DQ719726
 

Information on mRNA DQ719726

Description: Mus musculus piRNA piR-135048, 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: DQ719726
Position: chr12:56796794-56796823

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 |    30  100.0%         12     -  56796794  56796823              DQ719726     1    30    30
browser |    30  100.0%          1     -   5879479   5879508              DQ719726     1    30    30
browser |    30  100.0%          1     -   6505508   6505537              DQ719726     1    30    30
browser |    30  100.0%          1     +   8066111   8066140              DQ719726     1    30    30
browser |    30  100.0%          1     +   8228552   8228581              DQ719726     1    30    30
browser |    30  100.0%          1     -   8730519   8730548              DQ719726     1    30    30
browser |    30  100.0%          1     -  10804995  10805024              DQ719726     1    30    30
browser |    30  100.0%          1     +  13622976  13623005              DQ719726     1    30    30
browser |    30  100.0%          1     +  16810622  16810651              DQ719726     1    30    30
browser |    30  100.0%          1     +  18029216  18029245              DQ719726     1    30    30
browser |    30  100.0%          1     +  18589246  18589275              DQ719726     1    30    30
browser |    30  100.0%          1     +  19694830  19694859              DQ719726     1    30    30
browser |    30  100.0%          1     +  26455238  26455267              DQ719726     1    30    30
browser |    30  100.0%          1     -  26513084  26513113              DQ719726     1    30    30
browser |    30  100.0%          1     +  27221386  27221415              DQ719726     1    30    30
browser |    30  100.0%          1     -  29986214  29986243              DQ719726     1    30    30
browser |    30  100.0%          1     +  34388719  34388748              DQ719726     1    30    30
browser |    30  100.0%          1     -  47264928  47264957              DQ719726     1    30    30
browser |    30  100.0%          1     -  48400269  48400298              DQ719726     1    30    30
browser |    30  100.0%          1     -  53171759  53171788              DQ719726     1    30    30
browser |    30  100.0%          1     +  55819669  55819698              DQ719726     1    30    30
browser |    30  100.0%          1     +  56813522  56813551              DQ719726     1    30    30
browser |    30  100.0%          1     -  58367434  58367463              DQ719726     1    30    30
browser |    30  100.0%          1     -  58855742  58855771              DQ719726     1    30    30
browser |    30  100.0%          1     +  58972075  58972104              DQ719726     1    30    30
browser |    30  100.0%          1     -  60768928  60768957              DQ719726     1    30    30
browser |    30  100.0%          1     +  64424422  64424451              DQ719726     1    30    30
browser |    30  100.0%          1     -  66061697  66061726              DQ719726     1    30    30
browser |    30  100.0%          1     -  72169615  72169644              DQ719726     1    30    30
browser |    30  100.0%          1     -  74697510  74697539              DQ719726     1    30    30
browser |    30  100.0%          1     +  77646531  77646560              DQ719726     1    30    30
browser |    30  100.0%          1     +  79916929  79916958              DQ719726     1    30    30
browser |    30  100.0%          1     -  81546803  81546832              DQ719726     1    30    30
browser |    30  100.0%          1     -  87066285  87066314              DQ719726     1    30    30
browser |    30  100.0%          1     +  87390042  87390071              DQ719726     1    30    30
browser |    30  100.0%          1     +  89128970  89128999              DQ719726     1    30    30
browser |    30  100.0%          1     -  91403858  91403887              DQ719726     1    30    30
browser |    30  100.0%          1     +  93886452  93886481              DQ719726     1    30    30
browser |    30  100.0%          1     +  95625040  95625069              DQ719726     1    30    30
browser |    30  100.0%          1     +  97102651  97102680              DQ719726     1    30    30
browser |    30  100.0%          1     - 101910793 101910822              DQ719726     1    30    30
browser |    30  100.0%          1     + 102961553 102961582              DQ719726     1    30    30
browser |    30  100.0%          1     - 103137822 103137851              DQ719726     1    30    30
browser |    30  100.0%          1     - 108341510 108341539              DQ719726     1    30    30
browser |    30  100.0%          1     + 109543295 109543324              DQ719726     1    30    30
browser |    30  100.0%          1     - 111186279 111186308              DQ719726     1    30    30
browser |    30  100.0%          1     + 111633263 111633292              DQ719726     1    30    30
browser |    30  100.0%          1     - 112196988 112197017              DQ719726     1    30    30
browser |    30  100.0%          1     + 112859372 112859401              DQ719726     1    30    30
browser |    30  100.0%          1     + 112945970 112945999              DQ719726     1    30    30
browser |    30  100.0%          1     - 116580927 116580956              DQ719726     1    30    30
