AB352941
 

Information on mRNA AB352941

Description: Mus musculus non-coding RNA, oocyte_piRNA3757, 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: AB352941
Position: chr12:56795752-56795777

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%         12     -  56795752  56795777              AB352941     1    26    26
browser |    26  100.0%          1     -   5875687   5875712              AB352941     1    26    26
browser |    26  100.0%          1     -   6501716   6501741              AB352941     1    26    26
browser |    26  100.0%          1     +   8069904   8069929              AB352941     1    26    26
browser |    25  100.0%          1     +   8232349   8232373              AB352941     1    25    26
browser |    26  100.0%          1     -  11100893  11100918              AB352941     1    26    26
browser |    26  100.0%          1     -  11958464  11958489              AB352941     1    26    26
browser |    25  100.0%          1     +  16814418  16814442              AB352941     1    25    26
browser |    25  100.0%          1     +  18033006  18033030              AB352941     1    25    26
browser |    26  100.0%          1     +  18590292  18590317              AB352941     1    26    26
browser |    26  100.0%          1     +  19698626  19698651              AB352941     1    26    26
browser |    26  100.0%          1     -  26389373  26389398              AB352941     1    26    26
browser |    26  100.0%          1     +  34957131  34957156              AB352941     1    26    26
browser |    26  100.0%          1     +  37816554  37816579              AB352941     1    26    26
browser |    26  100.0%          1     +  38746893  38746918              AB352941     1    26    26
browser |    26  100.0%          1     +  40740462  40740487              AB352941     1    26    26
browser |    26  100.0%          1     +  45777367  45777392              AB352941     1    26    26
browser |    26  100.0%          1     +  48132301  48132326              AB352941     1    26    26
browser |    26  100.0%          1     +  55821276  55821301              AB352941     1    26    26
browser |    26  100.0%          1     +  56817318  56817343              AB352941     1    26    26
browser |    26  100.0%          1     -  58363642  58363667              AB352941     1    26    26
browser |    25  100.0%          1     -  60765137  60765161              AB352941     1    25    26
browser |    26  100.0%          1     -  62574400  62574425              AB352941     1    26    26
browser |    26  100.0%          1     -  64218465  64218490              AB352941     1    26    26
browser |    26  100.0%          1     +  64428218  64428243              AB352941     1    26    26
browser |    26  100.0%          1     -  65000598  65000623              AB352941     1    26    26
browser |    25  100.0%          1     -  66057910  66057934              AB352941     1    25    26
browser |    26  100.0%          1     -  67791715  67791740              AB352941     1    26    26
browser |    25  100.0%          1     -  69738352  69738376              AB352941     2    26    26
browser |    26  100.0%          1     -  74693721  74693746              AB352941     1    26    26
browser |    26  100.0%          1     -  76751122  76751147              AB352941     1    26    26
browser |    25  100.0%          1     -  81543012  81543036              AB352941     1    25    26
browser |    26  100.0%          1     +  82482573  82482598              AB352941     1    26    26
browser |    26  100.0%          1     -  84974729  84974754              AB352941     1    26    26
browser |    26  100.0%          1     +  87393838  87393863              AB352941     1    26    26
browser |    26  100.0%          1     -  91400069  91400094              AB352941     1    26    26
browser |    26  100.0%          1     +  97105947  97105972              AB352941     1    26    26
browser |    26  100.0%          1     - 101906998 101907023              AB352941     1    26    26
browser |    26  100.0%          1     + 102965349 102965374              AB352941     1    26    26
browser |    26  100.0%          1     - 103134030 103134055              AB352941     1    26    26
browser |    26  100.0%          1     - 104218423 104218448              AB352941     1    26    26
browser |    26  100.0%          1     - 108337718 108337743              AB352941     1    26    26
browser |    26  100.0%          1     - 109057534 109057559              AB352941     1    26    26
