AB350505
 

Information on mRNA AB350505

Description: Mus musculus non-coding RNA, oocyte_piRNA1321, 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: AB350505
Position: chr12:56795445-56795469

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     -  56795445  56795469              AB350505     1    25    25
browser |    25  100.0%          1     -   5875379   5875403              AB350505     1    25    25
browser |    25  100.0%          1     +   6242192   6242216              AB350505     1    25    25
browser |    25  100.0%          1     -   6501408   6501432              AB350505     1    25    25
browser |    25  100.0%          1     +   8070213   8070237              AB350505     1    25    25
browser |    25  100.0%          1     +   8232648   8232672              AB350505     1    25    25
browser |    25  100.0%          1     -  10800899  10800923              AB350505     1    25    25
browser |    25  100.0%          1     +  16814726  16814750              AB350505     1    25    25
browser |    25  100.0%          1     +  18590600  18590624              AB350505     1    25    25
browser |    25  100.0%          1     +  19698934  19698958              AB350505     1    25    25
browser |    25  100.0%          1     +  21654305  21654329              AB350505     1    25    25
browser |    25  100.0%          1     +  23344596  23344620              AB350505     1    25    25
browser |    25  100.0%          1     -  26389064  26389088              AB350505     1    25    25
browser |    25  100.0%          1     +  26459341  26459365              AB350505     1    25    25
browser |    25  100.0%          1     -  26510264  26510288              AB350505     1    25    25
browser |    25  100.0%          1     +  27225490  27225514              AB350505     1    25    25
browser |    25  100.0%          1     -  29982618  29982642              AB350505     1    25    25
browser |    25  100.0%          1     +  34389606  34389630              AB350505     1    25    25
browser |    25  100.0%          1     +  34957439  34957463              AB350505     1    25    25
browser |    25  100.0%          1     +  35833820  35833844              AB350505     1    25    25
browser |    25  100.0%          1     -  37318699  37318723              AB350505     1    25    25
browser |    25  100.0%          1     +  38747201  38747225              AB350505     1    25    25
browser |    25  100.0%          1     +  45777676  45777700              AB350505     1    25    25
browser |    25  100.0%          1     -  47263407  47263431              AB350505     1    25    25
browser |    25  100.0%          1     +  48132611  48132635              AB350505     1    25    25
browser |    25  100.0%          1     -  48394306  48394330              AB350505     1    25    25
browser |    25  100.0%          1     -  53169596  53169620              AB350505     1    25    25
browser |    25  100.0%          1     -  58363335  58363359              AB350505     1    25    25
browser |    25  100.0%          1     -  58851645  58851669              AB350505     1    25    25
browser |    25  100.0%          1     -  60764829  60764853              AB350505     1    25    25
browser |    25  100.0%          1     -  74693414  74693438              AB350505     1    25    25
browser |    25  100.0%          1     -  76750813  76750837              AB350505     1    25    25
browser |    25  100.0%          1     -  81542704  81542728              AB350505     1    25    25
browser |    25  100.0%          1     +  82482881  82482905              AB350505     1    25    25
browser |    25  100.0%          1     -  84974422  84974446              AB350505     1    25    25
browser |    25  100.0%          1     -  87062185  87062209              AB350505     1    25    25
browser |    25  100.0%          1     +  87394147  87394171              AB350505     1    25    25
browser |    25  100.0%          1     +  89130103  89130127              AB350505     1    25    25
browser |    25  100.0%          1     -  91399761  91399785              AB350505     1    25    25
browser |    25  100.0%          1     -  93036029  93036053              AB350505     1    25    25
browser |    25  100.0%          1     +  93888190  93888214              AB350505     1    25    25
browser |    25  100.0%          1     +  97108115  97108139              AB350505     1    25    25
browser |    25  100.0%          1     - 101906691 101906715              AB350505     1    25    25
browser |    25  100.0%          1     + 102965658 102965682              AB350505     1    25    25
browser |    25  100.0%          1     - 103133723 103133747              AB350505     1    25    25
browser |    25  100.0%          1     + 103520916 103520940              AB350505     1    25    25
browser |    25  100.0%          1     - 104218113 104218137              AB350505     1    25    25
