DQ685908
 

Information on mRNA DQ685908

Description: Mus musculus piRNA piR-101230, 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: DQ685908
Position: chr12:56796138-56796159

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 |    22  100.0%         12     +  56796138  56796159              DQ685908     1    22    22
browser |    22  100.0%          1     +   6504852   6504873              DQ685908     1    22    22
browser |    22  100.0%          1     -  13623640  13623661              DQ685908     1    22    22
browser |    22  100.0%          1     -  18029880  18029901              DQ685908     1    22    22
browser |    22  100.0%          1     -  19695494  19695515              DQ685908     1    22    22
browser |    22  100.0%          1     +  26512428  26512449              DQ685908     1    22    22
browser |    22  100.0%          1     -  27222050  27222071              DQ685908     1    22    22
browser |    22  100.0%          1     -  40739896  40739917              DQ685908     1    22    22
browser |    22  100.0%          1     +  53171103  53171124              DQ685908     1    22    22
browser |    22  100.0%          1     -  55820333  55820354              DQ685908     1    22    22
browser |    22  100.0%          1     -  56814186  56814207              DQ685908     1    22    22
browser |    22  100.0%          1     +  60768272  60768293              DQ685908     1    22    22
browser |    22  100.0%          1     +  62577536  62577557              DQ685908     1    22    22
browser |    22  100.0%          1     -  64425086  64425107              DQ685908     1    22    22
browser |    22  100.0%          1     +  72168958  72168979              DQ685908     1    22    22
browser |    22  100.0%          1     -  76594182  76594203              DQ685908     1    22    22
browser |    22  100.0%          1     -  79917593  79917614              DQ685908     1    22    22
browser |    22  100.0%          1     +  81546147  81546168              DQ685908     1    22    22
browser |    22  100.0%          1     -  87390706  87390727              DQ685908     1    22    22
browser |    22  100.0%          1     +  91403202  91403223              DQ685908     1    22    22
browser |    22  100.0%          1     -  93887116  93887137              DQ685908     1    22    22
browser |    22  100.0%          1     -  97103315  97103336              DQ685908     1    22    22
browser |    22  100.0%          1     - 102962217 102962238              DQ685908     1    22    22
browser |    22  100.0%          1     + 103137166 103137187              DQ685908     1    22    22
browser |    22  100.0%          1     + 108340854 108340875              DQ685908     1    22    22
browser |    22  100.0%          1     - 111633927 111633948              DQ685908     1    22    22
browser |    22  100.0%          1     + 112196332 112196353              DQ685908     1    22    22
browser |    22  100.0%          1     - 112946634 112946655              DQ685908     1    22    22
browser |    22  100.0%          1     + 116580271 116580292              DQ685908     1    22    22
browser |    22  100.0%          1     - 125247422 125247443              DQ685908     1    22    22
browser |    22  100.0%          1     - 130464881 130464902              DQ685908     1    22    22
browser |    22  100.0%          1     - 140965975 140965996              DQ685908     1    22    22
browser |    22  100.0%          1     - 144262734 144262755              DQ685908     1    22    22
browser |    22  100.0%          1     - 145999501 145999522              DQ685908     1    22    22
browser |    22  100.0%          1     + 146161904 146161925              DQ685908     1    22    22
browser |    22  100.0%          1     + 146277207 146277228              DQ685908     1    22    22
browser |    22  100.0%          1     + 148047284 148047305              DQ685908     1    22    22
browser |    22  100.0%          1     + 148336743 148336764              DQ685908     1    22    22
browser |    22  100.0%          1     + 149386303 149386324              DQ685908     1    22    22
browser |    22  100.0%          1     + 154778964 154778985              DQ685908     1    22    22
browser |    22  100.0%          1     - 162670947 162670968              DQ685908     1    22    22
browser |    22  100.0%          1     + 166594470 166594491              DQ685908     1    22    22
browser |    22  100.0%          1     - 169372194 169372215              DQ685908     1    22    22
browser |    22  100.0%          1     - 169946181 169946202              DQ685908     1    22    22
