DQ708415
 

Information on mRNA DQ708415

Description: Mus musculus piRNA piR-123737, complete sequence.
Gene: n/a
Product: n/a
Author: Lau,N.C., Seto,A.G., Kim,J., Kuramochi-Miyagawa,S., Nakano,T., Bartel,D.P. and Kingston,R.E.
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: 2006-06-08
Version: 1
mRNA sequence: DQ708415
Position: chrX:15628619-15628639

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 |    21  100.0%          X     +  15628619  15628639              DQ708415     2    22    22
browser |    21  100.0%          1     +   3986281   3986301              DQ708415     2    22    22
browser |    21  100.0%          1     -   4074876   4074896              DQ708415     2    22    22
browser |    21  100.0%          1     +   6131413   6131433              DQ708415     2    22    22
browser |    21  100.0%          1     +   6471411   6471431              DQ708415     2    22    22
browser |    21  100.0%          1     +   7724570   7724590              DQ708415     2    22    22
browser |    21  100.0%          1     +   8233591   8233611              DQ708415     2    22    22
browser |    21  100.0%          1     -   8541128   8541148              DQ708415     2    22    22
browser |    21  100.0%          1     +   9435688   9435708              DQ708415     2    22    22
browser |    21  100.0%          1     +   9442394   9442414              DQ708415     2    22    22
browser |    21  100.0%          1     -  10927938  10927958              DQ708415     2    22    22
browser |    21  100.0%          1     +  12031932  12031952              DQ708415     2    22    22
browser |    21  100.0%          1     +  14011518  14011538              DQ708415     2    22    22
browser |    21  100.0%          1     -  14781756  14781776              DQ708415     2    22    22
browser |    21  100.0%          1     -  18229269  18229289              DQ708415     2    22    22
browser |    21  100.0%          1     +  18576652  18576672              DQ708415     2    22    22
browser |    21  100.0%          1     +  18660190  18660210              DQ708415     2    22    22
browser |    21  100.0%          1     +  20903272  20903292              DQ708415     2    22    22
browser |    21  100.0%          1     -  23637976  23637996              DQ708415     2    22    22
browser |    21  100.0%          1     -  24328238  24328258              DQ708415     2    22    22
browser |    21  100.0%          1     +  26241388  26241408              DQ708415     2    22    22
browser |    21  100.0%          1     +  26372551  26372571              DQ708415     2    22    22
browser |    21  100.0%          1     +  26446707  26446727              DQ708415     2    22    22
browser |    22  100.0%          1     +  26620482  26620503              DQ708415     1    22    22
browser |    21  100.0%          1     -  27270383  27270403              DQ708415     2    22    22
browser |    21  100.0%          1     -  28532846  28532866              DQ708415     2    22    22
browser |    21  100.0%          1     -  29642886  29642906              DQ708415     2    22    22
browser |    21  100.0%          1     -  30756518  30756538              DQ708415     2    22    22
browser |    21  100.0%          1     -  31596579  31596599              DQ708415     2    22    22
browser |    21  100.0%          1     -  31611744  31611764              DQ708415     2    22    22
browser |    21  100.0%          1     -  37452086  37452106              DQ708415     2    22    22
browser |    21  100.0%          1     -  38417461  38417481              DQ708415     2    22    22
browser |    21  100.0%          1     -  44959933  44959953              DQ708415     2    22    22
browser |    21  100.0%          1     -  81516212  81516232              DQ708415     2    22    22
browser |    21  100.0%          1     -  81972857  81972877              DQ708415     2    22    22
browser |    21  100.0%          1     -  92504431  92504451              DQ708415     2    22    22
browser |    21  100.0%          1     -  97626738  97626758              DQ708415     2    22    22
browser |    21  100.0%          1     +  99147218  99147238              DQ708415     2    22    22
browser |    21  100.0%          1     + 101009219 101009239              DQ708415     2    22    22
browser |    21  100.0%          1     + 101083210 101083230              DQ708415     2    22    22
browser |    21  100.0%          1     + 102110768 102110788              DQ708415     2    22    22
browser |    21  100.0%          1     + 103109858 103109878              DQ708415     2    22    22
browser |    21  100.0%          1     + 103777110 103777130              DQ708415     2    22    22
browser |    21  100.0%          1     + 104810132 104810152              DQ708415     2    22    22
browser |    21  100.0%          1     + 107950306 107950326              DQ708415     2    22    22
browser |    21  100.0%          1     - 111915645 111915665              DQ708415     2    22    22
browser |    21  100.0%          1     + 112898534 112898554              DQ708415     2    22    22