browser |    26  100.0%          1     + 109547088 109547113              AB352941     1    26    26
browser |    26  100.0%          1     + 110260859 110260884              AB352941     1    26    26
browser |    26  100.0%          1     - 110866465 110866490              AB352941     1    26    26
browser |    26  100.0%          1     + 112949766 112949791              AB352941     1    26    26
browser |    26  100.0%          1     - 120499708 120499733              AB352941     1    26    26
browser |    26  100.0%          1     + 126870970 126870995              AB352941     1    26    26
browser |    26  100.0%          1     - 127487129 127487154              AB352941     1    26    26
browser |    26  100.0%          1     - 127820891 127820916              AB352941     1    26    26
browser |    26  100.0%          1     + 130465824 130465849              AB352941     1    26    26
browser |    26  100.0%          1     - 137202785 137202810              AB352941     1    26    26
browser |    26  100.0%          1     + 139656664 139656689              AB352941     1    26    26
browser |    26  100.0%          1     + 140969105 140969130              AB352941     1    26    26
browser |    26  100.0%          1     - 142285153 142285178              AB352941     1    26    26
browser |    26  100.0%          1     - 142513751 142513776              AB352941     1    26    26
browser |    26  100.0%          1     - 144731558 144731583              AB352941     1    26    26
browser |    26  100.0%          1     - 148045465 148045490              AB352941     1    26    26
browser |    26  100.0%          1     + 148154084 148154109              AB352941     1    26    26
browser |    26  100.0%          1     + 148365298 148365323              AB352941     1    26    26
browser |    25  100.0%          1     + 149274956 149274980              AB352941     1    25    26
browser |    26  100.0%          1     + 149463270 149463295              AB352941     1    26    26
browser |    26  100.0%          1     + 152542714 152542739              AB352941     1    26    26
browser |    25  100.0%          1     - 159798462 159798486              AB352941     1    25    26
browser |    26  100.0%          1     - 160644575 160644600              AB352941     1    26    26
browser |    26  100.0%          1     + 162674079 162674104              AB352941     1    26    26
browser |    26  100.0%          1     - 163297191 163297216              AB352941     1    26    26
browser |    26  100.0%          1     + 166183151 166183176              AB352941     1    26    26
browser |    26  100.0%          1     + 169375323 169375348              AB352941     1    26    26
browser |    26  100.0%          1     + 169949314 169949339              AB352941     1    26    26
browser |    26  100.0%          1     - 176371760 176371785              AB352941     1    26    26
browser |    25  100.0%          1     + 178007631 178007655              AB352941     1    25    26
browser |    25  100.0%          1     - 181092217 181092241              AB352941     1    25    26
browser |    24  100.0%          1     + 181325918 181325941              AB352941     2    25    26
browser |    26  100.0%          1     + 191843739 191843764              AB352941     1    26    26
browser |    25  100.0%          1     + 195008612 195008636              AB352941     1    25    26
browser |    25  100.0%         10     -   3552057   3552081              AB352941     1    25    26
browser |    26  100.0%         10     -  19415770  19415795              AB352941     1    26    26
browser |    26  100.0%         10     +  19676105  19676130              AB352941     1    26    26
browser |    26  100.0%         10     +  21091306  21091331              AB352941     1    26    26
browser |    25  100.0%         10     -  21519344  21519368              AB352941     1    25    26
browser |    26  100.0%         10     -  22560289  22560314              AB352941     1    26    26
browser |    25  100.0%         10     -  23748345  23748369              AB352941     1    25    26
browser |    26  100.0%         10     +  24566334  24566359              AB352941     1    26    26
browser |    26  100.0%         10     -  24978568  24978593              AB352941     1    26    26
browser |    26  100.0%         10     +  30695944  30695969              AB352941     1    26    26
browser |    26  100.0%         10     +  30970629  30970654              AB352941     1    26    26
browser |    26  100.0%         10     +  31629718  31629743              AB352941     1    26    26
