AB352614
 

Information on mRNA AB352614

Description: Mus musculus non-coding RNA, oocyte_piRNA3430, 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: AB352614
Position: chr12:56794935-56794958

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%         12     -  56794935  56794958              AB352614     1    24    24
browser |    24  100.0%          1     -   3101890   3101913              AB352614     1    24    24
browser |    24  100.0%          1     -   4202696   4202719              AB352614     1    24    24
browser |    24  100.0%          1     -   5874868   5874891              AB352614     1    24    24
browser |    24  100.0%          1     -   5881626   5881649              AB352614     1    24    24
browser |    24  100.0%          1     +   6238354   6238377              AB352614     1    24    24
browser |    24  100.0%          1     +   6242705   6242728              AB352614     1    24    24
browser |    24  100.0%          1     -   6500898   6500921              AB352614     1    24    24
browser |    24  100.0%          1     -   6507666   6507689              AB352614     1    24    24
browser |    24  100.0%          1     -   7938049   7938072              AB352614     1    24    24
browser |    24  100.0%          1     +   8063951   8063974              AB352614     1    24    24
browser |    24  100.0%          1     +   8070719   8070742              AB352614     1    24    24
browser |    24  100.0%          1     +   8226450   8226473              AB352614     1    24    24
browser |    24  100.0%          1     +   8860249   8860272              AB352614     1    24    24
browser |    24  100.0%          1     -  10800394  10800417              AB352614     1    24    24
browser |    24  100.0%          1     -  10807180  10807203              AB352614     1    24    24
browser |    24  100.0%          1     -  11957647  11957670              AB352614     1    24    24
browser |    24  100.0%          1     -  11961858  11961881              AB352614     1    24    24
browser |    24  100.0%          1     -  12017155  12017178              AB352614     1    24    24
browser |    24  100.0%          1     +  14030957  14030980              AB352614     1    24    24
browser |    24  100.0%          1     +  14068819  14068842              AB352614     1    24    24
browser |    24  100.0%          1     -  16276037  16276060              AB352614     1    24    24
browser |    24  100.0%          1     -  16772784  16772807              AB352614     1    24    24
browser |    24  100.0%          1     +  16808518  16808541              AB352614     1    24    24
browser |    24  100.0%          1     +  16815232  16815255              AB352614     1    24    24
browser |    24  100.0%          1     -  16918669  16918692              AB352614     1    24    24
browser |    24  100.0%          1     +  18587084  18587107              AB352614     1    24    24
browser |    24  100.0%          1     +  18591105  18591128              AB352614     1    24    24
browser |    24  100.0%          1     +  19692600  19692623              AB352614     1    24    24
browser |    24  100.0%          1     +  19699445  19699468              AB352614     1    24    24
browser |    24  100.0%          1     +  21654812  21654835              AB352614     1    24    24
browser |    24  100.0%          1     +  24107724  24107747              AB352614     1    24    24
browser |    24  100.0%          1     -  26388559  26388582              AB352614     1    24    24
browser |    24  100.0%          1     -  81542194  81542217              AB352614     1    24    24
browser |    24  100.0%          1     -  81548921  81548944              AB352614     1    24    24
browser |    24  100.0%          1     +  82478780  82478803              AB352614     1    24    24
browser |    24  100.0%          1     +  82483393  82483416              AB352614     1    24    24
browser |    24  100.0%          1     -  84973912  84973935              AB352614     1    24    24
browser |    24  100.0%          1     -  84978242  84978265              AB352614     1    24    24
browser |    24  100.0%          1     -  87761002  87761025              AB352614     1    24    24
browser |    24  100.0%          1     +  88905157  88905180              AB352614     1    24    24
browser |    24  100.0%          1     +  89126816  89126839              AB352614     1    24    24
browser |    24  100.0%          1     +  89130614  89130637              AB352614     1    24    24
browser |    24  100.0%          1     -  91399251  91399274              AB352614     1    24    24
browser |    24  100.0%          1     -  91405992  91406015              AB352614     1    24    24
browser |    24  100.0%          1     +  93884325  93884348              AB352614     1    24    24
browser |    24  100.0%          1     +  93888701  93888724              AB352614     1    24    24
browser |    24  100.0%          1     +  97108621  97108644              AB352614     1    24    24
browser |    24  100.0%          1     -  98528399  98528422              AB352614     1    24    24
browser |    24  100.0%          1     - 101454303 101454326              AB352614     1    24    24
browser |    24  100.0%          1     - 101906186 101906209              AB352614     1    24    24
browser |    24  100.0%          1     - 101912978 101913001              AB352614     1    24    24
browser |    24  100.0%          1     + 102959411 102959434              AB352614     1    24    24