browser |    21  100.0%          1     + 113281882 113281902              DQ708415     2    22    22
browser |    21  100.0%          1     - 113780283 113780303              DQ708415     2    22    22
browser |    21  100.0%          1     + 115135622 115135642              DQ708415     2    22    22
browser |    21  100.0%          1     + 121906121 121906141              DQ708415     2    22    22
browser |    21  100.0%          1     - 121940141 121940161              DQ708415     2    22    22
browser |    21  100.0%          1     + 121969904 121969924              DQ708415     2    22    22
browser |    21  100.0%          1     - 125946770 125946790              DQ708415     2    22    22
browser |    21  100.0%          1     + 126449880 126449900              DQ708415     2    22    22
browser |    21  100.0%          1     + 133278069 133278089              DQ708415     2    22    22
browser |    21  100.0%          1     - 133386724 133386744              DQ708415     2    22    22
browser |    21  100.0%          1     + 133464005 133464025              DQ708415     2    22    22
browser |    21  100.0%          1     - 137000450 137000470              DQ708415     2    22    22
browser |    21  100.0%          1     - 139956018 139956038              DQ708415     2    22    22
browser |    21  100.0%          1     - 141391942 141391962              DQ708415     2    22    22
browser |    21  100.0%          1     - 143541008 143541028              DQ708415     2    22    22
browser |    21  100.0%          1     - 147555829 147555849              DQ708415     2    22    22
browser |    21  100.0%          1     - 154473881 154473901              DQ708415     2    22    22
browser |    21  100.0%          1     - 157337989 157338009              DQ708415     2    22    22
browser |    22  100.0%          1     - 159910886 159910907              DQ708415     1    22    22
browser |    21  100.0%          1     + 168573867 168573887              DQ708415     2    22    22
browser |    21  100.0%          1     - 170679371 170679391              DQ708415     2    22    22
browser |    20  100.0%          1     - 170681759 170681778              DQ708415     2    21    22
browser |    20  100.0%          1     + 171380876 171380895              DQ708415     2    21    22
browser |    21  100.0%          1     + 171588786 171588806              DQ708415     2    22    22
browser |    20  100.0%          1     + 171764601 171764620              DQ708415     2    21    22
browser |    21  100.0%          1     + 173271645 173271665              DQ708415     2    22    22
browser |    20  100.0%          1     - 173595525 173595544              DQ708415     2    21    22
browser |    20  100.0%          1     - 173741493 173741512              DQ708415     2    21    22
browser |    20  100.0%          1     - 175616263 175616282              DQ708415     2    21    22
browser |    21  100.0%          1     + 176097036 176097056              DQ708415     2    22    22
browser |    20  100.0%          1     - 176476712 176476731              DQ708415     2    21    22
browser |    21  100.0%          1     + 176669769 176669789              DQ708415     2    22    22
browser |    20  100.0%          1     + 183603453 183603472              DQ708415     3    22    22
browser |    21  100.0%          1     + 183891253 183891273              DQ708415     2    22    22
browser |    20  100.0%          1     + 189218632 189218651              DQ708415     2    21    22
browser |    21  100.0%          1     - 193738073 193738093              DQ708415     2    22    22
browser |    21  100.0%          1     - 194163321 194163341              DQ708415     2    22    22
browser |    21  100.0%          1     + 194237534 194237554              DQ708415     2    22    22
browser |    21  100.0%         10     -   5959875   5959895              DQ708415     2    22    22
browser |    21  100.0%         10     +   6450942   6450962              DQ708415     2    22    22
browser |    21  100.0%         10     -   7461376   7461396              DQ708415     2    22    22
browser |    21  100.0%         10     +  10314526  10314546              DQ708415     2    22    22
browser |    21  100.0%         10     +  10636341  10636361              DQ708415     2    22    22
browser |    21  100.0%         10     -  11794979  11794999              DQ708415     2    22    22
browser |    21  100.0%         10     +  18426066  18426086              DQ708415     2    22    22
browser |    21  100.0%         10     -  22060352  22060372              DQ708415     2    22    22
browser |    21  100.0%         10     -  22250589  22250609              DQ708415     2    22    22
browser |    21  100.0%         10     +  24862298  24862318              DQ708415     2    22    22
browser |    21  100.0%         10     -  27240241  27240261              DQ708415     2    22    22
browser |    21  100.0%         10     -  29260336  29260356              DQ708415     2    22    22
browser |    21  100.0%         10     +  31099192  31099212              DQ708415     2    22    22
browser |    21  100.0%         10     +  33687076  33687096              DQ708415     2    22    22
