AB351842
 

Information on mRNA AB351842

Description: Mus musculus non-coding RNA, oocyte_piRNA2658, 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: AB351842
Position: chrX:15607061-15607086

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 |    26  100.0%          X     +  15607061  15607086              AB351842     1    26    26
browser |    26  100.0%          1     -   4155490   4155515              AB351842     1    26    26
browser |    26  100.0%          1     -   4155698   4155723              AB351842     1    26    26
browser |    26  100.0%          1     -   4155906   4155931              AB351842     1    26    26
browser |    26  100.0%          1     +   4258035   4258060              AB351842     1    26    26
browser |    26  100.0%          1     +   5500606   5500631              AB351842     1    26    26
browser |    26  100.0%          1     +   5890352   5890377              AB351842     1    26    26
browser |    26  100.0%          1     -   6221243   6221268              AB351842     1    26    26
browser |    26  100.0%          1     -   8288674   8288699              AB351842     1    26    26
browser |    26  100.0%          1     -   8288882   8288907              AB351842     1    26    26
browser |    26  100.0%          1     +   8758644   8758669              AB351842     1    26    26
browser |    26  100.0%          1     +   8758852   8758877              AB351842     1    26    26
browser |    26  100.0%          1     +   8759060   8759085              AB351842     1    26    26
browser |    26  100.0%          1     +   8759268   8759293              AB351842     1    26    26
browser |    26  100.0%          1     +   8759476   8759501              AB351842     1    26    26
browser |    26  100.0%          1     -   9121050   9121075              AB351842     1    26    26
browser |    26  100.0%          1     -   9121258   9121283              AB351842     1    26    26
browser |    26  100.0%          1     +   9245778   9245803              AB351842     1    26    26
browser |    26  100.0%          1     +   9245986   9246011              AB351842     1    26    26
browser |    26  100.0%          1     +   9246194   9246219              AB351842     1    26    26
browser |    26  100.0%          1     -  10863085  10863110              AB351842     1    26    26
browser |    26  100.0%          1     +  11744531  11744556              AB351842     1    26    26
browser |    26  100.0%          1     -  11799476  11799501              AB351842     1    26    26
browser |    26  100.0%          1     -  11799684  11799709              AB351842     1    26    26
browser |    26  100.0%          1     -  11799892  11799917              AB351842     1    26    26
browser |    26  100.0%          1     +  11924080  11924105              AB351842     1    26    26
browser |    26  100.0%          1     +  12287566  12287591              AB351842     1    26    26
browser |    26  100.0%          1     -  15064838  15064863              AB351842     1    26    26
browser |    26  100.0%          1     +  15090662  15090687              AB351842     1    26    26
browser |    26  100.0%          1     -  15812787  15812812              AB351842     1    26    26
browser |    26  100.0%          1     -  15812995  15813020              AB351842     1    26    26
browser |    26  100.0%          1     -  15813619  15813644              AB351842     1    26    26
browser |    26  100.0%          1     +  16523123  16523148              AB351842     1    26    26
browser |    26  100.0%          1     -  80671448  80671473              AB351842     1    26    26
browser |    26  100.0%          1     -  80671656  80671681              AB351842     1    26    26
browser |    26  100.0%          1     -  83440534  83440559              AB351842     1    26    26
browser |    26  100.0%          1     +  83593171  83593196              AB351842     1    26    26
browser |    26  100.0%          1     +  84099582  84099607              AB351842     1    26    26
browser |    26  100.0%          1     +  84099790  84099815              AB351842     1    26    26
browser |    26  100.0%          1     +  84241391  84241416              AB351842     1    26    26
browser |    26  100.0%          1     +  84241599  84241624              AB351842     1    26    26
browser |    26  100.0%          1     +  84241807  84241832              AB351842     1    26    26
browser |    26  100.0%          1     +  84678482  84678507              AB351842     1    26    26
browser |    26  100.0%          1     +  84678690  84678715              AB351842     1    26    26
browser |    26  100.0%          1     +  84678898  84678923              AB351842     1    26    26
browser |    26  100.0%          1     -  84998324  84998349              AB351842     1    26    26
browser |    26  100.0%          1     -  84998733  84998758              AB351842     1    26    26
browser |    26  100.0%          1     -  85044944  85044969              AB351842     1    26    26
browser |    26  100.0%          1     +  85125539  85125564              AB351842     1    26    26
browser |    26  100.0%          1     -  85317643  85317668              AB351842     1    26    26
browser |    26  100.0%          1     -  87962348  87962373              AB351842     1    26    26
browser |    26  100.0%          1     -  87962556  87962581              AB351842     1    26    26
browser |    26  100.0%          1     -  87962972  87962997              AB351842     1    26    26
browser |    26  100.0%          1     +  89144500  89144525              AB351842     1    26    26
browser |    26  100.0%          1     +  89144708  89144733              AB351842     1    26    26
