AB341276
 

Information on mRNA AB341276

Description: Mus musculus non-coding RNA, oocyte_clustered_small_RNA6477, 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: AB341276
Position: chrX:15589622-15589648

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     -  15589622  15589648              AB341276     1    26    26
browser |    24  100.0%          1     +   8208723   8208746              AB341276     1    24    26
browser |    26  100.0%          1     -  15282314  15282340              AB341276     1    26    26
browser |    24  100.0%          1     -  86002220  86002243              AB341276     1    24    26
browser |    26  100.0%          1     -  91161342  91161368              AB341276     1    26    26
browser |    24  100.0%          1     + 102724327 102724350              AB341276     1    24    26
browser |    26  100.0%          1     + 148842511 148842537              AB341276     1    26    26
browser |    26  100.0%          1     + 164346465 164346491              AB341276     1    26    26
browser |    26  100.0%          1     - 166283197 166283223              AB341276     1    26    26
browser |    24  100.0%         10     -  14985542  14985565              AB341276     1    24    26
browser |    26  100.0%         10     -  31012649  31012675              AB341276     1    26    26
browser |    26  100.0%         10     +  31607325  31607351              AB341276     1    26    26
browser |    26  100.0%         10     +  32615473  32615499              AB341276     1    26    26
browser |    24  100.0%         10     -  33585003  33585026              AB341276     1    24    26
browser |    26  100.0%         10     -  37828298  37828324              AB341276     1    26    26
browser |    24  100.0%         10     +  95577922  95577945              AB341276     1    24    26
browser |    26  100.0%         10     + 118061027 118061052              AB341276     1    26    26
browser |    26  100.0%         10     - 118110227 118110252              AB341276     1    26    26
browser |    24  100.0%         10     - 118203160 118203183              AB341276     1    24    26
browser |    26  100.0%         11     +  13785822  13785848              AB341276     1    26    26
browser |    26  100.0%         11     +  23549982  23550008              AB341276     1    26    26
browser |    26  100.0%         11     -  47525563  47525589              AB341276     1    26    26
browser |    26  100.0%         11     -  69536366  69536392              AB341276     1    26    26
browser |    26  100.0%         11     -  75508003  75508029              AB341276     1    26    26
browser |    24  100.0%         11     -  92039478  92039501              AB341276     1    24    26
browser |    26  100.0%         11     + 116634820 116634846              AB341276     1    26    26
browser |    26  100.0%         12     +   8254551   8254577              AB341276     1    26    26
browser |    26  100.0%         12     -  57798066  57798092              AB341276     1    26    26
browser |    24  100.0%         12     + 117754483 117754506              AB341276     1    24    26
browser |    26  100.0%         13     -  31271832  31271858              AB341276     1    26    26
browser |    24  100.0%         13     +  77512995  77513018              AB341276     1    24    26
browser |    26  100.0%         13     -  92222672  92222698              AB341276     1    26    26
browser |    26  100.0%         14     +   4471631   4471657              AB341276     1    26    26
browser |    26  100.0%         14     -   9636284   9636310              AB341276     1    26    26
browser |    24  100.0%         14     -  20865086  20865109              AB341276     1    24    26
browser |    26  100.0%         14     +  69288622  69288648              AB341276     1    26    26
browser |    24  100.0%         15     +  11998330  11998353              AB341276     1    24    26
browser |    26  100.0%         15     -  16463387  16463413              AB341276     1    26    26
browser |    26  100.0%         15     -  22208480  22208506              AB341276     1    26    26
browser |    26  100.0%         15     +  40125898  40125924              AB341276     1    26    26
browser |    24  100.0%         15     +  49303018  49303041              AB341276     1    24    26
browser |    24  100.0%         15     -  91605986  91606009              AB341276     1    24    26
browser |    26  100.0%         16     +  33391624  33391650              AB341276     1    26    26
browser |    24  100.0%         16     +  94094671  94094695              AB341276     3    26    26
browser |    24  100.0%         17     +  18408236  18408259              AB341276     1    24    26
browser |    26  100.0%         17     -  51092112  51092138              AB341276     1    26    26
browser |    26  100.0%         18     -  26208748  26208774              AB341276     1    26    26