browser |    21  100.0%         10     +  33687761  33687781              DQ708415     2    22    22
browser |    21  100.0%         10     -  33897833  33897853              DQ708415     2    22    22
browser |    21  100.0%         10     -  33995324  33995344              DQ708415     2    22    22
browser |    21  100.0%         10     -  34496500  34496520              DQ708415     2    22    22
browser |    21  100.0%         10     -  34730453  34730473              DQ708415     2    22    22
browser |    21  100.0%         10     +  35752675  35752695              DQ708415     2    22    22
browser |    21  100.0%         10     -  36507241  36507261              DQ708415     2    22    22
browser |    21  100.0%         10     +  37921631  37921651              DQ708415     2    22    22
browser |    21  100.0%         10     -  38343209  38343229              DQ708415     2    22    22
browser |    21  100.0%         10     -  38993054  38993074              DQ708415     2    22    22
browser |    21  100.0%         10     -  40076771  40076791              DQ708415     2    22    22
browser |    21  100.0%         10     -  40404739  40404759              DQ708415     2    22    22
browser |    21  100.0%         10     +  45979729  45979749              DQ708415     2    22    22
browser |    21  100.0%         10     +  46251696  46251716              DQ708415     2    22    22
browser |    21  100.0%         10     +  46899986  46900006              DQ708415     2    22    22
browser |    21  100.0%         10     +  51675856  51675876              DQ708415     2    22    22
browser |    21  100.0%         10     +  52943027  52943047              DQ708415     2    22    22
browser |    21  100.0%         10     +  54167281  54167301              DQ708415     2    22    22
browser |    21  100.0%         10     +  80901205  80901225              DQ708415     2    22    22
browser |    21  100.0%         10     +  83312705  83312725              DQ708415     2    22    22
browser |    21  100.0%         10     +  85678918  85678938              DQ708415     2    22    22
browser |    21  100.0%         10     -  86465886  86465906              DQ708415     2    22    22
browser |    21  100.0%         10     +  89526175  89526195              DQ708415     2    22    22
browser |    21  100.0%         10     -  89717235  89717255              DQ708415     2    22    22
browser |    21  100.0%         10     +  90531524  90531544              DQ708415     2    22    22
browser |    20  100.0%         10     -  91876115  91876134              DQ708415     3    22    22
browser |    20  100.0%         10     +  93631369  93631388              DQ708415     3    22    22
browser |    20  100.0%         10     +  93739646  93739665              DQ708415     2    21    22
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browser |    21  100.0%         10     + 100765190 100765210              DQ708415     2    22    22
browser |    21  100.0%         10     + 101772940 101772960              DQ708415     2    22    22
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browser |    20  100.0%         10     - 104129390 104129409              DQ708415     2    21    22
browser |    21  100.0%         10     + 111267067 111267087              DQ708415     2    22    22
browser |    21  100.0%         10     + 114467862 114467882              DQ708415     2    22    22
browser |    21  100.0%         10     + 118971046 118971066              DQ708415     2    22    22
browser |    20  100.0%         10     - 121563460 121563479              DQ708415     3    22    22
browser |    20  100.0%         10     - 122462945 122462964              DQ708415     2    21    22
browser |    20  100.0%         10     - 125068975 125068994              DQ708415     2    21    22
browser |    20  100.0%         10     - 126397812 126397831              DQ708415     2    21    22
browser |    21  100.0%         10     + 126578863 126578883              DQ708415     2    22    22
browser |    21  100.0%         11     +   3778108   3778128              DQ708415     2    22    22
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browser |    21  100.0%         11     +   9599313   9599333              DQ708415     2    22    22
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View details of parts of alignment within browser window
.
View table schema

Go to Mouse mRNAs track controls

Data last updated at UCSC: 2020-08-18

Description

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

Display Conventions and Configuration

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

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

To use the filter:

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

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

Methods

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

Credits

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

References

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

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

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