DQ694443
 

Information on mRNA DQ694443

Description: Mus musculus piRNA piR-109765, 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: DQ694443
Position: chrX:15628617-15628644

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 |    28  100.0%          X     -  15628617  15628644              DQ694443     1    28    28
browser |    28  100.0%          1     -   3986279   3986306              DQ694443     1    28    28
browser |    28  100.0%          1     +   4074871   4074898              DQ694443     1    28    28
browser |    28  100.0%          1     -   6131411   6131438              DQ694443     1    28    28
browser |    28  100.0%          1     -   6471409   6471436              DQ694443     1    28    28
browser |    28  100.0%          1     -   7724568   7724595              DQ694443     1    28    28
browser |    28  100.0%          1     -   8233589   8233616              DQ694443     1    28    28
browser |    28  100.0%          1     +   8541123   8541150              DQ694443     1    28    28
browser |    28  100.0%          1     -   9435686   9435713              DQ694443     1    28    28
browser |    28  100.0%          1     -   9442392   9442419              DQ694443     1    28    28
browser |    28  100.0%          1     +  10927933  10927960              DQ694443     1    28    28
browser |    28  100.0%          1     -  12031930  12031957              DQ694443     1    28    28
browser |    28  100.0%          1     +  14781751  14781778              DQ694443     1    28    28
browser |    28  100.0%          1     +  18229264  18229291              DQ694443     1    28    28
browser |    28  100.0%          1     -  18576650  18576677              DQ694443     1    28    28
browser |    28  100.0%          1     +  23637971  23637998              DQ694443     1    28    28
browser |    28  100.0%          1     +  24328233  24328260              DQ694443     1    28    28
browser |    28  100.0%          1     -  26446705  26446732              DQ694443     1    28    28
browser |    28  100.0%          1     +  27270378  27270405              DQ694443     1    28    28
browser |    28  100.0%          1     +  28532841  28532868              DQ694443     1    28    28
browser |    28  100.0%          1     +  30756513  30756540              DQ694443     1    28    28
browser |    28  100.0%          1     +  31596574  31596601              DQ694443     1    28    28
browser |    28  100.0%          1     +  31611739  31611766              DQ694443     1    28    28
browser |    28  100.0%          1     -  35745922  35745949              DQ694443     1    28    28
browser |    28  100.0%          1     -  35793619  35793646              DQ694443     1    28    28
browser |    28  100.0%          1     +  37452081  37452108              DQ694443     1    28    28
browser |    28  100.0%          1     +  38417456  38417483              DQ694443     1    28    28
browser |    28  100.0%          1     -  40572105  40572132              DQ694443     1    28    28
browser |    28  100.0%          1     +  44959928  44959955              DQ694443     1    28    28
browser |    28  100.0%          1     -  46285587  46285614              DQ694443     1    28    28
browser |    28  100.0%          1     -  46583951  46583978              DQ694443     1    28    28
browser |    28  100.0%          1     +  46622462  46622489              DQ694443     1    28    28
browser |    28  100.0%          1     -  50142732  50142759              DQ694443     1    28    28
browser |    26  100.0%          1     +  81516207  81516232              DQ694443     1    26    28
browser |    28  100.0%          1     +  81972852  81972879              DQ694443     1    28    28
browser |    26  100.0%          1     +  92504426  92504451              DQ694443     1    26    28
browser |    28  100.0%          1     +  97626733  97626760              DQ694443     1    28    28
browser |    28  100.0%          1     -  99147216  99147243              DQ694443     1    28    28
browser |    28  100.0%          1     - 101009217 101009244              DQ694443     1    28    28
browser |    28  100.0%          1     - 101083208 101083235              DQ694443     1    28    28
browser |    28  100.0%          1     - 102110766 102110793              DQ694443     1    28    28
browser |    28  100.0%          1     - 103109856 103109883              DQ694443     1    28    28
browser |    28  100.0%          1     - 103777108 103777135              DQ694443     1    28    28
browser |    28  100.0%          1     - 104810130 104810157              DQ694443     1    28    28
browser |    28  100.0%          1     - 107950304 107950331              DQ694443     1    28    28
browser |    28  100.0%          1     + 111915640 111915667              DQ694443     1    28    28
browser |    27  100.0%          1     - 112898533 112898559              DQ694443     1    27    28
