AB350238
 

Information on mRNA AB350238

Description: Mus musculus non-coding RNA, oocyte_piRNA1054, 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: AB350238
Position: chr12:56795444-56795468

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     -  56795444  56795468              AB350238     1    25    25
browser |    25  100.0%          1     -   5875378   5875402              AB350238     1    25    25
browser |    25  100.0%          1     +   6242193   6242217              AB350238     1    25    25
browser |    25  100.0%          1     -   6501407   6501431              AB350238     1    25    25
browser |    25  100.0%          1     +   8070214   8070238              AB350238     1    25    25
browser |    25  100.0%          1     +   8232649   8232673              AB350238     1    25    25
browser |    25  100.0%          1     -  10800898  10800922              AB350238     1    25    25
browser |    25  100.0%          1     +  16814727  16814751              AB350238     1    25    25
browser |    25  100.0%          1     +  18590601  18590625              AB350238     1    25    25
browser |    25  100.0%          1     +  19698935  19698959              AB350238     1    25    25
browser |    25  100.0%          1     +  21654306  21654330              AB350238     1    25    25
browser |    25  100.0%          1     +  23344597  23344621              AB350238     1    25    25
browser |    25  100.0%          1     -  26389063  26389087              AB350238     1    25    25
browser |    25  100.0%          1     +  26459342  26459366              AB350238     1    25    25
browser |    25  100.0%          1     -  26510263  26510287              AB350238     1    25    25
browser |    25  100.0%          1     +  27225491  27225515              AB350238     1    25    25
browser |    25  100.0%          1     -  29982617  29982641              AB350238     1    25    25
browser |    25  100.0%          1     +  34389607  34389631              AB350238     1    25    25
browser |    25  100.0%          1     +  34957440  34957464              AB350238     1    25    25
browser |    25  100.0%          1     +  35833821  35833845              AB350238     1    25    25
browser |    25  100.0%          1     -  37318698  37318722              AB350238     1    25    25
browser |    25  100.0%          1     +  38747202  38747226              AB350238     1    25    25
browser |    25  100.0%          1     +  45777677  45777701              AB350238     1    25    25
browser |    25  100.0%          1     -  47263406  47263430              AB350238     1    25    25
browser |    25  100.0%          1     -  48394305  48394329              AB350238     1    25    25
browser |    25  100.0%          1     -  53169595  53169619              AB350238     1    25    25
browser |    25  100.0%          1     -  58363334  58363358              AB350238     1    25    25
browser |    25  100.0%          1     -  58851644  58851668              AB350238     1    25    25
browser |    25  100.0%          1     -  60764828  60764852              AB350238     1    25    25
browser |    25  100.0%          1     -  74693413  74693437              AB350238     1    25    25
browser |    25  100.0%          1     -  76750812  76750836              AB350238     1    25    25
browser |    25  100.0%          1     -  81542703  81542727              AB350238     1    25    25
browser |    25  100.0%          1     +  82482882  82482906              AB350238     1    25    25
browser |    25  100.0%          1     -  84974421  84974445              AB350238     1    25    25
browser |    25  100.0%          1     -  87062184  87062208              AB350238     1    25    25
browser |    25  100.0%          1     +  87394148  87394172              AB350238     1    25    25
browser |    25  100.0%          1     +  89130104  89130128              AB350238     1    25    25
browser |    25  100.0%          1     -  91399760  91399784              AB350238     1    25    25
browser |    25  100.0%          1     -  93036028  93036052              AB350238     1    25    25
browser |    25  100.0%          1     +  93888191  93888215              AB350238     1    25    25
browser |    25  100.0%          1     +  97108116  97108140              AB350238     1    25    25
browser |    25  100.0%          1     - 101906690 101906714              AB350238     1    25    25
browser |    25  100.0%          1     + 102965659 102965683              AB350238     1    25    25
browser |    25  100.0%          1     - 103133722 103133746              AB350238     1    25    25
browser |    25  100.0%          1     + 103520917 103520941              AB350238     1    25    25
browser |    25  100.0%          1     - 104218112 104218136              AB350238     1    25    25
browser |    25  100.0%          1     - 107967351 107967375              AB350238     1    25    25
browser |    25  100.0%          1     - 108337409 108337433              AB350238     1    25    25
