AB352377
 

Information on mRNA AB352377

Description: Mus musculus non-coding RNA, oocyte_piRNA3193, 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: AB352377
Position: chrX:15611156-15611182

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%          X     +  15611156  15611182              AB352377     1    27    27
browser |    27  100.0%          1     -   3159797   3159823              AB352377     1    27    27
browser |    27  100.0%          1     -   3571648   3571674              AB352377     1    27    27
browser |    27  100.0%          1     -   3897065   3897091              AB352377     1    27    27
browser |    27  100.0%          1     -   3993654   3993680              AB352377     1    27    27
browser |    27  100.0%          1     +   4514991   4515017              AB352377     1    27    27
browser |    27  100.0%          1     +   4635268   4635294              AB352377     1    27    27
browser |    27  100.0%          1     -   5400116   5400142              AB352377     1    27    27
browser |    27  100.0%          1     +   5425521   5425547              AB352377     1    27    27
browser |    27  100.0%          1     -   7400832   7400858              AB352377     1    27    27
browser |    27  100.0%          1     +   8511097   8511123              AB352377     1    27    27
browser |    27  100.0%          1     -  11687035  11687061              AB352377     1    27    27
browser |    27  100.0%          1     -  11848956  11848982              AB352377     1    27    27
browser |    27  100.0%          1     +  11962691  11962717              AB352377     1    27    27
browser |    27  100.0%          1     -  13803056  13803082              AB352377     1    27    27
browser |    27  100.0%          1     +  14188352  14188378              AB352377     1    27    27
browser |    27  100.0%          1     +  14521926  14521952              AB352377     1    27    27
browser |    27  100.0%          1     -  15330053  15330079              AB352377     1    27    27
browser |    27  100.0%          1     +  16522380  16522406              AB352377     1    27    27
browser |    27  100.0%          1     -  17455467  17455493              AB352377     1    27    27
browser |    27  100.0%          1     +  17541761  17541787              AB352377     1    27    27
browser |    27  100.0%          1     -  17988315  17988341              AB352377     1    27    27
browser |    27  100.0%          1     +  18034829  18034855              AB352377     1    27    27
browser |    27  100.0%          1     +  18520777  18520803              AB352377     1    27    27
browser |    27  100.0%          1     +  18612803  18612829              AB352377     1    27    27
browser |    27  100.0%          1     +  18889398  18889424              AB352377     1    27    27
browser |    27  100.0%          1     +  19446984  19447010              AB352377     1    27    27
browser |    27  100.0%          1     +  19473298  19473324              AB352377     1    27    27
browser |    27  100.0%          1     -  19792541  19792567              AB352377     1    27    27
browser |    27  100.0%          1     +  20319443  20319469              AB352377     1    27    27
browser |    27  100.0%          1     -  20350098  20350124              AB352377     1    27    27
browser |    27  100.0%          1     -  21267536  21267562              AB352377     1    27    27
browser |    27  100.0%          1     -  23336738  23336764              AB352377     1    27    27
browser |    27  100.0%          1     +  80116161  80116187              AB352377     1    27    27
browser |    27  100.0%          1     +  81402430  81402456              AB352377     1    27    27
browser |    27  100.0%          1     +  83801592  83801618              AB352377     1    27    27
browser |    27  100.0%          1     +  84552238  84552264              AB352377     1    27    27
browser |    27  100.0%          1     -  84947572  84947598              AB352377     1    27    27
browser |    27  100.0%          1     +  85124638  85124664              AB352377     1    27    27
browser |    27  100.0%          1     +  85281565  85281591              AB352377     1    27    27
browser |    27  100.0%          1     +  85405956  85405982              AB352377     1    27    27
browser |    27  100.0%          1     -  85484239  85484265              AB352377     1    27    27
browser |    27  100.0%          1     +  86706913  86706939              AB352377     1    27    27
browser |    27  100.0%          1     +  86827780  86827806              AB352377     1    27    27
browser |    27  100.0%          1     +  94083270  94083296              AB352377     1    27    27
browser |    27  100.0%          1     -  94652547  94652573              AB352377     1    27    27
browser |    27  100.0%          1     -  97346745  97346771              AB352377     1    27    27
browser |    27  100.0%          1     +  98298847  98298873              AB352377     1    27    27
browser |    27  100.0%          1     -  98927967  98927993              AB352377     1    27    27
browser |    27  100.0%          1     - 101048116 101048142              AB352377     1    27    27
browser |    27  100.0%          1     + 101173949 101173975              AB352377     1    27    27
browser |    27  100.0%          1     + 101234629 101234655              AB352377     1    27    27
browser |    27  100.0%          1     - 101688023 101688049              AB352377     1    27    27
browser |    27  100.0%          1     - 102015827 102015853              AB352377     1    27    27
browser |    27  100.0%          1     - 103077445 103077471              AB352377     1    27    27
browser |    27  100.0%          1     + 103220641 103220667              AB352377     1    27    27
browser |    27  100.0%          1     + 103607592 103607618              AB352377     1    27    27
browser |    27  100.0%          1     + 104149860 104149886              AB352377     1    27    27
browser |    27  100.0%          1     - 104943404 104943430              AB352377     1    27    27
browser |    27  100.0%          1     - 104950646 104950672              AB352377     1    27    27
browser |    27  100.0%          1     - 106778522 106778548              AB352377     1    27    27
browser |    27  100.0%          1     - 107132375 107132401              AB352377     1    27    27
browser |    27  100.0%          1     - 107849675 107849701              AB352377     1    27    27
browser |    27  100.0%          1     - 108251122 108251148              AB352377     1    27    27
