DQ707787
 

Information on mRNA DQ707787

Description: Mus musculus piRNA piR-123109, 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: DQ707787
Position: chrX:15592631-15592656

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 |    26  100.0%          X     +  15592631  15592656              DQ707787     1    26    29
browser |    29  100.0%          1     +   3168854   3168883              DQ707787     1    29    29
browser |    26  100.0%          1     +   6070776   6070801              DQ707787     1    26    29
browser |    26  100.0%          1     -  44803611  44803636              DQ707787     1    26    29
browser |    26  100.0%          1     -  59414771  59414796              DQ707787     1    26    29
browser |    26  100.0%          1     +  59695292  59695317              DQ707787     1    26    29
browser |    26  100.0%          1     -  65746378  65746403              DQ707787     1    26    29
browser |    26  100.0%          1     -  77986938  77986963              DQ707787     1    26    29
browser |    26  100.0%          1     +  86165205  86165230              DQ707787     1    26    29
browser |    27  100.0%          1     -  90530108  90530135              DQ707787     3    29    29
browser |    26  100.0%          1     + 136937041 136937066              DQ707787     1    26    29
browser |    26  100.0%          1     - 136971066 136971091              DQ707787     1    26    29
browser |    26  100.0%          1     - 155390300 155390325              DQ707787     1    26    29
browser |    26  100.0%          1     - 165133347 165133372              DQ707787     1    26    29
browser |    26  100.0%         10     -  52223093  52223118              DQ707787     1    26    29
browser |    29  100.0%         10     -  56437287  56437316              DQ707787     1    29    29
browser |    26  100.0%         10     +  93483028  93483053              DQ707787     1    26    29
browser |    26  100.0%         10     -  97053906  97053931              DQ707787     1    26    29
browser |    26  100.0%         10     - 115297257 115297282              DQ707787     1    26    29
browser |    29  100.0%         11     +   4161394   4161422              DQ707787     1    29    29
browser |    26  100.0%         11     -  26544410  26544435              DQ707787     1    26    29
browser |    26  100.0%         11     -  43474501  43474526              DQ707787     1    26    29
browser |    26  100.0%         11     -  60478086  60478111              DQ707787     1    26    29
browser |    26  100.0%         11     -  60528213  60528238              DQ707787     1    26    29
browser |    26  100.0%         11     -  60579327  60579352              DQ707787     1    26    29
browser |    26  100.0%         11     -  69734560  69734585              DQ707787     1    26    29
browser |    26  100.0%         11     +  77609069  77609094              DQ707787     1    26    29
browser |    26  100.0%         11     +  89014093  89014118              DQ707787     1    26    29
browser |    26  100.0%         11     + 117233693 117233718              DQ707787     1    26    29
browser |    26  100.0%         11     + 120474113 120474138              DQ707787     1    26    29
browser |    26  100.0%         12     -   3624982   3625007              DQ707787     1    26    29
browser |    26  100.0%         12     +  16844914  16844939              DQ707787     1    26    29
browser |    26  100.0%         12     -  63257475  63257500              DQ707787     1    26    29
browser |    26  100.0%         12     +  89451670  89451695              DQ707787     1    26    29
browser |    26  100.0%         12     -  96370947  96370972              DQ707787     1    26    29
browser |    29  100.0%         12     -  98378664  98378692              DQ707787     1    29    29
browser |    26  100.0%         12     + 111117542 111117567              DQ707787     1    26    29
browser |    26  100.0%         13     -  11413231  11413256              DQ707787     1    26    29
browser |    26  100.0%         13     -  36383691  36383716              DQ707787     1    26    29
browser |    26  100.0%         13     +  61953209  61953234              DQ707787     1    26    29
browser |    26  100.0%         13     +  62164890  62164915              DQ707787     1    26    29
browser |    26  100.0%         13     +  62278866  62278891              DQ707787     1    26    29
browser |    26  100.0%         13     -  62699590  62699615              DQ707787     1    26    29
browser |    26  100.0%         13     - 100789276 100789301              DQ707787     1    26    29
browser |    26  100.0%         13     - 117529490 117529515              DQ707787     1    26    29
browser |    29  100.0%         14     +  14864026  14864055              DQ707787     1    29    29
browser |    29  100.0%         14     +  15414704  15414733              DQ707787     1    29    29
browser |    29  100.0%         14     +  15485727  15485756              DQ707787     1    29    29
