DQ720098
 

Information on mRNA DQ720098

Description: Mus musculus piRNA piR-135420, 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: DQ720098
Position: chrX:15609121-15609149

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     +  15609121  15609149              DQ720098     1    29    29
browser |    29  100.0%          1     -   3248751   3248779              DQ720098     1    29    29
browser |    29  100.0%          1     -   3312072   3312100              DQ720098     1    29    29
browser |    29  100.0%          1     -   4153467   4153495              DQ720098     1    29    29
browser |    29  100.0%          1     +   5019544   5019572              DQ720098     1    29    29
browser |    29  100.0%          1     -   5108914   5108942              DQ720098     1    29    29
browser |    29  100.0%          1     -   5340923   5340951              DQ720098     1    29    29
browser |    29  100.0%          1     +   5502873   5502901              DQ720098     1    29    29
browser |    29  100.0%          1     +   5809026   5809054              DQ720098     1    29    29
browser |    29  100.0%          1     +   6989631   6989659              DQ720098     1    29    29
browser |    29  100.0%          1     -   7556327   7556355              DQ720098     1    29    29
browser |    29  100.0%          1     +   8002336   8002364              DQ720098     1    29    29
browser |    29  100.0%          1     -   8286652   8286680              DQ720098     1    29    29
browser |    29  100.0%          1     +   8736534   8736562              DQ720098     1    29    29
browser |    29  100.0%          1     +   8761495   8761523              DQ720098     1    29    29
browser |    29  100.0%          1     +   9248213   9248241              DQ720098     1    29    29
browser |    29  100.0%          1     +  10455346  10455374              DQ720098     1    29    29
browser |    29  100.0%          1     -  10956467  10956495              DQ720098     1    29    29
browser |    29  100.0%          1     +  11746592  11746620              DQ720098     1    29    29
browser |    29  100.0%          1     -  11797433  11797461              DQ720098     1    29    29
browser |    29  100.0%          1     +  11877848  11877876              DQ720098     1    29    29
browser |    29  100.0%          1     +  12147825  12147853              DQ720098     1    29    29
browser |    29  100.0%          1     +  12289628  12289656              DQ720098     1    29    29
browser |    29  100.0%          1     -  13884417  13884445              DQ720098     1    29    29
browser |    29  100.0%          1     -  15043485  15043513              DQ720098     1    29    29
browser |    29  100.0%          1     -  15062774  15062802              DQ720098     1    29    29
browser |    29  100.0%          1     +  15092724  15092752              DQ720098     1    29    29
browser |    29  100.0%          1     +  15300664  15300692              DQ720098     1    29    29
browser |    29  100.0%          1     -  15565648  15565676              DQ720098     1    29    29
browser |    29  100.0%          1     -  15810765  15810793              DQ720098     1    29    29
browser |    29  100.0%          1     -  16002313  16002341              DQ720098     1    29    29
browser |    29  100.0%          1     -  16024242  16024270              DQ720098     1    29    29
browser |    29  100.0%          1     +  16525384  16525412              DQ720098     1    29    29
browser |    29  100.0%          1     -  80669426  80669454              DQ720098     1    29    29
browser |    29  100.0%          1     -  80756858  80756886              DQ720098     1    29    29
browser |    29  100.0%          1     +  81471275  81471303              DQ720098     1    29    29
browser |    29  100.0%          1     +  82526250  82526278              DQ720098     1    29    29
browser |    29  100.0%          1     +  83349599  83349627              DQ720098     1    29    29
browser |    29  100.0%          1     -  83438512  83438540              DQ720098     1    29    29
browser |    29  100.0%          1     +  83595232  83595260              DQ720098     1    29    29
browser |    29  100.0%          1     +  83653080  83653108              DQ720098     1    29    29
browser |    29  100.0%          1     +  84101809  84101837              DQ720098     1    29    29
browser |    29  100.0%          1     +  84244450  84244478              DQ720098     1    29    29
browser |    29  100.0%          1     +  84431936  84431964              DQ720098     1    29    29
browser |    29  100.0%          1     +  84680917  84680945              DQ720098     1    29    29
browser |    29  100.0%          1     -  85032949  85032977              DQ720098     1    29    29
browser |    29  100.0%          1     -  85042679  85042707              DQ720098     1    29    29
browser |    29  100.0%          1     -  85315621  85315649              DQ720098     1    29    29
browser |    29  100.0%          1     -  87960324  87960352              DQ720098     1    29    29
browser |    29  100.0%          1     +  89147351  89147379              DQ720098     1    29    29
browser |    29  100.0%          1     -  92343905  92343933              DQ720098     1    29    29
browser |    29  100.0%          1     +  94031113  94031141              DQ720098     1    29    29
browser |    29  100.0%          1     -  94125713  94125741              DQ720098     1    29    29
browser |    29  100.0%          1     -  94167649  94167677              DQ720098     1    29    29
browser |    29  100.0%          1     -  94319797  94319825              DQ720098     1    29    29
browser |    29  100.0%          1     +  94329367  94329395              DQ720098     1    29    29
browser |    29  100.0%          1     -  94406876  94406904              DQ720098     1    29    29
browser |    29  100.0%          1     +  94851534  94851562              DQ720098     1    29    29
