AB351219
 

Information on mRNA AB351219

Description: Mus musculus non-coding RNA, oocyte_piRNA2035, 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: AB351219
Position: chr12:56795394-56795415

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 |    22  100.0%         12     -  56795394  56795415              AB351219     1    22    22
browser |    22  100.0%          1     -   4628088   4628109              AB351219     1    22    22
browser |    22  100.0%          1     -   5875328   5875349              AB351219     1    22    22
browser |    22  100.0%          1     +   6242246   6242267              AB351219     1    22    22
browser |    22  100.0%          1     -   6501357   6501378              AB351219     1    22    22
browser |    22  100.0%          1     +   8070267   8070288              AB351219     1    22    22
browser |    22  100.0%          1     +   8232702   8232723              AB351219     1    22    22
browser |    22  100.0%          1     -   8729321   8729342              AB351219     1    22    22
browser |    22  100.0%          1     -  10800848  10800869              AB351219     1    22    22
browser |    22  100.0%          1     -  11958106  11958127              AB351219     1    22    22
browser |    22  100.0%          1     -  12017606  12017627              AB351219     1    22    22
browser |    22  100.0%          1     +  14032925  14032946              AB351219     1    22    22
browser |    22  100.0%          1     +  16814780  16814801              AB351219     1    22    22
browser |    22  100.0%          1     +  18590654  18590675              AB351219     1    22    22
browser |    22  100.0%          1     +  19698988  19699009              AB351219     1    22    22
browser |    22  100.0%          1     +  21654359  21654380              AB351219     1    22    22
browser |    22  100.0%          1     +  23344650  23344671              AB351219     1    22    22
browser |    22  100.0%          1     -  26389013  26389034              AB351219     1    22    22
browser |    22  100.0%          1     +  26459395  26459416              AB351219     1    22    22
browser |    22  100.0%          1     -  26510213  26510234              AB351219     1    22    22
browser |    22  100.0%          1     +  27177373  27177394              AB351219     1    22    22
browser |    22  100.0%          1     +  27225544  27225565              AB351219     1    22    22
browser |    22  100.0%          1     -  29982567  29982588              AB351219     1    22    22
browser |    22  100.0%          1     +  31045921  31045942              AB351219     1    22    22
browser |    22  100.0%          1     +  34389660  34389681              AB351219     1    22    22
browser |    22  100.0%          1     +  34957493  34957514              AB351219     1    22    22
browser |    22  100.0%          1     +  35833874  35833895              AB351219     1    22    22
browser |    22  100.0%          1     -  37318648  37318669              AB351219     1    22    22
browser |    22  100.0%          1     -  47263356  47263377              AB351219     1    22    22
browser |    22  100.0%          1     -  48394255  48394276              AB351219     1    22    22
browser |    22  100.0%          1     -  48841787  48841808              AB351219     1    22    22
browser |    22  100.0%          1     -  53169545  53169566              AB351219     1    22    22
browser |    22  100.0%          1     -  58363284  58363305              AB351219     1    22    22
browser |    22  100.0%          1     -  81542653  81542674              AB351219     1    22    22
browser |    22  100.0%          1     +  82482935  82482956              AB351219     1    22    22
browser |    22  100.0%          1     -  84974371  84974392              AB351219     1    22    22
browser |    22  100.0%          1     -  87062134  87062155              AB351219     1    22    22
browser |    22  100.0%          1     +  87394201  87394222              AB351219     1    22    22
browser |    22  100.0%          1     +  89130157  89130178              AB351219     1    22    22
browser |    22  100.0%          1     -  91399710  91399731              AB351219     1    22    22
browser |    22  100.0%          1     -  93035978  93035999              AB351219     1    22    22
browser |    22  100.0%          1     +  93888244  93888265              AB351219     1    22    22
browser |    22  100.0%          1     -  95963781  95963802              AB351219     1    22    22
browser |    22  100.0%          1     +  97108169  97108190              AB351219     1    22    22
browser |    22  100.0%          1     -  98528851  98528872              AB351219     1    22    22
browser |    22  100.0%          1     - 101906640 101906661              AB351219     1    22    22
browser |    22  100.0%          1     + 102079312 102079333              AB351219     1    22    22
browser |    22  100.0%          1     + 102965712 102965733              AB351219     1    22    22
browser |    22  100.0%          1     - 103133672 103133693              AB351219     1    22    22