browser |    25  100.0%          1     - 107967352 107967376              AB350505     1    25    25
browser |    25  100.0%          1     - 108337410 108337434              AB350505     1    25    25
browser |    25  100.0%          1     - 109057225 109057249              AB350505     1    25    25
browser |    25  100.0%          1     + 109547396 109547420              AB350505     1    25    25
browser |    25  100.0%          1     + 110261168 110261192              AB350505     1    25    25
browser |    25  100.0%          1     - 110866158 110866182              AB350505     1    25    25
browser |    25  100.0%          1     - 111182183 111182207              AB350505     1    25    25
browser |    25  100.0%          1     + 111637366 111637390              AB350505     1    25    25
browser |    25  100.0%          1     - 112492848 112492872              AB350505     1    25    25
browser |    25  100.0%          1     + 112862359 112862383              AB350505     1    25    25
browser |    25  100.0%          1     + 112950075 112950099              AB350505     1    25    25
browser |    25  100.0%          1     + 114117384 114117408              AB350505     1    25    25
browser |    25  100.0%          1     - 115813918 115813942              AB350505     1    25    25
browser |    25  100.0%          1     - 116576828 116576852              AB350505     1    25    25
browser |    25  100.0%          1     + 125250859 125250883              AB350505     1    25    25
browser |    25  100.0%          1     + 126356553 126356577              AB350505     1    25    25
browser |    25  100.0%          1     + 126871280 126871304              AB350505     1    25    25
browser |    25  100.0%          1     - 159798153 159798177              AB350505     1    25    25
browser |    25  100.0%          1     - 160644266 160644290              AB350505     1    25    25
browser |    25  100.0%          1     + 162674388 162674412              AB350505     1    25    25
browser |    25  100.0%          1     - 163296883 163296907              AB350505     1    25    25
browser |    25  100.0%          1     - 166591526 166591550              AB350505     1    25    25
browser |    25  100.0%          1     + 169375631 169375655              AB350505     1    25    25
browser |    25  100.0%          1     + 169949622 169949646              AB350505     1    25    25
browser |    25  100.0%          1     - 174870371 174870395              AB350505     1    25    25
browser |    25  100.0%          1     - 176371453 176371477              AB350505     1    25    25
browser |    25  100.0%          1     + 177891857 177891881              AB350505     1    25    25
browser |    25  100.0%          1     + 178007940 178007964              AB350505     1    25    25
browser |    25  100.0%          1     - 181091909 181091933              AB350505     1    25    25
browser |    25  100.0%          1     + 181326225 181326249              AB350505     1    25    25
browser |    25  100.0%          1     + 191844049 191844073              AB350505     1    25    25
browser |    25  100.0%          1     + 195008920 195008944              AB350505     1    25    25
browser |    25  100.0%         10     -   3267156   3267180              AB350505     1    25    25
browser |    25  100.0%         10     -   3551748   3551772              AB350505     1    25    25
browser |    25  100.0%         10     +   9726695   9726719              AB350505     1    25    25
browser |    25  100.0%         10     +  11576290  11576314              AB350505     1    25    25
browser |    25  100.0%         10     -  19415463  19415487              AB350505     1    25    25
browser |    25  100.0%         10     +  21091614  21091638              AB350505     1    25    25
browser |    25  100.0%         10     -  21519036  21519060              AB350505     1    25    25
browser |    25  100.0%         10     -  22559982  22560006              AB350505     1    25    25
browser |    25  100.0%         10     -  23748037  23748061              AB350505     1    25    25
browser |    25  100.0%         10     +  24566644  24566668              AB350505     1    25    25
browser |    25  100.0%         10     -  24978261  24978285              AB350505     1    25    25
browser |    25  100.0%         10     +  25848355  25848379              AB350505     1    25    25
browser |    25  100.0%         10     +  30696253  30696277              AB350505     1    25    25
browser |    25  100.0%         10     +  30970939  30970963              AB350505     1    25    25
browser |    25  100.0%         10     +  31364882  31364906              AB350505     1    25    25
browser |    25  100.0%         10     +  31630026  31630050              AB350505     1    25    25
browser |    25  100.0%         10     +  33766198  33766222              AB350505     1    25    25
