.0%         12     -  39482046  39482071              AB338368     1    25    25
browser |    25  100.0%         12     -  63344868  63344893              AB338368     1    25    25
browser |    25  100.0%         12     + 101336169 101336194              AB338368     1    25    25
browser |    25  100.0%         12     + 105273218 105273243              AB338368     1    25    25
browser |    23  100.0%         12     - 114905129 114905151              AB338368     1    23    25
browser |    25  100.0%         12     - 118318388 118318413              AB338368     1    25    25
browser |    25  100.0%         13     -   4921287   4921312              AB338368     1    25    25
browser |    25  100.0%         13     +  11013648  11013673              AB338368     1    25    25
browser |    25  100.0%         13     +  19184849  19184874              AB338368     1    25    25
browser |    25  100.0%         13     -  23390371  23390396              AB338368     1    25    25
browser |    25  100.0%         13     -  51186846  51186871              AB338368     1    25    25
browser |    25  100.0%         13     -  52204969  52204994              AB338368     1    25    25
browser |    25  100.0%         13     +  54570975  54571000              AB338368     1    25    25
browser |    25  100.0%         13     +  82357948  82357973              AB338368     1    25    25
browser |    25  100.0%         13     +  84571271  84571296              AB338368     1    25    25
browser |    25  100.0%         13     +  85555366  85555391              AB338368     1    25    25
browser |    25  100.0%         13     -  93671242  93671267              AB338368     1    25    25
browser |    25  100.0%         14     -   4871624   4871649              AB338368     1    25    25
browser |    25  100.0%         14     +   5090966   5090991              AB338368     1    25    25
browser |    25  100.0%         14     +   7005629   7005654              AB338368     1    25    25
browser |    25  100.0%         14     -   8421512   8421537              AB338368     1    25    25
browser |    25  100.0%         14     -  23585618  23585643              AB338368     1    25    25
browser |    25  100.0%         14     +  55467215  55467240              AB338368     1    25    25
browser |    25  100.0%         14     -  80819717  80819742              AB338368     1    25    25
browser |    25  100.0%         14     -  86369381  86369406              AB338368     1    25    25
browser |    25  100.0%         14     +  87845481  87845506              AB338368     1    25    25
browser |    25  100.0%         14     -  89103978  89104003              AB338368     1    25    25
browser |    25  100.0%         14     +  89277208  89277233              AB338368     1    25    25
browser |    25  100.0%         14     +  95805625  95805650              AB338368     1    25    25
browser |    23  100.0%         14     - 101819153 101819175              AB338368     1    23    25
browser |    25  100.0%         14     - 103873101 103873126              AB338368     1    25    25
browser |    25  100.0%         14     - 110292887 110292912              AB338368     1    25    25
browser |    25  100.0%         14     + 119682146 119682171              AB338368     1    25    25
browser |    23  100.0%         15     -   9499704   9499726              AB338368     1    23    25
browser |    25  100.0%         15     -  71470219  71470244              AB338368     1    25    25
browser |    25  100.0%         15     +  82492659  82492684              AB338368     1    25    25
browser |    25  100.0%         15     +  88923901  88923926              AB338368     1    25    25
browser |    23  100.0%         15     -  93996537  93996559              AB338368     1    23    25
browser |    25  100.0%         16     -   5460913   5460937              AB338368     1    25    25
browser |    25  100.0%         16     +   8887769   8887794              AB338368     1    25    25
browser |    25  100.0%         16     -  16752969  16752994              AB338368     1    25    25
browser |    25  100.0%         16     +  17773706  17773731              AB338368     1    25    25
browser |    25  100.0%         16     -  46940681  46940706              AB338368     1    25    25
browser |    23  100.0%         16     -  48005747  48005769              AB338368     1    23    25
browser |    23  100.0%         16     +  61147847  61147869              AB338368     1    23    25
browser |    25  100.0%         16     -  69759586  69759611              AB338368     1    25    25
browser |    25  100.0%         16     +  75438269  75438294              AB338368     1    25    25
browser |    25  100.0%         16     +  77826689  77826714              AB338368     1    25    25
browser |    25  100.0%         16     +  79343398  79343423              AB338368     1    25    25
browser |    25  100.0%         16     +  80826193  80826218              AB338368     1    25    25
browser |    25  100.0%         16     +  83200291  83200316              AB338368     1    25    25