browser |    26  100.0%          1     +  89145124  89145149              AB351842     1    26    26
browser |    26  100.0%          1     +  89145332  89145357              AB351842     1    26    26
browser |    26  100.0%          1     -  92346165  92346190              AB351842     1    26    26
browser |    26  100.0%          1     -  94169915  94169940              AB351842     1    26    26
browser |    26  100.0%          1     -  94321819  94321844              AB351842     1    26    26
browser |    26  100.0%          1     -  94322027  94322052              AB351842     1    26    26
browser |    26  100.0%          1     -  94322235  94322260              AB351842     1    26    26
browser |    26  100.0%          1     +  94327305  94327330              AB351842     1    26    26
browser |    26  100.0%          1     -  94409165  94409190              AB351842     1    26    26
browser |    26  100.0%          1     +  96119150  96119175              AB351842     1    26    26
browser |    26  100.0%          1     - 157711416 157711441              AB351842     1    26    26
browser |    26  100.0%          1     - 158416141 158416166              AB351842     1    26    26
browser |    26  100.0%          1     - 159542064 159542089              AB351842     1    26    26
browser |    26  100.0%          1     + 160249871 160249896              AB351842     1    26    26
browser |    26  100.0%          1     - 162097584 162097609              AB351842     1    26    26
browser |    26  100.0%          1     - 162097792 162097817              AB351842     1    26    26
browser |    26  100.0%          1     + 163599441 163599466              AB351842     1    26    26
browser |    26  100.0%          1     + 163640445 163640470              AB351842     1    26    26
browser |    26  100.0%          1     - 164557358 164557383              AB351842     1    26    26
browser |    26  100.0%          1     - 164557566 164557591              AB351842     1    26    26
browser |    26  100.0%          1     + 164744269 164744294              AB351842     1    26    26
browser |    26  100.0%          1     + 164853846 164853871              AB351842     1    26    26
browser |    26  100.0%          1     + 166428049 166428074              AB351842     1    26    26
browser |    26  100.0%          1     + 166428683 166428708              AB351842     1    26    26
browser |    26  100.0%          1     + 166429099 166429124              AB351842     1    26    26
browser |    26  100.0%          1     + 166429307 166429332              AB351842     1    26    26
browser |    26  100.0%          1     - 167308398 167308423              AB351842     1    26    26
browser |    26  100.0%          1     - 168940794 168940819              AB351842     1    26    26
browser |    26  100.0%          1     + 169112472 169112497              AB351842     1    26    26
browser |    26  100.0%          1     + 172544613 172544638              AB351842     1    26    26
browser |    26  100.0%          1     + 172559548 172559573              AB351842     1    26    26
browser |    26  100.0%          1     + 172559756 172559781              AB351842     1    26    26
browser |    26  100.0%          1     - 172712150 172712175              AB351842     1    26    26
browser |    26  100.0%          1     - 172712358 172712383              AB351842     1    26    26
browser |    26  100.0%          1     - 172989831 172989856              AB351842     1    26    26
browser |    26  100.0%          1     - 173087966 173087991              AB351842     1    26    26
browser |    26  100.0%          1     - 173088382 173088407              AB351842     1    26    26
browser |    26  100.0%          1     - 173088590 173088615              AB351842     1    26    26
browser |    26  100.0%          1     - 174615174 174615199              AB351842     1    26    26
browser |    26  100.0%          1     + 176110239 176110264              AB351842     1    26    26
browser |    26  100.0%          1     + 176110447 176110472              AB351842     1    26    26
browser |    26  100.0%          1     + 194926145 194926170              AB351842     1    26    26
browser |    26  100.0%         10     -   3532773   3532798              AB351842     1    26    26
browser |    26  100.0%         10     +   5338826   5338851              AB351842     1    26    26
browser |    26  100.0%         10     +   5339034   5339059              AB351842     1    26    26
browser |    26  100.0%         10     +   5339450   5339475              AB351842     1    26    26
browser |    26  100.0%         10     +   6604925   6604950              AB351842     1    26    26
browser |    26  100.0%         10     +   6605133   6605158              AB351842     1    26    26
browser |    26  100.0%         10     -   8195568   8195593              AB351842     1    26    26
browser |    26  100.0%         10     -  10022849  10022874              AB351842     1    26    26
browser |    26  100.0%         10     +  10460547  10460572              AB351842     1    26    26
browser |    26  100.0%         10     +  10460963  10460988              AB351842     1    26    26
browser |    26  100.0%         10     +  11498978  11499003              AB351842     1    26    26
browser |    26  100.0%         10     +  12142361  12142386              AB351842     1    26    26
browser |    26  100.0%         10     +  12142777  12142802              AB351842     1    26    26
browser |    26  100.0%         10     -  15217965  15217990              AB351842     1    26    26
browser |    26  100.0%         10     -  15218381  15218406              AB351842     1    26    26
browser |    26  100.0%         10     -  15448539  15448564              AB351842     1    26    26