browser |    29  100.0%          1     -  94886143  94886171              DQ720098     1    29    29
browser |    29  100.0%          1     -  95164069  95164097              DQ720098     1    29    29
browser |    29  100.0%          1     -  95443109  95443137              DQ720098     1    29    29
browser |    29  100.0%          1     +  95713485  95713513              DQ720098     1    29    29
browser |    29  100.0%          1     +  96023387  96023415              DQ720098     1    29    29
browser |    29  100.0%          1     +  96121376  96121404              DQ720098     1    29    29
browser |    29  100.0%          1     -  96914366  96914394              DQ720098     1    29    29
browser |    29  100.0%          1     - 157438293 157438321              DQ720098     1    29    29
browser |    29  100.0%          1     - 157708770 157708798              DQ720098     1    29    29
browser |    29  100.0%          1     - 158414078 158414106              DQ720098     1    29    29
browser |    29  100.0%          1     - 159539998 159540026              DQ720098     1    29    29
browser |    29  100.0%          1     + 160251890 160251918              DQ720098     1    29    29
browser |    29  100.0%          1     - 160469493 160469521              DQ720098     1    29    29
browser |    29  100.0%          1     - 162095562 162095590              DQ720098     1    29    29
browser |    29  100.0%          1     + 162168945 162168973              DQ720098     1    29    29
browser |    29  100.0%          1     - 162844190 162844218              DQ720098     1    29    29
browser |    29  100.0%          1     + 163540184 163540212              DQ720098     1    29    29
browser |    29  100.0%          1     + 163601503 163601531              DQ720098     1    29    29
browser |    29  100.0%          1     - 163638310 163638338              DQ720098     1    29    29
browser |    29  100.0%          1     - 164555335 164555363              DQ720098     1    29    29
browser |    29  100.0%          1     + 164746332 164746360              DQ720098     1    29    29
browser |    29  100.0%          1     + 164855910 164855938              DQ720098     1    29    29
browser |    29  100.0%          1     - 166372434 166372462              DQ720098     1    29    29
browser |    29  100.0%          1     + 166431326 166431354              DQ720098     1    29    29
browser |    29  100.0%          1     + 166817612 166817640              DQ720098     1    29    29
browser |    29  100.0%          1     - 167306330 167306358              DQ720098     1    29    29
browser |    29  100.0%          1     - 168443162 168443190              DQ720098     1    29    29
browser |    29  100.0%          1     - 168454743 168454771              DQ720098     1    29    29
browser |    29  100.0%          1     - 168475083 168475111              DQ720098     1    29    29
browser |    29  100.0%          1     - 168684989 168685017              DQ720098     1    29    29
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browser |    29  100.0%          1     + 169004934 169004962              DQ720098     1    29    29
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browser |    29  100.0%          1     + 189124957 189124985              DQ720098     1    29    29
browser |    29  100.0%         10     +   3573765   3573793              DQ720098     1    29    29
browser |    29  100.0%         10     +   5341469   5341497              DQ720098     1    29    29
browser |    29  100.0%         10     -   6163291   6163319              DQ720098     1    29    29
browser |    29  100.0%         10     -   6235081   6235109              DQ720098     1    29    29
browser |    29  100.0%         10     +   6575858   6575886              DQ720098     1    29    29
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browser |    29  100.0%         10     +   6607152   6607180              DQ720098     1    29    29
browser |    29  100.0%         10     +   6730395   6730423              DQ720098     1    29    29
browser |    29  100.0%         10     +   7348336   7348364              DQ720098     1    29    29
browser |    29  100.0%         10     +   8141312   8141340              DQ720098     1    29    29
browser |    29  100.0%         10     -   8193302   8193330              DQ720098     1    29    29
browser |    29  100.0%         10     -  10020786  10020814              DQ720098     1    29    29
browser |    29  100.0%         10     +  10462982  10463010              DQ720098     1    29    29
browser |    29  100.0%         10     -  11404740  11404768              DQ720098     1    29    29
browser |    29  100.0%         10     +  11458025  11458053              DQ720098     1    29    29
browser |    29  100.0%         10     +  11501040  11501068              DQ720098     1    29    29
browser |    29  100.0%         10     -  11668023  11668051              DQ720098     1    29    29
browser |    29  100.0%         10     +  12144795  12144823              DQ720098     1    29    29
browser |    29  100.0%         10     +  12180143  12180171              DQ720098     1    29    29
browser |    29  100.0%         10     +  12233313  12233341              DQ720098     1    29    29
browser |    29  100.0%         10     -  14169542  14169570              DQ720098     1    29    29
browser |    29  100.0%         10     -  14362946  14362974              DQ720098     1    29    29
browser |    29  100.0%         10     +  14801491  14801519              DQ720098     1    29    29
browser |    29  100.0%         10     -  14878249  14878277              DQ720098     1    29    29
browser |    29  100.0%         10     -  15215943  15215971              DQ720098     1    29    29
browser |    29  100.0%         10     -  15260862  15260890              DQ720098     1    29    29
browser |    29  100.0%         10     -  15344021  15344049              DQ720098     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