DQ598704
 

Information on mRNA DQ598704

Description: Homo sapiens piRNA piR-36770, 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: DQ598704
Position: chr3:1243685-1243708

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 |    24  100.0%          3     -   1243685   1243708              DQ598704     3    26    26
browser |    26  100.0%          1     +   5046680   5046705              DQ598704     1    26    26
browser |    26  100.0%          1     +   5114951   5114976              DQ598704     1    26    26
browser |    26  100.0%          1     +  68388098  68388123              DQ598704     1    26    26
browser |    26  100.0%          1     + 183615480 183615505              DQ598704     1    26    26
browser |    26  100.0%          1     + 209450768 209450793              DQ598704     1    26    26
browser |    26  100.0%          1     + 212911337 212911362              DQ598704     1    26    26
browser |    26  100.0%          1     - 215413818 215413843              DQ598704     1    26    26
browser |    26  100.0%          1     - 218597667 218597692              DQ598704     1    26    26
browser |    26  100.0%          1     + 221967788 221967813              DQ598704     1    26    26
browser |    26  100.0%          1     - 221976981 221977006              DQ598704     1    26    26
browser |    26  100.0%          1     - 223028279 223028304              DQ598704     1    26    26
browser |    26  100.0%         10     -  17630721  17630746              DQ598704     1    26    26
browser |    26  100.0%         10     -  52037639  52037664              DQ598704     1    26    26
browser |    26  100.0%         10     -  53502910  53502935              DQ598704     1    26    26
browser |    26  100.0%         10     +  54168587  54168612              DQ598704     1    26    26
browser |    26  100.0%         10     -  58864894  58864919              DQ598704     1    26    26
browser |    26  100.0%         10     +  76820401  76820426              DQ598704     1    26    26
browser |    26  100.0%         10     -  90084916  90084941              DQ598704     1    26    26
browser |    26  100.0%         11     +  42122408  42122433              DQ598704     1    26    26
browser |    26  100.0%         11     +  96589757  96589782              DQ598704     1    26    26
browser |    26  100.0%         11     - 130757383 130757408              DQ598704     1    26    26
browser |    26  100.0%         12     +  20765209  20765234              DQ598704     1    26    26
browser |    26  100.0%         12     -  20820878  20820903              DQ598704     1    26    26
browser |    26  100.0%         12     -  67770524  67770549              DQ598704     1    26    26
browser |    26  100.0%         12     +  70087232  70087257              DQ598704     1    26    26
browser |    26  100.0%         12     +  79541700  79541725              DQ598704     1    26    26
browser |    26  100.0%         12     +  86940631  86940656              DQ598704     1    26    26
browser |    26  100.0%  12_KQ759760v1_fix     +    172253    172278              DQ598704     1    26    26
browser |    26  100.0%         13     +  56042144  56042169              DQ598704     1    26    26
browser |    26  100.0%         13     -  56116295  56116320              DQ598704     1    26    26
browser |    26  100.0%         13     -  66230251  66230276              DQ598704     1    26    26
browser |    26  100.0%         13     -  88516700  88516725              DQ598704     1    26    26
browser |    26  100.0%         13     -  90852463  90852488              DQ598704     1    26    26
browser |    26  100.0%         13     + 109267176 109267201              DQ598704     1    26    26
browser |    26  100.0%         14     -  31249180  31249205              DQ598704     1    26    26
browser |    26  100.0%         14     +  98987032  98987057              DQ598704     1    26    26
browser |    26  100.0%         15     +  35240602  35240627              DQ598704     1    26    26
browser |    26  100.0%         15     -  36289517  36289542              DQ598704     1    26    26
browser |    26  100.0%         15     -  53430711  53430736              DQ598704     1    26    26
browser |    26  100.0%         16     -  59521515  59521540              DQ598704     1    26    26
browser |    26  100.0%         16     -  70620341  70620366              DQ598704     1    26    26
browser |    26  100.0%         16     -  86745898  86745923              DQ598704     1    26    26
browser |    26  100.0%         17     +  34185108  34185133              DQ598704     1    26    26
browser |    26  100.0%         19     +   5550305   5550330              DQ598704     1    26    26
browser |    26  100.0%         19     +  20157368  20157393              DQ598704     1    26    26
browser |    26  100.0%         19     -  36159275  36159300              DQ598704     1    26    26
