DQ563217
 

Information on mRNA DQ563217

Description: Mus musculus piRNA piR-3329, complete sequence.
Gene: n/a
Product: n/a
Author: Girard,A., Sachidanandam,R., Hannon,G.J. and Carmell,M.A.
Organism: Mus musculus
Tissue: n/a
Development stage: n/a
Cell line: n/a
Sex: n/a
Library: n/a
Clone: n/a
CDS: n/a
Date: 2008-11-02
Version: 1
mRNA sequence: DQ563217
Position: chrX:15607364-15607392

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 |    29  100.0%          X     -  15607364  15607392              DQ563217     1    29    29
browser |    29  100.0%          1     +   4155185   4155213              DQ563217     1    29    29
browser |    29  100.0%          1     -   4258338   4258366              DQ563217     1    29    29
browser |    29  100.0%          1     +   5110673   5110701              DQ563217     1    29    29
browser |    29  100.0%          1     -   5494056   5494084              DQ563217     1    29    29
browser |    29  100.0%          1     -   5501116   5501144              DQ563217     1    29    29
browser |    29  100.0%          1     -   5891071   5891099              DQ563217     1    29    29
browser |    29  100.0%          1     -   6097547   6097575              DQ563217     1    29    29
browser |    29  100.0%          1     +   7558086   7558114              DQ563217     1    29    29
browser |    29  100.0%          1     +   8288369   8288397              DQ563217     1    29    29
browser |    29  100.0%          1     -   8759778   8759806              DQ563217     1    29    29
browser |    29  100.0%          1     +   9120745   9120773              DQ563217     1    29    29
browser |    29  100.0%          1     -   9191646   9191674              DQ563217     1    29    29
browser |    29  100.0%          1     -   9246496   9246524              DQ563217     1    29    29
browser |    29  100.0%          1     +  10497888  10497916              DQ563217     1    29    29
browser |    29  100.0%          1     +  10862800  10862828              DQ563217     1    29    29
browser |    29  100.0%          1     -  11744834  11744862              DQ563217     1    29    29
browser |    29  100.0%          1     +  11799171  11799199              DQ563217     1    29    29
browser |    29  100.0%          1     -  12146066  12146094              DQ563217     1    29    29
browser |    29  100.0%          1     -  12287869  12287897              DQ563217     1    29    29
browser |    29  100.0%          1     +  13890135  13890163              DQ563217     1    29    29
browser |    29  100.0%          1     +  15064532  15064560              DQ563217     1    29    29
browser |    29  100.0%          1     -  15090965  15090993              DQ563217     1    29    29
browser |    29  100.0%          1     +  15812482  15812510              DQ563217     1    29    29
browser |    29  100.0%          1     +  16026001  16026029              DQ563217     1    29    29
browser |    29  100.0%          1     -  16523627  16523655              DQ563217     1    29    29
browser |    29  100.0%          1     +  17404856  17404884              DQ563217     1    29    29
browser |    29  100.0%          1     -  17544419  17544447              DQ563217     1    29    29
browser |    29  100.0%          1     +  17755787  17755815              DQ563217     1    29    29
browser |    29  100.0%          1     +  17774846  17774874              DQ563217     1    29    29
browser |    29  100.0%          1     -  18998259  18998287              DQ563217     1    29    29
browser |    29  100.0%          1     +  19201634  19201662              DQ563217     1    29    29
browser |    29  100.0%          1     -  19910181  19910209              DQ563217     1    29    29
browser |    29  100.0%          1     +  80671143  80671171              DQ563217     1    29    29
browser |    29  100.0%          1     -  83347843  83347871              DQ563217     1    29    29
browser |    29  100.0%          1     +  83440229  83440257              DQ563217     1    29    29
browser |    29  100.0%          1     -  83593474  83593502              DQ563217     1    29    29
browser |    29  100.0%          1     -  83651321  83651349              DQ563217     1    29    29
browser |    29  100.0%          1     -  84100092  84100120              DQ563217     1    29    29
browser |    29  100.0%          1     -  84242733  84242761              DQ563217     1    29    29
browser |    29  100.0%          1     -  84430219  84430247              DQ563217     1    29    29
browser |    29  100.0%          1     -  84679200  84679228              DQ563217     1    29    29
browser |    29  100.0%          1     +  84998018  84998046              DQ563217     1    29    29
browser |    29  100.0%          1     +  85044437  85044465              DQ563217     1    29    29
browser |    29  100.0%          1     -  85201786  85201814              DQ563217     1    29    29
browser |    29  100.0%          1     +  85317336  85317364              DQ563217     1    29    29