browser |    22  100.0%          1     + 174873002 174873023              DQ685908     1    22    22
browser |    22  100.0%          1     - 177888446 177888467              DQ685908     1    22    22
browser |    22  100.0%          1     - 178004499 178004520              DQ685908     1    22    22
browser |    22  100.0%          1     - 183299107 183299128              DQ685908     1    22    22
browser |    22  100.0%          1     - 195005483 195005504              DQ685908     1    22    22
browser |    22  100.0%         10     -   8477872   8477893              DQ685908     1    22    22
browser |    22  100.0%         10     -  11572851  11572872              DQ685908     1    22    22
browser |    22  100.0%         10     +  19890633  19890654              DQ685908     1    22    22
browser |    22  100.0%         10     +  21522479  21522500              DQ685908     1    22    22
browser |    22  100.0%         10     +  22403370  22403391              DQ685908     1    22    22
browser |    22  100.0%         10     +  23751480  23751501              DQ685908     1    22    22
browser |    22  100.0%         10     -  25847144  25847165              DQ685908     1    22    22
browser |    22  100.0%         10     -  30692812  30692833              DQ685908     1    22    22
browser |    22  100.0%         10     -  30967497  30967518              DQ685908     1    22    22
browser |    22  100.0%         10     -  51761924  51761945              DQ685908     1    22    22
browser |    22  100.0%         10     -  56599672  56599693              DQ685908     1    22    22
browser |    22  100.0%         10     -  57016592  57016613              DQ685908     1    22    22
browser |    22  100.0%         10     -  70630085  70630106              DQ685908     1    22    22
browser |    22  100.0%         10     -  77789436  77789457              DQ685908     1    22    22
browser |    22  100.0%         10     +  81510635  81510656              DQ685908     1    22    22
browser |    22  100.0%         10     +  81669763  81669784              DQ685908     1    22    22
browser |    22  100.0%         10     +  83305991  83306012              DQ685908     1    22    22
browser |    22  100.0%         10     -  88489677  88489698              DQ685908     1    22    22
browser |    22  100.0%         10     +  94202194  94202215              DQ685908     1    22    22
browser |    22  100.0%         10     +  97162573  97162594              DQ685908     1    22    22
browser |    22  100.0%         10     -  99177816  99177837              DQ685908     1    22    22
browser |    22  100.0%         10     - 107838189 107838210              DQ685908     1    22    22
browser |    22  100.0%         10     - 110534960 110534981              DQ685908     1    22    22
browser |    22  100.0%         10     + 116446427 116446448              DQ685908     1    22    22
browser |    22  100.0%         10     - 117909383 117909404              DQ685908     1    22    22
browser |    22  100.0%         10     - 122344503 122344524              DQ685908     1    22    22
browser |    22  100.0%         10     + 122672913 122672934              DQ685908     1    22    22
browser |    21  100.0%         10     - 123698081 123698101              DQ685908     1    21    22
browser |    22  100.0%         10     - 124415055 124415076              DQ685908     1    22    22
browser |    22  100.0%         10     + 124519107 124519128              DQ685908     1    22    22
browser |    22  100.0%         10     - 129764003 129764024              DQ685908     1    22    22
browser |    22  100.0%         11     +   6095754   6095775              DQ685908     1    22    22
browser |    22  100.0%         11     +   7529946   7529967              DQ685908     1    22    22
browser |    22  100.0%         11     -  10713156  10713177              DQ685908     1    22    22
browser |    22  100.0%         11     -  12748438  12748459              DQ685908     1    22    22
browser |    22  100.0%         11     +  18760718  18760739              DQ685908     1    22    22
browser |    22  100.0%         11     +  19517687  19517708              DQ685908     1    22    22
browser |    22  100.0%         11     -  38375168  38375189              DQ685908     1    22    22
browser |    22  100.0%         11     +  39958814  39958835              DQ685908     1    22    22
browser |    21  100.0%         11     +  54471662  54471682              DQ685908     1    21    22
browser |    22  100.0%         11     +  55136025  55136046              DQ685908     1    22    22
