JV075075
 

Information on mRNA JV075075

Description: TSA: Macaca mulatta Mamu_405838 mRNA sequence.
Gene: n/a
Product: n/a
Author: Zimin,A.V., Cornish,A.S., Maudhoo,M.D., Gibbs,R.M., Zhang,X., Pandey,S., Meehan,D.T., Wipfler,K., Bosinger,S.E., Johnson,Z.P., Tharp,G.K., Marcais,G., Roberts,M., Ferguson,B., Fox,H.S., Treangen,T., Salzberg,S.L., Yorke,J.A. and Norgren,R.B. Jr.
Organism: Macaca mulatta
Tissue: testis
Development stage: n/a
Cell line: n/a
Sex: n/a
Library: n/a
Clone: n/a
CDS: n/a
Date: 2014-10-04
Version: 1
mRNA sequence: JV075075
Position: chr14:69637428-70295018

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 |   146   95.9%         14     -  69637428  70295018              JV075075    26   201   201
browser |   150   96.0%          1     +  38560251  39407913              JV075075    31   200   201
browser |    73   98.7%         14     +  24388975  25030143              JV075075    32   104   201
browser |   173   96.0%         17     -  13871248  14538411              JV075075    22   198   201
browser |   120   95.9%         17     +  39410089  39638121              JV075075    22   200   201
browser |   164   96.4%         20     +  17915039  19021568              JV075075    34   198   201
browser |   192   95.9%          6     + 175354797 176356997              JV075075     2   198   201
browser |   170   95.3%          X     + 112584947 113543341              JV075075     1   201   201
View table schema

Go to Rhesus mRNAs track controls

Data last updated at UCSC: 2020-08-22

Description

The mRNA track shows alignments between rhesus 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 rhesus 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