browser |    30  100.0%          1     - 117634585 117634614              DQ719726     1    30    30
browser |    30  100.0%          1     - 125276028 125276057              DQ719726     1    30    30
browser |    30  100.0%          1     - 127490921 127490950              DQ719726     1    30    30
browser |    30  100.0%          1     - 127807720 127807749              DQ719726     1    30    30
browser |    30  100.0%          1     - 137203827 137203856              DQ719726     1    30    30
browser |    30  100.0%          1     + 140746713 140746742              DQ719726     1    30    30
browser |    30  100.0%          1     + 140965311 140965340              DQ719726     1    30    30
browser |    30  100.0%          1     + 144262070 144262099              DQ719726     1    30    30
browser |    30  100.0%          1     + 145998837 145998866              DQ719726     1    30    30
browser |    30  100.0%          1     + 149271160 149271189              DQ719726     1    30    30
browser |    30  100.0%          1     + 149459470 149459499              DQ719726     1    30    30
browser |    30  100.0%          1     - 154779620 154779649              DQ719726     1    30    30
browser |    30  100.0%          1     - 159802253 159802282              DQ719726     1    30    30
browser |    30  100.0%          1     + 162670283 162670312              DQ719726     1    30    30
browser |    30  100.0%          1     + 166181921 166181950              DQ719726     1    30    30
browser |    30  100.0%          1     - 166595126 166595155              DQ719726     1    30    30
browser |    30  100.0%          1     + 169371530 169371559              DQ719726     1    30    30
browser |    30  100.0%          1     + 169945517 169945546              DQ719726     1    30    30
browser |    30  100.0%          1     - 174873658 174873687              DQ719726     1    30    30
browser |    30  100.0%          1     - 176375552 176375581              DQ719726     1    30    30
browser |    30  100.0%          1     + 177887782 177887811              DQ719726     1    30    30
browser |    30  100.0%          1     + 178003835 178003864              DQ719726     1    30    30
browser |    30  100.0%          1     + 179723730 179723759              DQ719726     1    30    30
browser |    30  100.0%          1     - 181096009 181096038              DQ719726     1    30    30
browser |    30  100.0%          1     + 181322624 181322653              DQ719726     1    30    30
browser |    30  100.0%          1     + 195004819 195004848              DQ719726     1    30    30
browser |    30  100.0%         10     -   3555849   3555878              DQ719726     1    30    30
browser |    30  100.0%         10     +   8477208   8477237              DQ719726     1    30    30
browser |    30  100.0%         10     +  11572187  11572216              DQ719726     1    30    30
browser |    30  100.0%         10     -  19419562  19419591              DQ719726     1    30    30
browser |    30  100.0%         10     -  19891289  19891318              DQ719726     1    30    30
browser |    30  100.0%         10     -  21523135  21523164              DQ719726     1    30    30
browser |    30  100.0%         10     -  22404026  22404055              DQ719726     1    30    30
browser |    30  100.0%         10     -  22564081  22564110              DQ719726     1    30    30
browser |    30  100.0%         10     -  23752136  23752165              DQ719726     1    30    30
browser |    30  100.0%         10     -  24980208  24980237              DQ719726     1    30    30
browser |    30  100.0%         10     +  25846480  25846509              DQ719726     1    30    30
browser |    30  100.0%         10     +  30692148  30692177              DQ719726     1    30    30
browser |    30  100.0%         10     +  30966833  30966862              DQ719726     1    30    30
browser |    30  100.0%         10     +  31360775  31360804              DQ719726     1    30    30
browser |    30  100.0%         10     -  34622739  34622768              DQ719726     1    30    30
browser |    30  100.0%         10     +  41718702  41718731              DQ719726     1    30    30
browser |    30  100.0%         10     +  51761260  51761289              DQ719726     1    30    30
browser |    30  100.0%         10     +  56599008  56599037              DQ719726     1    30    30
browser |    30  100.0%         10     +  57015928  57015957              DQ719726     1    30    30
browser |    30  100.0%         10     +  62941930  62941959              DQ719726     1    30    30
browser |    30  100.0%         10     -  65478542  65478571              DQ719726     1    30    30
browser |    30  100.0%         10     -  66563157  66563186              DQ719726     1    30    30
browser |    30  100.0%         10     +  70629421  70629450              DQ719726     1    30    30
browser |    30  100.0%         10     +  71529418  71529447              DQ719726     1    30    30
browser |    30  100.0%         10     +  77788772  77788801              DQ719726     1    30    30
browser |    30  100.0%         10     -  78656706  78656735              DQ719726     1    30    30
browser |    30  100.0%         10     -  81511291  81511320              DQ719726     1    30    30
