AB350713
 

Information on mRNA AB350713

Description: Mus musculus non-coding RNA, oocyte_piRNA1529, 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: AB350713
Position: chr12:56797427-56797448

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 |    22  100.0%         12     -  56797427  56797448              AB350713     1    22    22
browser |    22  100.0%          1     -   5880112   5880133              AB350713     1    22    22
browser |    22  100.0%          1     -   6506141   6506162              AB350713     1    22    22
browser |    22  100.0%          1     +   8065486   8065507              AB350713     1    22    22
browser |    22  100.0%          1     +   8227927   8227948              AB350713     1    22    22
browser |    22  100.0%          1     -   8731152   8731173              AB350713     1    22    22
browser |    22  100.0%          1     -  10805628  10805649              AB350713     1    22    22
browser |    22  100.0%          1     -  12019452  12019473              AB350713     1    22    22
browser |    22  100.0%          1     +  13622351  13622372              AB350713     1    22    22
browser |    22  100.0%          1     +  16809997  16810018              AB350713     1    22    22
browser |    22  100.0%          1     +  18028591  18028612              AB350713     1    22    22
browser |    22  100.0%          1     +  18588621  18588642              AB350713     1    22    22
browser |    22  100.0%          1     +  19694205  19694226              AB350713     1    22    22
browser |    22  100.0%          1     -  22071005  22071026              AB350713     1    22    22
browser |    22  100.0%          1     +  23341762  23341783              AB350713     1    22    22
browser |    22  100.0%          1     -  26391901  26391922              AB350713     1    22    22
browser |    22  100.0%          1     +  26454613  26454634              AB350713     1    22    22
browser |    22  100.0%          1     -  26513717  26513738              AB350713     1    22    22
browser |    22  100.0%          1     +  27220761  27220782              AB350713     1    22    22
browser |    22  100.0%          1     -  29986847  29986868              AB350713     1    22    22
browser |    22  100.0%          1     +  34388094  34388115              AB350713     1    22    22
browser |    22  100.0%          1     +  35829090  35829111              AB350713     1    22    22
browser |    22  100.0%          1     +  38745479  38745500              AB350713     1    22    22
browser |    22  100.0%          1     +  40738770  40738791              AB350713     1    22    22
browser |    22  100.0%          1     +  45774843  45774864              AB350713     1    22    22
browser |    22  100.0%          1     -  47265561  47265582              AB350713     1    22    22
browser |    22  100.0%          1     +  48129777  48129798              AB350713     1    22    22
browser |    22  100.0%          1     -  48400902  48400923              AB350713     1    22    22
browser |    22  100.0%          1     -  53172392  53172413              AB350713     1    22    22
browser |    22  100.0%          1     -  58368067  58368088              AB350713     1    22    22
browser |    22  100.0%          1     -  58856375  58856396              AB350713     1    22    22
browser |    22  100.0%          1     -  60769561  60769582              AB350713     1    22    22
browser |    22  100.0%          1     -  62578825  62578846              AB350713     1    22    22
browser |    22  100.0%          1     -  81547436  81547457              AB350713     1    22    22
browser |    22  100.0%          1     +  82480340  82480361              AB350713     1    22    22
browser |    22  100.0%          1     -  83209040  83209061              AB350713     1    22    22
browser |    22  100.0%          1     -  87066918  87066939              AB350713     1    22    22
browser |    22  100.0%          1     +  87389417  87389438              AB350713     1    22    22
browser |    22  100.0%          1     +  89128345  89128366              AB350713     1    22    22
browser |    22  100.0%          1     -  91404491  91404512              AB350713     1    22    22
browser |    22  100.0%          1     +  93885827  93885848              AB350713     1    22    22
browser |    22  100.0%          1     +  95624415  95624436              AB350713     1    22    22
browser |    22  100.0%          1     +  97102026  97102047              AB350713     1    22    22
browser |    22  100.0%          1     -  98529688  98529709              AB350713     1    22    22
browser |    22  100.0%          1     - 101911426 101911447              AB350713     1    22    22
browser |    22  100.0%          1     + 102960928 102960949              AB350713     1    22    22
browser |    22  100.0%          1     - 103138455 103138476              AB350713     1    22    22
browser |    22  100.0%          1     + 103407559 103407580              AB350713     1    22    22
browser |    22  100.0%          1     + 103518090 103518111              AB350713     1    22    22
browser |    22  100.0%          1     - 104220951 104220972              AB350713     1    22    22
browser |    22  100.0%          1     - 108342143 108342164              AB350713     1    22    22
browser |    22  100.0%          1     - 109060002 109060023              AB350713     1    22    22
browser |    22  100.0%          1     + 109542670 109542691              AB350713     1    22    22
browser |    22  100.0%          1     + 110258335 110258356              AB350713     1    22    22
browser |    22  100.0%          1     - 111186912 111186933              AB350713     1    22    22
browser |    22  100.0%          1     + 111632638 111632659              AB350713     1    22    22
browser |    22  100.0%          1     - 112197632 112197653              AB350713     1    22    22