browser |    29  100.0%          1     +  87962043  87962071              DQ563217     1    29    29
browser |    29  100.0%          1     -  89145634  89145662              DQ563217     1    29    29
browser |    29  100.0%          1     +  94169408  94169436              DQ563217     1    29    29
browser |    29  100.0%          1     +  94321514  94321542              DQ563217     1    29    29
browser |    29  100.0%          1     -  94327608  94327636              DQ563217     1    29    29
browser |    29  100.0%          1     +  94408860  94408888              DQ563217     1    29    29
browser |    29  100.0%          1     +  95165786  95165814              DQ563217     1    29    29
browser |    29  100.0%          1     -  95711726  95711754              DQ563217     1    29    29
browser |    29  100.0%          1     -  96119660  96119688              DQ563217     1    29    29
browser |    29  100.0%          1     -  96500604  96500632              DQ563217     1    29    29
browser |    29  100.0%          1     +  98548047  98548075              DQ563217     1    29    29
browser |    29  100.0%          1     +  98578433  98578461              DQ563217     1    29    29
browser |    29  100.0%          1     +  98773594  98773622              DQ563217     1    29    29
browser |    29  100.0%          1     -  98874939  98874967              DQ563217     1    29    29
browser |    29  100.0%          1     -  99111602  99111630              DQ563217     1    29    29
browser |    29  100.0%          1     -  99131425  99131453              DQ563217     1    29    29
browser |    29  100.0%          1     +  99278987  99279015              DQ563217     1    29    29
browser |    29  100.0%          1     +  99751392  99751420              DQ563217     1    29    29
browser |    29  100.0%          1     + 100247725 100247753              DQ563217     1    29    29
browser |    29  100.0%          1     + 157710487 157710515              DQ563217     1    29    29
browser |    29  100.0%          1     + 158415837 158415865              DQ563217     1    29    29
browser |    29  100.0%          1     - 160250173 160250201              DQ563217     1    29    29
browser |    29  100.0%          1     + 162097279 162097307              DQ563217     1    29    29
browser |    29  100.0%          1     + 162845949 162845977              DQ563217     1    29    29
browser |    29  100.0%          1     - 163599744 163599772              DQ563217     1    29    29
browser |    29  100.0%          1     + 163640068 163640096              DQ563217     1    29    29
browser |    29  100.0%          1     + 164557052 164557080              DQ563217     1    29    29
browser |    29  100.0%          1     - 164854151 164854179              DQ563217     1    29    29
browser |    29  100.0%          1     + 166374182 166374210              DQ563217     1    29    29
browser |    29  100.0%          1     - 166429609 166429637              DQ563217     1    29    29
browser |    29  100.0%          1     + 167308090 167308118              DQ563217     1    29    29
browser |    29  100.0%          1     + 168686744 168686772              DQ563217     1    29    29
browser |    29  100.0%          1     - 168811576 168811604              DQ563217     1    29    29
browser |    29  100.0%          1     + 168940489 168940517              DQ563217     1    29    29
browser |    29  100.0%          1     - 169112976 169113004              DQ563217     1    29    29
browser |    29  100.0%          1     + 170089459 170089487              DQ563217     1    29    29
browser |    29  100.0%          1     - 171346670 171346698              DQ563217     1    29    29
browser |    29  100.0%          1     - 172544916 172544944              DQ563217     1    29    29
browser |    29  100.0%          1     + 173087661 173087689              DQ563217     1    29    29
browser |    29  100.0%          1     - 173368322 173368350              DQ563217     1    29    29
browser |    29  100.0%          1     - 173846053 173846081              DQ563217     1    29    29
browser |    29  100.0%          1     + 174541118 174541146              DQ563217     1    29    29
browser |    29  100.0%          1     + 174841482 174841510              DQ563217     1    29    29
browser |    29  100.0%          1     - 175224673 175224701              DQ563217     1    29    29
browser |    29  100.0%          1     - 176110749 176110777              DQ563217     1    29    29
browser |    29  100.0%          1     + 193491949 193491977              DQ563217     1    29    29
browser |    29  100.0%          1     - 193763156 193763184              DQ563217     1    29    29
browser |    29  100.0%          1     + 194737699 194737727              DQ563217     1    29    29
browser |    29  100.0%          1     - 194926449 194926477              DQ563217     1    29    29
browser |    29  100.0%         10     +   4787252   4787280              DQ563217     1    29    29
browser |    29  100.0%         10     -   5339752   5339780              DQ563217     1    29    29