browser |    22  100.0%         11     -  61314107  61314128              DQ685908     1    22    22
browser |    22  100.0%         11     +  66842331  66842352              DQ685908     1    22    22
browser |    22  100.0%         11     +  74114781  74114802              DQ685908     1    22    22
browser |    22  100.0%         11     -  74778066  74778087              DQ685908     1    22    22
browser |    22  100.0%         11     -  79766217  79766238              DQ685908     1    22    22
browser |    22  100.0%         11     -  84954372  84954393              DQ685908     1    22    22
browser |    22  100.0%         11     +  88806045  88806066              DQ685908     1    22    22
browser |    22  100.0%         11     -  90795359  90795380              DQ685908     1    22    22
browser |    22  100.0%         11     +  90855262  90855283              DQ685908     1    22    22
browser |    22  100.0%         11     -  91992729  91992750              DQ685908     1    22    22
browser |    22  100.0%         11     -  98506933  98506954              DQ685908     1    22    22
browser |    22  100.0%         11     +  99605208  99605229              DQ685908     1    22    22
browser |    22  100.0%         11     + 106185589 106185610              DQ685908     1    22    22
browser |    22  100.0%         11     - 113805865 113805886              DQ685908     1    22    22
browser |    22  100.0%         11     + 115649988 115650009              DQ685908     1    22    22
browser |    22  100.0%         11     - 116679232 116679253              DQ685908     1    22    22
browser |    22  100.0%         11     - 117393527 117393548              DQ685908     1    22    22
browser |    22  100.0%         12     -   3055213   3055234              DQ685908     1    22    22
browser |    22  100.0%         12     +   3385071   3385092              DQ685908     1    22    22
browser |    22  100.0%         12     -   6569381   6569402              DQ685908     1    22    22
browser |    22  100.0%         12     -   6855872   6855893              DQ685908     1    22    22
browser |    22  100.0%         12     +  14648420  14648441              DQ685908     1    22    22
browser |    22  100.0%         12     -  17175060  17175081              DQ685908     1    22    22
browser |    22  100.0%         12     -  18012649  18012670              DQ685908     1    22    22
browser |    22  100.0%         12     +  18329350  18329371              DQ685908     1    22    22
browser |    22  100.0%         12     +  19312502  19312523              DQ685908     1    22    22
browser |    22  100.0%         12     -  19827350  19827371              DQ685908     1    22    22
browser |    22  100.0%         12     +  19849737  19849758              DQ685908     1    22    22
browser |    22  100.0%         12     -  32080840  32080861              DQ685908     1    22    22
browser |    22  100.0%         12     -  41416347  41416368              DQ685908     1    22    22
browser |    22  100.0%         12     -  48581802  48581823              DQ685908     1    22    22
browser |    22  100.0%         12     -  49044412  49044433              DQ685908     1    22    22
browser |    22  100.0%         12     +  60757943  60757964              DQ685908     1    22    22
browser |    22  100.0%         12     +  65078206  65078227              DQ685908     1    22    22
browser |    22  100.0%         12     -  65682893  65682914              DQ685908     1    22    22
browser |    22  100.0%         12     +  65852264  65852285              DQ685908     1    22    22
browser |    22  100.0%         12     +  70712197  70712218              DQ685908     1    22    22
browser |    22  100.0%         12     +  70969046  70969067              DQ685908     1    22    22
browser |    22  100.0%         12     -  76794209  76794230              DQ685908     1    22    22
browser |    22  100.0%         12     +  79612876  79612897              DQ685908     1    22    22
browser |    22  100.0%         12     +  94239067  94239088              DQ685908     1    22    22
browser |    22  100.0%         12     +  96198468  96198489              DQ685908     1    22    22
browser |    22  100.0%         12     -  98324332  98324353              DQ685908     1    22    22
browser |    22  100.0%         12     - 109871193 109871214              DQ685908     1    22    22
browser |    22  100.0%         12     - 114599883 114599904              DQ685908     1    22    22
browser |    22  100.0%         13     -   4391290   4391311              DQ685908     1    22    22