browser |    25  100.0%          1     - 109057224 109057248              AB350238     1    25    25
browser |    25  100.0%          1     + 109547397 109547421              AB350238     1    25    25
browser |    25  100.0%          1     + 110261169 110261193              AB350238     1    25    25
browser |    25  100.0%          1     - 110866157 110866181              AB350238     1    25    25
browser |    25  100.0%          1     - 111182182 111182206              AB350238     1    25    25
browser |    25  100.0%          1     + 111637367 111637391              AB350238     1    25    25
browser |    25  100.0%          1     - 112492847 112492871              AB350238     1    25    25
browser |    25  100.0%          1     + 112862360 112862384              AB350238     1    25    25
browser |    25  100.0%          1     + 112950076 112950100              AB350238     1    25    25
browser |    25  100.0%          1     + 114117385 114117409              AB350238     1    25    25
browser |    25  100.0%          1     - 115813917 115813941              AB350238     1    25    25
browser |    25  100.0%          1     - 116576827 116576851              AB350238     1    25    25
browser |    25  100.0%          1     + 125250860 125250884              AB350238     1    25    25
browser |    25  100.0%          1     + 126356554 126356578              AB350238     1    25    25
browser |    25  100.0%          1     + 126871281 126871305              AB350238     1    25    25
browser |    25  100.0%          1     - 159798152 159798176              AB350238     1    25    25
browser |    25  100.0%          1     - 160644265 160644289              AB350238     1    25    25
browser |    25  100.0%          1     + 162674389 162674413              AB350238     1    25    25
browser |    25  100.0%          1     - 163296882 163296906              AB350238     1    25    25
browser |    25  100.0%          1     - 166591525 166591549              AB350238     1    25    25
browser |    25  100.0%          1     + 169375632 169375656              AB350238     1    25    25
browser |    25  100.0%          1     + 169949623 169949647              AB350238     1    25    25
browser |    25  100.0%          1     - 174870370 174870394              AB350238     1    25    25
browser |    25  100.0%          1     - 176371452 176371476              AB350238     1    25    25
browser |    25  100.0%          1     + 177891858 177891882              AB350238     1    25    25
browser |    25  100.0%          1     + 178007941 178007965              AB350238     1    25    25
browser |    25  100.0%          1     - 181091908 181091932              AB350238     1    25    25
browser |    25  100.0%          1     + 181326226 181326250              AB350238     1    25    25
browser |    25  100.0%          1     + 191844050 191844074              AB350238     1    25    25
browser |    25  100.0%          1     + 195008921 195008945              AB350238     1    25    25
browser |    25  100.0%         10     -   3267155   3267179              AB350238     1    25    25
browser |    25  100.0%         10     -   3551747   3551771              AB350238     1    25    25
browser |    25  100.0%         10     +   9726696   9726720              AB350238     1    25    25
browser |    25  100.0%         10     +  11576291  11576315              AB350238     1    25    25
browser |    25  100.0%         10     -  19415462  19415486              AB350238     1    25    25
browser |    25  100.0%         10     +  21091615  21091639              AB350238     1    25    25
browser |    25  100.0%         10     -  21519035  21519059              AB350238     1    25    25
browser |    25  100.0%         10     -  22559981  22560005              AB350238     1    25    25
browser |    25  100.0%         10     -  23748036  23748060              AB350238     1    25    25
browser |    25  100.0%         10     +  24566645  24566669              AB350238     1    25    25
browser |    25  100.0%         10     -  24978260  24978284              AB350238     1    25    25
browser |    25  100.0%         10     +  25848356  25848380              AB350238     1    25    25
browser |    25  100.0%         10     +  30696254  30696278              AB350238     1    25    25
browser |    25  100.0%         10     +  30970940  30970964              AB350238     1    25    25
browser |    25  100.0%         10     +  31364883  31364907              AB350238     1    25    25
browser |    25  100.0%         10     +  31630027  31630051              AB350238     1    25    25
browser |    25  100.0%         10     +  33766199  33766223              AB350238     1    25    25
browser |    25  100.0%         10     -  34618639  34618663              AB350238     1    25    25
browser |    25  100.0%         10     +  41722805  41722829              AB350238     1    25    25
browser |    25  100.0%         10     -  45431817  45431841              AB350238     1    25    25
