AB351534
 

Information on mRNA AB351534

Description: Mus musculus non-coding RNA, oocyte_piRNA2350, 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: AB351534
Position: chr12:56959562-56959597

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 |    36  100.0%         12     -  56959562  56959597              AB351534     1    36    36
browser |    36  100.0%          1     +   5635932   5635967              AB351534     1    36    36
browser |    36  100.0%          1     -   8859548   8859583              AB351534     1    36    36
browser |    36  100.0%          1     +  10801075  10801110              AB351534     1    36    36
browser |    36  100.0%          1     +  12017833  12017868              AB351534     1    36    36
browser |    36  100.0%          1     -  16814539  16814574              AB351534     1    36    36
browser |    36  100.0%          1     +  22066464  22066499              AB351534     1    36    36
browser |    36  100.0%          1     -  23344407  23344442              AB351534     1    36    36
browser |    36  100.0%          1     +  28496311  28496346              AB351534     1    36    36
browser |    36  100.0%          1     -  29697097  29697132              AB351534     1    36    36
browser |    36  100.0%          1     +  29982794  29982829              AB351534     1    36    36
browser |    36  100.0%          1     +  30727854  30727889              AB351534     1    36    36
browser |    36  100.0%          1     -  31511819  31511854              AB351534     1    36    36
browser |    36  100.0%          1     +  37318875  37318910              AB351534     1    36    36
browser |    36  100.0%          1     -  37816674  37816709              AB351534     1    36    36
browser |    36  100.0%          1     -  44333776  44333811              AB351534     1    36    36
browser |    36  100.0%          1     -  44401065  44401100              AB351534     1    36    36
browser |    36  100.0%          1     +  47263592  47263627              AB351534     1    36    36
browser |    36  100.0%          1     +  47996008  47996043              AB351534     1    36    36
browser |    36  100.0%          1     -  48010083  48010118              AB351534     1    36    36
browser |    36  100.0%          1     +  48711470  48711505              AB351534     1    36    36
browser |    36  100.0%          1     -  50200614  50200649              AB351534     1    36    36
browser |    36  100.0%          1     -  52632272  52632307              AB351534     1    36    36
browser |    36  100.0%          1     -  53276352  53276387              AB351534     1    36    36
browser |    36  100.0%          1     -  53546646  53546681              AB351534     1    36    36
browser |    36  100.0%          1     +  57625217  57625252              AB351534     1    36    36
browser |    36  100.0%          1     +  58789636  58789671              AB351534     1    36    36
browser |    36  100.0%          1     +  58851822  58851857              AB351534     1    36    36
browser |    36  100.0%          1     +  59385376  59385411              AB351534     1    36    36
browser |    36  100.0%          1     +  64218334  64218369              AB351534     1    36    36
browser |    36  100.0%          1     -  65748796  65748831              AB351534     1    36    36
browser |    36  100.0%          1     -  65855786  65855821              AB351534     1    36    36
browser |    36  100.0%          1     -  75981372  75981407              AB351534     1    36    36
browser |    36  100.0%          1     -  81961854  81961889              AB351534     1    36    36
browser |    36  100.0%          1     +  86246472  86246507              AB351534     1    36    36
browser |    36  100.0%          1     -  95626370  95626405              AB351534     1    36    36
browser |    36  100.0%          1     +  96895701  96895736              AB351534     1    36    36
browser |    36  100.0%          1     -  97106042  97106077              AB351534     1    36    36
browser |    36  100.0%          1     + 100457712 100457747              AB351534     1    36    36
browser |    36  100.0%          1     - 102079062 102079097              AB351534     1    36    36
browser |    36  100.0%          1     - 103520729 103520764              AB351534     1    36    36
browser |    36  100.0%          1     + 108873982 108874017              AB351534     1    36    36
browser |    36  100.0%          1     - 108887190 108887225              AB351534     1    36    36
browser |    36  100.0%          1     - 111637179 111637214              AB351534     1    36    36
browser |    36  100.0%          1     + 112193072 112193107              AB351534     1    36    36
browser |    36  100.0%          1     + 112493024 112493059              AB351534     1    36    36
browser |    36  100.0%          1     - 117919524 117919559              AB351534     1    36    36
browser |    36  100.0%          1     + 118069659 118069694              AB351534     1    36    36
browser |    36  100.0%          1     + 125274855 125274890              AB351534     1    36    36
browser |    36  100.0%          1     - 128818400 128818435              AB351534     1    36    36
browser |    36  100.0%          1     + 136736764 136736799              AB351534     1    36    36
browser |    36  100.0%          1     + 143723950 143723985              AB351534     1    36    36
browser |    36  100.0%          1     + 146158926 146158961              AB351534     1    36    36
browser |    36  100.0%          1     - 161362595 161362630              AB351534     1    36    36
browser |    36  100.0%          1     - 169375444 169375479              AB351534     1    36    36
