AB352113
 

Information on mRNA AB352113

Description: Mus musculus non-coding RNA, oocyte_piRNA2929, 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: AB352113
Position: chrX:15589988-15590011

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 |    24  100.0%          X     -  15589988  15590011              AB352113     1    24    24
browser |    24  100.0%          1     -   3684191   3684214              AB352113     1    24    24
browser |    24  100.0%          1     +   4887162   4887185              AB352113     1    24    24
browser |    24  100.0%          1     -   5579990   5580013              AB352113     1    24    24
browser |    24  100.0%          1     -   7065287   7065310              AB352113     1    24    24
browser |    24  100.0%          1     +   7148852   7148875              AB352113     1    24    24
browser |    24  100.0%          1     +   7351158   7351181              AB352113     1    24    24
browser |    24  100.0%          1     +   7523443   7523466              AB352113     1    24    24
browser |    24  100.0%          1     -   7676754   7676777              AB352113     1    24    24
browser |    24  100.0%          1     -   7909268   7909291              AB352113     1    24    24
browser |    24  100.0%          1     +   8208360   8208383              AB352113     1    24    24
browser |    24  100.0%          1     -  11621594  11621617              AB352113     1    24    24
browser |    24  100.0%          1     -  11778013  11778036              AB352113     1    24    24
browser |    24  100.0%          1     -  12552615  12552638              AB352113     1    24    24
browser |    24  100.0%          1     +  12598823  12598846              AB352113     1    24    24
browser |    24  100.0%          1     -  13524162  13524185              AB352113     1    24    24
browser |    24  100.0%          1     -  14348099  14348122              AB352113     1    24    24
browser |    24  100.0%          1     -  15282681  15282704              AB352113     1    24    24
browser |    24  100.0%          1     -  15776973  15776996              AB352113     1    24    24
browser |    24  100.0%          1     -  16972942  16972965              AB352113     1    24    24
browser |    24  100.0%          1     -  18227679  18227702              AB352113     1    24    24
browser |    24  100.0%          1     +  20196900  20196923              AB352113     1    24    24
browser |    24  100.0%          1     +  24501986  24502009              AB352113     1    24    24
browser |    24  100.0%          1     +  30422686  30422709              AB352113     1    24    24
browser |    24  100.0%          1     +  30933214  30933237              AB352113     1    24    24
browser |    24  100.0%          1     +  31379010  31379033              AB352113     1    24    24
browser |    24  100.0%          1     -  31582246  31582269              AB352113     1    24    24
browser |    24  100.0%          1     +  32444921  32444944              AB352113     1    24    24
browser |    24  100.0%          1     -  33105067  33105090              AB352113     1    24    24
browser |    24  100.0%          1     +  45483094  45483117              AB352113     1    24    24
browser |    24  100.0%          1     +  47173374  47173397              AB352113     1    24    24
browser |    24  100.0%          1     +  49911657  49911680              AB352113     1    24    24
browser |    24  100.0%          1     +  52438792  52438815              AB352113     1    24    24
browser |    24  100.0%          1     -  84315070  84315093              AB352113     1    24    24
browser |    24  100.0%          1     +  85137010  85137033              AB352113     1    24    24
browser |    24  100.0%          1     +  85414443  85414466              AB352113     1    24    24
browser |    24  100.0%          1     +  87545415  87545438              AB352113     1    24    24
browser |    24  100.0%          1     +  91277330  91277353              AB352113     1    24    24
browser |    24  100.0%          1     +  92280466  92280489              AB352113     1    24    24
browser |    24  100.0%          1     +  97029200  97029223              AB352113     1    24    24
browser |    24  100.0%          1     -  97107549  97107572              AB352113     1    24    24
browser |    24  100.0%          1     +  99027944  99027967              AB352113     1    24    24
browser |    24  100.0%          1     +  99083586  99083609              AB352113     1    24    24
browser |    24  100.0%          1     + 101417700 101417723              AB352113     1    24    24
browser |    24  100.0%          1     - 101917271 101917294              AB352113     1    24    24