browser |    28  100.0%          1     - 113281880 113281907              DQ694443     1    28    28
browser |    28  100.0%          1     + 113780278 113780305              DQ694443     1    28    28
browser |    28  100.0%          1     - 115135620 115135647              DQ694443     1    28    28
browser |    28  100.0%          1     - 121906119 121906146              DQ694443     1    28    28
browser |    28  100.0%          1     + 121940136 121940163              DQ694443     1    28    28
browser |    28  100.0%          1     - 121969902 121969929              DQ694443     1    28    28
browser |    28  100.0%          1     - 133278067 133278094              DQ694443     1    28    28
browser |    28  100.0%          1     + 133386719 133386746              DQ694443     1    28    28
browser |    28  100.0%          1     - 133464003 133464030              DQ694443     1    28    28
browser |    28  100.0%          1     + 143541003 143541030              DQ694443     1    28    28
browser |    28  100.0%          1     + 147555824 147555851              DQ694443     1    28    28
browser |    28  100.0%          1     + 154473876 154473903              DQ694443     1    28    28
browser |    28  100.0%          1     + 154841603 154841630              DQ694443     1    28    28
browser |    28  100.0%          1     + 157337984 157338011              DQ694443     1    28    28
browser |    26  100.0%          1     + 159910881 159910906              DQ694443     1    26    28
browser |    28  100.0%          1     - 168573865 168573892              DQ694443     1    28    28
browser |    28  100.0%          1     + 170679366 170679393              DQ694443     1    28    28
browser |    28  100.0%          1     - 173271643 173271670              DQ694443     1    28    28
browser |    28  100.0%          1     - 176097034 176097061              DQ694443     1    28    28
browser |    26  100.0%          1     - 176669769 176669794              DQ694443     1    26    28
browser |    28  100.0%          1     - 183891251 183891278              DQ694443     1    28    28
browser |    28  100.0%          1     + 193738068 193738095              DQ694443     1    28    28
browser |    27  100.0%          1     + 194163316 194163342              DQ694443     1    27    28
browser |    28  100.0%          1     - 194237532 194237559              DQ694443     1    28    28
browser |    28  100.0%         10     +   5959870   5959897              DQ694443     1    28    28
browser |    28  100.0%         10     +   7461371   7461398              DQ694443     1    28    28
browser |    28  100.0%         10     -  10314524  10314551              DQ694443     1    28    28
browser |    28  100.0%         10     +  11794974  11795001              DQ694443     1    28    28
browser |    28  100.0%         10     -  18426064  18426091              DQ694443     1    28    28
browser |    28  100.0%         10     +  27240236  27240263              DQ694443     1    28    28
browser |    28  100.0%         10     +  29260331  29260358              DQ694443     1    28    28
browser |    28  100.0%         10     -  31099190  31099217              DQ694443     1    28    28
browser |    28  100.0%         10     -  33687074  33687101              DQ694443     1    28    28
browser |    28  100.0%         10     -  33687759  33687786              DQ694443     1    28    28
browser |    28  100.0%         10     +  33897828  33897855              DQ694443     1    28    28
browser |    28  100.0%         10     +  33995319  33995346              DQ694443     1    28    28
browser |    28  100.0%         10     +  34496495  34496522              DQ694443     1    28    28
browser |    28  100.0%         10     +  34730448  34730475              DQ694443     1    28    28
browser |    28  100.0%         10     -  35752673  35752700              DQ694443     1    28    28
browser |    28  100.0%         10     +  36507236  36507263              DQ694443     1    28    28
browser |    28  100.0%         10     +  38343204  38343231              DQ694443     1    28    28
browser |    28  100.0%         10     +  38993049  38993076              DQ694443     1    28    28
browser |    28  100.0%         10     +  40076766  40076793              DQ694443     1    28    28
browser |    28  100.0%         10     +  40404734  40404761              DQ694443     1    28    28
browser |    28  100.0%         10     -  45979727  45979754              DQ694443     1    28    28
browser |    28  100.0%         10     -  46251694  46251721              DQ694443     1    28    28
browser |    28  100.0%         10     -  46899984  46900011              DQ694443     1    28    28
browser |    28  100.0%         10     -  51675854  51675881              DQ694443     1    28    28
browser |    28  100.0%         10     -  54167279  54167306              DQ694443     1    28    28