browser |    22  100.0%          1     + 112858747 112858768              AB350713     1    22    22
browser |    22  100.0%          1     + 112945345 112945366              AB350713     1    22    22
browser |    22  100.0%          1     + 114114552 114114573              AB350713     1    22    22
browser |    22  100.0%          1     - 115816753 115816774              AB350713     1    22    22
browser |    22  100.0%          1     - 116581560 116581581              AB350713     1    22    22
browser |    22  100.0%          1     - 117635218 117635239              AB350713     1    22    22
browser |    22  100.0%          1     - 120502236 120502257              AB350713     1    22    22
browser |    22  100.0%          1     + 125246133 125246154              AB350713     1    22    22
browser |    22  100.0%          1     - 159802886 159802907              AB350713     1    22    22
browser |    22  100.0%          1     - 160647103 160647124              AB350713     1    22    22
browser |    22  100.0%          1     + 162669658 162669679              AB350713     1    22    22
browser |    22  100.0%          1     - 166595759 166595780              AB350713     1    22    22
browser |    22  100.0%          1     + 169944892 169944913              AB350713     1    22    22
browser |    22  100.0%          1     - 174874291 174874312              AB350713     1    22    22
browser |    22  100.0%          1     - 176376185 176376206              AB350713     1    22    22
browser |    22  100.0%          1     + 177887157 177887178              AB350713     1    22    22
browser |    22  100.0%          1     + 178003210 178003231              AB350713     1    22    22
browser |    22  100.0%          1     + 179723105 179723126              AB350713     1    22    22
browser |    22  100.0%          1     - 181096642 181096663              AB350713     1    22    22
browser |    22  100.0%          1     + 181321999 181322020              AB350713     1    22    22
browser |    22  100.0%          1     + 183297817 183297838              AB350713     1    22    22
browser |    22  100.0%          1     + 191841215 191841236              AB350713     1    22    22
browser |    22  100.0%          1     + 195004194 195004215              AB350713     1    22    22
browser |    22  100.0%         10     -   3556482   3556503              AB350713     1    22    22
browser |    22  100.0%         10     +   8476583   8476604              AB350713     1    22    22
browser |    22  100.0%         10     +  11571562  11571583              AB350713     1    22    22
browser |    22  100.0%         10     -  19420195  19420216              AB350713     1    22    22
browser |    22  100.0%         10     +  19674597  19674618              AB350713     1    22    22
browser |    22  100.0%         10     -  19891922  19891943              AB350713     1    22    22
browser |    22  100.0%         10     +  21088782  21088803              AB350713     1    22    22
browser |    22  100.0%         10     -  21523768  21523789              AB350713     1    22    22
browser |    22  100.0%         10     -  22404660  22404681              AB350713     1    22    22
browser |    22  100.0%         10     -  22564714  22564735              AB350713     1    22    22
browser |    22  100.0%         10     -  23752769  23752790              AB350713     1    22    22
browser |    22  100.0%         10     +  24563810  24563831              AB350713     1    22    22
browser |    22  100.0%         10     -  24980841  24980862              AB350713     1    22    22
browser |    22  100.0%         10     +  25845855  25845876              AB350713     1    22    22
browser |    22  100.0%         10     +  30358927  30358948              AB350713     1    22    22
browser |    22  100.0%         10     +  30691523  30691544              AB350713     1    22    22
browser |    22  100.0%         10     +  30966208  30966229              AB350713     1    22    22
browser |    22  100.0%         10     +  31360150  31360171              AB350713     1    22    22
browser |    22  100.0%         10     +  33764477  33764498              AB350713     1    22    22
browser |    22  100.0%         10     -  34616594  34616615              AB350713     1    22    22
browser |    22  100.0%         10     -  34623372  34623393              AB350713     1    22    22
browser |    22  100.0%         10     +  41718077  41718098              AB350713     1    22    22
browser |    22  100.0%         10     +  47548227  47548248              AB350713     1    22    22
browser |    22  100.0%         10     +  51760635  51760656              AB350713     1    22    22
browser |    22  100.0%         10     -  65479175  65479196              AB350713     1    22    22
browser |    22  100.0%         10     -  65790249  65790270              AB350713     1    22    22
browser |    22  100.0%         10     -  66563790  66563811              AB350713     1    22    22
browser |    22  100.0%         10     +  77857734  77857755              AB350713     1    22    22
browser |    22  100.0%         10     -  78657339  78657360              AB350713     1    22    22
browser |    22  100.0%         10     -  81511923  81511944              AB350713     1    22    22
browser |    22  100.0%         10     -  81671051  81671072              AB350713     1    22    22
browser |    22  100.0%         10     +  81805267  81805288              AB350713     1    22    22
browser |    22  100.0%         10     -  83307280  83307301              AB350713     1    22    22
browser |    22  100.0%         10     -  83512335  83512356              AB350713     1    22    22
browser |    22  100.0%         10     +  83624845  83624866              AB350713     1    22    22
browser |    22  100.0%         10     +  85552601  85552622              AB350713     1    22    22
