DQ585326
 

Information on mRNA DQ585326

Description: Homo sapiens piRNA piR-52438, complete sequence.
Gene: n/a
Product: n/a
Author: Girard,A., Sachidanandam,R., Hannon,G.J. and Carmell,M.A.
Organism: Homo sapiens
Tissue: n/a
Development stage: n/a
Cell line: n/a
Sex: n/a
Library: n/a
Clone: n/a
CDS: n/a
Date: 2008-11-02
Version: 1
mRNA sequence: DQ585326
Position: chr17:35195950-35195976

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 |    27  100.0%         17     -  35195950  35195976              DQ585326     1    27    27
browser |    27  100.0%          1     +  24798700  24798726              DQ585326     1    27    27
browser |    27  100.0%          1     +  39999098  39999124              DQ585326     1    27    27
browser |    27  100.0%          1     +  54232637  54232663              DQ585326     1    27    27
browser |    27  100.0%          1     +  86215157  86215183              DQ585326     1    27    27
browser |    27  100.0%          1     + 108675125 108675151              DQ585326     1    27    27
browser |    27  100.0%          1     - 117431146 117431172              DQ585326     1    27    27
browser |    27  100.0%          1     - 150729922 150729948              DQ585326     1    27    27
browser |    27  100.0%          1     + 150780920 150780946              DQ585326     1    27    27
browser |    27  100.0%          1     - 151652138 151652164              DQ585326     1    27    27
browser |    27  100.0%          1     - 174351027 174351053              DQ585326     1    27    27
browser |    27  100.0%         10     -  70688804  70688830              DQ585326     1    27    27
browser |    27  100.0%         10     + 100092235 100092261              DQ585326     1    27    27
browser |    27  100.0%         10     + 103128120 103128146              DQ585326     1    27    27
browser |    27  100.0%         11     +   2331802   2331828              DQ585326     1    27    27
browser |    27  100.0%         11     +  28429412  28429438              DQ585326     1    27    27
browser |    27  100.0%         11     +  41303142  41303168              DQ585326     1    27    27
browser |    27  100.0%         11     +  44662986  44663012              DQ585326     1    27    27
browser |    27  100.0%         11     +  62277975  62278001              DQ585326     1    27    27
browser |    27  100.0%         11     -  64173394  64173420              DQ585326     1    27    27
browser |    27  100.0%         11     +  65238673  65238699              DQ585326     1    27    27
browser |    27  100.0%         11     -  72503477  72503503              DQ585326     1    27    27
browser |    27  100.0%         11     -  93948183  93948209              DQ585326     1    27    27
browser |    27  100.0%         11     -  95322013  95322039              DQ585326     1    27    27
browser |    27  100.0%         11     - 118332673 118332699              DQ585326     1    27    27
browser |    27  100.0%         11     - 119508819 119508845              DQ585326     1    27    27
browser |    27  100.0%         12     -  37815855  37815881              DQ585326     1    27    27
browser |    27  100.0%         12     -  56076673  56076699              DQ585326     1    27    27
browser |    27  100.0%         12     +  66133977  66134003              DQ585326     1    27    27
browser |    27  100.0%         12     +  95946670  95946696              DQ585326     1    27    27
browser |    27  100.0%         12     - 110868668 110868694              DQ585326     1    27    27
browser |    27  100.0%         12     - 119919672 119919698              DQ585326     1    27    27
browser |    27  100.0%         12     + 121993022 121993048              DQ585326     1    27    27
browser |    27  100.0%         13     +  19778426  19778452              DQ585326     1    27    27
browser |    27  100.0%         13     +  42965838  42965864              DQ585326     1    27    27
browser |    27  100.0%         13     +  49377446  49377472              DQ585326     1    27    27
browser |    27  100.0%         14     +  70477010  70477036              DQ585326     1    27    27
browser |    27   96.3%         14     -  91558294  91558320              DQ585326     1    27    27
browser |    27  100.0%         14     -  92912627  92912653              DQ585326     1    27    27
browser |    27  100.0%         14     - 105079993 105080019              DQ585326     1    27    27
browser |    27   96.3%  14_KI270844v1_alt     -     22430     22456              DQ585326     1    27    27
browser |    27  100.0%  14_KI270847v1_alt     -     27189     27215              DQ585326     1    27    27
browser |    27  100.0%         15     -  88554415  88554441              DQ585326     1    27    27
browser |    27  100.0%         15     -  88942647  88942673              DQ585326     1    27    27
browser |    25  100.0%         15     +  89867067  89867091              DQ585326     1    25    27
browser |    27  100.0%         16     -   2802818   2802844              DQ585326     1    27    27
browser |    27  100.0%         16     -  56740962  56740988              DQ585326     1    27    27
browser |    27  100.0%         16     +  70203917  70203943              DQ585326     1    27    27
browser |    27   96.3%         17     +    598016    598042              DQ585326     1    27    27
