AB345589
 

Information on mRNA AB345589

Description: Mus musculus non-coding RNA, oocyte_clustered_small_RNA10790, complete sequence.
Gene: n/a
Product: n/a
Author: Watanabe,T., Totoki,Y., Toyoda,A., Kaneda,M., Kuramochi-Miyagawa,S., Obata,Y., Chiba,H., Kohara,Y., Kono,T., Nakano,T., Surani,M.A., Sakaki,Y. and Sasaki,H.
Organism: Mus musculus
Tissue: n/a
Development stage: growing stage
Cell line: n/a
Sex: n/a
Library: n/a
Clone: n/a
CDS: n/a
Date: 2008-04-24
Version: 1
mRNA sequence: AB345589
Position: chr12:56959199-56959224

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     +  56959199  56959224              AB345589     1    25    25
browser |    25  100.0%          1     -   5636449   5636474              AB345589     1    25    25
browser |    25  100.0%          1     -  11102121  11102146              AB345589     1    25    25
browser |    25  100.0%          1     -  11439204  11439229              AB345589     1    25    25
browser |    25  100.0%          1     +  14032169  14032194              AB345589     1    25    25
browser |    25  100.0%          1     +  21653063  21653088              AB345589     1    25    25
browser |    25  100.0%          1     +  27176766  27176791              AB345589     1    25    25
browser |    25  100.0%          1     +  31045314  31045339              AB345589     1    25    25
browser |    25  100.0%          1     +  31510296  31510321              AB345589     1    25    25
browser |    25  100.0%          1     +  34955121  34955146              AB345589     1    25    25
browser |    25  100.0%          1     -  37321598  37321623              AB345589     1    25    25
browser |    25  100.0%          1     +  37813948  37813973              AB345589     1    25    25
browser |    25  100.0%          1     +  44331049  44331074              AB345589     1    25    25
browser |    25  100.0%          1     -  47996381  47996406              AB345589     1    25    25
browser |    25  100.0%          1     +  48009576  48009601              AB345589     1    25    25
browser |    25  100.0%          1     -  48711843  48711868              AB345589     1    25    25
browser |    25  100.0%          1     +  52630141  52630166              AB345589     1    25    25
browser |    25  100.0%          1     +  53275989  53276014              AB345589     1    25    25
browser |    25  100.0%          1     -  57626743  57626768              AB345589     1    25    25
browser |    25  100.0%          1     -  59388166  59388191              AB345589     1    25    25
browser |    25  100.0%          1     +  65748433  65748458              AB345589     1    25    25
browser |    25  100.0%          1     -  67146311  67146336              AB345589     1    25    25
browser |    25  100.0%          1     -  93038349  93038374              AB345589     1    25    25
browser |    25  100.0%          1     -  96896074  96896099              AB345589     1    25    25
browser |    25  100.0%          1     + 108885671 108885696              AB345589     1    25    25
browser |    25  100.0%          1     - 112495924 112495949              AB345589     1    25    25
browser |    25  100.0%          1     - 117676329 117676354              AB345589     1    25    25
browser |    25  100.0%          1     - 121708261 121708286              AB345589     1    25    25
browser |    25  100.0%          1     + 128816878 128816903              AB345589     1    25    25
browser |    25  100.0%          1     + 129019306 129019331              AB345589     1    25    25
browser |    25  100.0%          1     - 136737281 136737306              AB345589     1    25    25
browser |    25  100.0%          1     + 161361078 161361103              AB345589     1    25    25
browser |    25  100.0%          1     - 163299204 163299229              AB345589     1    25    25
browser |    25  100.0%          1     + 171658696 171658721              AB345589     1    25    25
browser |    25  100.0%          1     - 177955926 177955951              AB345589     1    25    25
browser |    25  100.0%          1     + 185037174 185037199              AB345589     1    25    25
browser |    25  100.0%          1     + 191235209 191235234              AB345589     1    25    25
browser |    25  100.0%         10     +   7316179   7316204              AB345589     1    25    25
browser |    25  100.0%         10     +   9723778   9723803              AB345589     1    25    25
browser |    25  100.0%         10     -  15058279  15058304              AB345589     1    25    25
browser |    25  100.0%         10     -  28888941  28888966              AB345589     1    25    25
browser |    25  100.0%         10     +  31627109  31627134              AB345589     1    25    25
browser |    25  100.0%         10     +  32813806  32813831              AB345589     1    25    25
browser |    25  100.0%         10     -  35600289  35600314              AB345589     1    25    25
browser |    25  100.0%         10     -  39639441  39639466              AB345589     1    25    25
browser |    25  100.0%         10     +  43754476  43754501              AB345589     1    25    25
browser |    25  100.0%         10     -  47513538  47513563              AB345589     1    25    25