browser |    24  100.0%          1     - 102123519 102123542              AB352113     1    24    24
browser |    24  100.0%          1     - 105802674 105802697              AB352113     1    24    24
browser |    24  100.0%          1     - 107471703 107471726              AB352113     1    24    24
browser |    24  100.0%          1     - 108940766 108940789              AB352113     1    24    24
browser |    24  100.0%          1     - 109471227 109471250              AB352113     1    24    24
browser |    24  100.0%          1     + 110575509 110575532              AB352113     1    24    24
browser |    24  100.0%          1     + 111594041 111594064              AB352113     1    24    24
browser |    24  100.0%          1     + 113667265 113667288              AB352113     1    24    24
browser |    24  100.0%          1     + 120034355 120034378              AB352113     1    24    24
browser |    24  100.0%          1     - 132573494 132573517              AB352113     1    24    24
browser |    24  100.0%          1     + 133910609 133910632              AB352113     1    24    24
browser |    24  100.0%          1     - 135170850 135170873              AB352113     1    24    24
browser |    24  100.0%          1     - 141680477 141680500              AB352113     1    24    24
browser |    24  100.0%          1     + 145457603 145457626              AB352113     1    24    24
browser |    24  100.0%          1     - 148637206 148637229              AB352113     1    24    24
browser |    24  100.0%          1     + 149686793 149686816              AB352113     1    24    24
browser |    24  100.0%          1     - 149867260 149867283              AB352113     1    24    24
browser |    24  100.0%          1     - 151619876 151619899              AB352113     1    24    24
browser |    24  100.0%          1     - 158970742 158970765              AB352113     1    24    24
browser |    24  100.0%          1     + 167385347 167385370              AB352113     1    24    24
browser |    24  100.0%          1     + 177414639 177414662              AB352113     1    24    24
browser |    24  100.0%          1     - 178300385 178300408              AB352113     1    24    24
browser |    24  100.0%          1     + 185250668 185250691              AB352113     1    24    24
browser |    24  100.0%          1     + 190879460 190879483              AB352113     1    24    24
browser |    24  100.0%          1     + 191386286 191386309              AB352113     1    24    24
browser |    24  100.0%         10     +   5525276   5525299              AB352113     1    24    24
browser |    24  100.0%         10     -   6424643   6424666              AB352113     1    24    24
browser |    24  100.0%         10     -   7060129   7060152              AB352113     1    24    24
browser |    24  100.0%         10     -   9440812   9440835              AB352113     1    24    24
browser |    24  100.0%         10     +  10354599  10354622              AB352113     1    24    24
browser |    24  100.0%         10     -  12010377  12010400              AB352113     1    24    24
browser |    24  100.0%         10     -  15673411  15673434              AB352113     1    24    24
browser |    24  100.0%         10     +  17375972  17375995              AB352113     1    24    24
browser |    24  100.0%         10     +  18107098  18107121              AB352113     1    24    24
browser |    24  100.0%         10     -  24047279  24047302              AB352113     1    24    24
browser |    24  100.0%         10     +  26011559  26011582              AB352113     1    24    24
browser |    24  100.0%         10     +  26332028  26332051              AB352113     1    24    24
browser |    24  100.0%         10     +  29673653  29673676              AB352113     1    24    24
browser |    24  100.0%         10     +  37806670  37806693              AB352113     1    24    24
browser |    24  100.0%         10     -  38776923  38776946              AB352113     1    24    24
browser |    24  100.0%         10     +  40061716  40061739              AB352113     1    24    24
browser |    24  100.0%         10     +  40078736  40078759              AB352113     1    24    24
browser |    24  100.0%         10     -  41062336  41062359              AB352113     1    24    24
browser |    24  100.0%         10     -  45858304  45858327              AB352113     1    24    24
browser |    24  100.0%         10     +  46477441  46477464              AB352113     1    24    24
browser |    24  100.0%         10     -  46861602  46861625              AB352113     1    24    24
browser |    24  100.0%         10     +  48821448  48821471              AB352113     1    24    24
