AB345426
 

Information on mRNA AB345426

Description: Mus musculus non-coding RNA, oocyte_clustered_small_RNA10627, 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: AB345426
Position: chr12:57218071-57218091

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 |    21  100.0%         12     -  57218071  57218091              AB345426     1    21    23
browser |    21  100.0%          1     +  23956000  23956020              AB345426     1    21    23
browser |    21  100.0%          1     +  88050035  88050055              AB345426     1    21    23
browser |    21  100.0%          1     +  88073768  88073788              AB345426     1    21    23
browser |    21  100.0%          1     +  93663788  93663808              AB345426     1    21    23
browser |    21  100.0%          1     + 132195070 132195090              AB345426     1    21    23
browser |    22  100.0%          1     - 150035546 150035567              AB345426     2    23    23
browser |    21  100.0%          1     - 155991589 155991609              AB345426     1    21    23
browser |    23  100.0%          1     - 158170125 158170147              AB345426     1    23    23
browser |    21  100.0%          1     - 171119151 171119171              AB345426     1    21    23
browser |    21  100.0%          1     - 179521381 179521401              AB345426     1    21    23
browser |    21  100.0%          1     - 180052459 180052479              AB345426     1    21    23
browser |    21  100.0%          1     + 191838479 191838499              AB345426     1    21    23
browser |    21  100.0%          1     - 192936267 192936287              AB345426     1    21    23
browser |    21  100.0%          1     - 194648105 194648125              AB345426     1    21    23
browser |    21  100.0%         10     -   5267066   5267086              AB345426     1    21    23
browser |    21  100.0%         10     +  37271557  37271577              AB345426     1    21    23
browser |    21  100.0%         10     -  39188521  39188541              AB345426     1    21    23
browser |    21  100.0%         10     +  41468908  41468928              AB345426     1    21    23
browser |    21  100.0%         10     -  43348419  43348439              AB345426     1    21    23
browser |    21  100.0%         10     +  54125132  54125152              AB345426     1    21    23
browser |    21  100.0%         10     +  79934066  79934086              AB345426     1    21    23
browser |    21  100.0%         10     +  80302300  80302320              AB345426     1    21    23
browser |    21  100.0%         10     + 100107453 100107473              AB345426     1    21    23
browser |    21  100.0%         10     - 116476169 116476189              AB345426     1    21    23
browser |    21  100.0%         11     +  40105189  40105209              AB345426     1    21    23
browser |    21  100.0%         11     +  51957569  51957589              AB345426     1    21    23
browser |    21  100.0%         11     -  59495387  59495407              AB345426     1    21    23
browser |    21  100.0%         11     +  59946858  59946878              AB345426     1    21    23
browser |    21  100.0%         11     -  60140819  60140839              AB345426     1    21    23
browser |    21  100.0%         11     +  61074253  61074273              AB345426     1    21    23
browser |    21  100.0%         11     +  61830131  61830151              AB345426     1    21    23
browser |    21  100.0%         11     -  64276317  64276337              AB345426     1    21    23
browser |    21  100.0%         11     +  69662313  69662333              AB345426     1    21    23
browser |    21  100.0%         11     -  75620558  75620578              AB345426     1    21    23
browser |    21  100.0%         11     +  80608482  80608502              AB345426     1    21    23
browser |    21  100.0%         11     -  98968829  98968849              AB345426     1    21    23
browser |    21  100.0%         11     - 101638905 101638925              AB345426     1    21    23
browser |    21  100.0%         11     - 109213237 109213257              AB345426     1    21    23
browser |    21  100.0%         11     - 120825247 120825267              AB345426     1    21    23
browser |    21  100.0%         12     +  44120961  44120981              AB345426     1    21    23
browser |    21  100.0%         12     +  58586543  58586563              AB345426     1    21    23
browser |    21  100.0%         12     +  72087150  72087170              AB345426     1    21    23
browser |    21  100.0%         12     +  75324155  75324175              AB345426     1    21    23
browser |    21  100.0%         12     +  83832368  83832388              AB345426     1    21    23
browser |    22  100.0%         12     + 118558375 118558396              AB345426     1    22    23
browser |    21  100.0%         13     +  38612268  38612288              AB345426     1    21    23
browser |    21  100.0%         13     -  39948284  39948304              AB345426     1    21    23
browser |    21  100.0%         13     -  43705906  43705926              AB345426     1    21    23
browser |    21  100.0%         13     -  50058159  50058179              AB345426     1    21    23
browser |    22  100.0%         13     -  59382635  59382656              AB345426     1    22    23
browser |    23  100.0%         13     -  69168092  69168114              AB345426     1    23    23
browser |    21  100.0%         13     -  84268439  84268459              AB345426     1    21    23
browser |    21  100.0%         13     + 111877906 111877926              AB345426     1    21    23
browser |    21  100.0%         13     - 112440102 112440122              AB345426     1    21    23
browser |    21  100.0%         14     -  51569726  51569746              AB345426     1    21    23
