DQ723933
 

Information on mRNA DQ723933

Description: Mus musculus piRNA piR-139255, 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: DQ723933
Position: chr12:56960325-56960349

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 |    25  100.0%         12     -  56960325  56960349              DQ723933     1    25    25
browser |    25  100.0%          1     +  11437962  11437986              DQ723933     1    25    25
browser |    25  100.0%          1     +  11440327  11440351              DQ723933     1    25    25
browser |    24  100.0%          1     +  12035848  12035871              DQ723933     1    24    25
browser |    25  100.0%          1     +  17595040  17595064              DQ723933     1    25    25
browser |    25  100.0%          1     +  17597424  17597448              DQ723933     1    25    25
browser |    25  100.0%          1     -  22150571  22150595              DQ723933     1    25    25
browser |    25  100.0%          1     +  27406389  27406413              DQ723933     1    25    25
browser |    25  100.0%          1     -  51424154  51424178              DQ723933     1    25    25
browser |    25  100.0%          1     +  57624485  57624509              DQ723933     1    25    25
browser |    25  100.0%          1     +  57627896  57627920              DQ723933     1    25    25
browser |    25  100.0%          1     -  73149813  73149837              DQ723933     1    25    25
browser |    25  100.0%          1     +  78023193  78023217              DQ723933     1    25    25
browser |    25  100.0%          1     + 108873232 108873256              DQ723933     1    25    25
browser |    25  100.0%          1     + 108876723 108876747              DQ723933     1    25    25
browser |    25  100.0%          1     - 117917896 117917920              DQ723933     1    25    25
browser |    25  100.0%          1     - 117920285 117920309              DQ723933     1    25    25
browser |    25  100.0%          1     - 130676077 130676101              DQ723933     1    25    25
browser |    25  100.0%          1     - 144996099 144996123              DQ723933     1    25    25
browser |    24  100.0%          1     + 147235667 147235690              DQ723933     1    24    25
browser |    25  100.0%          1     - 153756290 153756314              DQ723933     1    25    25
browser |    25  100.0%         10     +  11776808  11776832              DQ723933     1    25    25
browser |    25  100.0%         10     +  11779448  11779472              DQ723933     1    25    25
browser |    25  100.0%         10     -  18114941  18114965              DQ723933     1    25    25
browser |    25  100.0%         10     -  18117231  18117255              DQ723933     1    25    25
browser |    25  100.0%         10     +  26539217  26539241              DQ723933     1    25    25
browser |    25  100.0%         10     -  27669307  27669331              DQ723933     1    25    25
browser |    25  100.0%         10     +  28886660  28886684              DQ723933     1    25    25
browser |    25  100.0%         10     +  28890159  28890183              DQ723933     1    25    25
browser |    25  100.0%         10     +  37837877  37837901              DQ723933     1    25    25
browser |    25  100.0%         10     +  47557027  47557051              DQ723933     1    25    25
browser |    25  100.0%         10     +  47559493  47559517              DQ723933     1    25    25
browser |    25  100.0%         10     +  55591874  55591898              DQ723933     1    25    25
browser |    25  100.0%         10     +  57441414  57441438              DQ723933     1    25    25
browser |    25  100.0%         10     +  77645447  77645471              DQ723933     1    25    25
browser |    25  100.0%         10     +  87345519  87345543              DQ723933     1    25    25
browser |    25  100.0%         10     - 103909557 103909581              DQ723933     1    25    25
browser |    25  100.0%         10     - 121976990 121977014              DQ723933     1    25    25
browser |    25  100.0%         10     - 121979229 121979253              DQ723933     1    25    25
browser |    25  100.0%         11     -  21547033  21547057              DQ723933     1    25    25
browser |    25  100.0%         11     - 108365936 108365960              DQ723933     1    25    25
browser |    25  100.0%         12     +  14644420  14644444              DQ723933     1    25    25
browser |    25  100.0%         12     +  14651345  14651369              DQ723933     1    25    25
browser |    25  100.0%         12     -  25907348  25907372              DQ723933     1    25    25
browser |    25  100.0%         12     +  26156728  26156752              DQ723933     1    25    25
browser |    25  100.0%         12     +  26159085  26159109              DQ723933     1    25    25
browser |    25  100.0%         12     +  43263291  43263315              DQ723933     1    25    25
browser |    25  100.0%         12     -  56957977  56958001              DQ723933     1    25    25
browser |    25  100.0%         12     -  76699889  76699913              DQ723933     1    25    25
browser |    25  100.0%         12     -  76702359  76702383              DQ723933     1    25    25