browser |    24  100.0%         10     -  52513655  52513678              AB352113     1    24    24
browser |    24  100.0%         10     -  61350763  61350786              AB352113     1    24    24
browser |    24  100.0%         10     -  62473630  62473653              AB352113     1    24    24
browser |    24  100.0%         10     -  62568478  62568501              AB352113     1    24    24
browser |    24  100.0%         10     +  65312212  65312235              AB352113     1    24    24
browser |    24  100.0%         10     -  65442502  65442525              AB352113     1    24    24
browser |    24  100.0%         10     -  69807294  69807317              AB352113     1    24    24
browser |    24  100.0%         10     +  71288465  71288488              AB352113     1    24    24
browser |    24  100.0%         10     +  72352234  72352257              AB352113     1    24    24
browser |    24  100.0%         10     +  82353734  82353757              AB352113     1    24    24
browser |    24  100.0%         10     +  85674851  85674874              AB352113     1    24    24
browser |    24  100.0%         10     +  87611533  87611556              AB352113     1    24    24
browser |    24  100.0%         10     -  87909378  87909401              AB352113     1    24    24
browser |    24  100.0%         10     +  95577566  95577589              AB352113     1    24    24
browser |    24  100.0%         10     -  97160199  97160222              AB352113     1    24    24
browser |    24  100.0%         10     -  97566698  97566721              AB352113     1    24    24
browser |    24  100.0%         10     -  97957141  97957164              AB352113     1    24    24
browser |    24  100.0%         10     + 103316885 103316908              AB352113     1    24    24
browser |    24  100.0%         10     - 106069470 106069493              AB352113     1    24    24
browser |    24  100.0%         10     + 108832504 108832527              AB352113     1    24    24
browser |    24  100.0%         10     + 110612758 110612781              AB352113     1    24    24
browser |    24  100.0%         10     + 112339425 112339448              AB352113     1    24    24
browser |    24  100.0%         10     + 113461748 113461771              AB352113     1    24    24
browser |    24  100.0%         10     + 116598642 116598665              AB352113     1    24    24
browser |    24  100.0%         10     + 124749704 124749727              AB352113     1    24    24
browser |    24  100.0%         10     - 126296537 126296560              AB352113     1    24    24
browser |    22  100.0%         10     + 126622010 126622031              AB352113     3    24    24
browser |    24  100.0%         10     + 128647135 128647158              AB352113     1    24    24
browser |    24  100.0%         10     - 128691346 128691369              AB352113     1    24    24
browser |    24  100.0%         10     + 129826615 129826638              AB352113     1    24    24
browser |    24  100.0%         11     +   7342155   7342178              AB352113     1    24    24
browser |    24  100.0%         11     +   7534693   7534716              AB352113     1    24    24
browser |    24  100.0%         11     -  10341251  10341274              AB352113     1    24    24
browser |    24  100.0%         11     -  21542276  21542299              AB352113     1    24    24
browser |    24  100.0%         11     -  22519581  22519604              AB352113     1    24    24
browser |    24  100.0%         11     +  23035896  23035919              AB352113     1    24    24
browser |    24  100.0%         11     +  23549373  23549396              AB352113     1    24    24
browser |    24  100.0%         11     +  24561872  24561895              AB352113     1    24    24
browser |    24  100.0%         11     +  33414849  33414872              AB352113     1    24    24
browser |    24  100.0%         11     +  40010912  40010935              AB352113     1    24    24
browser |    24  100.0%         11     -  40161963  40161986              AB352113     1    24    24
browser |    24  100.0%         11     +  45541686  45541709              AB352113     1    24    24
browser |    24  100.0%         11     +  46776464  46776487              AB352113     1    24    24
browser |    24  100.0%         11     +  48560700  48560723              AB352113     1    24    24
browser |    24  100.0%         11     -  48795260  48795283              AB352113     1    24    24
browser |    24  100.0%         11     -  58638302  58638325              AB352113     1    24    24
browser |    24  100.0%         11     -  59507400  59507423              AB352113     1    24    24