browser |    22  100.0%         10     +  86980021  86980042              AB350713     1    22    22
browser |    22  100.0%         10     +  88488388  88488409              AB350713     1    22    22
browser |    22  100.0%         10     -  90164070  90164091              AB350713     1    22    22
browser |    22  100.0%         10     -  94203483  94203504              AB350713     1    22    22
browser |    22  100.0%         10     -  95996759  95996780              AB350713     1    22    22
browser |    22  100.0%         10     -  96033943  96033964              AB350713     1    22    22
browser |    22  100.0%         10     -  97163862  97163883              AB350713     1    22    22
browser |    22  100.0%         10     +  99176527  99176548              AB350713     1    22    22
browser |    22  100.0%         10     -  99385635  99385656              AB350713     1    22    22
browser |    22  100.0%         10     + 104392754 104392775              AB350713     1    22    22
browser |    22  100.0%         10     - 104659006 104659027              AB350713     1    22    22
browser |    22  100.0%         10     + 104672971 104672992              AB350713     1    22    22
browser |    22  100.0%         10     + 105014490 105014511              AB350713     1    22    22
browser |    22  100.0%         10     + 121002179 121002200              AB350713     1    22    22
browser |    22  100.0%         10     - 122205325 122205346              AB350713     1    22    22
browser |    22  100.0%         10     + 122343225 122343246              AB350713     1    22    22
browser |    22  100.0%         10     - 122674202 122674223              AB350713     1    22    22
browser |    22  100.0%         10     + 123696792 123696813              AB350713     1    22    22
browser |    22  100.0%         10     + 124413766 124413787              AB350713     1    22    22
browser |    22  100.0%         10     + 124443187 124443208              AB350713     1    22    22
browser |    22  100.0%         10     - 124520396 124520417              AB350713     1    22    22
browser |    22  100.0%         10     + 129051206 129051227              AB350713     1    22    22
browser |    22  100.0%         10     - 129230241 129230262              AB350713     1    22    22
browser |    22  100.0%         10     + 129762714 129762735              AB350713     1    22    22
browser |    22  100.0%         10     - 130400450 130400471              AB350713     1    22    22
browser |    22  100.0%         11     -   6097043   6097064              AB350713     1    22    22
browser |    22  100.0%         11     -   7531235   7531256              AB350713     1    22    22
browser |    22  100.0%         11     -   9663534   9663555              AB350713     1    22    22
browser |    22  100.0%         11     +  10711867  10711888              AB350713     1    22    22
browser |    22  100.0%         11     +  12513477  12513498              AB350713     1    22    22
browser |    22  100.0%         11     +  12747148  12747169              AB350713     1    22    22
browser |    22  100.0%         11     -  12907671  12907692              AB350713     1    22    22
browser |    22  100.0%         11     -  14848253  14848274              AB350713     1    22    22
browser |    22  100.0%         11     +  15179247  15179268              AB350713     1    22    22
browser |    22  100.0%         11     -  15236409  15236430              AB350713     1    22    22
browser |    22  100.0%         11     -  18762007  18762028              AB350713     1    22    22
browser |    22  100.0%         11     -  19518976  19518997              AB350713     1    22    22
browser |    22  100.0%         11     +  20467933  20467954              AB350713     1    22    22
browser |    22  100.0%         11     +  22529335  22529356              AB350713     1    22    22
browser |    22  100.0%         11     -  23174134  23174155              AB350713     1    22    22
browser |    22  100.0%         11     +  26507077  26507098              AB350713     1    22    22
browser |    22  100.0%         11     -  27905520  27905541              AB350713     1    22    22
browser |    22  100.0%         11     +  28048850  28048871              AB350713     1    22    22
browser |    22  100.0%         11     +  29076115  29076136              AB350713     1    22    22
browser |    22  100.0%         11     -  29233150  29233171              AB350713     1    22    22
browser |    22  100.0%         11     -  31403114  31403135              AB350713     1    22    22
browser |    22  100.0%         11     +  61312818  61312839              AB350713     1    22    22
browser |    22  100.0%         11     +  63360107  63360128              AB350713     1    22    22
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browser |    22  100.0%         11     -  79635117  79635138              AB350713     1    22    22
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browser |    22  100.0%         12     -  52780539  52780560              AB350713     1    22    22
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browser |    22  100.0%         12     -  68674106  68674127              AB350713     1    22    22
browser |    22  100.0%         12     -  70713486  70713507              AB350713     1    22    22
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browser |    22  100.0%         12     -  79614165  79614186              AB350713     1    22    22
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browser |    22  100.0%         12     +  93477882  93477903              AB350713     1    22    22
browser |    22  100.0%         12     -  94008834  94008855              AB350713     1    22    22
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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