browser |    21  100.0%         14     +  60093572  60093592              AB345426     1    21    23
browser |    21  100.0%         14     + 121470437 121470457              AB345426     1    21    23
browser |    22  100.0%         15     -  64299746  64299767              AB345426     1    22    23
browser |    21  100.0%         15     -  80959475  80959495              AB345426     1    21    23
browser |    21  100.0%         15     +  81375939  81375959              AB345426     1    21    23
browser |    21  100.0%         15     +  82252472  82252492              AB345426     1    21    23
browser |    21  100.0%         15     +  97831602  97831622              AB345426     1    21    23
browser |    21  100.0%         15     + 100144469 100144489              AB345426     1    21    23
browser |    23  100.0%         16     -  11230318  11230340              AB345426     1    23    23
browser |    21  100.0%         16     -  21742517  21742537              AB345426     1    21    23
browser |    21  100.0%         16     +  29825889  29825909              AB345426     1    21    23
browser |    21  100.0%         16     +  72499465  72499485              AB345426     1    21    23
browser |    21  100.0%         16     +  87285990  87286010              AB345426     1    21    23
browser |    21  100.0%         16     +  92112312  92112332              AB345426     1    21    23
browser |    21  100.0%         17     -  24019301  24019321              AB345426     1    21    23
browser |    21  100.0%         17     -  25250682  25250702              AB345426     1    21    23
browser |    21  100.0%         17     -  26195766  26195786              AB345426     1    21    23
browser |    21  100.0%         17     -  27458688  27458708              AB345426     1    21    23
browser |    21  100.0%         17     -  27635262  27635282              AB345426     1    21    23
browser |    21  100.0%         17     +  30136834  30136854              AB345426     1    21    23
browser |    23  100.0%         17     +  56391893  56391915              AB345426     1    23    23
browser |    21  100.0%         18     -   4572918   4572938              AB345426     1    21    23
browser |    21  100.0%         18     +   7274248   7274268              AB345426     1    21    23
browser |    21  100.0%         18     +  36038101  36038121              AB345426     1    21    23
browser |    21  100.0%         18     +  36304192  36304212              AB345426     1    21    23
browser |    21  100.0%         18     +  78551241  78551261              AB345426     1    21    23
browser |    22  100.0%         18     -  80545475  80545496              AB345426     2    23    23
browser |    21  100.0%         19     -  22761860  22761880              AB345426     1    21    23
browser |    21  100.0%         19     +  45379015  45379035              AB345426     1    21    23
browser |    21  100.0%          2     -   3216252   3216272              AB345426     1    21    23
browser |    21  100.0%          2     -   4374881   4374901              AB345426     1    21    23
browser |    21  100.0%          2     +  18606819  18606839              AB345426     1    21    23
browser |    21  100.0%          2     -  21037615  21037635              AB345426     1    21    23
browser |    21  100.0%          2     -  28188710  28188730              AB345426     1    21    23
browser |    21  100.0%          2     +  33722850  33722870              AB345426     1    21    23
browser |    21  100.0%          2     -  34991590  34991610              AB345426     1    21    23
browser |    21  100.0%          2     -  48291686  48291706              AB345426     1    21    23
browser |    21  100.0%          2     -  49644434  49644454              AB345426     1    21    23
browser |    21  100.0%          2     + 101785975 101785995              AB345426     1    21    23
browser |    21  100.0%          2     - 109742740 109742760              AB345426     1    21    23
browser |    21  100.0%          2     - 115272154 115272174              AB345426     1    21    23
browser |    23  100.0%          2     + 121374255 121374277              AB345426     1    23    23
browser |    21  100.0%          2     + 127557819 127557839              AB345426     1    21    23
browser |    21  100.0%          2     - 153902489 153902509              AB345426     1    21    23
browser |    21  100.0%          2     - 170442496 170442516              AB345426     1    21    23
browser |    23  100.0%          2     - 173470435 173470457              AB345426     1    23    23
browser |    21  100.0%          2     + 179560239 179560259              AB345426     1    21    23
browser |    21  100.0%          3     +  53204189  53204209              AB345426     1    21    23
browser |    21  100.0%          3     +  65137682  65137702              AB345426     1    21    23
browser |    21  100.0%          3     +  86868550  86868570              AB345426     1    21    23
browser |    21  100.0%          3     +  90102745  90102765              AB345426     1    21    23
browser |    21  100.0%          3     -  98207395  98207415              AB345426     1    21    23
browser |    21  100.0%          3     -  98279138  98279158              AB345426     1    21    23
browser |    21  100.0%          3     - 115833349 115833369              AB345426     1    21    23
browser |    21  100.0%          4     +  56860391  56860411              AB345426     1    21    23
browser |    21  100.0%          4     +  62101866  62101886              AB345426     1    21    23
browser |    21  100.0%          4     +  63611065  63611085              AB345426     1    21    23
browser |    21  100.0%          4     - 119559763 119559783              AB345426     1    21    23
browser |    21  100.0%          4     - 120433334 120433354              AB345426     1    21    23
browser |    21  100.0%          4     - 123308961 123308981              AB345426     1    21    23