browser |    25  100.0%         12     -  84068615  84068639              DQ723933     1    25    25
browser |    25  100.0%         12     + 103762652 103762676              DQ723933     1    25    25
browser |    24  100.0%         12     + 115483897 115483920              DQ723933     2    25    25
browser |    25  100.0%         13     +   5294962   5294986              DQ723933     1    25    25
browser |    25  100.0%         13     -   9891883   9891907              DQ723933     1    25    25
browser |    25  100.0%         13     +  29449645  29449669              DQ723933     1    25    25
browser |    25  100.0%         13     -  41971688  41971712              DQ723933     1    25    25
browser |    25  100.0%         13     +  66145264  66145288              DQ723933     1    25    25
browser |    25  100.0%         13     +  66148851  66148875              DQ723933     1    25    25
browser |    25  100.0%         13     -  66767531  66767555              DQ723933     1    25    25
browser |    25  100.0%         13     +  81232126  81232150              DQ723933     1    25    25
browser |    25  100.0%         13     +  81234727  81234751              DQ723933     1    25    25
browser |    25  100.0%         13     +  87432241  87432265              DQ723933     1    25    25
browser |    25  100.0%         13     -  87532589  87532613              DQ723933     1    25    25
browser |    25  100.0%         13     + 103527359 103527383              DQ723933     1    25    25
browser |    25  100.0%         13     - 103845242 103845266              DQ723933     1    25    25
browser |    25  100.0%         13     - 106921925 106921949              DQ723933     1    25    25
browser |    25  100.0%         13     - 106924437 106924461              DQ723933     1    25    25
browser |    25  100.0%         13     + 115474639 115474663              DQ723933     1    25    25
browser |    25  100.0%         13     - 116062523 116062547              DQ723933     1    25    25
browser |    25  100.0%         14     +  15926855  15926879              DQ723933     1    25    25
browser |    25  100.0%         14     +  16244879  16244903              DQ723933     1    25    25
browser |    25  100.0%         14     +  16292108  16292132              DQ723933     1    25    25
browser |    25  100.0%         14     +  16776693  16776717              DQ723933     1    25    25
browser |    25  100.0%         14     +  17129244  17129268              DQ723933     1    25    25
browser |    25  100.0%         14     -  18225807  18225831              DQ723933     1    25    25
browser |    25  100.0%         14     +  98992599  98992623              DQ723933     1    25    25
browser |    25  100.0%         14     - 101818680 101818704              DQ723933     1    25    25
browser |    25  100.0%         14     - 101821239 101821263              DQ723933     1    25    25
browser |    25  100.0%         15     +  34552731  34552755              DQ723933     1    25    25
browser |    25  100.0%         15     -  97631997  97632021              DQ723933     1    25    25
browser |    25  100.0%         15     -  97634255  97634279              DQ723933     1    25    25
browser |    25  100.0%         15     - 103810513 103810537              DQ723933     1    25    25
browser |    25  100.0%         15     - 103817300 103817324              DQ723933     1    25    25
browser |    25  100.0%         16     +   6211332   6211356              DQ723933     1    25    25
browser |    25  100.0%         16     -  29073916  29073940              DQ723933     1    25    25
browser |    25  100.0%         16     -  48725409  48725433              DQ723933     1    25    25
browser |    25  100.0%         16     +  77147386  77147410              DQ723933     1    25    25
browser |    25  100.0%         16     +  77823730  77823754              DQ723933     1    25    25
browser |    25  100.0%         16     -  79274392  79274416              DQ723933     1    25    25
browser |    25  100.0%         17     +   5596856   5596880              DQ723933     1    25    25
browser |    25  100.0%         17     +  15823356  15823380              DQ723933     1    25    25
browser |    25  100.0%         17     +  15830153  15830177              DQ723933     1    25    25
browser |    25  100.0%         17     -  18340155  18340179              DQ723933     1    25    25
browser |    25  100.0%         17     +  27570243  27570267              DQ723933     1    25    25
browser |    25  100.0%         17     +  27573914  27573938              DQ723933     1    25    25
browser |    25  100.0%         17     -  29438087  29438111              DQ723933     1    25    25
browser |    25  100.0%         17     +  38843347  38843371              DQ723933     1    25    25
browser |    25  100.0%         17     -  61327469  61327493              DQ723933     1    25    25
browser |    25  100.0%         17     -  72661725  72661749              DQ723933     1    25    25
browser |    23  100.0%         17     +  83057688  83057710              DQ723933     3    25    25
browser |    25  100.0%         18     +   5110020   5110044              DQ723933     1    25    25