browser |    25  100.0%         10     -  34618640  34618664              AB350505     1    25    25
browser |    25  100.0%         10     +  41722804  41722828              AB350505     1    25    25
browser |    25  100.0%         10     -  45431818  45431842              AB350505     1    25    25
browser |    25  100.0%         10     +  50370731  50370755              AB350505     1    25    25
browser |    25  100.0%         10     +  51763175  51763199              AB350505     1    25    25
browser |    25  100.0%         10     +  54468761  54468785              AB350505     1    25    25
browser |    25  100.0%         10     -  55592444  55592468              AB350505     1    25    25
browser |    25  100.0%         10     +  56603112  56603136              AB350505     1    25    25
browser |    25  100.0%         10     +  57020032  57020056              AB350505     1    25    25
browser |    25  100.0%         10     -  65475511  65475535              AB350505     1    25    25
browser |    25  100.0%         10     -  65787415  65787439              AB350505     1    25    25
browser |    25  100.0%         10     -  66559061  66559085              AB350505     1    25    25
browser |    25  100.0%         10     -  78653110  78653134              AB350505     1    25    25
browser |    25  100.0%         10     +  80815843  80815867              AB350505     1    25    25
browser |    25  100.0%         10     +  81809992  81810016              AB350505     1    25    25
browser |    25  100.0%         10     -  83507603  83507627              AB350505     1    25    25
browser |    25  100.0%         10     +  83627625  83627649              AB350505     1    25    25
browser |    25  100.0%         10     +  84584916  84584940              AB350505     1    25    25
browser |    25  100.0%         10     +  85555717  85555741              AB350505     1    25    25
browser |    25  100.0%         10     -  85605109  85605133              AB350505     1    25    25
browser |    25  100.0%         10     +  88493098  88493122              AB350505     1    25    25
browser |    25  100.0%         10     +  88803219  88803243              AB350505     1    25    25
browser |    25  100.0%         10     -  90161287  90161311              AB350505     1    25    25
browser |    25  100.0%         10     -  94199254  94199278              AB350505     1    25    25
browser |    25  100.0%         10     -  95993925  95993949              AB350505     1    25    25
browser |    25  100.0%         10     -  96029211  96029235              AB350505     1    25    25
browser |    25  100.0%         10     -  97157239  97157263              AB350505     1    25    25
browser |    25  100.0%         10     -  98934876  98934900              AB350505     1    25    25
browser |    25  100.0%         10     +  99181253  99181277              AB350505     1    25    25
browser |    25  100.0%         10     + 104397480 104397504              AB350505     1    25    25
browser |    25  100.0%         10     - 104656169 104656193              AB350505     1    25    25
browser |    25  100.0%         10     + 105016827 105016851              AB350505     1    25    25
browser |    25  100.0%         10     - 109151895 109151919              AB350505     1    25    25
browser |    25  100.0%         10     + 111893425 111893449              AB350505     1    25    25
browser |    25  100.0%         10     - 113559426 113559450              AB350505     1    25    25
browser |    25  100.0%         10     - 116442984 116443008              AB350505     1    25    25
browser |    25  100.0%         10     + 117911545 117911569              AB350505     1    25    25
browser |    25  100.0%         10     + 121004342 121004366              AB350505     1    25    25
browser |    25  100.0%         10     - 122202781 122202805              AB350505     1    25    25
browser |    25  100.0%         10     + 124418497 124418521              AB350505     1    25    25
browser |    25  100.0%         10     + 124446003 124446027              AB350505     1    25    25
browser |    25  100.0%         10     - 124517171 124517195              AB350505     1    25    25
browser |    25  100.0%         10     - 129225509 129225533              AB350505     1    25    25
browser |    25  100.0%         10     + 129764693 129764717              AB350505     1    25    25
browser |    25  100.0%         10     - 130396828 130396852              AB350505     1    25    25
browser |    25  100.0%         11     -   6092309   6092333              AB350505     1    25    25
browser |    25  100.0%         11     +   6484950   6484974              AB350505     1    25    25
browser |    25  100.0%         11     -   7526506   7526530              AB350505     1    25    25
browser |    25  100.0%         11     -   9658804   9658828              AB350505     1    25    25