browser |    28  100.0%         10     +  59997615  59997642              DQ694443     1    28    28
browser |    28  100.0%         10     -  63940699  63940726              DQ694443     1    28    28
browser |    28  100.0%         10     -  65897232  65897259              DQ694443     1    28    28
browser |    28  100.0%         10     -  77405305  77405332              DQ694443     1    28    28
browser |    28  100.0%         10     -  77575532  77575559              DQ694443     1    28    28
browser |    28  100.0%         10     +  78810672  78810699              DQ694443     1    28    28
browser |    28  100.0%         10     -  80901203  80901230              DQ694443     1    28    28
browser |    28  100.0%         10     -  83312703  83312730              DQ694443     1    28    28
browser |    28  100.0%         10     -  85678916  85678943              DQ694443     1    28    28
browser |    28  100.0%         10     +  86465881  86465908              DQ694443     1    28    28
browser |    28  100.0%         10     -  89526173  89526200              DQ694443     1    28    28
browser |    28  100.0%         10     +  89717230  89717257              DQ694443     1    28    28
browser |    28  100.0%         10     -  90531522  90531549              DQ694443     1    28    28
browser |    25  100.0%         10     +  91876110  91876134              DQ694443     1    25    28
browser |    28  100.0%         10     -  94235847  94235874              DQ694443     1    28    28
browser |    28  100.0%         10     +  94819440  94819467              DQ694443     1    28    28
browser |    28  100.0%         10     -  95884357  95884384              DQ694443     1    28    28
browser |    28  100.0%         10     +  95890108  95890135              DQ694443     1    28    28
browser |    26  100.0%         10     +  96113107  96113132              DQ694443     1    26    28
browser |    28  100.0%         10     - 100765188 100765215              DQ694443     1    28    28
browser |    28  100.0%         10     - 101772938 101772965              DQ694443     1    28    28
browser |    28  100.0%         10     - 103324645 103324672              DQ694443     1    28    28
browser |    28  100.0%         10     - 111267065 111267092              DQ694443     1    28    28
browser |    28  100.0%         10     - 114467860 114467887              DQ694443     1    28    28
browser |    28  100.0%         10     - 118971044 118971071              DQ694443     1    28    28
browser |    28  100.0%         10     - 126578861 126578888              DQ694443     1    28    28
browser |    28  100.0%         11     +   4081251   4081278              DQ694443     1    28    28
browser |    28  100.0%         11     -   4354738   4354765              DQ694443     1    28    28
browser |    28  100.0%         11     -   7832247   7832274              DQ694443     1    28    28
browser |    28  100.0%         11     -   9599311   9599338              DQ694443     1    28    28
browser |    28  100.0%         11     +  10349698  10349725              DQ694443     1    28    28
browser |    28  100.0%         11     -  12126708  12126735              DQ694443     1    28    28
browser |    27  100.0%         11     -  12868169  12868195              DQ694443     2    28    28
browser |    28  100.0%         11     -  15072385  15072412              DQ694443     1    28    28
browser |    28  100.0%         11     -  21142958  21142985              DQ694443     1    28    28
browser |    28  100.0%         11     -  21344870  21344897              DQ694443     1    28    28
browser |    28  100.0%         11     +  22868195  22868222              DQ694443     1    28    28
browser |    28  100.0%         11     +  24730569  24730596              DQ694443     1    28    28
browser |    28  100.0%         11     +  26989139  26989166              DQ694443     1    28    28
browser |    28  100.0%         11     -  30985444  30985471              DQ694443     1    28    28
browser |    28  100.0%         11     +  31470915  31470942              DQ694443     1    28    28
browser |    28  100.0%         11     -  31743947  31743974              DQ694443     1    28    28
browser |    28  100.0%         11     -  32040417  32040444              DQ694443     1    28    28
browser |    28  100.0%         11     +  41994378  41994405              DQ694443     1    28    28
browser |    28  100.0%         11     -  42655497  42655524              DQ694443     1    28    28
browser |    28  100.0%         11     +  47547128  47547155              DQ694443     1    28    28
browser |    28  100.0%         11     +  47564196  47564223              DQ694443     1    28    28
browser |    28  100.0%         11     -  48777259  48777286              DQ694443     1    28    28
browser |    28  100.0%         11     +  50928180  50928207              DQ694443     1    28    28
