DQ726602
 

Information on mRNA DQ726602

Description: Mus musculus piRNA piR-141924, 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: DQ726602
Position: chr12:56988411-56988439

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%         12     +  56988411  56988439              DQ726602     1    29    32
browser |    29  100.0%          1     +  62932407  62932435              DQ726602     1    29    32
browser |    32  100.0%          1     -  90366089  90366120              DQ726602     1    32    32
browser |    31  100.0%          1     +  95609480  95609510              DQ726602     1    31    32
browser |    30  100.0%          1     + 123048677 123048706              DQ726602     1    30    32
browser |    29  100.0%          1     + 134039212 134039240              DQ726602     1    29    32
browser |    29  100.0%          1     + 164345530 164345558              DQ726602     1    29    32
browser |    32  100.0%          1     + 177626774 177626805              DQ726602     1    32    32
browser |    32  100.0%          1     - 184714835 184714866              DQ726602     1    32    32
browser |    30  100.0%         10     -  29487830  29487859              DQ726602     1    30    32
browser |    32  100.0%         10     +  35254400  35254431              DQ726602     1    32    32
browser |    29  100.0%         10     +  52121923  52121951              DQ726602     1    29    32
browser |    32  100.0%         10     -  60488574  60488605              DQ726602     1    32    32
browser |    29  100.0%         10     -  88499669  88499697              DQ726602     1    29    32
browser |    29  100.0%         10     + 116703224 116703252              DQ726602     1    29    32
browser |    28  100.0%         11     +  15405434  15405461              DQ726602     1    28    32
browser |    30  100.0%         11     -  92040530  92040559              DQ726602     3    32    32
browser |    32  100.0%         11     + 100378606 100378637              DQ726602     1    32    32
browser |    32  100.0%         12     -  28496986  28497017              DQ726602     1    32    32
browser |    29  100.0%         12     +  38003087  38003115              DQ726602     4    32    32
browser |    29  100.0%         12     -  52216906  52216934              DQ726602     1    29    32
browser |    29  100.0%         12     -  54986629  54986658              DQ726602     1    29    32
browser |    32  100.0%         12     +  75823172  75823203              DQ726602     1    32    32
browser |    32  100.0%         12     -  80654559  80654590              DQ726602     1    32    32
browser |    29  100.0%         12     + 104483484 104483512              DQ726602     1    29    32
browser |    32  100.0%         13     -  14134251  14134282              DQ726602     1    32    32
browser |    32  100.0%         13     +  19125644  19125675              DQ726602     1    32    32
browser |    32  100.0%         13     -  42736578  42736609              DQ726602     1    32    32
browser |    32  100.0%         13     -  43488506  43488537              DQ726602     1    32    32
browser |    30  100.0%         13     -  71446559  71446588              DQ726602     3    32    32
browser |    32  100.0%         13     +  88794577  88794608              DQ726602     1    32    32
browser |    32  100.0%         13     - 110510236 110510267              DQ726602     1    32    32
browser |    32  100.0%         14     -  68072341  68072372              DQ726602     1    32    32
browser |    32  100.0%         14     -  70605721  70605752              DQ726602     1    32    32
browser |    30  100.0%         14     + 106810513 106810542              DQ726602     1    30    32
browser |    32  100.0%         15     -   9146151   9146182              DQ726602     1    32    32
browser |    32  100.0%         15     -  21297452  21297483              DQ726602     1    32    32
browser |    29  100.0%         15     +  45318493  45318521              DQ726602     1    29    32
browser |    29  100.0%         15     -  59316242  59316270              DQ726602     1    29    32
browser |    29  100.0%         15     -  75121333  75121361              DQ726602     1    29    32
browser |    32  100.0%         15     +  84913384  84913415              DQ726602     1    32    32
browser |    28  100.0%         15     -  98037428  98037455              DQ726602     4    31    32
browser |    32  100.0%         16     +  10618178  10618209              DQ726602     1    32    32
browser |    30  100.0%         16     +  12605323  12605352              DQ726602     3    32    32