browser |    22  100.0%          1     + 103520970 103520991              AB351219     1    22    22
browser |    22  100.0%          1     - 107967301 107967322              AB351219     1    22    22
browser |    22  100.0%          1     - 108337359 108337380              AB351219     1    22    22
browser |    22  100.0%          1     + 108887440 108887461              AB351219     1    22    22
browser |    22  100.0%          1     - 109057174 109057195              AB351219     1    22    22
browser |    22  100.0%          1     + 109547450 109547471              AB351219     1    22    22
browser |    22  100.0%          1     + 110261222 110261243              AB351219     1    22    22
browser |    22  100.0%          1     - 110866107 110866128              AB351219     1    22    22
browser |    22  100.0%          1     - 111182132 111182153              AB351219     1    22    22
browser |    22  100.0%          1     + 111637420 111637441              AB351219     1    22    22
browser |    22  100.0%          1     - 112192845 112192866              AB351219     1    22    22
browser |    22  100.0%          1     - 112492797 112492818              AB351219     1    22    22
browser |    22  100.0%          1     + 112862413 112862434              AB351219     1    22    22
browser |    22  100.0%          1     + 112950129 112950150              AB351219     1    22    22
browser |    22  100.0%          1     + 114117438 114117459              AB351219     1    22    22
browser |    22  100.0%          1     + 125250913 125250934              AB351219     1    22    22
browser |    22  100.0%          1     - 159798102 159798123              AB351219     1    22    22
browser |    22  100.0%          1     - 160644215 160644236              AB351219     1    22    22
browser |    22  100.0%          1     + 162674442 162674463              AB351219     1    22    22
browser |    22  100.0%          1     - 163296832 163296853              AB351219     1    22    22
browser |    22  100.0%          1     - 166591475 166591496              AB351219     1    22    22
browser |    22  100.0%          1     + 169375685 169375706              AB351219     1    22    22
browser |    22  100.0%          1     + 169949676 169949697              AB351219     1    22    22
browser |    22  100.0%          1     + 172096515 172096536              AB351219     1    22    22
browser |    22  100.0%          1     - 174870320 174870341              AB351219     1    22    22
browser |    22  100.0%          1     - 176371402 176371423              AB351219     1    22    22
browser |    22  100.0%          1     + 177891911 177891932              AB351219     1    22    22
browser |    21  100.0%          1     + 178007995 178008015              AB351219     2    22    22
browser |    22  100.0%          1     + 180443180 180443201              AB351219     1    22    22
browser |    22  100.0%          1     + 181326279 181326300              AB351219     1    22    22
browser |    22  100.0%          1     + 191844103 191844124              AB351219     1    22    22
browser |    22  100.0%          1     + 192641749 192641770              AB351219     1    22    22
browser |    22  100.0%          1     + 195008974 195008995              AB351219     1    22    22
browser |    22  100.0%         10     -   3267105   3267126              AB351219     1    22    22
browser |    22  100.0%         10     -   3551697   3551718              AB351219     1    22    22
browser |    22  100.0%         10     +   8481366   8481387              AB351219     1    22    22
browser |    22  100.0%         10     +   9726749   9726770              AB351219     1    22    22
browser |    22  100.0%         10     +  11576344  11576365              AB351219     1    22    22
browser |    22  100.0%         10     -  11777324  11777345              AB351219     1    22    22
browser |    22  100.0%         10     -  19415412  19415433              AB351219     1    22    22
browser |    22  100.0%         10     +  19676476  19676497              AB351219     1    22    22
browser |    22  100.0%         10     +  21091668  21091689              AB351219     1    22    22
browser |    22  100.0%         10     -  21518985  21519006              AB351219     1    22    22
browser |    22  100.0%         10     -  22399888  22399909              AB351219     1    22    22
browser |    22  100.0%         10     -  22559931  22559952              AB351219     1    22    22
browser |    22  100.0%         10     -  23747986  23748007              AB351219     1    22    22
browser |    22  100.0%         10     +  24566698  24566719              AB351219     1    22    22
browser |    22  100.0%         10     -  24978210  24978231              AB351219     1    22    22
browser |    22  100.0%         10     +  25848409  25848430              AB351219     1    22    22
browser |    22  100.0%         10     -  26607610  26607631              AB351219     1    22    22
browser |    22  100.0%         10     +  30696307  30696328              AB351219     1    22    22
