AB351233
 

Information on mRNA AB351233

Description: Mus musculus non-coding RNA, oocyte_piRNA2049, 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: AB351233
Position: chr12:56797405-56797441

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 |    37  100.0%         12     -  56797405  56797441              AB351233     1    37    37
browser |    37  100.0%          1     -   5880090   5880126              AB351233     1    37    37
browser |    37  100.0%          1     -   6506119   6506155              AB351233     1    37    37
browser |    37  100.0%          1     +   8065493   8065529              AB351233     1    37    37
browser |    37  100.0%          1     +   8227934   8227970              AB351233     1    37    37
browser |    37  100.0%          1     -   8731130   8731166              AB351233     1    37    37
browser |    37  100.0%          1     -  10805606  10805642              AB351233     1    37    37
browser |    37  100.0%          1     -  12019430  12019466              AB351233     1    37    37
browser |    37  100.0%          1     +  13622358  13622394              AB351233     1    37    37
browser |    37  100.0%          1     +  16810004  16810040              AB351233     1    37    37
browser |    37  100.0%          1     +  18028598  18028634              AB351233     1    37    37
browser |    37  100.0%          1     +  18588628  18588664              AB351233     1    37    37
browser |    37  100.0%          1     +  19694212  19694248              AB351233     1    37    37
browser |    37  100.0%          1     -  22070983  22071019              AB351233     1    37    37
browser |    37  100.0%          1     +  26454620  26454656              AB351233     1    37    37
browser |    37  100.0%          1     -  26513695  26513731              AB351233     1    37    37
browser |    37  100.0%          1     +  27220768  27220804              AB351233     1    37    37
browser |    37  100.0%          1     -  29986825  29986861              AB351233     1    37    37
browser |    37  100.0%          1     +  34388101  34388137              AB351233     1    37    37
browser |    37  100.0%          1     +  35829097  35829133              AB351233     1    37    37
browser |    37  100.0%          1     +  40738777  40738813              AB351233     1    37    37
browser |    37  100.0%          1     -  47265539  47265575              AB351233     1    37    37
browser |    37  100.0%          1     -  48400880  48400916              AB351233     1    37    37
browser |    37  100.0%          1     -  53172370  53172406              AB351233     1    37    37
browser |    37  100.0%          1     +  55819050  55819086              AB351233     1    37    37
browser |    37  100.0%          1     +  56812904  56812940              AB351233     1    37    37
browser |    37  100.0%          1     -  58368045  58368081              AB351233     1    37    37
browser |    37  100.0%          1     -  58856353  58856389              AB351233     1    37    37
browser |    37  100.0%          1     +  58971457  58971493              AB351233     1    37    37
browser |    37  100.0%          1     -  60769539  60769575              AB351233     1    37    37
browser |    37  100.0%          1     -  62578803  62578839              AB351233     1    37    37
browser |    37  100.0%          1     -  64222865  64222901              AB351233     1    37    37
browser |    37  100.0%          1     +  64423804  64423840              AB351233     1    37    37
browser |    37  100.0%          1     -  81547414  81547450              AB351233     1    37    37
browser |    37  100.0%          1     +  82480347  82480383              AB351233     1    37    37
browser |    37  100.0%          1     -  83209018  83209054              AB351233     1    37    37
browser |    37  100.0%          1     -  87066896  87066932              AB351233     1    37    37
browser |    37  100.0%          1     +  87389424  87389460              AB351233     1    37    37
browser |    37  100.0%          1     +  89128352  89128388              AB351233     1    37    37
browser |    37  100.0%          1     -  91404469  91404505              AB351233     1    37    37
browser |    37  100.0%          1     +  93885834  93885870              AB351233     1    37    37
browser |    37  100.0%          1     +  95624422  95624458              AB351233     1    37    37
browser |    37  100.0%          1     +  97102033  97102069              AB351233     1    37    37
browser |    37  100.0%          1     - 101911404 101911440              AB351233     1    37    37