browser |    29  100.0%         16     +  15669133  15669161              DQ726602     4    32    32
browser |    32  100.0%         16     -  16575393  16575424              DQ726602     1    32    32
browser |    32  100.0%         16     -  32941079  32941110              DQ726602     1    32    32
browser |    32  100.0%         16     +  53715255  53715287              DQ726602     1    32    32
browser |    32  100.0%         16     -  68496759  68496790              DQ726602     1    32    32
browser |    32  100.0%         16     -  83894785  83894816              DQ726602     1    32    32
browser |    32  100.0%         16     +  94441060  94441091              DQ726602     1    32    32
browser |    29  100.0%         17     -  26397865  26397893              DQ726602     1    29    32
browser |    32  100.0%         17     -  34645504  34645535              DQ726602     1    32    32
browser |    29  100.0%         17     +  48686978  48687006              DQ726602     1    29    32
browser |    32  100.0%         17     -  55995896  55995927              DQ726602     1    32    32
browser |    28  100.0%         17     -  57466394  57466421              DQ726602     1    28    32
browser |    29  100.0%         18     +  13091013  13091041              DQ726602     1    29    32
browser |    29  100.0%         18     -  24361943  24361971              DQ726602     1    29    32
browser |    28  100.0%         18     -  27873558  27873585              DQ726602     2    29    32
browser |    32  100.0%         18     -  51197718  51197749              DQ726602     1    32    32
browser |    28  100.0%         18     +  52290545  52290572              DQ726602     3    30    32
browser |    32  100.0%         18     -  86409001  86409032              DQ726602     1    32    32
browser |    29  100.0%         19     +  44166037  44166065              DQ726602     1    29    32
browser |    32  100.0%         19     +  44957984  44958015              DQ726602     1    32    32
browser |    32  100.0%          2     -   3319875   3319906              DQ726602     1    32    32
browser |    32  100.0%          2     -  19919027  19919058              DQ726602     1    32    32
browser |    29  100.0%          2     -  22505361  22505389              DQ726602     1    29    32
browser |    32  100.0%          2     -  39446925  39446956              DQ726602     1    32    32
browser |    29  100.0%          2     + 124969839 124969867              DQ726602     1    29    32
browser |    32  100.0%          2     + 127471174 127471205              DQ726602     1    32    32
browser |    29  100.0%          2     + 152045320 152045348              DQ726602     4    32    32
browser |    32  100.0%          2     + 160888604 160888635              DQ726602     1    32    32
browser |    32  100.0%          2     - 168566552 168566583              DQ726602     1    32    32
browser |    29  100.0%          2     - 171870452 171870480              DQ726602     1    29    32
browser |    32  100.0%          3     -  20217227  20217258              DQ726602     1    32    32
browser |    30  100.0%          3     -  20727979  20728008              DQ726602     1    30    32
browser |    29  100.0%          3     +  22278156  22278184              DQ726602     1    29    32
browser |    31  100.0%          3     -  36613685  36613715              DQ726602     1    31    32
browser |    32  100.0%          3     -  71666299  71666330              DQ726602     1    32    32
browser |    32  100.0%          3     +  87502217  87502248              DQ726602     1    32    32
browser |    32  100.0%          3     +  98238295  98238326              DQ726602     1    32    32
browser |    32  100.0%          3     + 110161612 110161643              DQ726602     1    32    32
browser |    28  100.0%          3     - 143877331 143877358              DQ726602     2    29    32
browser |    32  100.0%          3     - 146493129 146493160              DQ726602     1    32    32
browser |    30  100.0%          3     + 153597879 153597908              DQ726602     3    32    32
browser |    29  100.0%          4     +  26149879  26149907              DQ726602     1    29    32
browser |    29  100.0%          4     -  43279842  43279870              DQ726602     4    32    32
browser |    29  100.0%          4     +  46547762  46547790              DQ726602     1    29    32
browser |    30  100.0%          4     -  90680047  90680076              DQ726602     1    30    32
browser |    30  100.0%          4     -  94402390  94402419              DQ726602     3    32    32
browser |    28  100.0%          4     -  98639542  98639569              DQ726602     5    32    32