browser |    24  100.0%         11     +  69081209  69081232              AB352113     1    24    24
browser |    24  100.0%         11     +  71157282  71157305              AB352113     1    24    24
browser |    23  100.0%         11     +  74058478  74058500              AB352113     2    24    24
browser |    24  100.0%         11     +  77146516  77146539              AB352113     1    24    24
browser |    24  100.0%         11     -  77191257  77191280              AB352113     1    24    24
browser |    24  100.0%         11     -  81397902  81397925              AB352113     1    24    24
browser |    23  100.0%         11     -  83576835  83576857              AB352113     1    23    24
browser |    24  100.0%         11     -  83618674  83618697              AB352113     1    24    24
browser |    22  100.0%         11     +  91058491  91058512              AB352113     1    22    24
browser |    24  100.0%         11     -  92716187  92716210              AB352113     1    24    24
browser |    24  100.0%         11     -  95212597  95212620              AB352113     1    24    24
browser |    24  100.0%         11     +  96134828  96134851              AB352113     1    24    24
browser |    23  100.0%         11     + 103559275 103559297              AB352113     1    23    24
browser |    24  100.0%         11     + 110929881 110929904              AB352113     1    24    24
browser |    24  100.0%         11     + 115027050 115027073              AB352113     1    24    24
browser |    24  100.0%         11     + 121096929 121096952              AB352113     1    24    24
browser |    24  100.0%         12     -   3169721   3169744              AB352113     1    24    24
browser |    24  100.0%         12     -   3766772   3766795              AB352113     1    24    24
browser |    24  100.0%         12     +   8959840   8959863              AB352113     1    24    24
browser |    24  100.0%         12     -  10536484  10536507              AB352113     1    24    24
browser |    23  100.0%         12     +  12358920  12358942              AB352113     1    23    24
browser |    24  100.0%         12     +  13113035  13113058              AB352113     1    24    24
browser |    24  100.0%         12     +  20637511  20637534              AB352113     1    24    24
browser |    24  100.0%         12     -  23993469  23993492              AB352113     1    24    24
browser |    24  100.0%         12     -  29450158  29450181              AB352113     1    24    24
browser |    24  100.0%         12     -  30106593  30106616              AB352113     1    24    24
browser |    24  100.0%         12     +  31213237  31213260              AB352113     1    24    24
browser |    24  100.0%         12     +  32268230  32268253              AB352113     1    24    24
browser |    24  100.0%         12     +  32593204  32593227              AB352113     1    24    24
browser |    22  100.0%         12     -  48053102  48053123              AB352113     1    22    24
browser |    24  100.0%         12     +  48194851  48194874              AB352113     1    24    24
browser |    24  100.0%         12     -  48454747  48454770              AB352113     1    24    24
browser |    24  100.0%         12     +  51080553  51080576              AB352113     1    24    24
browser |    24  100.0%         12     +  51082051  51082074              AB352113     1    24    24
browser |    23  100.0%         12     +  54617250  54617272              AB352113     1    23    24
browser |    24  100.0%         12     +  58342162  58342185              AB352113     1    24    24
browser |    24  100.0%         12     +  58706324  58706347              AB352113     1    24    24
browser |    24  100.0%         12     +  64511302  64511325              AB352113     1    24    24
browser |    24  100.0%         12     +  71285233  71285256              AB352113     1    24    24
browser |    24  100.0%         12     -  72318630  72318653              AB352113     1    24    24
browser |    24  100.0%         12     +  81873424  81873447              AB352113     1    24    24
browser |    24  100.0%         12     +  84524161  84524184              AB352113     1    24    24
browser |    24  100.0%         12     +  91563078  91563101              AB352113     1    24    24
browser |    24  100.0%         12     +  96077435  96077458              AB352113     1    24    24
browser |    24  100.0%         12     +  96617126  96617149              AB352113     1    24    24
browser |    24  100.0%         12     - 101214483 101214506              AB352113     1    24    24
browser |    24  100.0%         12     + 101464852 101464875              AB352113     1    24    24