browser |    36  100.0%          1     - 169949435 169949470              AB351534     1    36    36
browser |    36  100.0%          1     - 171659059 171659094              AB351534     1    36    36
browser |    36  100.0%          1     + 176371629 176371664              AB351534     1    36    36
browser |    36  100.0%          1     + 177955409 177955444              AB351534     1    36    36
browser |    36  100.0%          1     - 179727645 179727680              AB351534     1    36    36
browser |    36  100.0%          1     - 181326038 181326073              AB351534     1    36    36
browser |    36  100.0%          1     - 191235572 191235607              AB351534     1    36    36
browser |    36  100.0%          1     - 192641499 192641534              AB351534     1    36    36
browser |    36  100.0%          1     - 195008733 195008768              AB351534     1    36    36
browser |    36  100.0%         10     +   3267332   3267367              AB351534     1    36    36
browser |    36  100.0%         10     +   6517767   6517802              AB351534     1    36    36
browser |    36  100.0%         10     -   7192962   7192997              AB351534     1    36    36
browser |    36  100.0%         10     -   7316686   7316721              AB351534     1    36    36
browser |    36  100.0%         10     -   8481125   8481160              AB351534     1    36    36
browser |    36  100.0%         10     -   9726508   9726543              AB351534     1    36    36
browser |    36  100.0%         10     +  11777560  11777595              AB351534     1    36    36
browser |    36  100.0%         10     +  14486354  14486389              AB351534     1    36    36
browser |    36  100.0%         10     +  15056742  15056777              AB351534     1    36    36
browser |    36  100.0%         10     -  15812570  15812605              AB351534     1    36    36
browser |    36  100.0%         10     -  19676226  19676261              AB351534     1    36    36
browser |    36  100.0%         10     +  19887369  19887404              AB351534     1    36    36
browser |    36  100.0%         10     +  22400130  22400165              AB351534     1    36    36
browser |    36  100.0%         10     +  24978437  24978472              AB351534     1    36    36
browser |    36  100.0%         10     +  26607846  26607881              AB351534     1    36    36
browser |    36  100.0%         10     -  32814140  32814175              AB351534     1    36    36
browser |    36  100.0%         10     +  34615993  34616028              AB351534     1    36    36
browser |    36  100.0%         10     -  38468827  38468862              AB351534     1    36    36
browser |    36  100.0%         10     +  39637903  39637938              AB351534     1    36    36
browser |    36  100.0%         10     -  43754983  43755018              AB351534     1    36    36
browser |    36  100.0%         10     -  47549645  47549680              AB351534     1    36    36
browser |    36  100.0%         10     +  47557773  47557808              AB351534     1    36    36
browser |    36  100.0%         10     +  47909432  47909467              AB351534     1    36    36
browser |    36  100.0%         10     +  48627973  48628008              AB351534     1    36    36
browser |    36  100.0%         10     +  48869020  48869055              AB351534     1    36    36
browser |    36  100.0%         10     -  62447976  62448011              AB351534     1    36    36
browser |    36  100.0%         10     -  62945848  62945883              AB351534     1    36    36
browser |    36  100.0%         10     -  71533330  71533365              AB351534     1    36    36
browser |    36  100.0%         10     +  73385149  73385184              AB351534     1    36    36
browser |    36  100.0%         10     -  74714222  74714257              AB351534     1    36    36
browser |    36  100.0%         10     -  76758640  76758675              AB351534     1    36    36
browser |    36  100.0%         10     +  81507374  81507409              AB351534     1    36    36
browser |    36  100.0%         10     +  81666502  81666537              AB351534     1    36    36
browser |    36  100.0%         10     +  82408255  82408290              AB351534     1    36    36
browser |    36  100.0%         10     -  82776713  82776748              AB351534     1    36    36
browser |    36  100.0%         10     +  83252168  83252203              AB351534     1    36    36
browser |    36  100.0%         10     +  83302729  83302764              AB351534     1    36    36
browser |    36  100.0%         10     +  85605285  85605320              AB351534     1    36    36
browser |    36  100.0%         10     -  86980608  86980643              AB351534     1    36    36
browser |    36  100.0%         10     -  88492911  88492946              AB351534     1    36    36
browser |    36  100.0%         10     -  88803032  88803067              AB351534     1    36    36
browser |    36  100.0%         10     +  91651328  91651363              AB351534     1    36    36
browser |    36  100.0%         10     -  92356374  92356409              AB351534     1    36    36
browser |    36  100.0%         10     +  92587375  92587410              AB351534     1    36    36
browser |    36  100.0%         10     +  95994103  95994138              AB351534     1    36    36
browser |    36  100.0%         10     +  97157415  97157450              AB351534     1    36    36
browser |    36  100.0%         10     +  99382762  99382797              AB351534     1    36    36
browser |    36  100.0%         10     - 100418602 100418637              AB351534     1    36    36
browser |    36  100.0%         10     - 103911361 103911396              AB351534     1    36    36