browser |    25  100.0%         10     -  47558271  47558296              AB345589     1    25    25
browser |    25  100.0%         10     +  54465844  54465869              AB345589     1    25    25
browser |    25  100.0%         10     +  74712698  74712723              AB345589     1    25    25
browser |    25  100.0%         10     +  82776206  82776231              AB345589     1    25    25
browser |    25  100.0%         10     +  88800844  88800869              AB345589     1    25    25
browser |    25  100.0%         10     -  91651701  91651726              AB345589     1    25    25
browser |    25  100.0%         10     +  92356011  92356036              AB345589     1    25    25
browser |    25  100.0%         10     + 103910854 103910879              AB345589     1    25    25
browser |    25  100.0%         10     - 122143266 122143291              AB345589     1    25    25
browser |    25  100.0%         10     - 124303654 124303679              AB345589     1    25    25
browser |    25  100.0%         11     -   7986363   7986388              AB345589     1    25    25
browser |    25  100.0%         11     -   9036311   9036336              AB345589     1    25    25
browser |    25  100.0%         11     +  15811303  15811328              AB345589     1    25    25
browser |    25  100.0%         11     +  15834603  15834628              AB345589     1    25    25
browser |    25  100.0%         11     -  29115419  29115444              AB345589     1    25    25
browser |    25  100.0%         11     +  29231493  29231518              AB345589     1    25    25
browser |    25  100.0%         11     +  31163976  31164001              AB345589     1    25    25
browser |    25  100.0%         11     +  43551506  43551531              AB345589     1    25    25
browser |    25  100.0%         11     +  67021824  67021849              AB345589     1    25    25
browser |    25  100.0%         11     - 108715696 108715721              AB345589     1    25    25
browser |    25  100.0%         11     + 116651348 116651373              AB345589     1    25    25
browser |    25  100.0%         12     +   4839019   4839044              AB345589     1    25    25
browser |    25  100.0%         12     +  17294659  17294684              AB345589     1    25    25
browser |    25  100.0%         12     -  23585636  23585661              AB345589     1    25    25
browser |    25  100.0%         12     +  24396844  24396869              AB345589     1    25    25
browser |    25  100.0%         12     +  25642876  25642901              AB345589     1    25    25
browser |    25  100.0%         12     -  26157988  26158013              AB345589     1    25    25
browser |    25  100.0%         12     +  32647413  32647438              AB345589     1    25    25
browser |    25  100.0%         12     +  32953286  32953311              AB345589     1    25    25
browser |    25  100.0%         12     +  36667134  36667159              AB345589     1    25    25
browser |    25  100.0%         12     -  44202333  44202358              AB345589     1    25    25
browser |    25  100.0%         12     -  54917769  54917794              AB345589     1    25    25
browser |    25  100.0%         12     -  64202079  64202104              AB345589     1    25    25
browser |    25  100.0%         12     +  65731254  65731279              AB345589     1    25    25
browser |    25  100.0%         12     +  65880604  65880629              AB345589     1    25    25
browser |    25  100.0%         12     +  74746266  74746291              AB345589     1    25    25
browser |    25  100.0%         12     +  88479591  88479616              AB345589     1    25    25
browser |    25  100.0%         12     +  91195434  91195459              AB345589     1    25    25
browser |    25  100.0%         12     + 114906113 114906138              AB345589     1    25    25
browser |    25  100.0%         12     + 118759619 118759644              AB345589     1    25    25
browser |    25  100.0%         13     -   4513556   4513581              AB345589     1    25    25
browser |    25  100.0%         13     -   8073386   8073411              AB345589     1    25    25
browser |    25  100.0%         13     -  11013048  11013073              AB345589     1    25    25
browser |    25  100.0%         13     +  11143053  11143078              AB345589     1    25    25
browser |    25  100.0%         13     -  15274503  15274528              AB345589     1    25    25
browser |    25  100.0%         13     +  23391031  23391056              AB345589     1    25    25
browser |    25  100.0%         13     +  27473179  27473204              AB345589     1    25    25
browser |    25  100.0%         13     -  33960058  33960083              AB345589     1    25    25
browser |    25  100.0%         13     +  39863626  39863651              AB345589     1    25    25
browser |    25  100.0%         13     +  50060354  50060379              AB345589     1    25    25
browser |    25  100.0%         13     -  50712509  50712534              AB345589     1    25    25
browser |    25  100.0%         13     +  51187598  51187623              AB345589     1    25    25