browser |    26  100.0%         10     +  33765890  33765915              AB352941     1    26    26
browser |    26  100.0%         10     -  34618947  34618972              AB352941     1    26    26
browser |    26  100.0%         10     +  41722496  41722521              AB352941     1    26    26
browser |    26  100.0%         10     -  45432125  45432150              AB352941     1    26    26
browser |    26  100.0%         10     -  55592752  55592777              AB352941     1    26    26
browser |    26  100.0%         10     +  57019724  57019749              AB352941     1    26    26
browser |    26  100.0%         10     +  59221721  59221746              AB352941     1    26    26
browser |    26  100.0%         10     +  62447855  62447880              AB352941     1    26    26
browser |    25  100.0%         10     -  65787725  65787749              AB352941     1    25    26
browser |    25  100.0%         10     -  66559369  66559393              AB352941     1    25    26
browser |    26  100.0%         10     +  70633217  70633242              AB352941     1    26    26
browser |    26  100.0%         10     +  77792568  77792593              AB352941     1    26    26
browser |    26  100.0%         10     +  77860258  77860283              AB352941     1    26    26
browser |    26  100.0%         10     -  78653417  78653442              AB352941     1    26    26
browser |    26  100.0%         10     +  80815535  80815560              AB352941     1    26    26
browser |    25  100.0%         10     +  81809684  81809708              AB352941     1    25    26
browser |    26  100.0%         10     -  83507910  83507935              AB352941     1    26    26
browser |    26  100.0%         10     +  83627315  83627340              AB352941     1    26    26
browser |    26  100.0%         10     +  84584606  84584631              AB352941     1    26    26
browser |    25  100.0%         10     +  85555409  85555433              AB352941     1    25    26
browser |    25  100.0%         10     -  85605417  85605441              AB352941     1    25    26
browser |    25  100.0%         10     +  88802911  88802935              AB352941     1    25    26
browser |    26  100.0%         10     -  90161596  90161621              AB352941     1    26    26
browser |    26  100.0%         10     -  94199562  94199587              AB352941     1    26    26
browser |    25  100.0%         10     -  95994235  95994259              AB352941     1    25    26
browser |    25  100.0%         10     -  96029519  96029543              AB352941     1    25    26
browser |    26  100.0%         10     -  98935183  98935208              AB352941     1    26    26
browser |    25  100.0%         10     +  99180945  99180969              AB352941     1    25    26
browser |    25  100.0%         10     + 100418481 100418505              AB352941     1    25    26
browser |    26  100.0%         10     - 104656478 104656503              AB352941     1    26    26
browser |    26  100.0%         10     + 104677392 104677417              AB352941     1    26    26
browser |    25  100.0%         10     + 105016518 105016542              AB352941     1    25    26
browser |    26  100.0%         10     - 105509637 105509662              AB352941     1    26    26
browser |    25  100.0%         10     + 107841321 107841345              AB352941     1    25    26
browser |    26  100.0%         10     - 109152203 109152228              AB352941     1    26    26
browser |    26  100.0%         10     + 110535526 110535551              AB352941     1    26    26
browser |    26  100.0%         10     + 111893117 111893142              AB352941     1    26    26
browser |    26  100.0%         10     - 116443291 116443316              AB352941     1    26    26
browser |    26  100.0%         10     + 121004034 121004059              AB352941     1    26    26
browser |    25  100.0%         10     - 122140663 122140687              AB352941     1    25    26
browser |    25  100.0%         10     - 122203090 122203114              AB352941     1    25    26
browser |    26  100.0%         10     + 124418188 124418213              AB352941     1    26    26
browser |    26  100.0%         10     + 124445693 124445718              AB352941     1    26    26
browser |    26  100.0%         10     - 129225816 129225841              AB352941     1    26    26
browser |    25  100.0%         10     + 129764385 129764409              AB352941     1    25    26
browser |    26  100.0%         11     -   6092617   6092642              AB352941     1    26    26