browser |    36  100.0%         10     + 104411967 104412002              AB351534     1    36    36
browser |    36  100.0%         10     - 110837749 110837784              AB351534     1    36    36
browser |    36  100.0%         10     + 113559602 113559637              AB351534     1    36    36
browser |    36  100.0%         10     - 121978475 121978510              AB351534     1    36    36
browser |    36  100.0%         10     + 122140531 122140566              AB351534     1    36    36
browser |    36  100.0%         10     - 122347752 122347787              AB351534     1    36    36
browser |    36  100.0%         10     - 123701656 123701691              AB351534     1    36    36
browser |    36  100.0%         10     + 124303281 124303316              AB351534     1    36    36
browser |    36  100.0%         10     - 129051823 129051858              AB351534     1    36    36
browser |    36  100.0%         10     + 129225685 129225720              AB351534     1    36    36
browser |    36  100.0%         11     -   5311926   5311961              AB351534     1    36    36
browser |    36  100.0%         11     -   6749109   6749144              AB351534     1    36    36
browser |    36  100.0%         11     +   7984849   7984884              AB351534     1    36    36
browser |    36  100.0%         11     +   9035794   9035829              AB351534     1    36    36
browser |    36  100.0%         11     +   9658981   9659016              AB351534     1    36    36
browser |    36  100.0%         11     -  10716408  10716443              AB351534     1    36    36
browser |    36  100.0%         11     -  12751688  12751723              AB351534     1    36    36
browser |    36  100.0%         11     -  13824675  13824710              AB351534     1    36    36
browser |    36  100.0%         11     +  14847652  14847687              AB351534     1    36    36
browser |    36  100.0%         11     +  15233537  15233572              AB351534     1    36    36
browser |    36  100.0%         11     -  15811666  15811701              AB351534     1    36    36
browser |    36  100.0%         11     -  15836792  15836827              AB351534     1    36    36
browser |    36  100.0%         11     +  16155238  16155273              AB351534     1    36    36
browser |    36  100.0%         11     -  16181644  16181679              AB351534     1    36    36
browser |    36  100.0%         11     +  18757451  18757486              AB351534     1    36    36
browser |    36  100.0%         11     +  19739720  19739755              AB351534     1    36    36
browser |    36  100.0%         11     +  20460210  20460245              AB351534     1    36    36
browser |    36  100.0%         11     +  23193778  23193813              AB351534     1    36    36
browser |    36  100.0%         11     -  27087109  27087144              AB351534     1    36    36
browser |    36  100.0%         11     -  29232000  29232035              AB351534     1    36    36
browser |    36  100.0%         11     -  31164482  31164517              AB351534     1    36    36
browser |    36  100.0%         11     +  31398561  31398596              AB351534     1    36    36
browser |    36  100.0%         11     -  31725958  31725993              AB351534     1    36    36
browser |    36  100.0%         11     +  54468395  54468430              AB351534     1    36    36
browser |    36  100.0%         11     +  65343608  65343643              AB351534     1    36    36
browser |    36  100.0%         11     +  66839650  66839685              AB351534     1    36    36
browser |    36  100.0%         11     +  70932196  70932231              AB351534     1    36    36
browser |    36  100.0%         11     +  70957584  70957619              AB351534     1    36    36
browser |    36  100.0%         11     -  79766883  79766918              AB351534     1    36    36
browser |    36  100.0%         11     +  85331308  85331343              AB351534     1    36    36
browser |    36  100.0%         11     +  88802783  88802818              AB351534     1    36    36
browser |    36  100.0%         11     + 108715323 108715358              AB351534     1    36    36
browser |    36  100.0%         11     - 116654127 116654162              AB351534     1    36    36
browser |    36  100.0%         11     - 120964642 120964677              AB351534     1    36    36
browser |    36  100.0%         12     +   3084726   3084761              AB351534     1    36    36
browser |    36  100.0%         12     -   3112237   3112272              AB351534     1    36    36
browser |    36  100.0%         12     +   3381803   3381838              AB351534     1    36    36
browser |    36  100.0%         12     -   4839382   4839417              AB351534     1    36    36
browser |    36  100.0%         12     -   6859120   6859155              AB351534     1    36    36
browser |    36  100.0%         12     +  14645161  14645196              AB351534     1    36    36
browser |    36  100.0%         12     -  17980153  17980188              AB351534     1    36    36
browser |    36  100.0%         12     -  18182444  18182479              AB351534     1    36    36
browser |    36  100.0%         12     -  19761298  19761333              AB351534     1    36    36
browser |    36  100.0%         12     -  19830597  19830632              AB351534     1    36    36
browser |    36  100.0%         12     +  19849358  19849393              AB351534     1    36    36
browser |    36  100.0%         12     +  19865189  19865224              AB351534     1    36    36
browser |    36  100.0%         12     +  22426108  22426143              AB351534     1    36    36
browser |    36  100.0%         12     +  23585119  23585154              AB351534     1    36    36