browser |    24  100.0%          1     + 102966169 102966192              AB352614     1    24    24
browser |    24  100.0%          1     - 103133219 103133242              AB352614     1    24    24
browser |    24  100.0%          1     - 103139972 103139995              AB352614     1    24    24
browser |    24  100.0%          1     + 103516459 103516482              AB352614     1    24    24
browser |    24  100.0%          1     + 103521428 103521451              AB352614     1    24    24
browser |    24  100.0%          1     - 104217608 104217631              AB352614     1    24    24
browser |    24  100.0%          1     - 104222497 104222520              AB352614     1    24    24
browser |    24  100.0%          1     + 105865905 105865928              AB352614     1    24    24
browser |    24  100.0%          1     - 107966841 107966864              AB352614     1    24    24
browser |    24  100.0%          1     + 108887883 108887906              AB352614     1    24    24
browser |    24  100.0%          1     + 109541143 109541166              AB352614     1    24    24
browser |    24  100.0%          1     + 109547901 109547924              AB352614     1    24    24
browser |    24  100.0%          1     - 159804378 159804401              AB352614     1    24    24
browser |    24  100.0%          1     - 160643761 160643784              AB352614     1    24    24
browser |    24  100.0%          1     - 160648553 160648576              AB352614     1    24    24
browser |    24  100.0%          1     - 163520862 163520885              AB352614     1    24    24
browser |    24  100.0%          1     + 166411858 166411881              AB352614     1    24    24
browser |    24  100.0%          1     - 166768007 166768030              AB352614     1    24    24
browser |    24  100.0%          1     + 169370009 169370032              AB352614     1    24    24
browser |    24  100.0%          1     + 169376143 169376166              AB352614     1    24    24
browser |    24  100.0%          1     + 169943387 169943410              AB352614     1    24    24
browser |    24  100.0%          1     + 169950134 169950157              AB352614     1    24    24
browser |    24  100.0%          1     - 174869861 174869884              AB352614     1    24    24
browser |    24  100.0%          1     - 174875809 174875832              AB352614     1    24    24
browser |    24  100.0%          1     - 176370943 176370966              AB352614     1    24    24
browser |    24  100.0%          1     - 176377685 176377708              AB352614     1    24    24
browser |    24  100.0%          1     + 178001700 178001723              AB352614     1    24    24
browser |    24  100.0%          1     + 178008451 178008474              AB352614     1    24    24
browser |    24  100.0%          1     - 179225465 179225488              AB352614     1    24    24
browser |    24  100.0%          1     - 181091399 181091422              AB352614     1    24    24
browser |    24  100.0%          1     - 181098128 181098151              AB352614     1    24    24
browser |    24  100.0%          1     + 181320495 181320518              AB352614     1    24    24
browser |    24  100.0%          1     + 181326731 181326754              AB352614     1    24    24
browser |    24  100.0%          1     + 182047299 182047322              AB352614     1    24    24
browser |    24  100.0%          1     - 188754607 188754630              AB352614     1    24    24
browser |    24  100.0%          1     + 191839745 191839768              AB352614     1    24    24
browser |    24  100.0%          1     + 194336152 194336175              AB352614     1    24    24
browser |    24  100.0%         10     -   3551238   3551261              AB352614     1    24    24
browser |    24  100.0%         10     -   3557983   3558006              AB352614     1    24    24
browser |    24  100.0%         10     +   6171260   6171283              AB352614     1    24    24
browser |    24  100.0%         10     +  13544878  13544901              AB352614     1    24    24
browser |    24  100.0%         10     +  17900416  17900439              AB352614     1    24    24
browser |    24  100.0%         10     -  19414953  19414976              AB352614     1    24    24
browser |    24  100.0%         10     -  19421712  19421735              AB352614     1    24    24
browser |    24  100.0%         10     +  21087125  21087148              AB352614     1    24    24
browser |    24  100.0%         10     +  21092125  21092148              AB352614     1    24    24
browser |    24  100.0%         10     -  21518526  21518549              AB352614     1    24    24
browser |    24  100.0%         10     -  21525377  21525400              AB352614     1    24    24
browser |    24  100.0%         10     -  22399436  22399459              AB352614     1    24    24
browser |    24  100.0%         10     -  22406344  22406367              AB352614     1    24    24
browser |    24  100.0%         10     -  22559472  22559495              AB352614     1    24    24
browser |    24  100.0%         10     -  22566400  22566423              AB352614     1    24    24
browser |    24  100.0%         10     -  23744292  23744315              AB352614     1    24    24
browser |    24  100.0%         10     +  24562349  24562372              AB352614     1    24    24