browser |    22  100.0%         10     +  30970993  30971014              AB351219     1    22    22
browser |    22  100.0%         10     +  31364936  31364957              AB351219     1    22    22
browser |    22  100.0%         10     +  31630080  31630101              AB351219     1    22    22
browser |    22  100.0%         10     +  32814381  32814402              AB351219     1    22    22
browser |    22  100.0%         10     +  33766252  33766273              AB351219     1    22    22
browser |    22  100.0%         10     -  34618589  34618610              AB351219     1    22    22
browser |    22  100.0%         10     -  37728150  37728171              AB351219     1    22    22
browser |    22  100.0%         10     +  41722858  41722879              AB351219     1    22    22
browser |    22  100.0%         10     -  43646439  43646460              AB351219     1    22    22
browser |    22  100.0%         10     -  45431767  45431788              AB351219     1    22    22
browser |    22  100.0%         10     +  47549895  47549916              AB351219     1    22    22
browser |    22  100.0%         10     -  47909196  47909217              AB351219     1    22    22
browser |    22  100.0%         10     -  48627737  48627758              AB351219     1    22    22
browser |    22  100.0%         10     +  50370785  50370806              AB351219     1    22    22
browser |    22  100.0%         10     +  80815897  80815918              AB351219     1    22    22
browser |    22  100.0%         10     -  81507147  81507168              AB351219     1    22    22
browser |    22  100.0%         10     -  81666275  81666296              AB351219     1    22    22
browser |    22  100.0%         10     +  81810046  81810067              AB351219     1    22    22
browser |    22  100.0%         10     -  83302502  83302523              AB351219     1    22    22
browser |    22  100.0%         10     +  83627679  83627700              AB351219     1    22    22
browser |    22  100.0%         10     +  84584970  84584991              AB351219     1    22    22
browser |    22  100.0%         10     +  85555771  85555792              AB351219     1    22    22
browser |    22  100.0%         10     -  85605058  85605079              AB351219     1    22    22
browser |    22  100.0%         10     +  88493152  88493173              AB351219     1    22    22
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browser |    22  100.0%         10     -  90161236  90161257              AB351219     1    22    22
browser |    22  100.0%         10     -  94199203  94199224              AB351219     1    22    22
browser |    22  100.0%         10     -  95993874  95993895              AB351219     1    22    22
browser |    22  100.0%         10     -  96029160  96029181              AB351219     1    22    22
browser |    22  100.0%         10     -  97157188  97157209              AB351219     1    22    22
browser |    22  100.0%         10     +  99181307  99181328              AB351219     1    22    22
browser |    22  100.0%         10     + 100418843 100418864              AB351219     1    22    22
browser |    22  100.0%         10     + 104397534 104397555              AB351219     1    22    22
browser |    22  100.0%         10     - 104656118 104656139              AB351219     1    22    22
browser |    22  100.0%         10     + 104677755 104677776              AB351219     1    22    22
browser |    22  100.0%         10     + 105016881 105016902              AB351219     1    22    22
browser |    22  100.0%         10     - 105509277 105509298              AB351219     1    22    22
browser |    22  100.0%         10     - 109151844 109151865              AB351219     1    22    22
browser |    22  100.0%         10     + 121004396 121004417              AB351219     1    22    22
browser |    22  100.0%         10     - 122669530 122669551              AB351219     1    22    22
browser |    22  100.0%         10     + 124418551 124418572              AB351219     1    22    22
browser |    22  100.0%         10     + 124446057 124446078              AB351219     1    22    22
browser |    22  100.0%         10     - 124517120 124517141              AB351219     1    22    22
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browser |    22  100.0%         10     - 130396777 130396798              AB351219     1    22    22
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browser |    22  100.0%         11     -   6092258   6092279              AB351219     1    22    22
browser |    22  100.0%         11     +   6485004   6485025              AB351219     1    22    22
browser |    22  100.0%         11     +   6749359   6749380              AB351219     1    22    22
browser |    22  100.0%         11     -   7526455   7526476              AB351219     1    22    22
browser |    22  100.0%         11     -   9658753   9658774              AB351219     1    22    22
browser |    22  100.0%         11     +  10716649  10716670              AB351219     1    22    22
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browser |    22  100.0%         12     -  18325859  18325880              AB351219     1    22    22