browser |    36  100.0%         12     -  24745065  24745100              AB351534     1    36    36
browser |    36  100.0%         12     +  26157471  26157506              AB351534     1    36    36
browser |    36  100.0%         12     +  27283136  27283171              AB351534     1    36    36
browser |    36  100.0%         12     -  32649544  32649579              AB351534     1    36    36
browser |    36  100.0%         12     -  32955421  32955456              AB351534     1    36    36
browser |    36  100.0%         12     -  36667497  36667532              AB351534     1    36    36
browser |    36  100.0%         12     -  39485217  39485252              AB351534     1    36    36
browser |    36  100.0%         12     -  40233253  40233288              AB351534     1    36    36
browser |    36  100.0%         12     +  44813485  44813520              AB351534     1    36    36
browser |    36  100.0%         12     +  52220541  52220576              AB351534     1    36    36
browser |    36  100.0%         12     -  54407279  54407314              AB351534     1    36    36
browser |    36  100.0%         12     -  54676244  54676279              AB351534     1    36    36
browser |    36  100.0%         12     +  60754682  60754717              AB351534     1    36    36
browser |    36  100.0%         12     +  64200568  64200603              AB351534     1    36    36
browser |    36  100.0%         12     +  65832357  65832392              AB351534     1    36    36
browser |    36  100.0%         12     +  66454797  66454832              AB351534     1    36    36
browser |    36  100.0%         12     +  70965785  70965820              AB351534     1    36    36
browser |    36  100.0%         12     -  90737462  90737497              AB351534     1    36    36
browser |    36  100.0%         12     -  91195797  91195832              AB351534     1    36    36
browser |    36  100.0%         12     -  96906126  96906161              AB351534     1    36    36
browser |    36  100.0%         12     -  98327585  98327620              AB351534     1    36    36
browser |    36  100.0%         12     + 105267480 105267515              AB351534     1    36    36
browser |    36  100.0%         12     + 109788062 109788097              AB351534     1    36    36
browser |    34  100.0%         12     - 112852713 112852746              AB351534     3    36    36
browser |    36  100.0%         12     + 113160222 113160257              AB351534     1    36    36
browser |    36  100.0%         12     - 114489822 114489857              AB351534     1    36    36
browser |    36  100.0%         12     - 114603136 114603171              AB351534     1    36    36
browser |    36  100.0%         12     - 118759982 118760017              AB351534     1    36    36
browser |    36  100.0%         13     -   3400986   3401021              AB351534     1    36    36
browser |    36  100.0%         13     +   4510816   4510851              AB351534     1    36    36
browser |    36  100.0%         13     +   4952706   4952741              AB351534     1    36    36
browser |    36  100.0%         13     +   5031039   5031074              AB351534     1    36    36
browser |    36  100.0%         13     +   5295714   5295749              AB351534     1    36    36
browser |    36  100.0%         13     +   6317865   6317900              AB351534     1    36    36
browser |    36  100.0%         13     +   7326418   7326453              AB351534     1    36    36
browser |    36  100.0%         13     +   7652790   7652825              AB351534     1    36    36
browser |    36  100.0%         13     +   9903774   9903809              AB351534     1    36    36
browser |    36  100.0%         13     -  10828768  10828803              AB351534     1    36    36
browser |    36  100.0%         13     +  10940220  10940255              AB351534     1    36    36
browser |    36  100.0%         13     -  12877406  12877441              AB351534     1    36    36
browser |    36  100.0%         13     +  15274130  15274165              AB351534     1    36    36
browser |    36  100.0%         13     +  19179015  19179050              AB351534     1    36    36
browser |    36  100.0%         13     -  22305255  22305290              AB351534     1    36    36
browser |    36  100.0%         13     +  22413615  22413650              AB351534     1    36    36
browser |    36  100.0%         13     -  23391394  23391429              AB351534     1    36    36
browser |    36  100.0%         13     +  23823929  23823964              AB351534     1    36    36
browser |    36  100.0%         13     -  24413246  24413281              AB351534     1    36    36
browser |    36  100.0%         13     -  32488963  32488998              AB351534     1    36    36
browser |    36  100.0%         13     +  33959541  33959576              AB351534     1    36    36
browser |    36  100.0%         13     -  39863989  39864024              AB351534     1    36    36
browser |    36  100.0%         13     +  50712136  50712171              AB351534     1    36    36
browser |    36  100.0%         13     -  51189099  51189134              AB351534     1    36    36
browser |    36  100.0%         13     -  52207060  52207095              AB351534     1    36    36
browser |    36  100.0%         13     -  54922662  54922697              AB351534     1    36    36
browser |    36  100.0%         13     +  59270403  59270438              AB351534     1    36    36
browser |    36  100.0%         13     -  65032158  65032193              AB351534     1    36    36
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View details of parts of alignment within browser window
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Go to Mouse mRNAs track controls