browser |    29  100.0%         14     +  15921963  15921992              DQ707787     1    29    29
browser |    29  100.0%         14     +  16239993  16240022              DQ707787     1    29    29
browser |    29  100.0%         14     +  16287217  16287246              DQ707787     1    29    29
browser |    29  100.0%         14     +  16629302  16629331              DQ707787     1    29    29
browser |    29  100.0%         14     +  16707218  16707247              DQ707787     1    29    29
browser |    29  100.0%         14     +  17175038  17175067              DQ707787     1    29    29
browser |    29  100.0%         14     +  17237902  17237931              DQ707787     1    29    29
browser |    29  100.0%         14     -  17770657  17770686              DQ707787     1    29    29
browser |    29  100.0%         14     -  17998153  17998182              DQ707787     1    29    29
browser |    29  100.0%         14     -  18230686  18230715              DQ707787     1    29    29
browser |    26  100.0%         14     -  18314804  18314829              DQ707787     1    26    29
browser |    29  100.0%         14     -  18400333  18400362              DQ707787     1    29    29
browser |    29  100.0%         14     -  19291689  19291718              DQ707787     1    29    29
browser |    29  100.0%         14     -  19350367  19350396              DQ707787     1    29    29
browser |    26  100.0%         14     +  57147101  57147126              DQ707787     1    26    29
browser |    26  100.0%         14     -  60478927  60478952              DQ707787     1    26    29
browser |    26  100.0%         14     -  91083455  91083480              DQ707787     1    26    29
browser |    26  100.0%         14     -  98838863  98838888              DQ707787     1    26    29
browser |    26  100.0%         15     +  80105101  80105126              DQ707787     1    26    29
browser |    26  100.0%         15     -  97834708  97834733              DQ707787     1    26    29
browser |    26  100.0%         16     +  32176479  32176504              DQ707787     1    26    29
browser |    26  100.0%         16     +  55637669  55637694              DQ707787     1    26    29
browser |    26  100.0%         16     -  65193143  65193168              DQ707787     1    26    29
browser |    26  100.0%         17     -  23797811  23797836              DQ707787     1    26    29
browser |    26  100.0%         17     -  24911160  24911185              DQ707787     1    26    29
browser |    26  100.0%         17     +  28297718  28297743              DQ707787     1    26    29
browser |    26  100.0%         17     -  29691204  29691531              DQ707787     1    26    29
browser |    29  100.0%         17     +  59643424  59643452              DQ707787     1    29    29
browser |    26  100.0%         18     -  73995354  73995379              DQ707787     1    26    29
browser |    26  100.0%         18     +  79177983  79178008              DQ707787     1    26    29
browser |    29  100.0%         18     -  84951440  84951469              DQ707787     1    29    29
browser |    26  100.0%         18     -  90147758  90147783              DQ707787     1    26    29
browser |    26  100.0%         19     +   6408450   6408475              DQ707787     1    26    29
browser |    26  100.0%         19     -  10383332  10383357              DQ707787     1    26    29
browser |    26  100.0%         19     -  28667111  28667136              DQ707787     1    26    29
browser |    26  100.0%          2     -  28209820  28209845              DQ707787     1    26    29
browser |    26  100.0%          2     +  34646365  34646390              DQ707787     1    26    29
browser |    26  100.0%          2     -  51283813  51283838              DQ707787     1    26    29
browser |    26  100.0%          2     +  57172064  57172089              DQ707787     1    26    29
browser |    26  100.0%          2     -  60065493  60065518              DQ707787     1    26    29
browser |    26  100.0%          2     +  86694945  86694970              DQ707787     1    26    29
browser |    26  100.0%          2     - 104616498 104616523              DQ707787     1    26    29
browser |    26  100.0%          2     + 126851219 126851244              DQ707787     1    26    29
browser |    26  100.0%          3     +   4648815   4648840              DQ707787     1    26    29
browser |    26  100.0%          3     -  34785434  34785459              DQ707787     1    26    29
browser |    26  100.0%          3     +  51365385  51365410              DQ707787     1    26    29
browser |    29  100.0%          3     -  65866926  65866954              DQ707787     1    29    29
browser |    26  100.0%          3     +  74258583  74258608              DQ707787     1    26    29
browser |    26  100.0%          3     -  89029514  89029539              DQ707787     1    26    29
browser |    26  100.0%          3     +  98041535  98041560              DQ707787     1    26    29
browser |    26  100.0%          3     - 108027100 108027125              DQ707787     1    26    29