browser |    30  100.0%         10     -  81670419  81670448              DQ719726     1    30    30
browser |    30  100.0%         10     +  81805892  81805921              DQ719726     1    30    30
browser |    30  100.0%         10     -  83306647  83306676              DQ719726     1    30    30
browser |    30  100.0%         10     -  83511702  83511731              DQ719726     1    30    30
browser |    30  100.0%         10     +  85553226  85553255              DQ719726     1    30    30
browser |    30  100.0%         10     +  88489013  88489042              DQ719726     1    30    30
browser |    30  100.0%         10     -  94202850  94202879              DQ719726     1    30    30
browser |    30  100.0%         10     -  96033310  96033339              DQ719726     1    30    30
browser |    30  100.0%         10     -  97163229  97163258              DQ719726     1    30    30
browser |    30  100.0%         10     +  99177152  99177181              DQ719726     1    30    30
browser |    30  100.0%         10     + 104393379 104393408              DQ719726     1    30    30
browser |    30  100.0%         10     + 104673596 104673625              DQ719726     1    30    30
browser |    30  100.0%         10     + 105015115 105015144              DQ719726     1    30    30
browser |    30  100.0%         10     + 107837525 107837554              DQ719726     1    30    30
browser |    30  100.0%         10     - 109155996 109156025              DQ719726     1    30    30
browser |    30  100.0%         10     + 110534296 110534325              DQ719726     1    30    30
browser |    30  100.0%         10     - 113563522 113563551              DQ719726     1    30    30
browser |    30  100.0%         10     - 116447083 116447112              DQ719726     1    30    30
browser |    30  100.0%         10     + 117908719 117908748              DQ719726     1    30    30
browser |    30  100.0%         10     + 121002804 121002833              DQ719726     1    30    30
browser |    30  100.0%         10     - 122204692 122204721              DQ719726     1    30    30
browser |    30  100.0%         10     - 122673569 122673598              DQ719726     1    30    30
browser |    30  100.0%         10     + 123697416 123697445              DQ719726     1    30    30
browser |    30  100.0%         10     + 124414391 124414420              DQ719726     1    30    30
browser |    30  100.0%         10     - 124519763 124519792              DQ719726     1    30    30
browser |    30  100.0%         10     - 129229608 129229637              DQ719726     1    30    30
browser |    30  100.0%         10     + 129763339 129763368              DQ719726     1    30    30
browser |    30  100.0%         10     - 130399817 130399846              DQ719726     1    30    30
browser |    30  100.0%         11     -   6096410   6096439              DQ719726     1    30    30
browser |    30  100.0%         11     -   7530602   7530631              DQ719726     1    30    30
browser |    30  100.0%         11     -   9662901   9662930              DQ719726     1    30    30
browser |    30  100.0%         11     +  10712492  10712521              DQ719726     1    30    30
browser |    30  100.0%         11     +  12514102  12514131              DQ719726     1    30    30
browser |    30  100.0%         11     +  12747774  12747803              DQ719726     1    30    30
browser |    30  100.0%         11     +  15179872  15179901              DQ719726     1    30    30
browser |    30  100.0%         11     -  18761374  18761403              DQ719726     1    30    30
browser |    30  100.0%         11     -  19518343  19518372              DQ719726     1    30    30
browser |    30  100.0%         11     +  20468558  20468587              DQ719726     1    30    30
browser |    30  100.0%         11     -  23173501  23173530              DQ719726     1    30    30
browser |    30  100.0%         11     -  23195114  23195143              DQ719726     1    30    30
browser |    30  100.0%         11     -  27904887  27904916              DQ719726     1    30    30
browser |    30  100.0%         11     +  28049475  28049504              DQ719726     1    30    30
browser |    30  100.0%         11     -  31402481  31402510              DQ719726     1    30    30
browser |    30  100.0%         11     -  39959470  39959499              DQ719726     1    30    30
browser |    30  100.0%         11     -  54472318  54472347              DQ719726     1    30    30
browser |    30  100.0%         11     -  55136681  55136710              DQ719726     1    30    30
browser |    30  100.0%         11     +  61313443  61313472              DQ719726     1    30    30
browser |    30  100.0%         11     +  63360732  63360761              DQ719726     1    30    30
browser |    30  100.0%         11     -  65347528  65347557              DQ719726     1    30    30
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browser |    30  100.0%         13     -  10944125  10944154              DQ719726     1    30    30
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browser |    30  100.0%         13     -  19182954  19182983              DQ719726     1    30    30
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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