browser |    25  100.0%         18     +   5113424   5113448              DQ723933     1    25    25
browser |    25  100.0%         18     +  24166474  24166498              DQ723933     1    25    25
browser |    25  100.0%         18     +  24169886  24169910              DQ723933     1    25    25
browser |    25  100.0%         19     +   5008144   5008168              DQ723933     1    25    25
browser |    25  100.0%         19     +  11399744  11399768              DQ723933     1    25    25
browser |    25  100.0%         19     +  11402623  11402647              DQ723933     1    25    25
browser |    25  100.0%          2     +  57853835  57853859              DQ723933     1    25    25
browser |    25  100.0%          2     +  57856151  57856175              DQ723933     1    25    25
browser |    25  100.0%          2     -  93389398  93389422              DQ723933     1    25    25
browser |    25  100.0%          2     + 120466624 120466648              DQ723933     1    25    25
browser |    25  100.0%          2     + 120469645 120469669              DQ723933     1    25    25
browser |    25  100.0%          2     - 138624168 138624192              DQ723933     1    25    25
browser |    25  100.0%          2     + 138775325 138775349              DQ723933     1    25    25
browser |    25  100.0%          2     + 172148289 172148313              DQ723933     1    25    25
browser |    25  100.0%          2     - 179958409 179958433              DQ723933     1    25    25
browser |    25  100.0%          3     -   4069175   4069199              DQ723933     1    25    25
browser |    25  100.0%          3     -   4071605   4071629              DQ723933     1    25    25
browser |    25  100.0%          3     +   9974034   9974058              DQ723933     1    25    25
browser |    25  100.0%          3     +  20234259  20234283              DQ723933     1    25    25
browser |    25  100.0%          3     +  23739956  23739980              DQ723933     1    25    25
browser |    25  100.0%          3     -  98969874  98969898              DQ723933     1    25    25
browser |    25  100.0%          3     - 122447955 122447979              DQ723933     1    25    25
browser |    25  100.0%          3     - 122450526 122450550              DQ723933     1    25    25
browser |    25  100.0%          3     + 132249567 132249591              DQ723933     1    25    25
browser |    25  100.0%          3     - 151446376 151446400              DQ723933     1    25    25
browser |    25  100.0%          4     -  47068082  47068106              DQ723933     1    25    25
browser |    25  100.0%          4     -  47071344  47071368              DQ723933     1    25    25
browser |    25  100.0%          4     -  52615100  52615124              DQ723933     1    25    25
browser |    25  100.0%          4     -  73352587  73352611              DQ723933     1    25    25
browser |    25  100.0%          4     +  74376549  74376573              DQ723933     1    25    25
browser |    25  100.0%          4     -  79308810  79308834              DQ723933     1    25    25
browser |    25  100.0%          4     -  87055489  87055513              DQ723933     1    25    25
browser |    25  100.0%          4     - 100741094 100741118              DQ723933     1    25    25
browser |    25  100.0%          4     + 135094922 135094946              DQ723933     1    25    25
browser |    25  100.0%          4     + 142513085 142513109              DQ723933     1    25    25
browser |    25  100.0%          5     -  18127216  18127240              DQ723933     1    25    25
browser |    25  100.0%          5     -  23390121  23390145              DQ723933     1    25    25
browser |    25  100.0%          5     -  23393186  23393210              DQ723933     1    25    25
browser |    25  100.0%          5     -  23931494  23931518              DQ723933     1    25    25
browser |    25  100.0%          5     -  23934808  23934832              DQ723933     1    25    25
browser |    25  100.0%          5     -  31913323  31913347              DQ723933     1    25    25
browser |    25  100.0%          5     -  32735715  32735739              DQ723933     1    25    25
browser |    25  100.0%          5     -  89978664  89978688              DQ723933     1    25    25
browser |    25  100.0%          5     + 104181668 104181692              DQ723933     1    25    25
browser |    25  100.0%          5     + 134065195 134065219              DQ723933     1    25    25
browser |    25  100.0%          6     +  26860148  26860172              DQ723933     1    25    25
browser |    25  100.0%          6     -  75599655  75599679              DQ723933     1    25    25
browser |    25  100.0%          6     -  78915170  78915194              DQ723933     1    25    25
browser |    25  100.0%          6     -  93045471  93045495              DQ723933     1    25    25
browser |    25  100.0%          6     - 128666517 128666541              DQ723933     1    25    25
browser |    25  100.0%          6     - 128670546 128670570              DQ723933     1    25    25
browser |    25  100.0%          6     - 138200005 138200029              DQ723933     1    25    25