browser |    24  100.0%         19     -  36263357  36263380              DQ598704     3    26    26
browser |    26  100.0%          2     -   7876535   7876560              DQ598704     1    26    26
browser |    24  100.0%          2     +  60419457  60419480              DQ598704     1    24    26
browser |    26  100.0%          2     +  66245762  66245787              DQ598704     1    26    26
browser |    26  100.0%          2     +  67333411  67333436              DQ598704     1    26    26
browser |    26  100.0%          2     -  71088917  71088942              DQ598704     1    26    26
browser |    26  100.0%          2     + 164297687 164297712              DQ598704     1    26    26
browser |    26  100.0%          2     - 165714369 165714394              DQ598704     1    26    26
browser |    26  100.0%          2     - 187674346 187674371              DQ598704     1    26    26
browser |    26  100.0%          2     + 192132254 192132279              DQ598704     1    26    26
browser |    26  100.0%          2     + 199248760 199248785              DQ598704     1    26    26
browser |    26  100.0%          2     - 218177904 218177929              DQ598704     1    26    26
browser |    26  100.0%         20     -  12344149  12344174              DQ598704     1    26    26
browser |    26  100.0%         20     +  12755706  12755731              DQ598704     1    26    26
browser |    26  100.0%         20     -  19755019  19755044              DQ598704     1    26    26
browser |    26  100.0%         20     +  40095176  40095201              DQ598704     1    26    26
browser |    26  100.0%         20     +  40270892  40270917              DQ598704     1    26    26
browser |    26  100.0%         22     +  27743820  27743845              DQ598704     1    26    26
browser |    25  100.0%          3     - 104443792 104443816              DQ598704     1    25    26
browser |    26  100.0%          3     - 112421435 112421460              DQ598704     1    26    26
browser |    26  100.0%          3     - 115797377 115797402              DQ598704     1    26    26
browser |    26  100.0%          3     - 116109192 116109217              DQ598704     1    26    26
browser |    26  100.0%          3     - 191899281 191899306              DQ598704     1    26    26
browser |    24  100.0%          4     -  23725896  23725919              DQ598704     3    26    26
browser |    26  100.0%          4     +  24325043  24325068              DQ598704     1    26    26
browser |    26  100.0%          4     +  24502841  24502866              DQ598704     1    26    26
browser |    26  100.0%          4     -  61768166  61768191              DQ598704     1    26    26
browser |    26  100.0%          4     -  91658500  91658525              DQ598704     1    26    26
browser |    26  100.0%          4     + 119995752 119995777              DQ598704     1    26    26
browser |    26  100.0%          4     - 135171169 135171194              DQ598704     1    26    26
browser |    26  100.0%          4     + 145700938 145700963              DQ598704     1    26    26
browser |    26  100.0%          4     + 156602112 156602137              DQ598704     1    26    26
browser |    26  100.0%          4     + 162710932 162710957              DQ598704     1    26    26
browser |    26  100.0%          4     - 167439682 167439707              DQ598704     1    26    26
browser |    26  100.0%          4     - 179168768 179168793              DQ598704     1    26    26
browser |    26  100.0%          4     + 182816352 182816377              DQ598704     1    26    26
browser |    25  100.0%          4     - 189483341 189483365              DQ598704     1    25    26
browser |    26   96.2%          4     + 189927651 189927676              DQ598704     1    26    26
browser |    26   96.2%  4_KI270896v1_alt     +    265181    265206              DQ598704     1    26    26
browser |    25  100.0%  4_KI270925v1_alt     -    121484    121508              DQ598704     1    25    26
browser |    26   96.2%  4_KQ983257v1_fix     +     20581     20606              DQ598704     1    26    26
browser |    26   96.2%  4_KQ983258v1_alt     +     20581     20606              DQ598704     1    26    26
browser |    26  100.0%          5     +   5517386   5517411              DQ598704     1    26    26
browser |    26  100.0%          5     +   7265415   7265440              DQ598704     1    26    26
browser |    26  100.0%          5     +  12491667  12491692              DQ598704     1    26    26
browser |    26  100.0%          5     +  18540138  18540163              DQ598704     1    26    26
browser |    26  100.0%          5     -  18672736  18672761              DQ598704     1    26    26
browser |    26  100.0%          5     +  84700311  84700336              DQ598704     1    26    26
browser |    26  100.0%          5     + 110531671 110531696              DQ598704     1    26    26
browser |    26  100.0%          5     - 153453587 153453612              DQ598704     1    26    26