browser |    37  100.0%          1     + 102960935 102960971              AB351233     1    37    37
browser |    37  100.0%          1     - 103138433 103138469              AB351233     1    37    37
browser |    37  100.0%          1     - 108342121 108342157              AB351233     1    37    37
browser |    37  100.0%          1     + 109542677 109542713              AB351233     1    37    37
browser |    37  100.0%          1     - 111186890 111186926              AB351233     1    37    37
browser |    37  100.0%          1     + 111632645 111632681              AB351233     1    37    37
browser |    37  100.0%          1     - 112197610 112197646              AB351233     1    37    37
browser |    37  100.0%          1     + 112858754 112858790              AB351233     1    37    37
browser |    37  100.0%          1     + 112945352 112945388              AB351233     1    37    37
browser |    37  100.0%          1     - 116581538 116581574              AB351233     1    37    37
browser |    37  100.0%          1     + 125246140 125246176              AB351233     1    37    37
browser |    37  100.0%          1     + 126353318 126353354              AB351233     1    37    37
browser |    37  100.0%          1     - 127491532 127491568              AB351233     1    37    37
browser |    37  100.0%          1     - 127808331 127808367              AB351233     1    37    37
browser |    37  100.0%          1     + 130463599 130463635              AB351233     1    37    37
browser |    37  100.0%          1     - 137204438 137204474              AB351233     1    37    37
browser |    37  100.0%          1     + 140746095 140746131              AB351233     1    37    37
browser |    37  100.0%          1     + 140964693 140964729              AB351233     1    37    37
browser |    37  100.0%          1     - 146163171 146163207              AB351233     1    37    37
browser |    37  100.0%          1     - 146278474 146278510              AB351233     1    37    37
browser |    37  100.0%          1     - 148048551 148048587              AB351233     1    37    37
browser |    37  100.0%          1     - 159802864 159802900              AB351233     1    37    37
browser |    37  100.0%          1     + 162669665 162669701              AB351233     1    37    37
browser |    37  100.0%          1     - 166595737 166595773              AB351233     1    37    37
browser |    37  100.0%          1     - 174874269 174874305              AB351233     1    37    37
browser |    37  100.0%          1     - 176376163 176376199              AB351233     1    37    37
browser |    37  100.0%          1     + 177887164 177887200              AB351233     1    37    37
browser |    37  100.0%          1     + 178003217 178003253              AB351233     1    37    37
browser |    37  100.0%          1     + 179723112 179723148              AB351233     1    37    37
browser |    37  100.0%          1     - 181096620 181096656              AB351233     1    37    37
browser |    37  100.0%          1     + 181322006 181322042              AB351233     1    37    37
browser |    37  100.0%          1     + 183297824 183297860              AB351233     1    37    37
browser |    37  100.0%          1     + 195004201 195004237              AB351233     1    37    37
browser |    37  100.0%         10     -   3556460   3556496              AB351233     1    37    37
browser |    37  100.0%         10     +   8476590   8476626              AB351233     1    37    37
browser |    37  100.0%         10     +  11571569  11571605              AB351233     1    37    37
browser |    37  100.0%         10     -  19420173  19420209              AB351233     1    37    37
browser |    37  100.0%         10     +  19674604  19674640              AB351233     1    37    37
browser |    37  100.0%         10     -  19891900  19891936              AB351233     1    37    37
browser |    37  100.0%         10     -  21523746  21523782              AB351233     1    37    37
browser |    37  100.0%         10     -  22404638  22404674              AB351233     1    37    37
browser |    37  100.0%         10     -  22564692  22564728              AB351233     1    37    37
browser |    37  100.0%         10     -  23752747  23752783              AB351233     1    37    37
browser |    37  100.0%         10     -  24980819  24980855              AB351233     1    37    37
browser |    37  100.0%         10     +  25845862  25845898              AB351233     1    37    37
browser |    37  100.0%         10     +  30358934  30358970              AB351233     1    37    37