browser |    25  100.0%         11     +  10716595  10716619              AB350505     1    25    25
browser |    25  100.0%         11     -  12458107  12458131              AB350505     1    25    25
browser |    25  100.0%         11     +  12518207  12518231              AB350505     1    25    25
browser |    25  100.0%         11     +  12751875  12751899              AB350505     1    25    25
browser |    25  100.0%         11     -  12904834  12904858              AB350505     1    25    25
browser |    25  100.0%         11     +  15183976  15184000              AB350505     1    25    25
browser |    25  100.0%         11     +  15836979  15837003              AB350505     1    25    25
browser |    25  100.0%         11     +  16181831  16181855              AB350505     1    25    25
browser |    25  100.0%         11     -  18757275  18757299              AB350505     1    25    25
browser |    25  100.0%         11     -  19516994  19517018              AB350505     1    25    25
browser |    25  100.0%         11     -  19739544  19739568              AB350505     1    25    25
browser |    25  100.0%         11     +  20470316  20470340              AB350505     1    25    25
browser |    25  100.0%         11     -  22286071  22286095              AB350505     1    25    25
browser |    25  100.0%         11     +  22532167  22532191              AB350505     1    25    25
browser |    25  100.0%         11     -  23169401  23169425              AB350505     1    25    25
browser |    25  100.0%         11     +  26509909  26509933              AB350505     1    25    25
browser |    25  100.0%         11     -  27901897  27901921              AB350505     1    25    25
browser |    25  100.0%         11     +  28053576  28053600              AB350505     1    25    25
browser |    25  100.0%         11     +  29078949  29078973              AB350505     1    25    25
browser |    25  100.0%         11     +  38377331  38377355              AB350505     1    25    25
browser |    25  100.0%         11     -  39955376  39955400              AB350505     1    25    25
browser |    25  100.0%         11     -  51556671  51556695              AB350505     1    25    25
browser |    25  100.0%         11     -  74111338  74111362              AB350505     1    25    25
browser |    25  100.0%         11     +  74435344  74435368              AB350505     1    25    25
browser |    25  100.0%         11     +  74781507  74781531              AB350505     1    25    25
browser |    25  100.0%         11     -  79124438  79124462              AB350505     1    25    25
browser |    25  100.0%         11     +  81442651  81442675              AB350505     1    25    25
browser |    25  100.0%         11     -  82225642  82225666              AB350505     1    25    25
browser |    25  100.0%         11     -  85177215  85177239              AB350505     1    25    25
browser |    25  100.0%         11     +  86740156  86740180              AB350505     1    25    25
browser |    25  100.0%         11     -  88802607  88802631              AB350505     1    25    25
browser |    25  100.0%         11     -  90721266  90721290              AB350505     1    25    25
browser |    25  100.0%         11     +  90798242  90798266              AB350505     1    25    25
browser |    25  100.0%         11     -  90851819  90851843              AB350505     1    25    25
browser |    25  100.0%         11     +  91996169  91996193              AB350505     1    25    25
browser |    25  100.0%         11     +  98510374  98510398              AB350505     1    25    25
browser |    25  100.0%         11     -  99604349  99604373              AB350505     1    25    25
browser |    25  100.0%         11     + 100559526 100559550              AB350505     1    25    25
browser |    25  100.0%         11     - 105919900 105919924              AB350505     1    25    25
browser |    25  100.0%         11     - 106184335 106184359              AB350505     1    25    25
browser |    25  100.0%         11     - 108290898 108290922              AB350505     1    25    25
browser |    25  100.0%         11     + 108545170 108545194              AB350505     1    25    25
browser |    25  100.0%         11     + 109914378 109914402              AB350505     1    25    25
browser |    25  100.0%         11     + 111079616 111079640              AB350505     1    25    25
browser |    25  100.0%         11     - 111107291 111107315              AB350505     1    25    25
browser |    25  100.0%         11     + 113809306 113809330              AB350505     1    25    25
browser |    25  100.0%         11     - 115646544 115646568              AB350505     1    25    25
browser |    25  100.0%         11     + 116284662 116284686              AB350505     1    25    25
browser |    25  100.0%         11     + 116682672 116682696              AB350505     1    25    25