browser |    26  100.0%          5     - 180418603 180418628              DQ598704     1    26    26
browser |    26  100.0%          6     -   6031659   6031684              DQ598704     1    26    26
browser |    26  100.0%          6     -  77664430  77664455              DQ598704     1    26    26
browser |    26  100.0%          6     -  81349007  81349032              DQ598704     1    26    26
browser |    26  100.0%          6     -  90674089  90674114              DQ598704     1    26    26
browser |    26  100.0%          6     -  94557824  94557849              DQ598704     1    26    26
browser |    26  100.0%          6     + 102294755 102294780              DQ598704     1    26    26
browser |    26  100.0%          6     - 114426201 114426226              DQ598704     1    26    26
browser |    26  100.0%          6     + 115033714 115033739              DQ598704     1    26    26
browser |    26  100.0%          6     - 121624317 121624342              DQ598704     1    26    26
browser |    26  100.0%          6     + 131325232 131325257              DQ598704     1    26    26
browser |    25  100.0%          6     + 144925006 144925030              DQ598704     2    26    26
browser |    26  100.0%          7     -  32841780  32841805              DQ598704     1    26    26
browser |    26  100.0%          7     -  42874485  42874510              DQ598704     1    26    26
browser |    26  100.0%          7     - 113237456 113237481              DQ598704     1    26    26
browser |    24  100.0%          7     + 121317401 121317424              DQ598704     1    24    26
browser |    24  100.0%          7     + 139463079 139463102              DQ598704     3    26    26
browser |    26  100.0%          7     - 143541099 143541124              DQ598704     1    26    26
browser |    26  100.0%          7     + 143788337 143788362              DQ598704     1    26    26
browser |    26   96.2%          7     - 148313952 148313977              DQ598704     1    26    26
browser |    26  100.0%  7_KZ208912v1_fix     -    160463    160488              DQ598704     1    26    26
browser |    26  100.0%  7_KZ208912v1_fix     +    332656    332681              DQ598704     1    26    26
browser |    26  100.0%          8     +  68975002  68975027              DQ598704     1    26    26
browser |    26  100.0%          8     +  71676742  71676767              DQ598704     1    26    26
browser |    26  100.0%          8     +  85064759  85064784              DQ598704     1    26    26
browser |    26  100.0%          8     -  90094083  90094108              DQ598704     1    26    26
browser |    26  100.0%          8     +  91949833  91949858              DQ598704     1    26    26
browser |    26  100.0%          8     +  97176910  97176935              DQ598704     1    26    26
browser |    26  100.0%          8     +  97202754  97202779              DQ598704     1    26    26
browser |    26  100.0%          8     +  99945700  99945725              DQ598704     1    26    26
browser |    25  100.0%          8     + 115816437 115816461              DQ598704     1    25    26
browser |    26  100.0%          8     - 132084115 132084140              DQ598704     1    26    26
browser |    26  100.0%          8     - 135771024 135771049              DQ598704     1    26    26
browser |    26  100.0%          9     -  21489579  21489604              DQ598704     1    26    26
browser |    26  100.0%          9     +  74087494  74087519              DQ598704     1    26    26
browser |    26  100.0%          9     -  82704588  82704613              DQ598704     1    26    26
browser |    26  100.0%          9     +  99671995  99672020              DQ598704     1    26    26
browser |    26  100.0%          9     + 115475192 115475217              DQ598704     1    26    26
browser |    26  100.0%          9     - 115843082 115843107              DQ598704     1    26    26
browser |    26  100.0%          9     - 118489551 118489576              DQ598704     1    26    26
browser |    26  100.0%          X     -   3557004   3557029              DQ598704     1    26    26
browser |    26  100.0%          X     +   4893421   4893446              DQ598704     1    26    26
browser |    26  100.0%          X     +  87683721  87683746              DQ598704     1    26    26
browser |    26  100.0%          X     -  90777195  90777220              DQ598704     1    26    26
browser |    26  100.0%          X     -  92276939  92276964              DQ598704     1    26    26
browser |    26  100.0%          X     - 109869091 109869116              DQ598704     1    26    26
browser |    26  100.0%          X     - 119321641 119321666              DQ598704     1    26    26
browser |    26  100.0%          X     + 122223866 122223891              DQ598704     1    26    26

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

Go to Human mRNAs track controls

Data last updated: 2020-02-04


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