DQ598192
 

Information on mRNA DQ598192

Description: Homo sapiens piRNA piR-36258, 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: DQ598192
Position: chr6:28789810-28789841

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 |    31   96.8%          6     -  28789810  28789841              DQ598192     1    32    32
browser |    31  100.0%          6     +  28607156  28607187              DQ598192     1    32    32
browser |    31  100.0%          6     +  28710589  28710620              DQ598192     1    32    32
browser |    31  100.0%          6     +  28719704  28719735              DQ598192     1    32    32
browser |    31  100.0%          6     +  28729315  28729346              DQ598192     1    32    32
browser |    31  100.0%          6     -  28796004  28796035              DQ598192     1    32    32
browser |    31  100.0%          6     -  28838484  28838515              DQ598192     1    32    32
browser |    31  100.0%          6     -  28863725  28863756              DQ598192     1    32    32
browser |    31   96.8%  6_GL000250v2_alt     -     55395     55426              DQ598192     1    32    32
browser |    31  100.0%  6_GL000250v2_alt     -     61587     61618              DQ598192     1    32    32
browser |    31  100.0%  6_GL000250v2_alt     -    104069    104100              DQ598192     1    32    32
browser |    31  100.0%  6_GL000250v2_alt     -    129309    129340              DQ598192     1    32    32
browser |    31  100.0%  6_GL000251v2_alt     +     97032     97063              DQ598192     1    32    32
browser |    31   96.8%  6_GL000251v2_alt     -    185783    185814              DQ598192     1    32    32
browser |    31  100.0%  6_GL000251v2_alt     +    200382    200413              DQ598192     1    32    32
browser |    31  100.0%  6_GL000251v2_alt     +    210383    210414              DQ598192     1    32    32
browser |    31  100.0%  6_GL000251v2_alt     +    219991    220022              DQ598192     1    32    32
browser |    31  100.0%  6_GL000251v2_alt     -    286675    286706              DQ598192     1    32    32
browser |    31  100.0%  6_GL000251v2_alt     -    329003    329034              DQ598192     1    32    32
browser |    31  100.0%  6_GL000251v2_alt     -    354265    354296              DQ598192     1    32    32
browser |    31   96.8%  6_GL000252v2_alt     -     55403     55434              DQ598192     1    32    32
browser |    31  100.0%  6_GL000252v2_alt     -     61595     61626              DQ598192     1    32    32
browser |    31  100.0%  6_GL000252v2_alt     -    104086    104117              DQ598192     1    32    32
browser |    31  100.0%  6_GL000252v2_alt     -    129327    129358              DQ598192     1    32    32
browser |    31   96.8%  6_GL000253v2_alt     -     55388     55419              DQ598192     1    32    32
browser |    31  100.0%  6_GL000253v2_alt     -     61577     61608              DQ598192     1    32    32
browser |    31  100.0%  6_GL000253v2_alt     -    104046    104077              DQ598192     1    32    32
browser |    31  100.0%  6_GL000253v2_alt     -    129283    129314              DQ598192     1    32    32
browser |    31   96.8%  6_GL000254v2_alt     -     55403     55434              DQ598192     1    32    32
browser |    31  100.0%  6_GL000254v2_alt     -     61597     61628              DQ598192     1    32    32
browser |    31  100.0%  6_GL000254v2_alt     -    104082    104113              DQ598192     1    32    32
browser |    31  100.0%  6_GL000254v2_alt     -    129319    129350              DQ598192     1    32    32
browser |    31  100.0%  6_GL000255v2_alt     -     61593     61624              DQ598192     1    32    32
browser |    31  100.0%  6_GL000255v2_alt     -    104065    104096              DQ598192     1    32    32
browser |    31  100.0%  6_GL000255v2_alt     -    129307    129338              DQ598192     1    32    32
browser |    31  100.0%  6_GL000256v2_alt     +     19126     19157              DQ598192     1    32    32
browser |    31  100.0%  6_GL000256v2_alt     +     29032     29063              DQ598192     1    32    32
browser |    31  100.0%  6_GL000256v2_alt     +     38661     38692              DQ598192     1    32    32
browser |    31  100.0%  6_GL000256v2_alt     -    105333    105364              DQ598192     1    32    32
browser |    31  100.0%  6_GL000256v2_alt     -    147732    147763              DQ598192     1    32    32
browser |    31  100.0%  6_GL000256v2_alt     -    172970    173001              DQ598192     1    32    32

View details of parts of alignment within browser window
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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