browser |    23  100.0%         16     +  88765438  88765460              AB338368     1    23    25
browser |    25  100.0%         17     +  15829835  15829860              AB338368     1    25    25
browser |    23  100.0%         17     -  18340649  18340671              AB338368     1    23    25
browser |    25  100.0%         17     +  23342280  23342305              AB338368     1    25    25
browser |    25  100.0%         17     -  50224841  50224866              AB338368     1    25    25
browser |    25  100.0%         17     -  53675682  53675707              AB338368     1    25    25
browser |    25  100.0%         17     -  61327787  61327812              AB338368     1    25    25
browser |    25  100.0%         18     -   7059046   7059071              AB338368     1    25    25
browser |    25  100.0%         18     +  24169476  24169501              AB338368     1    25    25
browser |    25  100.0%         18     -  63325758  63325783              AB338368     1    25    25
browser |    25  100.0%         18     -  71771001  71771026              AB338368     1    25    25
browser |    25  100.0%         19     -  45175349  45175374              AB338368     1    25    25
browser |    25  100.0%         19     -  45191717  45191742              AB338368     1    25    25
browser |    25  100.0%         19     +  59652903  59652928              AB338368     1    25    25
browser |    25  100.0%          2     -   8381050   8381074              AB338368     1    25    25
browser |    25  100.0%          2     -  14388368  14388393              AB338368     1    25    25
browser |    25  100.0%          2     +  36246204  36246229              AB338368     1    25    25
browser |    25  100.0%          2     +  39910604  39910629              AB338368     1    25    25
browser |    25  100.0%          2     +  46278393  46278418              AB338368     1    25    25
browser |    25  100.0%          2     +  71779196  71779221              AB338368     1    25    25
browser |    25  100.0%          2     -  73578556  73578581              AB338368     1    25    25
browser |    25  100.0%          2     +  87426541  87426566              AB338368     1    25    25
browser |    25  100.0%          2     + 122638174 122638199              AB338368     1    25    25
browser |    25  100.0%          2     - 123356124 123356149              AB338368     1    25    25
browser |    25  100.0%          2     - 123358934 123358959              AB338368     1    25    25
browser |    25  100.0%          2     - 123361712 123361737              AB338368     1    25    25
browser |    25  100.0%          2     - 123364482 123364507              AB338368     1    25    25
browser |    25  100.0%          2     + 129366560 129366585              AB338368     1    25    25
browser |    25  100.0%          2     - 149280659 149280684              AB338368     1    25    25
browser |    25  100.0%          3     -   9796628   9796653              AB338368     1    25    25
browser |    25  100.0%          3     -  20742538  20742563              AB338368     1    25    25
browser |    25  100.0%          3     + 116998161 116998186              AB338368     1    25    25
browser |    25  100.0%          3     - 124622641 124622666              AB338368     1    25    25
browser |    25  100.0%          3     - 140853951 140853976              AB338368     1    25    25
browser |    25  100.0%          4     -   7165839   7165864              AB338368     1    25    25
browser |    25  100.0%          4     -  21074229  21074254              AB338368     1    25    25
browser |    25  100.0%          4     -  25922281  25922306              AB338368     1    25    25
browser |    25  100.0%          4     -  38508796  38508821              AB338368     1    25    25
browser |    25  100.0%          4     -  57979932  57979957              AB338368     1    25    25
browser |    25  100.0%          4     +  59032531  59032556              AB338368     1    25    25
browser |    25  100.0%          4     +  63495361  63495386              AB338368     1    25    25
browser |    25  100.0%          4     +  71659206  71659231              AB338368     1    25    25
browser |    25  100.0%          4     +  78753274  78753299              AB338368     1    25    25
browser |    25  100.0%          4     +  80728226  80728251              AB338368     1    25    25
browser |    25  100.0%          4     + 106253228 106253253              AB338368     1    25    25
browser |    25  100.0%          4     + 111395800 111395825              AB338368     1    25    25
browser |    25  100.0%          4     + 141580128 141580153              AB338368     1    25    25
browser |    25  100.0%          5     +  13276654  13276679              AB338368     1    25    25
browser |    25  100.0%          5     -  18326591  18326616              AB338368     1    25    25
browser |    25  100.0%          5     +  20183549  20183574              AB338368     1    25    25
browser |    25  100.0%          5     +  30434729  30434754              AB338368     1    25    25
