Human mRNAs from GenBank

Display mode:  hide dense squish pack full   Filter: red green blue exclude include Combination Logic: and or

accession:	author:	library:	tissue:
cell:	keyword:	gene:	product:
description:

Color track by codons or bases: OFF genomic codons mRNA codons nonsynonymous mRNA codons mRNA bases different mRNA bases
Help on mRNA coloring

Alignment Gap/Insertion Display Options
Draw double horizontal lines when both genome and query have an insertion
Draw a vertical blue line for an insertion at the beginning or end of the query, orange for insertion in the middle of the query
Draw a vertical green line where query has a polyA tail insertion
Help on alignment gap/insertion display options

Description

The mRNA track shows alignments between human mRNAs in GenBank and the genome.

NOTE: As of April, 2008, we are again including GenBank sequences that contain the following URL as part of the record:

http://fulllength.invitrogen.com

Some transcripts from this library are suspect. Some of these entries are the result of alignment to pseudogenes, followed by a "correction" of the mRNA to match the genomic sequence. It is therefore not the sequence of the actual mRNA and makes it appear that the mRNA is transcribed. Invitrogen no longer sells the clones. This collection also contains a large amount of very good transcript evidence that can be quite useful. We have created a table, gbWarn, which lists problematic mRNAs and ESTs by accession. In a future release, we will be providing a better indication of the problematic transcripts in the genome browser display.

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, click here. Several types of alignment gap may also be colored; for more information, click here.

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, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL. GenBank: update. Nucleic Acids Res. 2004 Jan 1;32(Database issue):D23-6.

Kent WJ. BLAT - the BLAST-like alignment tool. Genome Res. 2002 Apr;12(4):656-64.