Data last updated at UCSC: 2020-08-18

Description

The mRNA track shows alignments between mouse mRNAs in GenBank and the genome.

Display Conventions and Configuration

This track follows the display conventions for PSL alignment tracks. In dense display mode, the items that are more darkly shaded indicate matches of better quality.

The description page for this track has a filter that can be used to change the display mode, alter the color, and include/exclude a subset of items within the track. This may be helpful when many items are shown in the track display, especially when only some are relevant to the current task.

To use the filter:

  1. Type a term in one or more of the text boxes to filter the mRNA display. For example, to apply the filter to all mRNAs expressed in a specific organ, type the name of the organ in the tissue box. To view the list of valid terms for each text box, consult the table in the Table Browser that corresponds to the factor on which you wish to filter. For example, the "tissue" table contains all the types of tissues that can be entered into the tissue text box. Multiple terms may be entered at once, separated by a space. Wildcards may also be used in the filter.
  2. If filtering on more than one value, choose the desired combination logic. If "and" is selected, only mRNAs that match all filter criteria will be highlighted. If "or" is selected, mRNAs that match any one of the filter criteria will be highlighted.
  3. Choose the color or display characteristic that should be used to highlight or include/exclude the filtered items. If "exclude" is chosen, the browser will not display mRNAs that match the filter criteria. If "include" is selected, the browser will display only those mRNAs that match the filter criteria.

This track may also be configured to display codon coloring, a feature that allows the user to quickly compare mRNAs against the genomic sequence. For more information about this option, go to the Codon and Base Coloring for Alignment Tracks page. Several types of alignment gap may also be colored; for more information, go to the Alignment Insertion/Deletion Display Options page.

Methods

GenBank mouse mRNAs were aligned against the genome using the blat program. When a single mRNA aligned in multiple places, the alignment having the highest base identity was found. Only alignments having a base identity level within 0.5% of the best and at least 96% base identity with the genomic sequence were kept.

Credits

The mRNA track was produced at UCSC from mRNA sequence data submitted to the international public sequence databases by scientists worldwide.

References

Benson DA, Cavanaugh M, Clark K, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW. GenBank. Nucleic Acids Res. 2013 Jan;41(Database issue):D36-42. PMID: 23193287; PMC: PMC3531190

Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL. GenBank: update. Nucleic Acids Res. 2004 Jan 1;32(Database issue):D23-6. PMID: 14681350; PMC: PMC308779

Kent WJ. BLAT - the BLAST-like alignment tool. Genome Res. 2002 Apr;12(4):656-64. PMID: 11932250; PMC: PMC187518