browser |    29  100.0%         10     -   6574107   6574135              DQ563217     1    29    29
browser |    29  100.0%         10     -   6605435   6605463              DQ563217     1    29    29
browser |    29  100.0%         10     -   7346577   7346605              DQ563217     1    29    29
browser |    29  100.0%         10     -   8139553   8139581              DQ563217     1    29    29
browser |    29  100.0%         10     +   8195061   8195089              DQ563217     1    29    29
browser |    29  100.0%         10     +  10022543  10022571              DQ563217     1    29    29
browser |    29  100.0%         10     -  10461265  10461293              DQ563217     1    29    29
browser |    29  100.0%         10     +  11406498  11406526              DQ563217     1    29    29
browser |    29  100.0%         10     -  11499281  11499309              DQ563217     1    29    29
browser |    29  100.0%         10     +  11671557  11671585              DQ563217     1    29    29
browser |    29  100.0%         10     -  12143079  12143107              DQ563217     1    29    29
browser |    29  100.0%         10     -  14799731  14799759              DQ563217     1    29    29
browser |    29  100.0%         10     +  14880008  14880036              DQ563217     1    29    29
browser |    29  100.0%         10     +  15217660  15217688              DQ563217     1    29    29
browser |    29  100.0%         10     +  15345780  15345808              DQ563217     1    29    29
browser |    29  100.0%         10     +  15476463  15476491              DQ563217     1    29    29
browser |    29  100.0%         10     +  15500982  15501010              DQ563217     1    29    29
browser |    29  100.0%         10     +  15656022  15656050              DQ563217     1    29    29
browser |    29  100.0%         10     -  17013474  17013502              DQ563217     1    29    29
browser |    29  100.0%         10     -  22498063  22498091              DQ563217     1    29    29
browser |    29  100.0%         10     -  22635447  22635475              DQ563217     1    29    29
browser |    29  100.0%         10     -  23357525  23357553              DQ563217     1    29    29
browser |    29  100.0%         10     +  25545506  25545534              DQ563217     1    29    29
browser |    29  100.0%         10     +  27235616  27235644              DQ563217     1    29    29
browser |    29  100.0%         10     +  27694220  27694248              DQ563217     1    29    29
browser |    29  100.0%         10     -  28810944  28810972              DQ563217     1    29    29
browser |    29  100.0%         10     -  28953333  28953361              DQ563217     1    29    29
browser |    29  100.0%         10     +  29316452  29316480              DQ563217     1    29    29
browser |    29  100.0%         10     -  29835971  29835999              DQ563217     1    29    29
browser |    29  100.0%         10     +  33453953  33453981              DQ563217     1    29    29
browser |    29  100.0%         10     -  85692071  85692099              DQ563217     1    29    29
browser |    29  100.0%         10     +  87244624  87244652              DQ563217     1    29    29
browser |    29  100.0%         10     -  87931958  87931986              DQ563217     1    29    29
browser |    29  100.0%         10     +  89800318  89800346              DQ563217     1    29    29
browser |    29  100.0%         10     +  89895622  89895650              DQ563217     1    29    29
browser |    29  100.0%         10     -  91169129  91169157              DQ563217     1    29    29
browser |    29  100.0%         10     +  91770341  91770369              DQ563217     1    29    29
browser |    29  100.0%         10     +  92895739  92895767              DQ563217     1    29    29
browser |    29  100.0%         10     +  93251184  93251212              DQ563217     1    29    29
browser |    29  100.0%         10     -  97882201  97882229              DQ563217     1    29    29
browser |    29  100.0%         10     -  98173803  98173831              DQ563217     1    29    29
browser |    29  100.0%         10     +  99560492  99560520              DQ563217     1    29    29
browser |    29  100.0%         10     +  99726462  99726490              DQ563217     1    29    29
browser |    29  100.0%         10     + 100157327 100157355              DQ563217     1    29    29
browser |    29  100.0%         10     + 101183274 101183302              DQ563217     1    29    29
browser |    29  100.0%         10     + 101287255 101287283              DQ563217     1    29    29
browser |    29  100.0%         10     - 101403734 101403762              DQ563217     1    29    29
browser |    29  100.0%         10     - 102152060 102152088              DQ563217     1    29    29
browser |    29  100.0%         10     + 103354503 103354531              DQ563217     1    29    29
browser |    29  100.0%         10     + 103410976 103411004              DQ563217     1    29    29