browser |    24  100.0%         10     +  24567150  24567173              AB352614     1    24    24
browser |    24  100.0%         10     -  24977757  24977780              AB352614     1    24    24
browser |    24  100.0%         10     -  24982368  24982391              AB352614     1    24    24
browser |    24  100.0%         10     +  25844339  25844362              AB352614     1    24    24
browser |    24  100.0%         10     +  25848867  25848890              AB352614     1    24    24
browser |    24  100.0%         10     -  26610381  26610404              AB352614     1    24    24
browser |    24  100.0%         10     -  30013523  30013546              AB352614     1    24    24
browser |    24  100.0%         10     +  30690010  30690033              AB352614     1    24    24
browser |    24  100.0%         10     +  30696762  30696785              AB352614     1    24    24
browser |    24  100.0%         10     +  30964585  30964608              AB352614     1    24    24
browser |    24  100.0%         10     +  30971445  30971468              AB352614     1    24    24
browser |    24  100.0%         10     +  31358647  31358670              AB352614     1    24    24
browser |    24  100.0%         10     +  31365394  31365417              AB352614     1    24    24
browser |    24  100.0%         10     +  31626138  31626161              AB352614     1    24    24
browser |    24  100.0%         10     -  34615304  34615327              AB352614     1    24    24
browser |    24  100.0%         10     +  80811892  80811915              AB352614     1    24    24
browser |    24  100.0%         10     +  80816355  80816378              AB352614     1    24    24
browser |    24  100.0%         10     -  81506696  81506719              AB352614     1    24    24
browser |    24  100.0%         10     -  81513560  81513583              AB352614     1    24    24
browser |    24  100.0%         10     -  81665824  81665847              AB352614     1    24    24
browser |    24  100.0%         10     -  81672688  81672711              AB352614     1    24    24
browser |    24  100.0%         10     +  81803746  81803769              AB352614     1    24    24
browser |    24  100.0%         10     +  81810504  81810527              AB352614     1    24    24
browser |    24  100.0%         10     -  82407567  82407590              AB352614     1    24    24
browser |    24  100.0%         10     -  82410979  82411002              AB352614     1    24    24
browser |    24  100.0%         10     -  83302051  83302074              AB352614     1    24    24
browser |    24  100.0%         10     -  83308848  83308871              AB352614     1    24    24
browser |    24  100.0%         10     -  83507093  83507116              AB352614     1    24    24
browser |    24  100.0%         10     -  83513818  83513841              AB352614     1    24    24
browser |    24  100.0%         10     +  83623360  83623383              AB352614     1    24    24
browser |    24  100.0%         10     +  83628131  83628154              AB352614     1    24    24
browser |    24  100.0%         10     +  84580474  84580497              AB352614     1    24    24
browser |    24  100.0%         10     +  84585422  84585445              AB352614     1    24    24
browser |    24  100.0%         10     +  85556223  85556246              AB352614     1    24    24
browser |    24  100.0%         10     -  90160782  90160805              AB352614     1    24    24
browser |    24  100.0%         10     -  90165550  90165573              AB352614     1    24    24
browser |    24  100.0%         10     -  92606833  92606856              AB352614     1    24    24
browser |    24  100.0%         10     -  94198744  94198767              AB352614     1    24    24
browser |    24  100.0%         10     -  94205069  94205092              AB352614     1    24    24
browser |    24  100.0%         10     -  94372436  94372459              AB352614     1    24    24
browser |    24  100.0%         10     +  95210019  95210042              AB352614     1    24    24
browser |    24  100.0%         10     +  97377678  97377701              AB352614     1    24    24
browser |    24  100.0%         10     + 104391156 104391179              AB352614     1    24    24
browser |    24  100.0%         10     + 104397986 104398009              AB352614     1    24    24
browser |    24  100.0%         10     + 104671478 104671501              AB352614     1    24    24
browser |    24  100.0%         10     + 104678213 104678236              AB352614     1    24    24
browser |    24  100.0%         10     + 105013002 105013025              AB352614     1    24    24
browser |    24  100.0%         11     +   3998970   3998993              AB352614     1    24    24
browser |    24  100.0%         11     +   5312634   5312657              AB352614     1    24    24
browser |    24  100.0%         11     +   5485496   5485519              AB352614     1    24    24
browser |    24  100.0%         11     -   7987606   7987629              AB352614     1    24    24
browser |    24  100.0%         11     -   9035112   9035135              AB352614     1    24    24
browser |    24  100.0%         11     -   9037352   9037375              AB352614     1    24    24
browser |    24  100.0%         11     -   9658294   9658317              AB352614     1    24    24
browser |    24  100.0%         11     -   9665025   9665048              AB352614     1    24    24
