AB349742
 

Information on mRNA AB349742

Description: Mus musculus non-coding RNA, oocyte_piRNA558, 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: AB349742
Position: chr12:56795631-56795655

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     -  56795631  56795655              AB349742     1    25    25
browser |    25  100.0%          1     -   4628325   4628349              AB349742     1    25    25
browser |    25  100.0%          1     +   5818412   5818436              AB349742     1    25    25
browser |    25  100.0%          1     -   5875566   5875590              AB349742     1    25    25
browser |    25  100.0%          1     +   6242006   6242030              AB349742     1    25    25
browser |    25  100.0%          1     -   6501595   6501619              AB349742     1    25    25
browser |    25  100.0%          1     +   7681385   7681409              AB349742     1    25    25
browser |    25  100.0%          1     +   8070026   8070050              AB349742     1    25    25
browser |    25  100.0%          1     +   8232471   8232495              AB349742     1    25    25
browser |    25  100.0%          1     -   8729567   8729591              AB349742     1    25    25
browser |    25  100.0%          1     -  11100772  11100796              AB349742     1    25    25
browser |    25  100.0%          1     -  11438715  11438739              AB349742     1    25    25
browser |    25  100.0%          1     -  11958343  11958367              AB349742     1    25    25
browser |    25  100.0%          1     -  18323813  18323837              AB349742     1    25    25
browser |    25  100.0%          1     +  18590414  18590438              AB349742     1    25    25
browser |    25  100.0%          1     +  19698748  19698772              AB349742     1    25    25
browser |    25  100.0%          1     -  26389252  26389276              AB349742     1    25    25
browser |    25  100.0%          1     +  26459155  26459179              AB349742     1    25    25
browser |    25  100.0%          1     -  26510450  26510474              AB349742     1    25    25
browser |    25  100.0%          1     +  27177130  27177154              AB349742     1    25    25
browser |    25  100.0%          1     +  27225304  27225328              AB349742     1    25    25
browser |    25  100.0%          1     +  28929769  28929793              AB349742     1    25    25
browser |    25  100.0%          1     +  34389420  34389444              AB349742     1    25    25
browser |    25  100.0%          1     +  34957253  34957277              AB349742     1    25    25
browser |    25  100.0%          1     +  35833633  35833657              AB349742     1    25    25
browser |    25  100.0%          1     +  38747015  38747039              AB349742     1    25    25
browser |    25  100.0%          1     +  40740584  40740608              AB349742     1    25    25
browser |    25  100.0%          1     -  48394492  48394516              AB349742     1    25    25
browser |    25  100.0%          1     -  48842024  48842048              AB349742     1    25    25
browser |    25  100.0%          1     -  53169783  53169807              AB349742     1    25    25
browser |    25  100.0%          1     -  58363521  58363545              AB349742     1    25    25
browser |    25  100.0%          1     -  60765015  60765039              AB349742     1    25    25
browser |    25  100.0%          1     -  62574279  62574303              AB349742     1    25    25
browser |    25  100.0%          1     -  81542890  81542914              AB349742     1    25    25
browser |    25  100.0%          1     +  82482695  82482719              AB349742     1    25    25
browser |    25  100.0%          1     -  84974608  84974632              AB349742     1    25    25
browser |    25  100.0%          1     -  87062372  87062396              AB349742     1    25    25
browser |    25  100.0%          1     +  87393960  87393984              AB349742     1    25    25
browser |    25  100.0%          1     +  89129917  89129941              AB349742     1    25    25
browser |    25  100.0%          1     -  91399948  91399972              AB349742     1    25    25
browser |    25  100.0%          1     -  93036215  93036239              AB349742     1    25    25
browser |    25  100.0%          1     +  93888003  93888027              AB349742     1    25    25
browser |    25  100.0%          1     -  95964027  95964051              AB349742     1    25    25
browser |    25  100.0%          1     -  98529097  98529121              AB349742     1    25    25
browser |    25  100.0%          1     + 102965471 102965495              AB349742     1    25    25
browser |    25  100.0%          1     - 103133909 103133933              AB349742     1    25    25
browser |    25  100.0%          1     - 104218302 104218326              AB349742     1    25    25
browser |    25  100.0%          1     - 107967538 107967562              AB349742     1    25    25
browser |    25  100.0%          1     + 108066560 108066584              AB349742     1    25    25