browser |    26  100.0%         10     -  15448747  15448772              AB351842     1    26    26
browser |    26  100.0%         10     -  15449149  15449174              AB351842     1    26    26
browser |    26  100.0%         10     -  15476768  15476793              AB351842     1    26    26
browser |    26  100.0%         10     -  15476976  15477001              AB351842     1    26    26
browser |    26  100.0%         10     -  15501288  15501313              AB351842     1    26    26
browser |    26  100.0%         10     -  15656535  15656560              AB351842     1    26    26
browser |    26  100.0%         10     -  15656743  15656768              AB351842     1    26    26
browser |    26  100.0%         10     +  17013171  17013196              AB351842     1    26    26
browser |    26  100.0%         10     -  27235921  27235946              AB351842     1    26    26
browser |    26  100.0%         10     -  27236336  27236361              AB351842     1    26    26
browser |    26  100.0%         10     -  27694525  27694550              AB351842     1    26    26
browser |    26  100.0%         10     +  28783744  28783769              AB351842     1    26    26
browser |    26  100.0%         10     +  28810226  28810251              AB351842     1    26    26
browser |    26  100.0%         10     +  28810642  28810667              AB351842     1    26    26
browser |    26  100.0%         10     +  29835253  29835278              AB351842     1    26    26
browser |    26  100.0%         10     +  29835669  29835694              AB351842     1    26    26
browser |    26  100.0%         10     +  85691567  85691592              AB351842     1    26    26
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browser |    26  100.0%         10     +  86429805  86429830              AB351842     1    26    26
browser |    26  100.0%         10     -  87016320  87016345              AB351842     1    26    26
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browser |    26  100.0%         10     -  87244930  87244955              AB351842     1    26    26
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browser |    26  100.0%         10     +  91168203  91168228              AB351842     1    26    26
browser |    26  100.0%         10     +  91168619  91168644              AB351842     1    26    26
browser |    26  100.0%         10     +  91168827  91168852              AB351842     1    26    26
browser |    26  100.0%         10     -  91770647  91770672              AB351842     1    26    26
browser |    26  100.0%         10     -  91771063  91771088              AB351842     1    26    26
browser |    26  100.0%         10     -  92750960  92750985              AB351842     1    26    26
browser |    26  100.0%         10     -  92751168  92751193              AB351842     1    26    26
browser |    26  100.0%         10     -  92896260  92896285              AB351842     1    26    26
browser |    26  100.0%         10     -  93251491  93251516              AB351842     1    26    26
browser |    26  100.0%         10     -  93251690  93251715              AB351842     1    26    26
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browser |    26  100.0%         10     -  99560797  99560822              AB351842     1    26    26
browser |    26  100.0%         10     -  99561213  99561238              AB351842     1    26    26
browser |    26  100.0%         10     -  99726976  99727001              AB351842     1    26    26
browser |    26  100.0%         10     - 101287561 101287586              AB351842     1    26    26
browser |    26  100.0%         10     + 101402808 101402833              AB351842     1    26    26
browser |    26  100.0%         10     + 101403016 101403041              AB351842     1    26    26
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browser |    26  100.0%         10     - 101466855 101466880              AB351842     1    26    26
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browser |    26  100.0%         11     +   7820000   7820025              AB351842     1    26    26
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browser |    26  100.0%         11     -  12095492  12095517              AB351842     1    26    26
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browser |    25  100.0%         11     +  86068813  86068837              AB351842     2    26    26
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browser |    26  100.0%         11     -  99780566  99780591              AB351842     1    26    26
browser |    26  100.0%         11     - 104546038 104546063              AB351842     1    26    26
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browser |    26  100.0%         11     + 111344317 111344342              AB351842     1    26    26
browser |    26  100.0%         12     -   5884540   5884565              AB351842     1    26    26
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browser |    26  100.0%         12     +   6063356   6063381              AB351842     1    26    26
browser |    26  100.0%         12     +   6063564   6063589              AB351842     1    26    26
browser |    26  100.0%         12     -   6662537   6662562              AB351842     1    26    26
browser |    26  100.0%         12     +   6821415   6821440              AB351842     1    26    26
browser |    26  100.0%         12     +   7161783   7161808              AB351842     1    26    26
browser |    26  100.0%         12     +   7161991   7162016              AB351842     1    26    26
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browser |    26  100.0%         12     +  10962235  10962260              AB351842     1    26    26
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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