browser |    26  100.0%         18     -  81181588  81181614              AB341276     1    26    26
browser |    26  100.0%         19     +   5627356   5627382              AB341276     1    26    26
browser |    26  100.0%         19     -  56152551  56152577              AB341276     1    26    26
browser |    26  100.0%         19     -  57555294  57555320              AB341276     1    26    26
browser |    24  100.0%          2     -  29002185  29002208              AB341276     1    24    26
browser |    26  100.0%          2     +  43634977  43635003              AB341276     1    26    26
browser |    24  100.0%          2     +  81453016  81453039              AB341276     1    24    26
browser |    26  100.0%          2     + 134078698 134078724              AB341276     1    26    26
browser |    24  100.0%          2     + 174753049 174753072              AB341276     1    24    26
browser |    26  100.0%          3     -  14800744  14800770              AB341276     1    26    26
browser |    26  100.0%          3     -  17346387  17346413              AB341276     1    26    26
browser |    26  100.0%          3     +  44420798  44420824              AB341276     1    26    26
browser |    26  100.0%          4     -   7520378   7520404              AB341276     1    26    26
browser |    26  100.0%          4     -  54176071  54176097              AB341276     1    26    26
browser |    24  100.0%          4     +  54499298  54499321              AB341276     1    24    26
browser |    26  100.0%          4     +  98279195  98279221              AB341276     1    26    26
browser |    26  100.0%          4     - 108279003 108279029              AB341276     1    26    26
browser |    26  100.0%          5     -  81097650  81097676              AB341276     1    26    26
browser |    26  100.0%          5     +  85346876  85346902              AB341276     1    26    26
browser |    24  100.0%          5     - 147803453 147803476              AB341276     1    24    26
browser |    26  100.0%          6     -  16954621  16954647              AB341276     1    26    26
browser |    26  100.0%          6     +  38279329  38279355              AB341276     1    26    26
browser |    26  100.0%          6     +  40300137  40300163              AB341276     1    26    26
browser |    26  100.0%          6     - 102828274 102828300              AB341276     1    26    26
browser |    26  100.0%          6     - 102829813 102829839              AB341276     1    26    26
browser |    26  100.0%          7     -  63107827  63107853              AB341276     1    26    26
browser |    26  100.0%          7     - 116297046 116297072              AB341276     1    26    26
browser |    26  100.0%          7     + 128468020 128468046              AB341276     1    26    26
browser |    26  100.0%          7     - 134185021 134185047              AB341276     1    26    26
browser |    24  100.0%          8     -   3522107   3522130              AB341276     1    24    26
browser |    24  100.0%          8     -   4826165   4826188              AB341276     1    24    26
browser |    26  100.0%          8     +  25948154  25948180              AB341276     1    26    26
browser |    26  100.0%          8     +  28179518  28179544              AB341276     1    26    26
browser |    24  100.0%          8     +  74381513  74381536              AB341276     1    24    26
browser |    26  100.0%          9     +  19175478  19175504              AB341276     1    26    26
browser |    24  100.0%          9     +  38471586  38471609              AB341276     1    24    26
browser |    24  100.0%          9     +  71507971  71507994              AB341276     1    24    26
browser |    26  100.0%          9     +  89540648  89540674              AB341276     1    26    26
browser |    25  100.0%          X     -   9106023   9106048              AB341276     2    26    26
browser |    25  100.0%          X     +  10548580  10548604              AB341276     1    25    26
browser |    26  100.0%          X     -  78211254  78211280              AB341276     1    26    26
browser |    26  100.0%          X     + 122240760 122240786              AB341276     1    26    26
browser |    26  100.0%          X     + 122470240 122470266              AB341276     1    26    26
browser |    26  100.0%          X     + 122689227 122689253              AB341276     1    26    26
browser |    26  100.0%          X     + 122917013 122917039              AB341276     1    26    26
browser |    26  100.0%          X     + 149603173 149603199              AB341276     1    26    26
browser |    26  100.0%          X     + 156299188 156299214              AB341276     1    26    26
browser |    26  100.0%          X     - 159972699 159972725              AB341276     1    26    26

View details of parts of alignment within browser window
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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