browser |    24  100.0%         12     - 102283518 102283541              AB352113     1    24    24
browser |    23  100.0%         12     + 103438542 103438564              AB352113     1    23    24
browser |    24  100.0%         12     - 105430608 105430631              AB352113     1    24    24
browser |    24  100.0%         12     + 105436283 105436306              AB352113     1    24    24
browser |    24  100.0%         12     + 114131750 114131773              AB352113     1    24    24
browser |    22  100.0%         12     - 114276425 114276446              AB352113     1    22    24
browser |    24  100.0%         12     - 114325736 114325759              AB352113     1    24    24
browser |    24  100.0%         12     - 114951508 114951531              AB352113     1    24    24
browser |    24  100.0%         12     + 118181161 118181184              AB352113     1    24    24
browser |    24  100.0%         13     -   7960233   7960256              AB352113     1    24    24
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browser |    24  100.0%         13     +  11204142  11204165              AB352113     1    24    24
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browser |    24  100.0%         13     -  12799469  12799492              AB352113     1    24    24
browser |    24  100.0%         13     -  13164462  13164485              AB352113     1    24    24
browser |    24  100.0%         13     -  13490216  13490239              AB352113     1    24    24
browser |    24  100.0%         13     +  15449799  15449822              AB352113     1    24    24
browser |    24  100.0%         13     +  16130094  16130117              AB352113     1    24    24
browser |    24  100.0%         13     +  16654305  16654328              AB352113     1    24    24
browser |    24  100.0%         13     +  17345028  17345051              AB352113     1    24    24
browser |    24  100.0%         13     -  17497210  17497233              AB352113     1    24    24
browser |    24  100.0%         13     -  22857508  22857531              AB352113     1    24    24
browser |    24  100.0%         13     +  24957756  24957779              AB352113     1    24    24
browser |    24  100.0%         13     +  25840086  25840109              AB352113     1    24    24
browser |    24  100.0%         13     -  30512394  30512417              AB352113     1    24    24
browser |    24  100.0%         13     -  31272200  31272223              AB352113     1    24    24
browser |    24  100.0%         13     +  46594050  46594073              AB352113     1    24    24
browser |    24  100.0%         13     -  54693892  54693915              AB352113     1    24    24
browser |    24  100.0%         13     -  58733008  58733031              AB352113     1    24    24
browser |    24  100.0%         13     -  60610864  60610887              AB352113     1    24    24
browser |    24  100.0%         13     -  60913379  60913402              AB352113     1    24    24
browser |    24  100.0%         13     -  60973083  60973106              AB352113     1    24    24
browser |    24  100.0%         13     +  64447795  64447818              AB352113     1    24    24
browser |    24  100.0%         13     +  66443704  66443727              AB352113     1    24    24
browser |    24  100.0%         13     +  66593606  66593629              AB352113     1    24    24
browser |    24  100.0%         13     +  66725905  66725928              AB352113     1    24    24
browser |    24  100.0%         13     -  70159292  70159315              AB352113     1    24    24
browser |    22  100.0%         13     -  70390946  70390967              AB352113     1    22    24
browser |    24  100.0%         13     -  70549739  70549762              AB352113     1    24    24
browser |    24  100.0%         13     +  71454889  71454912              AB352113     1    24    24
browser |    24  100.0%         13     +  76750098  76750121              AB352113     1    24    24
browser |    24  100.0%         13     +  87567148  87567171              AB352113     1    24    24
browser |    24  100.0%         13     +  88492995  88493018              AB352113     1    24    24
browser |    24  100.0%         13     -  89350743  89350766              AB352113     1    24    24
browser |    22  100.0%         13     +  89623279  89623300              AB352113     3    24    24
browser |    22  100.0%         13     -  92420131  92420152              AB352113     3    24    24
browser |    22  100.0%         13     -  93243864  93243885              AB352113     1    22    24
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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