browser |    37  100.0%         10     +  30691530  30691566              AB351233     1    37    37
browser |    37  100.0%         10     +  30966215  30966251              AB351233     1    37    37
browser |    37  100.0%         10     +  31360157  31360193              AB351233     1    37    37
browser |    37  100.0%         10     -  34616572  34616608              AB351233     1    37    37
browser |    37  100.0%         10     -  34623350  34623386              AB351233     1    37    37
browser |    37  100.0%         10     +  41718084  41718120              AB351233     1    37    37
browser |    37  100.0%         10     -  43648459  43648495              AB351233     1    37    37
browser |    37  100.0%         10     +  47548234  47548270              AB351233     1    37    37
browser |    37  100.0%         10     +  51760642  51760678              AB351233     1    37    37
browser |    37  100.0%         10     +  56598390  56598426              AB351233     1    37    37
browser |    37  100.0%         10     +  57015310  57015346              AB351233     1    37    37
browser |    37  100.0%         10     +  62941312  62941348              AB351233     1    37    37
browser |    37  100.0%         10     -  65479153  65479189              AB351233     1    37    37
browser |    37  100.0%         10     -  66563768  66563804              AB351233     1    37    37
browser |    37  100.0%         10     +  77788154  77788190              AB351233     1    37    37
browser |    37  100.0%         10     -  78657317  78657353              AB351233     1    37    37
browser |    37  100.0%         10     -  81511901  81511937              AB351233     1    37    37
browser |    37  100.0%         10     -  81671029  81671065              AB351233     1    37    37
browser |    37  100.0%         10     +  81805274  81805310              AB351233     1    37    37
browser |    37  100.0%         10     -  83307258  83307294              AB351233     1    37    37
browser |    37  100.0%         10     -  83512313  83512349              AB351233     1    37    37
browser |    37  100.0%         10     +  85552608  85552644              AB351233     1    37    37
browser |    37  100.0%         10     +  88488395  88488431              AB351233     1    37    37
browser |    37  100.0%         10     -  94203461  94203497              AB351233     1    37    37
browser |    37  100.0%         10     -  96033921  96033957              AB351233     1    37    37
browser |    37  100.0%         10     -  97163840  97163876              AB351233     1    37    37
browser |    37  100.0%         10     +  99176534  99176570              AB351233     1    37    37
browser |    37  100.0%         10     -  99385613  99385649              AB351233     1    37    37
browser |    37  100.0%         10     + 104392761 104392797              AB351233     1    37    37
browser |    37  100.0%         10     + 104672978 104673014              AB351233     1    37    37
browser |    37  100.0%         10     + 105014497 105014533              AB351233     1    37    37
browser |    37  100.0%         10     + 107836907 107836943              AB351233     1    37    37
browser |    37  100.0%         10     - 109156607 109156643              AB351233     1    37    37
browser |    37  100.0%         10     - 113564133 113564169              AB351233     1    37    37
browser |    37  100.0%         10     + 117908101 117908137              AB351233     1    37    37
browser |    37  100.0%         10     + 121002186 121002222              AB351233     1    37    37
browser |    37  100.0%         10     - 122205303 122205339              AB351233     1    37    37
browser |    35  100.0%         10     + 122343232 122343266              AB351233     1    35    37
browser |    37  100.0%         10     - 122674180 122674216              AB351233     1    37    37
browser |    37  100.0%         10     + 123696799 123696835              AB351233     1    37    37
browser |    37  100.0%         10     + 124413773 124413809              AB351233     1    37    37
browser |    37  100.0%         10     - 124520374 124520410              AB351233     1    37    37
browser |    35  100.0%         10     + 129051213 129051247              AB351233     1    35    37
browser |    37  100.0%         10     - 129230219 129230255              AB351233     1    37    37
browser |    37  100.0%         10     + 129762721 129762757              AB351233     1    37    37
browser |    37  100.0%         10     - 130400428 130400464              AB351233     1    37    37