browser |    25  100.0%          1     - 108337597 108337621              AB349742     1    25    25
browser |    25  100.0%          1     - 109057413 109057437              AB349742     1    25    25
browser |    25  100.0%          1     + 109062233 109062257              AB349742     1    25    25
browser |    25  100.0%          1     + 109547210 109547234              AB349742     1    25    25
browser |    25  100.0%          1     + 110260981 110261005              AB349742     1    25    25
browser |    25  100.0%          1     - 110866344 110866368              AB349742     1    25    25
browser |    25  100.0%          1     - 111182369 111182393              AB349742     1    25    25
browser |    25  100.0%          1     + 112862173 112862197              AB349742     1    25    25
browser |    25  100.0%          1     + 112949888 112949912              AB349742     1    25    25
browser |    25  100.0%          1     + 114117198 114117222              AB349742     1    25    25
browser |    25  100.0%          1     - 115814104 115814128              AB349742     1    25    25
browser |    25  100.0%          1     - 116577014 116577038              AB349742     1    25    25
browser |    25  100.0%          1     + 125250673 125250697              AB349742     1    25    25
browser |    25  100.0%          1     + 126356367 126356391              AB349742     1    25    25
browser |    25  100.0%          1     + 126871092 126871116              AB349742     1    25    25
browser |    25  100.0%          1     + 129019670 129019694              AB349742     1    25    25
browser |    25  100.0%          1     - 159798339 159798363              AB349742     1    25    25
browser |    25  100.0%          1     - 160644454 160644478              AB349742     1    25    25
browser |    25  100.0%          1     + 162674201 162674225              AB349742     1    25    25
browser |    25  100.0%          1     - 163297070 163297094              AB349742     1    25    25
browser |    25  100.0%          1     + 166183273 166183297              AB349742     1    25    25
browser |    25  100.0%          1     + 166411158 166411182              AB349742     1    25    25
browser |    25  100.0%          1     + 172096275 172096299              AB349742     1    25    25
browser |    25  100.0%          1     - 174870557 174870581              AB349742     1    25    25
browser |    25  100.0%          1     + 177891670 177891694              AB349742     1    25    25
browser |    25  100.0%          1     + 178007753 178007777              AB349742     1    25    25
browser |    25  100.0%          1     - 181092095 181092119              AB349742     1    25    25
browser |    25  100.0%          1     + 183302358 183302382              AB349742     1    25    25
browser |    25  100.0%          1     + 191843861 191843885              AB349742     1    25    25
browser |    25  100.0%         10     -   3551935   3551959              AB349742     1    25    25
browser |    25  100.0%         10     -  19415649  19415673              AB349742     1    25    25
browser |    25  100.0%         10     +  21091428  21091452              AB349742     1    25    25
browser |    25  100.0%         10     -  21519222  21519246              AB349742     1    25    25
browser |    25  100.0%         10     -  22560168  22560192              AB349742     1    25    25
browser |    25  100.0%         10     +  24566456  24566480              AB349742     1    25    25
browser |    25  100.0%         10     +  25848169  25848193              AB349742     1    25    25
browser |    25  100.0%         10     -  28887422  28887446              AB349742     1    25    25
browser |    25  100.0%         10     +  30696066  30696090              AB349742     1    25    25
browser |    25  100.0%         10     +  30970751  30970775              AB349742     1    25    25
browser |    25  100.0%         10     +  31364696  31364720              AB349742     1    25    25
browser |    25  100.0%         10     +  31629840  31629864              AB349742     1    25    25
browser |    25  100.0%         10     +  33766012  33766036              AB349742     1    25    25
browser |    25  100.0%         10     -  34618826  34618850              AB349742     1    25    25
browser |    25  100.0%         10     -  35599926  35599950              AB349742     1    25    25
browser |    25  100.0%         10     +  41722618  41722642              AB349742     1    25    25
browser |    25  100.0%         10     -  43646685  43646709              AB349742     1    25    25
browser |    25  100.0%         10     -  45432004  45432028              AB349742     1    25    25
browser |    25  100.0%         10     -  47513050  47513074              AB349742     1    25    25
browser |    25  100.0%         10     +  50370545  50370569              AB349742     1    25    25
browser |    25  100.0%         10     +  51762989  51763013              AB349742     1    25    25
