DQ589596
 

Information on mRNA DQ589596

Description: Homo sapiens piRNA piR-56708, 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: DQ589596
Position: chr10:29143060-29143084

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%         10     -  29143060  29143084              DQ589596     3    27    27
browser |    25  100.0%          1     + 187836376 187836400              DQ589596     3    27    27
browser |    25  100.0%          1     - 218214400 218214424              DQ589596     3    27    27
browser |    25  100.0%         18     +  54712820  54712844              DQ589596     3    27    27
browser |    25  100.0%          2     +  98172163  98172187              DQ589596     3    27    27
browser |    25  100.0%          2     + 154191942 154191966              DQ589596     3    27    27
browser |    25  100.0%         20     -   8005947   8005971              DQ589596     3    27    27
browser |    27  100.0%         21     -  44485850  44485876              DQ589596     1    27    27
browser |    27  100.0%         21     -  44490799  44490825              DQ589596     1    27    27
browser |    25  100.0%          3     +   7959009   7959033              DQ589596     3    27    27
browser |    25  100.0%          3     -  66635166  66635190              DQ589596     3    27    27
browser |    25  100.0%          3     + 104192256 104192280              DQ589596     3    27    27
browser |    25  100.0%          3     - 145395800 145395824              DQ589596     3    27    27
browser |    25  100.0%          4     - 130783223 130783247              DQ589596     3    27    27
browser |    25  100.0%          5     +  25853391  25853415              DQ589596     3    27    27
browser |    25  100.0%          6     +   2937983   2938007              DQ589596     3    27    27
browser |    25  100.0%          6     - 107079336 107079360              DQ589596     3    27    27
browser |    25  100.0%          6     - 169912245 169912269              DQ589596     3    27    27
browser |    25  100.0%  6_KI270797v1_alt     -    190067    190091              DQ589596     3    27    27
browser |    25  100.0%          8     +  41499405  41499429              DQ589596     3    27    27
browser |    25  100.0%          8     -  63322519  63322543              DQ589596     3    27    27
browser |    25  100.0%          8     - 110115973 110115997              DQ589596     3    27    27
browser |    25  100.0%          8     + 111624153 111624177              DQ589596     3    27    27
browser |    25  100.0%          9     -   1521178   1521202              DQ589596     3    27    27
browser |    25  100.0%          X     +  81229445  81229469              DQ589596     3    27    27

View details of parts of alignment within browser window
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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