DQ598312
 

Information on mRNA DQ598312

Description: Homo sapiens piRNA piR-36378, 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: DQ598312
Position: chr6:27519529-27519557

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 |    29  100.0%          6     +  27519529  27519557              DQ598312     1    29    29
browser |    29  100.0%         11     +  34979530  34979558              DQ598312     1    29    29
browser |    29  100.0%         15     -  65869105  65869133              DQ598312     1    29    29
browser |    29  100.0%         17     +   8119752   8119780              DQ598312     1    29    29
browser |    29  100.0%          6     +  18836171  18836199              DQ598312     1    29    29
browser |    29  100.0%          6     +  27295433  27295461              DQ598312     1    29    29
browser |    29  100.0%          6     -  27547795  27547823              DQ598312     1    29    29
browser |    29   96.6%          6     +  28589379  28589407              DQ598312     1    29    29
browser |    29  100.0%          6     -  28941644  28941672              DQ598312     1    29    29
browser |    29   96.6%  6_GL000251v2_alt     +     79253     79281              DQ598312     1    29    29
browser |    29  100.0%  6_GL000251v2_alt     -    428050    428078              DQ598312     1    29    29
browser |    29  100.0%  6_GL000253v2_alt     -    207207    207235              DQ598312     1    29    29
browser |    29  100.0%  6_GL000254v2_alt     -    207397    207425              DQ598312     1    29    29
browser |    29  100.0%  6_GL000255v2_alt     -    207226    207254              DQ598312     1    29    29
browser |    29  100.0%  6_GL000256v2_alt     -    251038    251066              DQ598312     1    29    29

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