browser |    25  100.0%         10     +  54468575  54468599              AB349742     1    25    25
browser |    25  100.0%         10     -  55592631  55592655              AB349742     1    25    25
browser |    25  100.0%         10     +  56602926  56602950              AB349742     1    25    25
browser |    25  100.0%         10     +  57019846  57019870              AB349742     1    25    25
browser |    25  100.0%         10     +  59221843  59221867              AB349742     1    25    25
browser |    25  100.0%         10     -  65787603  65787627              AB349742     1    25    25
browser |    25  100.0%         10     -  66559247  66559271              AB349742     1    25    25
browser |    25  100.0%         10     +  70633339  70633363              AB349742     1    25    25
browser |    25  100.0%         10     -  78653296  78653320              AB349742     1    25    25
browser |    25  100.0%         10     +  80815657  80815681              AB349742     1    25    25
browser |    25  100.0%         10     +  81809806  81809830              AB349742     1    25    25
browser |    25  100.0%         10     -  83507789  83507813              AB349742     1    25    25
browser |    25  100.0%         10     +  83627437  83627461              AB349742     1    25    25
browser |    25  100.0%         10     +  84584728  84584752              AB349742     1    25    25
browser |    25  100.0%         10     +  85555531  85555555              AB349742     1    25    25
browser |    25  100.0%         10     -  90161475  90161499              AB349742     1    25    25
browser |    25  100.0%         10     -  94199441  94199465              AB349742     1    25    25
browser |    25  100.0%         10     -  96029397  96029421              AB349742     1    25    25
browser |    25  100.0%         10     +  99181067  99181091              AB349742     1    25    25
browser |    25  100.0%         10     + 104397294 104397318              AB349742     1    25    25
browser |    25  100.0%         10     - 104656357 104656381              AB349742     1    25    25
browser |    25  100.0%         10     + 104677514 104677538              AB349742     1    25    25
browser |    25  100.0%         10     + 105016640 105016664              AB349742     1    25    25
browser |    25  100.0%         10     - 105509516 105509540              AB349742     1    25    25
browser |    25  100.0%         10     + 107841443 107841467              AB349742     1    25    25
browser |    25  100.0%         10     - 109152082 109152106              AB349742     1    25    25
browser |    25  100.0%         10     + 110535648 110535672              AB349742     1    25    25
browser |    25  100.0%         10     - 116443170 116443194              AB349742     1    25    25
browser |    25  100.0%         10     + 117911359 117911383              AB349742     1    25    25
browser |    25  100.0%         10     + 121004156 121004180              AB349742     1    25    25
browser |    25  100.0%         10     - 122202968 122202992              AB349742     1    25    25
browser |    25  100.0%         10     - 122669767 122669791              AB349742     1    25    25
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browser |    25  100.0%         10     - 124517359 124517383              AB349742     1    25    25
browser |    25  100.0%         10     + 129764507 129764531              AB349742     1    25    25
browser |    25  100.0%         10     - 130397014 130397038              AB349742     1    25    25
browser |    25  100.0%         11     -   6092496   6092520              AB349742     1    25    25
browser |    25  100.0%         11     +   6484763   6484787              AB349742     1    25    25
browser |    25  100.0%         11     -   7526692   7526716              AB349742     1    25    25
browser |    25  100.0%         11     -  12458295  12458319              AB349742     1    25    25
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browser |    25  100.0%         11     -  12905022  12905046              AB349742     1    25    25
browser |    25  100.0%         11     +  15183790  15183814              AB349742     1    25    25
browser |    25  100.0%         11     -  19517180  19517204              AB349742     1    25    25
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browser |    25  100.0%         11     -  22286259  22286283              AB349742     1    25    25
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browser |    25  100.0%         11     -  23169588  23169612              AB349742     1    25    25
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browser |    25  100.0%         11     -  27366114  27366138              AB349742     1    25    25
browser |    25  100.0%         11     -  27902084  27902108              AB349742     1    25    25
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browser |    25  100.0%         11     -  39955562  39955586              AB349742     1    25    25
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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