browser |    28  100.0%         11     +  52471260  52471287              DQ694443     1    28    28
browser |    28  100.0%         11     +  53831805  53831832              DQ694443     1    28    28
browser |    28  100.0%         11     +  59911217  59911244              DQ694443     1    28    28
browser |    28  100.0%         11     +  67118106  67118133              DQ694443     1    28    28
browser |    28  100.0%         11     -  68644079  68644106              DQ694443     1    28    28
browser |    28  100.0%         11     +  70029976  70030003              DQ694443     1    28    28
browser |    28  100.0%         11     -  70220189  70220216              DQ694443     1    28    28
browser |    27  100.0%         11     -  73473925  73473951              DQ694443     1    27    28
browser |    28  100.0%         11     +  82975498  82975525              DQ694443     1    28    28
browser |    25  100.0%         11     -  83120192  83120216              DQ694443     4    28    28
browser |    26  100.0%         11     +  86033377  86033402              DQ694443     1    26    28
browser |    28  100.0%         11     -  87359038  87359065              DQ694443     1    28    28
browser |    26  100.0%         11     +  91966488  91966513              DQ694443     3    28    28
browser |    28  100.0%         11     +  92119656  92119683              DQ694443     1    28    28
browser |    25  100.0%         11     -  95332669  95332693              DQ694443     1    25    28
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browser |    28  100.0%         11     - 101512470 101512497              DQ694443     1    28    28
browser |    25  100.0%         11     - 103213585 103213609              DQ694443     1    25    28
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browser |    28  100.0%         11     - 103522510 103522537              DQ694443     1    28    28
browser |    28  100.0%         11     - 104995396 104995423              DQ694443     1    28    28
browser |    25  100.0%         11     + 105695523 105695547              DQ694443     1    25    28
browser |    28  100.0%         11     + 109042043 109042070              DQ694443     1    28    28
browser |    28  100.0%         11     - 119197167 119197194              DQ694443     1    28    28
browser |    28  100.0%         12     -   4290643   4290670              DQ694443     1    28    28
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browser |    28  100.0%         12     - 106998099 106998126              DQ694443     1    28    28
browser |    25  100.0%         12     - 108711475 108711499              DQ694443     1    25    28
browser |    25  100.0%         12     - 112489260 112489284              DQ694443     1    25    28
browser |    25  100.0%         12     - 118569309 118569333              DQ694443     1    25    28
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browser |    26  100.0%         13     -   7931055   7931080              DQ694443     3    28    28
browser |    28  100.0%         13     -  11455244  11455271              DQ694443     1    28    28
browser |    28  100.0%         13     -  15017616  15017643              DQ694443     1    28    28
browser |    27  100.0%         13     +  21543730  21543756              DQ694443     2    28    28
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browser |    28  100.0%         13     -  31280934  31280961              DQ694443     1    28    28
browser |    28  100.0%         13     -  33749972  33749999              DQ694443     1    28    28
browser |    28  100.0%         13     -  33757273  33757300              DQ694443     1    28    28
browser |    28  100.0%         13     +  38686643  38686670              DQ694443     1    28    28
browser |    28  100.0%         13     -  40905773  40905800              DQ694443     1    28    28
browser |    28  100.0%         13     -  45160910  45160937              DQ694443     1    28    28
browser |    28  100.0%         13     -  49163428  49163455              DQ694443     1    28    28
browser |    28  100.0%         13     -  54952620  54952647              DQ694443     1    28    28
browser |    28  100.0%         13     +  56466809  56466836              DQ694443     1    28    28
browser |    27  100.0%         13     +  68938633  68938659              DQ694443     1    27    28
browser |    28  100.0%         13     -  69581172  69581199              DQ694443     1    28    28
browser |    28  100.0%         13     +  74332062  74332089              DQ694443     1    28    28
browser |    28  100.0%         13     +  75563524  75563551              DQ694443     1    28    28
browser |    28  100.0%         13     +  77319259  77319286              DQ694443     1    28    28
browser |    28  100.0%         13     +  77794261  77794288              DQ694443     1    28    28
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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