browser |    27  100.0%          1     - 108447603 108447629              AB352377     1    27    27
browser |    27  100.0%          1     + 158164198 158164224              AB352377     1    27    27
browser |    27  100.0%          1     - 158472085 158472111              AB352377     1    27    27
browser |    27  100.0%          1     + 158711884 158711910              AB352377     1    27    27
browser |    27  100.0%          1     + 161895780 161895806              AB352377     1    27    27
browser |    27  100.0%          1     - 161943750 161943776              AB352377     1    27    27
browser |    27  100.0%          1     + 162651929 162651955              AB352377     1    27    27
browser |    27  100.0%          1     + 163616086 163616112              AB352377     1    27    27
browser |    27  100.0%          1     + 165236958 165236984              AB352377     1    27    27
browser |    27  100.0%          1     + 165359500 165359526              AB352377     1    27    27
browser |    27  100.0%          1     - 166298670 166298696              AB352377     1    27    27
browser |    27  100.0%          1     + 166701549 166701575              AB352377     1    27    27
browser |    27  100.0%          1     + 166744505 166744531              AB352377     1    27    27
browser |    27  100.0%          1     + 167820633 167820659              AB352377     1    27    27
browser |    27  100.0%          1     - 172499967 172499993              AB352377     1    27    27
browser |    27  100.0%          1     + 173820024 173820050              AB352377     1    27    27
browser |    27  100.0%          1     - 175625323 175625349              AB352377     1    27    27
browser |    27  100.0%          1     - 176370615 176370641              AB352377     1    27    27
browser |    27  100.0%          1     - 177042539 177042565              AB352377     1    27    27
browser |    27  100.0%          1     - 177758883 177758909              AB352377     1    27    27
browser |    27  100.0%          1     - 185838295 185838321              AB352377     1    27    27
browser |    27  100.0%          1     - 186326058 186326084              AB352377     1    27    27
browser |    27  100.0%          1     + 187130209 187130235              AB352377     1    27    27
browser |    27  100.0%          1     + 190348873 190348899              AB352377     1    27    27
browser |    27  100.0%          1     + 192757285 192757311              AB352377     1    27    27
browser |    27  100.0%          1     + 193152820 193152846              AB352377     1    27    27
browser |    27  100.0%          1     + 193816060 193816086              AB352377     1    27    27
browser |    27  100.0%          1     - 194596205 194596231              AB352377     1    27    27
browser |    27  100.0%         10     +   5044690   5044716              AB352377     1    27    27
browser |    27  100.0%         10     -   8190092   8190118              AB352377     1    27    27
browser |    27  100.0%         10     +   9907172   9907198              AB352377     1    27    27
browser |    27  100.0%         10     -  10444609  10444635              AB352377     1    27    27
browser |    27  100.0%         10     +  10500682  10500708              AB352377     1    27    27
browser |    27  100.0%         10     +  10855603  10855629              AB352377     1    27    27
browser |    27  100.0%         10     -  11248339  11248365              AB352377     1    27    27
browser |    27  100.0%         10     +  12269821  12269847              AB352377     1    27    27
browser |    27  100.0%         10     -  12875114  12875140              AB352377     1    27    27
browser |    27  100.0%         10     +  13775029  13775055              AB352377     1    27    27
browser |    27  100.0%         10     +  14587708  14587734              AB352377     1    27    27
browser |    27  100.0%         10     +  15515609  15515635              AB352377     1    27    27
browser |    27  100.0%         10     +  16572427  16572453              AB352377     1    27    27
browser |    27  100.0%         10     +  16700760  16700786              AB352377     1    27    27
browser |    27  100.0%         10     +  17023575  17023601              AB352377     1    27    27
browser |    27  100.0%         10     +  17687272  17687298              AB352377     1    27    27
browser |    27  100.0%         10     -  18026904  18026930              AB352377     1    27    27
browser |    27  100.0%         10     +  19661264  19661290              AB352377     1    27    27
browser |    27  100.0%         10     -  19856878  19856904              AB352377     1    27    27
browser |    27  100.0%         10     +  19909976  19910002              AB352377     1    27    27
browser |    27  100.0%         10     +  22739504  22739530              AB352377     1    27    27
browser |    27  100.0%         10     -  23347410  23347436              AB352377     1    27    27
browser |    27  100.0%         10     +  23512018  23512044              AB352377     1    27    27
browser |    27  100.0%         10     -  31544575  31544601              AB352377     1    27    27
browser |    27  100.0%         10     -  31874192  31874218              AB352377     1    27    27
browser |    27  100.0%         10     -  32843900  32843926              AB352377     1    27    27
browser |    27  100.0%         10     -  33380781  33380807              AB352377     1    27    27
browser |    27  100.0%         10     -  36519235  36519261              AB352377     1    27    27
browser |    27  100.0%         10     -  37579666  37579692              AB352377     1    27    27
browser |    27  100.0%         10     -  38136088  38136114              AB352377     1    27    27
browser |    27  100.0%         10     -  38644416  38644442              AB352377     1    27    27
browser |    27  100.0%         10     -  46791007  46791033              AB352377     1    27    27
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browser |    27  100.0%         10     -  87828002  87828028              AB352377     1    27    27
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browser |    27  100.0%         10     - 102264693 102264719              AB352377     1    27    27
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browser |    27  100.0%         10     - 103585700 103585726              AB352377     1    27    27
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browser |    27  100.0%         10     - 129425126 129425152              AB352377     1    27    27
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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