browser |    30  100.0%          4     -  99618648  99618677              DQ726602     1    30    32
browser |    29  100.0%          4     - 118784166 118784194              DQ726602     1    29    32
browser |    32  100.0%          4     - 124975044 124975075              DQ726602     1    32    32
browser |    32  100.0%          4     - 125133909 125133940              DQ726602     1    32    32
browser |    29  100.0%          4     + 133362238 133362266              DQ726602     1    29    32
browser |    29  100.0%          5     -  54332247  54332275              DQ726602     1    29    32
browser |    29  100.0%          5     -  66155411  66155439              DQ726602     1    29    32
browser |    32  100.0%          5     -  81098700  81098731              DQ726602     1    32    32
browser |    32  100.0%          5     - 116139514 116139545              DQ726602     1    32    32
browser |    30  100.0%          6     +  35726729  35726758              DQ726602     1    30    32
browser |    29  100.0%          6     +  57725526  57725554              DQ726602     1    29    32
browser |    32  100.0%          6     -  58655429  58655460              DQ726602     1    32    32
browser |    32  100.0%          6     +  90031529  90031560              DQ726602     1    32    32
browser |    29  100.0%          6     - 115576985 115577013              DQ726602     4    32    32
browser |    29  100.0%          6     + 121270160 121270188              DQ726602     1    29    32
browser |    29  100.0%          6     + 143745872 143745900              DQ726602     1    29    32
browser |    32  100.0%          6     + 147445690 147445721              DQ726602     1    32    32
browser |    32  100.0%          7     +  18545010  18545041              DQ726602     1    32    32
browser |    29  100.0%          7     +  27533004  27533032              DQ726602     1    29    32
browser |    30  100.0%          7     -  45562236  45562265              DQ726602     1    30    32
browser |    28  100.0%          7     -  71575842  71575869              DQ726602     2    29    32
browser |    31  100.0%          7     - 109668160 109668190              DQ726602     1    31    32
browser |    29  100.0%          7     - 122694616 122694644              DQ726602     1    29    32
browser |    32  100.0%          7     - 127762620 127762651              DQ726602     1    32    32
browser |    28  100.0%          7     + 141599263 141599290              DQ726602     2    29    32
browser |    29  100.0%          8     +  15899218  15899246              DQ726602     1    29    32
browser |    29  100.0%          8     +  26429024  26429052              DQ726602     1    29    32
browser |    28  100.0%          8     +  35494674  35494701              DQ726602     2    29    32
browser |    30  100.0%          8     -  72159515  72159544              DQ726602     1    30    32
browser |    32  100.0%          8     +  96599779  96599810              DQ726602     1    32    32
browser |    29  100.0%          8     - 122936311 122936339              DQ726602     1    29    32
browser |    32  100.0%          9     -  12833722  12833753              DQ726602     1    32    32
browser |    31  100.0%          9     +  18316166  18316196              DQ726602     1    31    32
browser |    30  100.0%          9     +  57129961  57129990              DQ726602     3    32    32
browser |    32  100.0%          9     +  57208657  57208688              DQ726602     1    32    32
browser |    29  100.0%          9     -  81963250  81963278              DQ726602     1    29    32
browser |    30  100.0%          9     + 122669334 122669363              DQ726602     1    30    32
browser |    32  100.0%          X     -  12478136  12478167              DQ726602     1    32    32
browser |    29  100.0%          X     -  43149349  43149377              DQ726602     1    29    32
browser |    32  100.0%          X     -  52482619  52482650              DQ726602     1    32    32
browser |    32  100.0%          X     -  56876413  56876444              DQ726602     1    32    32
browser |    32  100.0%          X     -  68931122  68931154              DQ726602     1    32    32
browser |    29  100.0%          X     -  73144617  73144645              DQ726602     4    32    32
browser |    32  100.0%          X     +  92281629  92281660              DQ726602     1    32    32
browser |    32  100.0%          X     + 110237447 110237478              DQ726602     1    32    32
browser |    29  100.0%          X     - 150724422 150724450              DQ726602     1    29    32

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