browser |    27   96.3%         17     -   1403967   1403993              DQ585326     1    27    27
browser |    27  100.0%         17     -  19628830  19628856              DQ585326     1    27    27
browser |    27  100.0%         17     +  27033176  27033202              DQ585326     1    27    27
browser |    27  100.0%         17     +  42972377  42972403              DQ585326     1    27    27
browser |    27  100.0%  17_GL000258v2_alt     -    712015    712041              DQ585326     1    27    27
browser |    27  100.0%  17_GL000258v2_alt     +   1235122   1235148              DQ585326     1    27    27
browser |    27  100.0%         18     +  54342516  54342542              DQ585326     1    27    27
browser |    27  100.0%         19     -  34080529  34080555              DQ585326     1    27    27
browser |    27  100.0%         19     -  40109653  40109679              DQ585326     1    27    27
browser |    27  100.0%         19     +  40117234  40117260              DQ585326     1    27    27
browser |    27  100.0%          2     +    126249    126275              DQ585326     1    27    27
browser |    27  100.0%          2     +  41746133  41746159              DQ585326     1    27    27
browser |    27  100.0%          2     -  42607016  42607042              DQ585326     1    27    27
browser |    27  100.0%          2     -  55774678  55774704              DQ585326     1    27    27
browser |    27  100.0%          2     -  64513156  64513182              DQ585326     1    27    27
browser |    27  100.0%          2     +  96460846  96460872              DQ585326     1    27    27
browser |    27  100.0%          2     - 119845189 119845215              DQ585326     1    27    27
browser |    27  100.0%          2     - 127789638 127789664              DQ585326     1    27    27
browser |    27  100.0%          2     - 169787308 169787334              DQ585326     1    27    27
browser |    27  100.0%          2     - 186154946 186154972              DQ585326     1    27    27
browser |    27  100.0%          2     + 195567238 195567264              DQ585326     1    27    27
browser |    27  100.0%          2     - 197924094 197924120              DQ585326     1    27    27
browser |    27  100.0%          2     + 218845955 218845981              DQ585326     1    27    27
browser |    27  100.0%          2     + 222815736 222815762              DQ585326     1    27    27
browser |    27  100.0%         20     +   5026940   5026966              DQ585326     1    27    27
browser |    27  100.0%         20     +  32175387  32175413              DQ585326     1    27    27
browser |    27  100.0%         20     +  32723189  32723215              DQ585326     1    27    27
browser |    27  100.0%         20     +  35152918  35152944              DQ585326     1    27    27
browser |    27  100.0%         21     -  17293030  17293056              DQ585326     1    27    27
browser |    27  100.0%  21_KI270874v1_alt     -    149340    149366              DQ585326     1    27    27
browser |    27  100.0%         22     +  17560674  17560700              DQ585326     1    27    27
browser |    27  100.0%         22     -  31593932  31593958              DQ585326     1    27    27
browser |    27  100.0%          3     +  42797003  42797029              DQ585326     1    27    27
browser |    27  100.0%          3     +  48055259  48055285              DQ585326     1    27    27
browser |    27  100.0%          3     -  58551068  58551094              DQ585326     1    27    27
browser |    27  100.0%          3     -  58891361  58891387              DQ585326     1    27    27
browser |    27  100.0%          3     -  78584256  78584282              DQ585326     1    27    27
browser |    27  100.0%          3     -  98838983  98839009              DQ585326     1    27    27
browser |    27  100.0%          3     - 124368997 124369023              DQ585326     1    27    27
browser |    27  100.0%          3     + 128953660 128953686              DQ585326     1    27    27
browser |    27  100.0%          3     - 132472183 132472209              DQ585326     1    27    27
browser |    27  100.0%          3     - 179291644 179291670              DQ585326     1    27    27
browser |    27  100.0%          3     - 196762633 196762659              DQ585326     1    27    27
browser |    27  100.0%          4     -  48364812  48364838              DQ585326     1    27    27
browser |    27  100.0%          4     +  52464159  52464185              DQ585326     1    27    27
browser |    27  100.0%          5     -  34307646  34307672              DQ585326     1    27    27
browser |    27  100.0%          5     -  69063644  69063670              DQ585326     1    27    27
browser |    27  100.0%          5     +  82138897  82138923              DQ585326     1    27    27
browser |    27  100.0%          5     - 142077279 142077305              DQ585326     1    27    27
browser |    27  100.0%          5     - 168644365 168644391              DQ585326     1    27    27
browser |    27  100.0%          5     + 176304242 176304268              DQ585326     1    27    27
browser |    27  100.0%          5     + 176960686 176960712              DQ585326     1    27    27
browser |    27  100.0%          6     -  27486386  27486412              DQ585326     1    27    27
browser |    27   96.3%          6     +  29932108  29932134              DQ585326     1    27    27