browser |    25  100.0%         11     +   6484641   6484665              AB352941     1    25    26
browser |    25  100.0%         11     +  10716287  10716311              AB352941     1    25    26
browser |    26  100.0%         11     -  12458416  12458441              AB352941     1    26    26
browser |    25  100.0%         11     +  12517898  12517922              AB352941     1    25    26
browser |    26  100.0%         11     -  12905143  12905168              AB352941     1    26    26
browser |    26  100.0%         11     +  15183668  15183693              AB352941     1    26    26
browser |    26  100.0%         11     +  15836670  15836695              AB352941     1    26    26
browser |    25  100.0%         11     +  16181523  16181547              AB352941     1    25    26
browser |    26  100.0%         11     -  19517301  19517326              AB352941     1    26    26
browser |    25  100.0%         11     +  20470008  20470032              AB352941     1    25    26
browser |    26  100.0%         11     -  22286380  22286405              AB352941     1    26    26
browser |    25  100.0%         11     +  22531859  22531883              AB352941     1    25    26
browser |    26  100.0%         11     -  23169709  23169734              AB352941     1    26    26
browser |    25  100.0%         11     +  26509602  26509626              AB352941     2    26    26
browser |    26  100.0%         11     +  28053268  28053293              AB352941     1    26    26
browser |    26  100.0%         11     +  29078639  29078664              AB352941     1    26    26
browser |    25  100.0%         11     -  39955684  39955708              AB352941     1    25    26
browser |    26  100.0%         11     +  43553516  43553541              AB352941     1    26    26
browser |    26  100.0%         11     -  51556980  51557005              AB352941     1    26    26
browser |    25  100.0%         11     -  54468527  54468551              AB352941     1    25    26
browser |    25  100.0%         11     -  55132890  55132914              AB352941     1    25    26
browser |    25  100.0%         11     +  63364529  63364553              AB352941     2    26    26
browser |    25  100.0%         11     +  64687058  64687082              AB352941     2    26    26
browser |    26  100.0%         11     -  65343739  65343764              AB352941     1    26    26
browser |    25  100.0%         11     -  70932328  70932352              AB352941     1    25    26
browser |    26  100.0%         11     -  73627917  73627942              AB352941     1    26    26
browser |    26  100.0%         11     -  74111645  74111670              AB352941     1    26    26
browser |    26  100.0%         11     +  74435034  74435059              AB352941     1    26    26
browser |    26  100.0%         11     +  74781198  74781223              AB352941     1    26    26
browser |    25  100.0%         11     -  79124746  79124770              AB352941     1    25    26
browser |    26  100.0%         11     -  79633421  79633446              AB352941     1    26    26
browser |    26  100.0%         11     -  85177522  85177547              AB352941     1    26    26
browser |    26  100.0%         11     +  86739848  86739873              AB352941     1    26    26
browser |    26  100.0%         11     -  88802914  88802939              AB352941     1    26    26
browser |    25  100.0%         11     -  90721574  90721598              AB352941     1    25    26
browser |    26  100.0%         11     +  90797934  90797959              AB352941     1    26    26
browser |    25  100.0%         11     +  98510065  98510089              AB352941     1    25    26
browser |    25  100.0%         11     + 100559218 100559242              AB352941     1    25    26
browser |    26  100.0%         11     - 105920208 105920233              AB352941     1    26    26
browser |    25  100.0%         11     - 106184643 106184667              AB352941     1    25    26
browser |    26  100.0%         11     - 108291207 108291232              AB352941     1    26    26
browser |    26  100.0%         11     + 109914070 109914095              AB352941     1    26    26
browser |    25  100.0%         11     - 111107599 111107623              AB352941     1    25    26
browser |    26  100.0%         11     + 113808997 113809022              AB352941     1    26    26
browser |    26  100.0%         11     - 115646852 115646877              AB352941     1    26    26
browser |    26  100.0%         11     + 116284351 116284376              AB352941     1    26    26