browser |    37  100.0%         11     -   6097021   6097057              AB351233     1    37    37
browser |    37  100.0%         11     -   9663512   9663548              AB351233     1    37    37
browser |    37  100.0%         11     +  10711874  10711910              AB351233     1    37    37
browser |    37  100.0%         11     +  12513484  12513520              AB351233     1    37    37
browser |    37  100.0%         11     +  15179254  15179290              AB351233     1    37    37
browser |    37  100.0%         11     -  15236387  15236423              AB351233     1    37    37
browser |    37  100.0%         11     -  18761985  18762021              AB351233     1    37    37
browser |    37  100.0%         11     -  19518954  19518990              AB351233     1    37    37
browser |    37  100.0%         11     +  20467940  20467976              AB351233     1    37    37
browser |    37  100.0%         11     -  23174112  23174148              AB351233     1    37    37
browser |    37  100.0%         11     -  27905498  27905534              AB351233     1    37    37
browser |    37  100.0%         11     +  28048857  28048893              AB351233     1    37    37
browser |    37  100.0%         11     -  31403092  31403128              AB351233     1    37    37
browser |    37  100.0%         11     +  38373886  38373922              AB351233     1    37    37
browser |    37  100.0%         11     -  39960081  39960117              AB351233     1    37    37
browser |    37  100.0%         11     +  51330072  51330108              AB351233     1    37    37
browser |    37  100.0%         11     -  54472929  54472965              AB351233     1    37    37
browser |    37  100.0%         11     -  55137292  55137328              AB351233     1    37    37
browser |    37  100.0%         11     +  61312825  61312861              AB351233     1    37    37
browser |    37  100.0%         11     +  63360114  63360150              AB351233     1    37    37
browser |    37  100.0%         11     -  65348139  65348175              AB351233     1    37    37
browser |    37  100.0%         11     -  66843598  66843634              AB351233     1    37    37
browser |    37  100.0%         11     +  74021322  74021358              AB351233     1    37    37
browser |    37  100.0%         11     -  74116008  74116044              AB351233     1    37    37
browser |    37  100.0%         11     +  74432517  74432553              AB351233     1    37    37
browser |    37  100.0%         11     +  74776784  74776820              AB351233     1    37    37
browser |    37  100.0%         11     -  79635095  79635131              AB351233     1    37    37
browser |    37  100.0%         11     +  81437928  81437964              AB351233     1    37    37
browser |    37  100.0%         11     -  82227602  82227638              AB351233     1    37    37
browser |    37  100.0%         11     -  85181925  85181961              AB351233     1    37    37
browser |    37  100.0%         11     +  86738000  86738036              AB351233     1    37    37
browser |    37  100.0%         11     +  90794077  90794113              AB351233     1    37    37
browser |    37  100.0%         11     -  90856529  90856565              AB351233     1    37    37
browser |    37  100.0%         11     +  91991447  91991483              AB351233     1    37    37
browser |    37  100.0%         11     +  98505651  98505687              AB351233     1    37    37
browser |    37  100.0%         11     + 100555307 100555343              AB351233     1    37    37
browser |    37  100.0%         11     - 106186856 106186892              AB351233     1    37    37
browser |    37  100.0%         11     + 111074893 111074929              AB351233     1    37    37
browser |    37  100.0%         11     - 111112001 111112037              AB351233     1    37    37
browser |    37  100.0%         11     + 113804583 113804619              AB351233     1    37    37
browser |    37  100.0%         11     - 115651255 115651291              AB351233     1    37    37
browser |    37  100.0%         11     + 116677950 116677986              AB351233     1    37    37
browser |    37  100.0%         11     + 117392245 117392281              AB351233     1    37    37
browser |    37  100.0%         11     + 120213544 120213580              AB351233     1    37    37
browser |    37  100.0%         11     + 120962296 120962332              AB351233     1    37    37
browser |    37  100.0%         12     +   3053931   3053967              AB351233     1    37    37