browser |    27   96.3%          6     -  31067959  31067985              DQ585326     1    27    27
browser |    27   96.3%          6     -  31456450  31456476              DQ585326     1    27    27
browser |    27  100.0%          6     -  31855304  31855330              DQ585326     1    27    27
browser |    27  100.0%          6     -  32596734  32596760              DQ585326     1    27    27
browser |    27  100.0%          6     +  35339790  35339816              DQ585326     1    27    27
browser |    27  100.0%          6     -  47506738  47506764              DQ585326     1    27    27
browser |    27  100.0%          6     +  88946699  88946725              DQ585326     1    27    27
browser |    27  100.0%          6     + 109046138 109046164              DQ585326     1    27    27
browser |    27  100.0%          6     - 122850237 122850263              DQ585326     1    27    27
browser |    27  100.0%          6     + 162338307 162338333              DQ585326     1    27    27
browser |    27  100.0%  6_GL000250v2_alt     -   3187920   3187946              DQ585326     1    27    27
browser |    27   96.3%  6_GL000251v2_alt     +   1954262   1954288              DQ585326     1    27    27
browser |    27   96.3%  6_GL000251v2_alt     -   2550337   2550363              DQ585326     1    27    27
browser |    27  100.0%  6_GL000251v2_alt     -   3332720   3332746              DQ585326     1    27    27
browser |    27   96.3%  6_GL000252v2_alt     +   1730402   1730428              DQ585326     1    27    27
browser |    27   96.3%  6_GL000252v2_alt     -   2327331   2327357              DQ585326     1    27    27
browser |    27  100.0%  6_GL000252v2_alt     -   3103082   3103108              DQ585326     1    27    27
browser |    27  100.0%  6_GL000253v2_alt     -   3160520   3160546              DQ585326     1    27    27
browser |    27   96.3%  6_GL000253v2_alt     +   4074603   4074629              DQ585326     1    27    27
browser |    27   96.3%  6_GL000254v2_alt     -   2412075   2412101              DQ585326     1    27    27
browser |    27  100.0%  6_GL000254v2_alt     -   3197374   3197400              DQ585326     1    27    27
browser |    27   96.3%  6_GL000255v2_alt     +   1729625   1729651              DQ585326     1    27    27
browser |    27   96.3%  6_GL000255v2_alt     -   2325946   2325972              DQ585326     1    27    27
browser |    27  100.0%  6_GL000255v2_alt     -   3111276   3111302              DQ585326     1    27    27
browser |    27   96.3%  6_GL000256v2_alt     +   1775304   1775330              DQ585326     1    27    27
browser |    27   96.3%  6_GL000256v2_alt     -   2371404   2371430              DQ585326     1    27    27
browser |    27  100.0%  6_GL000256v2_alt     -   3156531   3156557              DQ585326     1    27    27
browser |    27  100.0%          7     +   1037299   1037325              DQ585326     1    27    27
browser |    27  100.0%          7     +   1069404   1069430              DQ585326     1    27    27
browser |    27  100.0%          7     +   2267367   2267393              DQ585326     1    27    27
browser |    27  100.0%          7     -  55221126  55221152              DQ585326     1    27    27
browser |    27  100.0%          7     +  64855566  64855592              DQ585326     1    27    27
browser |    27  100.0%          7     -  73285261  73285287              DQ585326     1    27    27
browser |    27  100.0%          7     - 100742803 100742829              DQ585326     1    27    27
browser |    27  100.0%          7     + 150197899 150197925              DQ585326     1    27    27
browser |    27  100.0%          8     -  61754018  61754044              DQ585326     1    27    27
browser |    27  100.0%          8     +  67310152  67310178              DQ585326     1    27    27
browser |    27  100.0%          9     +  81709595  81709621              DQ585326     1    27    27
browser |    27  100.0%          9     +  88625536  88625562              DQ585326     1    27    27
browser |    27  100.0%          9     - 107258444 107258470              DQ585326     1    27    27
browser |    27  100.0%          9     + 107775411 107775437              DQ585326     1    27    27
browser |    27  100.0%          9     + 111639981 111640007              DQ585326     1    27    27
browser |    27  100.0%          9     - 125329070 125329096              DQ585326     1    27    27
browser |    27  100.0%          9     + 125622851 125622877              DQ585326     1    27    27
browser |    27  100.0%          X     +  30601547  30601573              DQ585326     1    27    27
browser |    27  100.0%          X     -  42474920  42474946              DQ585326     1    27    27
browser |    27  100.0%          X     +  46274764  46274790              DQ585326     1    27    27
browser |    27  100.0%          X     -  52827724  52827750              DQ585326     1    27    27
browser |    27  100.0%          X     -  76219157  76219183              DQ585326     1    27    27

View details of parts of alignment within browser window
.
View table schema

Go to Human mRNAs track controls

Data last updated: 2019-10-03


p12 Note: Includes annotations on GRCh38.p12 patch sequences

Description

The mRNA track shows alignments between human 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 human 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