browser |    25  100.0%          6     - 138429678 138429702              DQ723933     1    25    25
browser |    25  100.0%          7     +   6089461   6089485              DQ723933     1    25    25
browser |    23  100.0%          7     -  24385343  24385365              DQ723933     3    25    25
browser |    25  100.0%          7     -  55059059  55059083              DQ723933     1    25    25
browser |    25  100.0%          7     -  55061638  55061662              DQ723933     1    25    25
browser |    25  100.0%          7     +  82999861  82999885              DQ723933     1    25    25
browser |    25  100.0%          7     + 106133388 106133412              DQ723933     1    25    25
browser |    25  100.0%          7     - 121196591 121196615              DQ723933     1    25    25
browser |    25  100.0%          7     - 121199171 121199195              DQ723933     1    25    25
browser |    25  100.0%          8     -  12069663  12069687              DQ723933     1    25    25
browser |    25  100.0%          9     +   9313220   9313244              DQ723933     1    25    25
browser |    24  100.0%          9     -  12444124  12444147              DQ723933     1    24    25
browser |    25  100.0%          9     -  12447277  12447301              DQ723933     1    25    25
browser |    25  100.0%          9     +  18957703  18957727              DQ723933     1    25    25
browser |    25  100.0%          9     +  18960173  18960197              DQ723933     1    25    25
browser |    25  100.0%          9     -  47238586  47238610              DQ723933     1    25    25
browser |    25  100.0%          9     -  93526352  93526376              DQ723933     1    25    25
browser |    25  100.0%          9     -  93533303  93533327              DQ723933     1    25    25
browser |    25  100.0%          9     + 122286833 122286857              DQ723933     1    25    25
browser |    25  100.0%          X     -  10004584  10004608              DQ723933     1    25    25
browser |    25  100.0%          X     +  62619380  62619404              DQ723933     1    25    25
browser |    25  100.0%          X     +  62622848  62622872              DQ723933     1    25    25
browser |    25  100.0%          X     +  66258932  66258956              DQ723933     1    25    25
browser |    25  100.0%          X     +  96801775  96801799              DQ723933     1    25    25
browser |    23  100.0%          X     +  96804159  96804181              DQ723933     3    25    25
browser |    25  100.0%          X     + 141953326 141953350              DQ723933     1    25    25
browser |    25  100.0%          X     + 141964007 141964031              DQ723933     1    25    25
browser |    25  100.0%          X     - 155305026 155305050              DQ723933     1    25    25
browser |    25  100.0%          X     - 163724981 163725005              DQ723933     1    25    25
browser |    25  100.0%          X     + 166120364 166120388              DQ723933     1    25    25
browser |    25  100.0%          Y     -   5502101   5502125              DQ723933     1    25    25
browser |    25  100.0%          Y     -   5508922   5508946              DQ723933     1    25    25
browser |    25  100.0%          Y     -   8390381   8390405              DQ723933     1    25    25
browser |    25  100.0%          Y     -   8653306   8653330              DQ723933     1    25    25
browser |    25  100.0%          Y     -   9285336   9285360              DQ723933     1    25    25
browser |    25  100.0%          Y     -   9429910   9429934              DQ723933     1    25    25
browser |    25  100.0%          Y     +  15105260  15105284              DQ723933     1    25    25
browser |    25  100.0%          Y     +  15112172  15112196              DQ723933     1    25    25
browser |    25  100.0%          Y     -  15359609  15359633              DQ723933     1    25    25
browser |    25  100.0%          Y     +  19817863  19817887              DQ723933     1    25    25
browser |    25  100.0%          Y     +  19824775  19824799              DQ723933     1    25    25
browser |    25  100.0%          Y     -  20072130  20072154              DQ723933     1    25    25
browser |    25  100.0%          Y     +  42326186  42326210              DQ723933     1    25    25
browser |    25  100.0%          Y     +  42333114  42333138              DQ723933     1    25    25
browser |    25  100.0%          Y     -  43171656  43171680              DQ723933     1    25    25
browser |    25  100.0%          Y     -  43178582  43178606              DQ723933     1    25    25
browser |    25  100.0%          Y     -  46184288  46184312              DQ723933     1    25    25
browser |    25  100.0%          Y     -  46191215  46191239              DQ723933     1    25    25
browser |    25  100.0%          Y     +  46435672  46435696              DQ723933     1    25    25
browser |    25  100.0%          Y     +  46442599  46442623              DQ723933     1    25    25
browser |    25  100.0%          Y     +  59353616  59353640              DQ723933     1    25    25
browser |    25  100.0%          Y     +  59360544  59360568              DQ723933     1    25    25

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