browser |    29  100.0%         10     + 103778197 103778225              DQ563217     1    29    29
browser |    29  100.0%         10     - 104330154 104330182              DQ563217     1    29    29
browser |    29  100.0%         10     + 104589638 104589666              DQ563217     1    29    29
browser |    29  100.0%         10     + 105760406 105760434              DQ563217     1    29    29
browser |    29  100.0%         10     - 105916863 105916891              DQ563217     1    29    29
browser |    29  100.0%         10     - 106149518 106149546              DQ563217     1    29    29
browser |    29  100.0%         10     - 107683142 107683170              DQ563217     1    29    29
browser |    29  100.0%         10     - 109243684 109243712              DQ563217     1    29    29
browser |    29  100.0%         10     - 110200850 110200878              DQ563217     1    29    29
browser |    29  100.0%         10     - 110464187 110464215              DQ563217     1    29    29
browser |    29  100.0%         10     - 110684002 110684030              DQ563217     1    29    29
browser |    29  100.0%         10     - 112342599 112342627              DQ563217     1    29    29
browser |    29  100.0%         11     +   7670509   7670537              DQ563217     1    29    29
browser |    29  100.0%         11     -   7820303   7820331              DQ563217     1    29    29
browser |    29  100.0%         11     +   9055567   9055595              DQ563217     1    29    29
browser |    29  100.0%         11     +   9314547   9314575              DQ563217     1    29    29
browser |    29  100.0%         11     +   9699803   9699831              DQ563217     1    29    29
browser |    29  100.0%         11     +  10044415  10044443              DQ563217     1    29    29
browser |    29  100.0%         11     -  10201210  10201238              DQ563217     1    29    29
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browser |    29  100.0%         11     -  11328343  11328371              DQ563217     1    29    29
browser |    29  100.0%         11     -  11562391  11562419              DQ563217     1    29    29
browser |    29  100.0%         11     +  12095187  12095215              DQ563217     1    29    29
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browser |    29  100.0%         11     -  18247700  18247728              DQ563217     1    29    29
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browser |    29  100.0%         11     +  26417163  26417191              DQ563217     1    29    29
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browser |    29  100.0%         11     - 111344620 111344648              DQ563217     1    29    29
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browser |    29  100.0%         12     -   6821718   6821746              DQ563217     1    29    29
browser |    29  100.0%         12     -   7162501   7162529              DQ563217     1    29    29
browser |    29  100.0%         12     +  10682057  10682085              DQ563217     1    29    29
browser |    29  100.0%         12     -  10935767  10935795              DQ563217     1    29    29
browser |    29  100.0%         12     -  10962538  10962566              DQ563217     1    29    29
browser |    29  100.0%         12     -  11022020  11022048              DQ563217     1    29    29
browser |    29  100.0%         12     +  12009439  12009467              DQ563217     1    29    29
browser |    29  100.0%         12     +  14595088  14595116              DQ563217     1    29    29
browser |    29  100.0%         12     -  14841955  14841983              DQ563217     1    29    29
browser |    29  100.0%         12     +  14897956  14897984              DQ563217     1    29    29
browser |    29  100.0%         12     -  14988740  14988768              DQ563217     1    29    29
browser |    29  100.0%         12     -  15242963  15242991              DQ563217     1    29    29
browser |    29  100.0%         12     +  15309239  15309267              DQ563217     1    29    29
browser |    29  100.0%         12     -  15429372  15429400              DQ563217     1    29    29
browser |    29  100.0%         12     +  15921691  15921719              DQ563217     1    29    29
browser |    29  100.0%         12     +  18212469  18212497              DQ563217     1    29    29
browser |    29  100.0%         12     +  22193617  22193645              DQ563217     1    29    29
browser |    29  100.0%         12     +  23352329  23352357              DQ563217     1    29    29
browser |    29  100.0%         12     +  24490884  24490912              DQ563217     1    29    29
browser |    29  100.0%         12     -  25797720  25797748              DQ563217     1    29    29
browser |    29  100.0%         12     -  26085759  26085787              DQ563217     1    29    29
browser |    29  100.0%         12     -  28241969  28241997              DQ563217     1    29    29
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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