browser |    22  100.0%         13     +   8003439   8003460              DQ685908     1    22    22
browser |    22  100.0%         13     +   9486953   9486974              DQ685908     1    22    22
browser |    22  100.0%         13     +   9908251   9908272              DQ685908     1    22    22
browser |    22  100.0%         13     -  11518802  11518823              DQ685908     1    22    22
browser |    22  100.0%         13     +  19182298  19182319              DQ685908     1    22    22
browser |    22  100.0%         13     -  22302005  22302026              DQ685908     1    22    22
browser |    21  100.0%         13     +  23827196  23827216              DQ685908     1    21    22
browser |    22  100.0%         13     +  28312647  28312668              DQ685908     1    22    22
browser |    22  100.0%         13     -  30556952  30556973              DQ685908     1    22    22
browser |    22  100.0%         13     -  32537375  32537396              DQ685908     1    22    22
browser |    22  100.0%         13     +  33135829  33135850              DQ685908     1    22    22
browser |    22  100.0%         13     -  34048825  34048846              DQ685908     1    22    22
browser |    22  100.0%         13     -  44420669  44420690              DQ685908     1    22    22
browser |    22  100.0%         13     -  45167431  45167452              DQ685908     1    22    22
browser |    22  100.0%         13     +  50886990  50887011              DQ685908     1    22    22
browser |    22  100.0%         13     +  56864950  56864971              DQ685908     1    22    22
browser |    21  100.0%         13     +  60173680  60173700              DQ685908     1    21    22
browser |    22  100.0%         13     +  60348770  60348791              DQ685908     1    22    22
browser |    22  100.0%         13     +  61096588  61096609              DQ685908     1    22    22
browser |    22  100.0%         13     +  62625096  62625117              DQ685908     1    22    22
browser |    22  100.0%         13     -  65028908  65028929              DQ685908     1    22    22
browser |    22  100.0%         13     -  66162941  66162962              DQ685908     1    22    22
browser |    22  100.0%         13     -  66379868  66379889              DQ685908     1    22    22
browser |    22  100.0%         13     +  77380422  77380443              DQ685908     1    22    22
browser |    22  100.0%         13     +  77820507  77820528              DQ685908     1    22    22
browser |    22  100.0%         13     -  79714474  79714495              DQ685908     1    22    22
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browser |    22  100.0%         13     - 102966483 102966504              DQ685908     1    22    22
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browser |    22  100.0%         13     + 111835045 111835066              DQ685908     1    22    22
browser |    22  100.0%         13     + 113700008 113700029              DQ685908     1    22    22
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browser |    22  100.0%         13     - 117435225 117435246              DQ685908     1    22    22
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browser |    22  100.0%         14     -   3459550   3459571              DQ685908     1    22    22
browser |    22  100.0%         14     +   6649406   6649427              DQ685908     1    22    22
browser |    22  100.0%         14     +   8133767   8133788              DQ685908     1    22    22
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browser |    22  100.0%         15     -   3198104   3198125              DQ685908     1    22    22
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browser |    22  100.0%         15     -  19052081  19052102              DQ685908     1    22    22
browser |    22  100.0%         15     +  21922062  21922083              DQ685908     1    22    22
browser |    22  100.0%         15     -  24324164  24324185              DQ685908     1    22    22
browser |    22  100.0%         15     +  26907128  26907149              DQ685908     1    22    22
browser |    22  100.0%         15     +  27290500  27290521              DQ685908     1    22    22
browser |    22  100.0%         15     -  38613089  38613110              DQ685908     1    22    22
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browser |    22  100.0%         15     -  47222838  47222859              DQ685908     1    22    22
browser |    22  100.0%         15     -  49188893  49188914              DQ685908     1    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