browser |    25  100.0%         13     +  52205556  52205581              AB345589     1    25    25
browser |    25  100.0%         13     -  54570153  54570178              AB345589     1    25    25
browser |    25  100.0%         13     +  54919936  54919961              AB345589     1    25    25
browser |    25  100.0%         13     +  62697491  62697516              AB345589     1    25    25
browser |    25  100.0%         13     -  62811011  62811036              AB345589     1    25    25
browser |    25  100.0%         13     -  64647936  64647961              AB345589     1    25    25
browser |    25  100.0%         13     -  66147533  66147558              AB345589     1    25    25
browser |    25  100.0%         13     -  75358193  75358218              AB345589     1    25    25
browser |    25  100.0%         13     -  75976439  75976464              AB345589     1    25    25
browser |    25  100.0%         13     -  76645503  76645528              AB345589     1    25    25
browser |    25  100.0%         13     -  76647946  76647971              AB345589     1    25    25
browser |    25  100.0%         13     -  81233389  81233414              AB345589     1    25    25
browser |    25  100.0%         13     +  82260458  82260483              AB345589     1    25    25
browser |    25  100.0%         13     -  84570513  84570538              AB345589     1    25    25
browser |    25  100.0%         13     -  85554778  85554803              AB345589     1    25    25
browser |    25  100.0%         13     -  86562119  86562144              AB345589     1    25    25
browser |    25  100.0%         13     + 106276148 106276173              AB345589     1    25    25
browser |    25  100.0%         13     + 106923186 106923211              AB345589     1    25    25
browser |    25  100.0%         13     + 118208251 118208276              AB345589     1    25    25
browser |    25  100.0%         13     + 118287046 118287071              AB345589     1    25    25
browser |    25  100.0%         14     -   5090284   5090309              AB345589     1    25    25
browser |    25  100.0%         14     -   7004801   7004826              AB345589     1    25    25
browser |    25  100.0%         14     +   8952443   8952468              AB345589     1    25    25
browser |    25  100.0%         14     -   9641543   9641568              AB345589     1    25    25
browser |    25  100.0%         14     -  11145016  11145041              AB345589     1    25    25
browser |    24  100.0%         14     +  15570548  15570572              AB345589     1    24    25
browser |    25  100.0%         14     +  23586374  23586399              AB345589     1    25    25
browser |    25  100.0%         14     +  29265499  29265524              AB345589     1    25    25
browser |    25  100.0%         14     +  29493604  29493629              AB345589     1    25    25
browser |    25  100.0%         14     +  33371164  33371189              AB345589     1    25    25
browser |    25  100.0%         14     +  37748384  37748409              AB345589     1    25    25
browser |    25  100.0%         14     +  39216506  39216531              AB345589     1    25    25
browser |    25  100.0%         14     -  42444014  42444039              AB345589     1    25    25
browser |    25  100.0%         14     +  52976463  52976488              AB345589     1    25    25
browser |    25  100.0%         14     +  53350178  53350203              AB345589     1    25    25
browser |    25  100.0%         14     +  65175304  65175329              AB345589     1    25    25
browser |    25  100.0%         14     +  71457428  71457453              AB345589     1    25    25
browser |    25  100.0%         14     +  72039856  72039881              AB345589     1    25    25
browser |    25  100.0%         14     -  80099301  80099326              AB345589     1    25    25
browser |    25  100.0%         14     +  80974884  80974909              AB345589     1    25    25
browser |    25  100.0%         14     -  84079936  84079961              AB345589     1    25    25
browser |    25  100.0%         14     +  84104501  84104526              AB345589     1    25    25
browser |    25  100.0%         14     +  84108294  84108319              AB345589     1    25    25
browser |    25  100.0%         14     -  85241439  85241464              AB345589     1    25    25
browser |    25  100.0%         14     -  87844699  87844724              AB345589     1    25    25
browser |    25  100.0%         14     -  89276533  89276558              AB345589     1    25    25
browser |    25  100.0%         14     +  92287949  92287974              AB345589     1    25    25
browser |    25  100.0%         14     -  98993859  98993884              AB345589     1    25    25
browser |    25  100.0%         14     + 101819969 101819994              AB345589     1    25    25
browser |    25  100.0%         14     + 106589058 106589083              AB345589     1    25    25
browser |    25  100.0%         14     + 109432673 109432698              AB345589     1    25    25
browser |    25  100.0%         14     - 110200989 110201014              AB345589     1    25    25
browser |    25  100.0%         14     - 110601828 110601853              AB345589     1    25    25