browser |    21  100.0%          4     + 123503734 123503754              AB345426     1    21    23
browser |    21  100.0%          4     + 126100205 126100225              AB345426     1    21    23
browser |    21  100.0%          4     - 128263652 128263672              AB345426     1    21    23
browser |    23  100.0%          4     - 130418876 130418898              AB345426     1    23    23
browser |    21  100.0%          4     - 130871061 130871081              AB345426     1    21    23
browser |    21  100.0%          4     + 131465151 131465171              AB345426     1    21    23
browser |    21  100.0%          4     + 156080193 156080213              AB345426     1    21    23
browser |    21  100.0%          5     +   3681144   3681164              AB345426     1    21    23
browser |    21  100.0%          5     -  32882872  32882892              AB345426     1    21    23
browser |    21  100.0%          5     -  33780125  33780145              AB345426     1    21    23
browser |    23  100.0%          5     -  84120488  84120510              AB345426     1    23    23
browser |    21  100.0%          5     + 114472729 114472749              AB345426     1    21    23
browser |    21  100.0%          5     - 150670764 150670784              AB345426     1    21    23
browser |    21  100.0%          6     +   7030084   7030104              AB345426     1    21    23
browser |    21  100.0%          6     +  28506162  28506182              AB345426     1    21    23
browser |    21  100.0%          6     -  47877698  47877718              AB345426     1    21    23
browser |    21  100.0%          6     +  53087381  53087401              AB345426     1    21    23
browser |    21  100.0%          6     +  92210478  92210498              AB345426     1    21    23
browser |    21  100.0%          6     +  94004931  94004951              AB345426     1    21    23
browser |    21  100.0%          6     - 113480285 113480305              AB345426     1    21    23
browser |    21  100.0%          6     - 115200191 115200211              AB345426     1    21    23
browser |    21  100.0%          7     +  27259215  27259235              AB345426     1    21    23
browser |    21  100.0%          7     -  34262458  34262478              AB345426     1    21    23
browser |    21  100.0%          7     +  44900328  44900348              AB345426     1    21    23
browser |    21  100.0%          7     +  67965864  67965884              AB345426     1    21    23
browser |    21  100.0%          7     + 126609805 126609825              AB345426     1    21    23
browser |    21  100.0%          7     - 127589324 127589344              AB345426     1    21    23
browser |    21  100.0%          7     + 128186806 128186826              AB345426     1    21    23
browser |    21  100.0%          7     + 130186996 130187016              AB345426     1    21    23
browser |    21  100.0%          8     +  75709819  75709839              AB345426     1    21    23
browser |    21  100.0%          8     +  83615085  83615105              AB345426     1    21    23
browser |    21  100.0%          8     -  85678870  85678890              AB345426     1    21    23
browser |    21  100.0%          8     +  90733748  90733768              AB345426     1    21    23
browser |    21  100.0%          8     + 105065440 105065460              AB345426     1    21    23
browser |    21  100.0%          8     - 106592378 106592398              AB345426     1    21    23
browser |    21  100.0%          8     + 112634024 112634044              AB345426     1    21    23
browser |    23  100.0%          9     +  35507454  35507476              AB345426     1    23    23
browser |    21  100.0%          9     +  43937234  43937254              AB345426     1    21    23
browser |    21  100.0%          9     -  44455847  44455867              AB345426     1    21    23
browser |    21  100.0%          9     -  58483457  58483477              AB345426     1    21    23
browser |    21  100.0%          9     -  69592186  69592206              AB345426     1    21    23
browser |    21  100.0%          9     +  84263822  84263842              AB345426     1    21    23
browser |    21  100.0%          9     -  94227971  94227991              AB345426     1    21    23
browser |    21  100.0%          9     +  94758021  94758041              AB345426     1    21    23
browser |    21  100.0%          9     -  96616890  96616910              AB345426     1    21    23
browser |    21  100.0%          9     + 103317218 103317238              AB345426     1    21    23
browser |    21  100.0%          9     + 119083240 119083260              AB345426     1    21    23
browser |    21  100.0%          9     - 119240598 119240618              AB345426     1    21    23
browser |    21  100.0%  Un_JH584304v1     -     43199     43219              AB345426     1    21    23
browser |    21  100.0%          X     +  47671181  47671201              AB345426     1    21    23
browser |    21  100.0%          X     -  63991287  63991307              AB345426     1    21    23
browser |    21  100.0%          X     -  65480870  65480890              AB345426     1    21    23
browser |    21  100.0%          X     -  97856109  97856129              AB345426     1    21    23
browser |    21  100.0%          X     + 102759824 102759844              AB345426     1    21    23
browser |    21  100.0%          X     + 104822916 104822936              AB345426     1    21    23
browser |    21  100.0%          X     - 161792090 161792110              AB345426     1    21    23
browser |    21  100.0%          X     + 165078208 165078228              AB345426     1    21    23
browser |    21  100.0%          X     - 167475117 167475137              AB345426     1    21    23

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