browser |    25  100.0%         10     +  50370732  50370756              AB350238     1    25    25
browser |    25  100.0%         10     +  51763176  51763200              AB350238     1    25    25
browser |    25  100.0%         10     +  54468762  54468786              AB350238     1    25    25
browser |    25  100.0%         10     -  55592443  55592467              AB350238     1    25    25
browser |    25  100.0%         10     +  56603113  56603137              AB350238     1    25    25
browser |    25  100.0%         10     +  57020033  57020057              AB350238     1    25    25
browser |    25  100.0%         10     -  65475510  65475534              AB350238     1    25    25
browser |    25  100.0%         10     -  65787414  65787438              AB350238     1    25    25
browser |    25  100.0%         10     -  66559060  66559084              AB350238     1    25    25
browser |    25  100.0%         10     -  78653109  78653133              AB350238     1    25    25
browser |    25  100.0%         10     +  80815844  80815868              AB350238     1    25    25
browser |    25  100.0%         10     +  81809993  81810017              AB350238     1    25    25
browser |    25  100.0%         10     -  83507602  83507626              AB350238     1    25    25
browser |    25  100.0%         10     +  83627626  83627650              AB350238     1    25    25
browser |    25  100.0%         10     +  84584917  84584941              AB350238     1    25    25
browser |    25  100.0%         10     +  85555718  85555742              AB350238     1    25    25
browser |    25  100.0%         10     -  85605108  85605132              AB350238     1    25    25
browser |    25  100.0%         10     +  88493099  88493123              AB350238     1    25    25
browser |    25  100.0%         10     +  88803220  88803244              AB350238     1    25    25
browser |    25  100.0%         10     -  90161286  90161310              AB350238     1    25    25
browser |    25  100.0%         10     -  94199253  94199277              AB350238     1    25    25
browser |    25  100.0%         10     -  95993924  95993948              AB350238     1    25    25
browser |    25  100.0%         10     -  96029210  96029234              AB350238     1    25    25
browser |    25  100.0%         10     -  97157238  97157262              AB350238     1    25    25
browser |    25  100.0%         10     -  98934875  98934899              AB350238     1    25    25
browser |    25  100.0%         10     +  99181254  99181278              AB350238     1    25    25
browser |    25  100.0%         10     + 104397481 104397505              AB350238     1    25    25
browser |    25  100.0%         10     - 104656168 104656192              AB350238     1    25    25
browser |    25  100.0%         10     + 105016828 105016852              AB350238     1    25    25
browser |    25  100.0%         10     - 109151894 109151918              AB350238     1    25    25
browser |    25  100.0%         10     + 111893426 111893450              AB350238     1    25    25
browser |    25  100.0%         10     - 113559425 113559449              AB350238     1    25    25
browser |    25  100.0%         10     - 116442983 116443007              AB350238     1    25    25
browser |    25  100.0%         10     + 117911546 117911570              AB350238     1    25    25
browser |    25  100.0%         10     + 121004343 121004367              AB350238     1    25    25
browser |    25  100.0%         10     - 122202780 122202804              AB350238     1    25    25
browser |    25  100.0%         10     + 124418498 124418522              AB350238     1    25    25
browser |    25  100.0%         10     + 124446004 124446028              AB350238     1    25    25
browser |    25  100.0%         10     - 124517170 124517194              AB350238     1    25    25
browser |    25  100.0%         10     - 129225508 129225532              AB350238     1    25    25
browser |    25  100.0%         10     + 129764694 129764718              AB350238     1    25    25
browser |    25  100.0%         10     - 130396827 130396851              AB350238     1    25    25
browser |    25  100.0%         11     -   6092308   6092332              AB350238     1    25    25
browser |    25  100.0%         11     +   6484951   6484975              AB350238     1    25    25
browser |    25  100.0%         11     -   7526505   7526529              AB350238     1    25    25
browser |    25  100.0%         11     -   9658803   9658827              AB350238     1    25    25
browser |    25  100.0%         11     +  10716596  10716620              AB350238     1    25    25
browser |    25  100.0%         11     -  12458106  12458130              AB350238     1    25    25
browser |    25  100.0%         11     +  12518208  12518232              AB350238     1    25    25