browser |    26  100.0%          3     + 125716083 125716108              DQ707787     1    26    29
browser |    26  100.0%          3     - 136233569 136233594              DQ707787     1    26    29
browser |    26  100.0%          4     +   6533617   6533642              DQ707787     1    26    29
browser |    26  100.0%          4     -  57763395  57763420              DQ707787     1    26    29
browser |    26  100.0%          4     -  62351134  62351159              DQ707787     1    26    29
browser |    26  100.0%          4     - 130580978 130581003              DQ707787     1    26    29
browser |    29  100.0%          4     + 131762929 131762958              DQ707787     1    29    29
browser |    26  100.0%          4     + 139083547 139083572              DQ707787     1    26    29
browser |    26  100.0%          4     + 144151557 144151582              DQ707787     1    26    29
browser |    26  100.0%          4     + 150496452 150496477              DQ707787     1    26    29
browser |    26  100.0%          4     + 152139277 152139302              DQ707787     1    26    29
browser |    26  100.0%          5     +   3380478   3380503              DQ707787     1    26    29
browser |    26  100.0%          5     +  55004332  55004357              DQ707787     1    26    29
browser |    26  100.0%          5     +  59435390  59435415              DQ707787     1    26    29
browser |    26  100.0%          5     -  77068904  77068929              DQ707787     1    26    29
browser |    26  100.0%          5     - 113835082 113835107              DQ707787     1    26    29
browser |    26  100.0%          6     -  38248905  38248930              DQ707787     1    26    29
browser |    26  100.0%          6     -  84739877  84739902              DQ707787     1    26    29
browser |    26  100.0%          6     -  85396740  85396765              DQ707787     1    26    29
browser |    29  100.0%          6     + 109116797 109116825              DQ707787     1    29    29
browser |    26  100.0%          6     - 120114934 120114959              DQ707787     1    26    29
browser |    26  100.0%          6     + 123160223 123160248              DQ707787     1    26    29
browser |    26  100.0%          7     -  28978549  28978574              DQ707787     1    26    29
browser |    26  100.0%          7     + 122821300 122821325              DQ707787     1    26    29
browser |    29  100.0%          7     + 122827353 122827381              DQ707787     1    29    29
browser |    26  100.0%          7     - 132547170 132547195              DQ707787     1    26    29
browser |    26  100.0%          8     +  11513137  11513162              DQ707787     1    26    29
browser |    26  100.0%          8     -  40800388  40800413              DQ707787     1    26    29
browser |    26  100.0%          8     +  52111098  52111123              DQ707787     1    26    29
browser |    26  100.0%          8     + 107492866 107492891              DQ707787     1    26    29
browser |    26  100.0%          8     + 107493147 107493172              DQ707787     1    26    29
browser |    26  100.0%          8     - 110714040 110714065              DQ707787     1    26    29
browser |    26  100.0%          8     + 125701682 125701707              DQ707787     1    26    29
browser |    26  100.0%          9     +  40888913  40888938              DQ707787     1    26    29
browser |    26  100.0%          9     +  43886313  43886338              DQ707787     1    26    29
browser |    26  100.0%          9     +  53565428  53565453              DQ707787     1    26    29
browser |    26  100.0%          9     -  58179511  58179536              DQ707787     1    26    29
browser |    29  100.0%          9     -  61865617  61865645              DQ707787     1    29    29
browser |    26  100.0%          9     -  83278815  83278840              DQ707787     1    26    29
browser |    26  100.0%          9     +  97087758  97087783              DQ707787     1    26    29
browser |    26  100.0%          9     +  99062959  99062984              DQ707787     1    26    29
browser |    27  100.0%          9     + 114481234 114481260              DQ707787     2    28    29
browser |    27  100.0%          X     +  36830727  36830753              DQ707787     1    27    29
browser |    26  100.0%          X     +  40132089  40132114              DQ707787     1    26    29
browser |    26  100.0%          X     -  52011300  52011325              DQ707787     1    26    29
browser |    26  100.0%          X     +  70458120  70458145              DQ707787     1    26    29
browser |    26  100.0%          X     -  92690730  92690755              DQ707787     1    26    29
browser |    26  100.0%          X     +  99463515  99463540              DQ707787     1    26    29
browser |    26  100.0%          X     + 101262276 101262301              DQ707787     1    26    29
browser |    26  100.0%          X     + 116814138 116814163              DQ707787     1    26    29

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