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browser |    22  100.0%         12     -  31408918  31408939              AB351219     1    22    22
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browser |    22  100.0%          X     - 113800435 113800456              AB351219     1    22    22
browser |    22  100.0%          X     - 113851917 113851938              AB351219     1    22    22
browser |    22  100.0%          X     + 115565218 115565239              AB351219     1    22    22
browser |    22  100.0%          X     - 117316960 117316981              AB351219     1    22    22
browser |    22  100.0%          X     - 118586357 118586378              AB351219     1    22    22
browser |    22  100.0%          X     + 119892812 119892833              AB351219     1    22    22
browser |    22  100.0%          X     + 122909312 122909333              AB351219     1    22    22
browser |    22  100.0%          X     + 124963386 124963407              AB351219     1    22    22
browser |    22  100.0%          X     + 125057497 125057518              AB351219     1    22    22
browser |    22  100.0%          X     - 157227607 157227628              AB351219     1    22    22
browser |    22  100.0%          X     + 157466292 157466313              AB351219     1    22    22
browser |    22  100.0%          X     + 157937093 157937114              AB351219     1    22    22
browser |    22  100.0%          X     + 159074989 159075010              AB351219     1    22    22
browser |    22  100.0%          X     + 160968051 160968072              AB351219     1    22    22
browser |    22  100.0%          X     + 161106983 161107004              AB351219     1    22    22
browser |    22  100.0%          X     - 161762412 161762433              AB351219     1    22    22
browser |    22  100.0%          X     + 164656234 164656255              AB351219     1    22    22
browser |    22  100.0%          X     + 166963702 166963723              AB351219     1    22    22
browser |    22  100.0%  X_GL456233v2_random     +    498317    498338              AB351219     1    22    22
browser |    22  100.0%          Y     +   2783455   2783476              AB351219     1    22    22
browser |    22  100.0%          Y     -   2875185   2875206              AB351219     1    22    22
browser |    22  100.0%          Y     +   3341799   3341820              AB351219     1    22    22
browser |    22  100.0%          Y     +   6772370   6772391              AB351219     1    22    22
browser |    22  100.0%          Y     -   8151869   8151890              AB351219     1    22    22
browser |    22  100.0%          Y     -  11210541  11210562              AB351219     1    22    22
browser |    22  100.0%          Y     +  12544567  12544588              AB351219     1    22    22
browser |    22  100.0%          Y     -  15895940  15895961              AB351219     1    22    22
browser |    22  100.0%          Y     +  17256441  17256462              AB351219     1    22    22
browser |    22  100.0%          Y     +  21229340  21229361              AB351219     1    22    22
browser |    22  100.0%          Y     -  21874086  21874107              AB351219     1    22    22
browser |    22  100.0%          Y     -  23481578  23481599              AB351219     1    22    22
browser |    22  100.0%          Y     +  35056694  35056715              AB351219     1    22    22
browser |    22  100.0%          Y     -  35704163  35704184              AB351219     1    22    22
browser |    22  100.0%          Y     -  39960098  39960119              AB351219     1    22    22
browser |    22  100.0%          Y     +  40111097  40111118              AB351219     1    22    22
browser |    22  100.0%          Y     -  42189221  42189242              AB351219     1    22    22
browser |    22  100.0%          Y     -  42464764  42464785              AB351219     1    22    22
browser |    22  100.0%          Y     -  43724402  43724423              AB351219     1    22    22
browser |    22  100.0%          Y     -  53871043  53871064              AB351219     1    22    22
browser |    22  100.0%          Y     -  69399537  69399558              AB351219     1    22    22
browser |    22  100.0%          Y     -  69686442  69686463              AB351219     1    22    22
browser |    22  100.0%          Y     -  73711073  73711094              AB351219     1    22    22
browser |    22  100.0%          Y     +  81110489  81110510              AB351219     1    22    22
browser |    22  100.0%          Y     -  82267006  82267027              AB351219     1    22    22
browser |    22  100.0%          Y     +  84726600  84726621              AB351219     1    22    22
browser |    22  100.0%          Y     -  85100731  85100752              AB351219     1    22    22
browser |    22  100.0%          Y     +  87791443  87791464              AB351219     1    22    22
browser |    22  100.0%          Y     +  88476134  88476155              AB351219     1    22    22

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