browser |    25  100.0%         14     - 111319481 111319506              AB345589     1    25    25
browser |    25  100.0%         14     - 114426978 114427003              AB345589     1    25    25
browser |    25  100.0%         14     - 119614411 119614436              AB345589     1    25    25
browser |    25  100.0%         15     -   6836243   6836268              AB345589     1    25    25
browser |    25  100.0%         15     -   8581376   8581401              AB345589     1    25    25
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browser |    25  100.0%         15     -  14740211  14740236              AB345589     1    25    25
browser |    25  100.0%         15     -  16455973  16455998              AB345589     1    25    25
browser |    25  100.0%         15     -  20158596  20158621              AB345589     1    25    25
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browser |    25  100.0%         15     -  29132804  29132829              AB345589     1    25    25
browser |    25  100.0%         15     -  32785546  32785571              AB345589     1    25    25
browser |    25  100.0%         15     -  33660591  33660616              AB345589     1    25    25
browser |    25  100.0%         15     -  34228816  34228841              AB345589     1    25    25
browser |    25  100.0%         15     -  38464124  38464149              AB345589     1    25    25
browser |    25  100.0%         15     -  45059338  45059363              AB345589     1    25    25
browser |    25  100.0%         15     -  46429218  46429243              AB345589     1    25    25
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browser |    25  100.0%         15     -  56667848  56667873              AB345589     1    25    25
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browser |    25  100.0%         15     +  65918219  65918244              AB345589     1    25    25
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browser |    25  100.0%         15     -  82491901  82491926              AB345589     1    25    25
browser |    25  100.0%         15     -  84032326  84032351              AB345589     1    25    25
browser |    25  100.0%         15     -  87400186  87400211              AB345589     1    25    25
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browser |    25  100.0%         15     +  97633129  97633154              AB345589     1    25    25
browser |    25  100.0%         15     + 103516221 103516246              AB345589     1    25    25
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browser |    25  100.0%         16     -  12154563  12154588              AB345589     1    25    25
browser |    25  100.0%         16     -  13301073  13301098              AB345589     1    25    25
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browser |    25  100.0%         17     -   8211481   8211506              AB345589     1    25    25
browser |    25  100.0%         17     -   8914904   8914929              AB345589     1    25    25
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browser |    25  100.0%         17     +  21439719  21439744              AB345589     1    25    25
browser |    25  100.0%         17     -  22853931  22853956              AB345589     1    25    25
browser |    25  100.0%         17     -  27487719  27487744              AB345589     1    25    25
browser |    25  100.0%         17     +  31772484  31772509              AB345589     1    25    25
browser |    25  100.0%         17     -  33959614  33959639              AB345589     1    25    25
browser |    25  100.0%         17     +  40020986  40021011              AB345589     1    25    25
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browser |    25  100.0%         17     +  52634509  52634534              AB345589     1    25    25
browser |    25  100.0%         17     +  52794778  52794803              AB345589     1    25    25
browser |    25  100.0%         17     +  53676434  53676459              AB345589     1    25    25
browser |    25  100.0%         17     -  54701964  54701989              AB345589     1    25    25
browser |    25  100.0%         17     -  54812538  54812563              AB345589     1    25    25
browser |    25  100.0%         17     +  60855543  60855568              AB345589     1    25    25
browser |    25  100.0%         17     +  61320371  61320396              AB345589     1    25    25
browser |    25  100.0%         17     +  67309253  67309278              AB345589     1    25    25
browser |    25  100.0%         17     +  67734419  67734444              AB345589     1    25    25
browser |    25  100.0%         17     +  78083436  78083461              AB345589     1    25    25
browser |    25  100.0%         17     +  78229008  78229033              AB345589     1    25    25
browser |    24  100.0%         17     +  81540213  81540237              AB345589     1    24    25
browser |    25  100.0%         17     -  83058959  83058984              AB345589     1    25    25
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View details of parts of alignment within browser window
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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