browser |    24  100.0%         11     +  10717101  10717124              AB352614     1    24    24
browser |    24  100.0%         11     -  12457602  12457625              AB352614     1    24    24
browser |    24  100.0%         11     -  12462557  12462580              AB352614     1    24    24
browser |    24  100.0%         11     +  12511929  12511952              AB352614     1    24    24
browser |    24  100.0%         11     +  12518712  12518735              AB352614     1    24    24
browser |    24  100.0%         11     -  12904329  12904352              AB352614     1    24    24
browser |    24  100.0%         11     -  12909166  12909189              AB352614     1    24    24
browser |    24  100.0%         11     +  13113129  13113152              AB352614     1    24    24
browser |    24  100.0%         11     -  14391935  14391958              AB352614     1    24    24
browser |    24  100.0%         11     +  15177709  15177732              AB352614     1    24    24
browser |    24  100.0%         11     +  15184487  15184510              AB352614     1    24    24
browser |    24  100.0%         11     +  15833698  15833721              AB352614     1    24    24
browser |    24  100.0%         11     +  15837485  15837508              AB352614     1    24    24
browser |    24  100.0%         11     -  16154550  16154573              AB352614     1    24    24
browser |    24  100.0%         11     -  16156875  16156898              AB352614     1    24    24
browser |    24  100.0%         11     -  17102926  17102949              AB352614     1    24    24
browser |    24  100.0%         11     -  19516490  19516513              AB352614     1    24    24
browser |    24  100.0%         11     -  19520536  19520559              AB352614     1    24    24
browser |    24  100.0%         11     +  20131604  20131627              AB352614     1    24    24
browser |    24  100.0%         11     -  22285566  22285589              AB352614     1    24    24
browser |    24  100.0%         11     +  22527721  22527744              AB352614     1    24    24
browser |    24  100.0%         11     +  22532672  22532695              AB352614     1    24    24
browser |    24  100.0%         11     +  26505466  26505489              AB352614     1    24    24
browser |    24  100.0%         11     +  26510421  26510444              AB352614     1    24    24
browser |    24  100.0%         11     +  80906528  80906551              AB352614     1    24    24
browser |    24  100.0%         11     +  81436327  81436350              AB352614     1    24    24
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browser |    24  100.0%         11     -  82225138  82225161              AB352614     1    24    24
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browser |    24  100.0%         11     -  90201521  90201544              AB352614     1    24    24
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browser |    24  100.0%         11     -  90725717  90725740              AB352614     1    24    24
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browser |    24  100.0%         11     -  90851309  90851332              AB352614     1    24    24
browser |    24  100.0%         11     -  90858056  90858079              AB352614     1    24    24
browser |    24  100.0%         11     +  91989888  91989911              AB352614     1    24    24
browser |    24  100.0%         11     +  91996681  91996704              AB352614     1    24    24
browser |    24  100.0%         11     -  94018655  94018678              AB352614     1    24    24
browser |    24  100.0%         11     +  98504124  98504147              AB352614     1    24    24
browser |    24  100.0%         11     +  98510885  98510908              AB352614     1    24    24
browser |    24  100.0%         11     -  99603839  99603862              AB352614     1    24    24
browser |    24  100.0%         11     -  99607997  99608020              AB352614     1    24    24
browser |    24  100.0%         11     + 100553741 100553764              AB352614     1    24    24
browser |    24  100.0%         11     + 100560032 100560055              AB352614     1    24    24
browser |    24  100.0%         11     - 104750743 104750766              AB352614     1    24    24
browser |    24  100.0%         11     - 104753112 104753135              AB352614     1    24    24
browser |    24  100.0%         11     - 106183831 106183854              AB352614     1    24    24
browser |    24  100.0%         11     + 108540746 108540769              AB352614     1    24    24
browser |    24  100.0%         12     +   3052359   3052382              AB352614     1    24    24
browser |    24  100.0%         12     +   3059162   3059185              AB352614     1    24    24
browser |    24  100.0%         12     -   3381116   3381139              AB352614     1    24    24
browser |    24  100.0%         12     -   3387894   3387917              AB352614     1    24    24
browser |    24  100.0%         12     -   6329646   6329669              AB352614     1    24    24
browser |    24  100.0%         12     +   6853043   6853066              AB352614     1    24    24
browser |    24  100.0%         12     +   6859810   6859833              AB352614     1    24    24
browser |    24  100.0%         12     +   8453196   8453219              AB352614     1    24    24
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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