browser |    37  100.0%         12     -   3386338   3386374              AB351233     1    37    37
browser |    37  100.0%         12     +   6568099   6568135              AB351233     1    37    37
browser |    37  100.0%         12     -  11159186  11159222              AB351233     1    37    37
browser |    37  100.0%         12     -  14649686  14649722              AB351233     1    37    37
browser |    37  100.0%         12     +  17173778  17173814              AB351233     1    37    37
browser |    37  100.0%         12     -  19313769  19313805              AB351233     1    37    37
browser |    37  100.0%         12     +  19826068  19826104              AB351233     1    37    37
browser |    37  100.0%         12     +  24447034  24447070              AB351233     1    37    37
browser |    37  100.0%         12     -  31413677  31413713              AB351233     1    37    37
browser |    37  100.0%         12     +  32079558  32079594              AB351233     1    37    37
browser |    37  100.0%         12     +  40453648  40453684              AB351233     1    37    37
browser |    37  100.0%         12     +  41415065  41415101              AB351233     1    37    37
browser |    37  100.0%         12     -  44817456  44817492              AB351233     1    37    37
browser |    37  100.0%         12     +  48580520  48580556              AB351233     1    37    37
browser |    37  100.0%         12     +  49043130  49043166              AB351233     1    37    37
browser |    37  100.0%         12     +  54673392  54673428              AB351233     1    37    37
browser |    37  100.0%         12     +  59488722  59488758              AB351233     1    37    37
browser |    37  100.0%         12     -  61338871  61338907              AB351233     1    37    37
browser |    37  100.0%         12     +  62583177  62583213              AB351233     1    37    37
browser |    37  100.0%         12     -  65079473  65079509              AB351233     1    37    37
browser |    37  100.0%         12     +  65681611  65681647              AB351233     1    37    37
browser |    37  100.0%         12     -  65853531  65853567              AB351233     1    37    37
browser |    37  100.0%         12     -  66459331  66459367              AB351233     1    37    37
browser |    37  100.0%         12     -  70713464  70713500              AB351233     1    37    37
browser |    37  100.0%         12     -  70970313  70970349              AB351233     1    37    37
browser |    37  100.0%         12     +  76792927  76792963              AB351233     1    37    37
browser |    37  100.0%         12     -  79614143  79614179              AB351233     1    37    37
browser |    37  100.0%         12     +  80465627  80465663              AB351233     1    37    37
browser |    37  100.0%         12     -  85453325  85453361              AB351233     1    37    37
browser |    37  100.0%         12     +  93477889  93477925              AB351233     1    37    37
browser |    37  100.0%         12     -  94008812  94008848              AB351233     1    37    37
browser |    37  100.0%         12     -  94240334  94240370              AB351233     1    37    37
browser |    37  100.0%         12     -  96199735  96199771              AB351233     1    37    37
browser |    37  100.0%         12     +  98323050  98323086              AB351233     1    37    37
browser |    37  100.0%         12     - 105272011 105272047              AB351233     1    37    37
browser |    37  100.0%         12     + 109869911 109869947              AB351233     1    37    37
browser |    37  100.0%         12     - 113163070 113163106              AB351233     1    37    37
browser |    37  100.0%         12     + 114598601 114598637              AB351233     1    37    37
browser |    35  100.0%         12     + 115523400 115523434              AB351233     1    35    37
browser |    37  100.0%         12     + 118319667 118319703              AB351233     1    37    37
browser |    37  100.0%         12     + 119556083 119556119              AB351233     1    37    37
browser |    37  100.0%         13     +   4390008   4390044              AB351233     1    37    37
browser |    37  100.0%         13     +   5329587   5329623              AB351233     1    37    37
browser |    37  100.0%         13     -   8004706   8004742              AB351233     1    37    37
browser |    37  100.0%         13     -   9488220   9488256              AB351233     1    37    37
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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