browser |    25  100.0%         11     +  12751876  12751900              AB350238     1    25    25
browser |    25  100.0%         11     -  12904833  12904857              AB350238     1    25    25
browser |    25  100.0%         11     +  15183977  15184001              AB350238     1    25    25
browser |    25  100.0%         11     +  15836980  15837004              AB350238     1    25    25
browser |    25  100.0%         11     +  16181832  16181856              AB350238     1    25    25
browser |    25  100.0%         11     -  18757274  18757298              AB350238     1    25    25
browser |    25  100.0%         11     -  19516993  19517017              AB350238     1    25    25
browser |    25  100.0%         11     -  19739543  19739567              AB350238     1    25    25
browser |    25  100.0%         11     +  20470317  20470341              AB350238     1    25    25
browser |    25  100.0%         11     -  22286070  22286094              AB350238     1    25    25
browser |    25  100.0%         11     +  22532168  22532192              AB350238     1    25    25
browser |    25  100.0%         11     -  23169400  23169424              AB350238     1    25    25
browser |    25  100.0%         11     +  26509910  26509934              AB350238     1    25    25
browser |    25  100.0%         11     -  27901896  27901920              AB350238     1    25    25
browser |    25  100.0%         11     +  28053577  28053601              AB350238     1    25    25
browser |    25  100.0%         11     +  29078950  29078974              AB350238     1    25    25
browser |    25  100.0%         11     +  38377332  38377356              AB350238     1    25    25
browser |    25  100.0%         11     -  39955375  39955399              AB350238     1    25    25
browser |    25  100.0%         11     -  51556670  51556694              AB350238     1    25    25
browser |    25  100.0%         11     -  74111337  74111361              AB350238     1    25    25
browser |    25  100.0%         11     +  74435345  74435369              AB350238     1    25    25
browser |    25  100.0%         11     +  74781508  74781532              AB350238     1    25    25
browser |    25  100.0%         11     -  79124437  79124461              AB350238     1    25    25
browser |    25  100.0%         11     +  81442652  81442676              AB350238     1    25    25
browser |    25  100.0%         11     -  82225641  82225665              AB350238     1    25    25
browser |    25  100.0%         11     -  85177214  85177238              AB350238     1    25    25
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browser |    25  100.0%         11     -  88802606  88802630              AB350238     1    25    25
browser |    25  100.0%         11     -  90721265  90721289              AB350238     1    25    25
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browser |    25  100.0%         11     -  90851818  90851842              AB350238     1    25    25
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browser |    25  100.0%         11     -  99604348  99604372              AB350238     1    25    25
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browser |    25  100.0%         11     - 105919899 105919923              AB350238     1    25    25
browser |    25  100.0%         11     - 106184334 106184358              AB350238     1    25    25
browser |    25  100.0%         11     - 108290897 108290921              AB350238     1    25    25
browser |    25  100.0%         11     + 108545171 108545195              AB350238     1    25    25
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browser |    25  100.0%         12     -  70708752  70708776              AB350238     1    25    25
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browser |    25  100.0%         12     -  79609431  79609455              AB350238     1    25    25
browser |    25  100.0%         12     +  80470350  80470374              AB350238     1    25    25
browser |    25  100.0%         12     +  81633780  81633804              AB350238     1    25    25
browser |    25  100.0%         12     -  82508680  82508704              AB350238     1    25    25
browser |    25  100.0%         12     -  85448617  85448641              AB350238     1    25    25
browser |    25  100.0%         12     +  88482562  88482586              AB350238     1    25    25
browser |    25  100.0%         12     +  93482610  93482634              AB350238     1    25    25
browser |    25  100.0%         12     -  94004101  94004125              AB350238     1    25    25
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browser |    25  100.0%         12     -  96197774  96197798              AB350238     1    25    25
browser |    25  100.0%         12     - 108046375 108046399              AB350238     1    25    25
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View details of parts of alignment within browser window
.
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