browser |    25  100.0%         11     + 117394958 117394982              AB350505     1    25    25
browser |    25  100.0%         11     + 120218266 120218290              AB350505     1    25    25
browser |    25  100.0%         11     + 120964829 120964853              AB350505     1    25    25
browser |    25  100.0%         12     +   3058651   3058675              AB350505     1    25    25
browser |    25  100.0%         12     +   3112424   3112448              AB350505     1    25    25
browser |    25  100.0%         12     -   3381626   3381650              AB350505     1    25    25
browser |    25  100.0%         12     +   6572822   6572846              AB350505     1    25    25
browser |    25  100.0%         12     +   8457586   8457610              AB350505     1    25    25
browser |    25  100.0%         12     -  11154474  11154498              AB350505     1    25    25
browser |    25  100.0%         12     +  17178500  17178524              AB350505     1    25    25
browser |    25  100.0%         12     -  19309059  19309083              AB350505     1    25    25
browser |    25  100.0%         12     +  25644260  25644284              AB350505     1    25    25
browser |    25  100.0%         12     -  31408969  31408993              AB350505     1    25    25
browser |    25  100.0%         12     +  32081531  32081555              AB350505     1    25    25
browser |    25  100.0%         12     +  32649731  32649755              AB350505     1    25    25
browser |    25  100.0%         12     +  32955609  32955633              AB350505     1    25    25
browser |    25  100.0%         12     +  40458372  40458396              AB350505     1    25    25
browser |    25  100.0%         12     +  41419788  41419812              AB350505     1    25    25
browser |    25  100.0%         12     +  44831520  44831544              AB350505     1    25    25
browser |    25  100.0%         12     -  49267944  49267968              AB350505     1    25    25
browser |    25  100.0%         12     -  52777703  52777727              AB350505     1    25    25
browser |    25  100.0%         12     -  61336725  61336749              AB350505     1    25    25
browser |    25  100.0%         12     -  65074764  65074788              AB350505     1    25    25
browser |    25  100.0%         12     -  65848821  65848845              AB350505     1    25    25
browser |    25  100.0%         12     -  66454621  66454645              AB350505     1    25    25
browser |    25  100.0%         12     -  68669374  68669398              AB350505     1    25    25
browser |    25  100.0%         12     +  68796310  68796334              AB350505     1    25    25
browser |    25  100.0%         12     -  70708753  70708777              AB350505     1    25    25
browser |    25  100.0%         12     -  73358610  73358634              AB350505     1    25    25
browser |    25  100.0%         12     +  76794899  76794923              AB350505     1    25    25
browser |    25  100.0%         12     -  79609432  79609456              AB350505     1    25    25
browser |    25  100.0%         12     +  80470349  80470373              AB350505     1    25    25
browser |    25  100.0%         12     +  81633779  81633803              AB350505     1    25    25
browser |    25  100.0%         12     -  82508681  82508705              AB350505     1    25    25
browser |    25  100.0%         12     -  85448618  85448642              AB350505     1    25    25
browser |    25  100.0%         12     +  88482561  88482585              AB350505     1    25    25
browser |    25  100.0%         12     +  93482609  93482633              AB350505     1    25    25
browser |    25  100.0%         12     -  94004102  94004126              AB350505     1    25    25
browser |    25  100.0%         12     -  94236127  94236151              AB350505     1    25    25
browser |    25  100.0%         12     -  96197775  96197799              AB350505     1    25    25
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View details of parts of alignment within browser window
.
View table schema

Go to Mouse mRNAs track controls

Data last updated at UCSC: 2020-08-18

Description

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

Display Conventions and Configuration

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

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

To use the filter:

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

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

Methods

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

Credits

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

References

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

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

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