browser |    25  100.0%         11     + 116682364 116682388              AB352941     1    25    26
browser |    25  100.0%         11     + 117394650 117394674              AB352941     1    25    26
browser |    25  100.0%         11     + 120964521 120964545              AB352941     1    25    26
browser |    26  100.0%         12     +   3058342   3058367              AB352941     1    26    26
browser |    26  100.0%         12     -   3084857   3084882              AB352941     1    26    26
browser |    26  100.0%         12     -   3381934   3381959              AB352941     1    26    26
browser |    26  100.0%         12     +   6572514   6572539              AB352941     1    26    26
browser |    26  100.0%         12     +   8457278   8457303              AB352941     1    26    26
browser |    25  100.0%         12     -  11154783  11154807              AB352941     1    25    26
browser |    26  100.0%         12     +  24451445  24451470              AB352941     1    26    26
browser |    26  100.0%         12     -  31409277  31409302              AB352941     1    26    26
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browser |    26  100.0%         12     +  40458063  40458088              AB352941     1    26    26
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browser |    26  100.0%         12     +  44831211  44831236              AB352941     1    26    26
browser |    25  100.0%         12     +  48584936  48584960              AB352941     2    26    26
browser |    25  100.0%         12     +  49047544  49047568              AB352941     1    25    26
browser |    26  100.0%         12     +  59493134  59493159              AB352941     1    26    26
browser |    26  100.0%         12     -  61337032  61337057              AB352941     1    26    26
browser |    26  100.0%         12     +  62584841  62584866              AB352941     1    26    26
browser |    26  100.0%         12     -  65075072  65075097              AB352941     1    26    26
browser |    26  100.0%         12     +  65686021  65686046              AB352941     1    26    26
browser |    25  100.0%         12     -  65849129  65849153              AB352941     1    25    26
browser |    25  100.0%         12     -  66454929  66454953              AB352941     1    25    26
browser |    26  100.0%         12     -  68669681  68669706              AB352941     1    26    26
browser |    26  100.0%         12     +  68796002  68796027              AB352941     1    26    26
browser |    26  100.0%         12     -  70709061  70709086              AB352941     1    26    26
browser |    26  100.0%         12     -  73358917  73358942              AB352941     1    26    26
browser |    26  100.0%         12     -  79609740  79609765              AB352941     1    26    26
browser |    26  100.0%         12     +  80470041  80470066              AB352941     1    26    26
browser |    26  100.0%         12     +  81633471  81633496              AB352941     1    26    26
browser |    25  100.0%         12     -  82508989  82509013              AB352941     1    25    26
browser |    25  100.0%         12     -  85448926  85448950              AB352941     1    25    26
browser |    25  100.0%         12     +  88482253  88482277              AB352941     1    25    26
browser |    26  100.0%         12     +  93482300  93482325              AB352941     1    26    26
browser |    25  100.0%         12     -  94004410  94004434              AB352941     1    25    26
browser |    26  100.0%         12     -  96198082  96198107              AB352941     1    26    26
browser |    26  100.0%         12     - 108046685 108046710              AB352941     1    26    26
browser |    25  100.0%         12     + 109874325 109874349              AB352941     1    25    26
browser |    26  100.0%         12     + 111358685 111358710              AB352941     1    26    26
browser |    26  100.0%         12     + 119560497 119560522              AB352941     1    26    26
browser |    26  100.0%         13     -   4117354   4117379              AB352941     1    26    26
browser |    26  100.0%         13     +   4394419   4394444              AB352941     1    26    26
browser |    26  100.0%         13     +   5332891   5332916              AB352941     1    26    26
browser |    26  100.0%         13     -   8000303   8000328              AB352941     1    26    26
browser |    26  100.0%         13     -   8520777   8520802              AB352941     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