browser |    25  100.0%          5     -  42988651  42988676              AB338368     1    25    25
browser |    25  100.0%          5     -  57807099  57807124              AB338368     1    25    25
browser |    25  100.0%          5     +  69205629  69205654              AB338368     1    25    25
browser |    25  100.0%          5     -  75466477  75466502              AB338368     1    25    25
browser |    25  100.0%          5     - 101763857 101763882              AB338368     1    25    25
browser |    25  100.0%          5     + 110084728 110084752              AB338368     1    25    25
browser |    25  100.0%          5     - 127038232 127038257              AB338368     1    25    25
browser |    25  100.0%          5     + 142054876 142054901              AB338368     1    25    25
browser |    25  100.0%          6     -  10359358  10359383              AB338368     1    25    25
browser |    25  100.0%          6     -  13528057  13528082              AB338368     1    25    25
browser |    23  100.0%          6     -  20321765  20321787              AB338368     1    23    25
browser |    25  100.0%          6     +  23893748  23893773              AB338368     1    25    25
browser |    25  100.0%          6     +  32666864  32666889              AB338368     1    25    25
browser |    25  100.0%          6     +  44119008  44119033              AB338368     1    25    25
browser |    23  100.0%          6     -  50589291  50589313              AB338368     1    23    25
browser |    25  100.0%          6     - 128666836 128666861              AB338368     1    25    25
browser |    23  100.0%          7     +   8583058   8583080              AB338368     1    23    25
browser |    25  100.0%          7     -  48055308  48055333              AB338368     1    25    25
browser |    25  100.0%          7     -  55059487  55059512              AB338368     1    25    25
browser |    25  100.0%          7     +  57774691  57774716              AB338368     1    25    25
browser |    25  100.0%          7     -  59149094  59149119              AB338368     1    25    25
browser |    25  100.0%          7     + 110608571 110608596              AB338368     1    25    25
browser |    25  100.0%          8     -   5268273   5268298              AB338368     1    25    25
browser |    25  100.0%          8     +   6550086   6550111              AB338368     1    25    25
browser |    25  100.0%          8     +  14856599  14856624              AB338368     1    25    25
browser |    25  100.0%          8     -  51848373  51848398              AB338368     1    25    25
browser |    25  100.0%          8     -  78027924  78027949              AB338368     1    25    25
browser |    25  100.0%          8     +  91503107  91503131              AB338368     1    25    25
browser |    25  100.0%          9     -   4491688   4491713              AB338368     1    25    25
browser |    25  100.0%          9     -  11554452  11554477              AB338368     1    25    25
browser |    25  100.0%          9     -  23652751  23652776              AB338368     1    25    25
browser |    25  100.0%          9     +  33131041  33131066              AB338368     1    25    25
browser |    25  100.0%          9     -  46507704  46507729              AB338368     1    25    25
browser |    25  100.0%          9     +  53927530  53927555              AB338368     1    25    25
browser |    25  100.0%          9     +  79942279  79942304              AB338368     1    25    25
browser |    25  100.0%          9     - 105484942 105484967              AB338368     1    25    25
browser |    25  100.0%          X     -   9252002   9252027              AB338368     1    25    25
browser |    25  100.0%          X     +  15525594  15525619              AB338368     1    25    25
browser |    25  100.0%          X     +  43105503  43105528              AB338368     1    25    25
browser |    25  100.0%          X     -  46436492  46436517              AB338368     1    25    25
browser |    23  100.0%          X     +  62622473  62622495              AB338368     1    23    25
browser |    25  100.0%          X     -  64790146  64790171              AB338368     1    25    25
browser |    25  100.0%          X     -  95726148  95726173              AB338368     1    25    25
browser |    25  100.0%          X     +  96532525  96532550              AB338368     1    25    25
browser |    25  100.0%          X     - 113321812 113321837              AB338368     1    25    25
browser |    23  100.0%          X     + 115633844 115633866              AB338368     1    23    25
browser |    25  100.0%          X     - 144817583 144817608              AB338368     1    25    25
browser |    25  100.0%          X     + 155105764 155105789              AB338368     1    25    25
browser |    23  100.0%          X     - 161103531 161103553              AB338368     1    23    25
browser |    25  100.0%          Y     +    693850    693875              AB338368     1    25    25

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