Rhesus sequence

[Wang, Yan]

Hello,

I try to pull a GCG sequence from the Rhesus assembly(BCM Mmul_8.0.1/rheMac8), somehow the sequences are all Non-Rhesus RefSeq Genes.

My question is that we can select so many species to do comparative analysis , where are those sequences from? Obviously, I can’t retrieve all the sequences.

 

Thanks,

Yan

 

 

 

 

[Jairo Navarro Gonzalez]

Hello Yan,

Thank you for using the UCSC Genome Browser and your inquiry.

You can learn more about the data in the Other RefSeq track from its description page, http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=rheMac8&g=xenoRefGene. From the methods section:

The RNAs were aligned against the rhesus genome using blat; those with an alignment of less than 15% were discarded. When a single RNA aligned in multiple places, the alignment having the highest base identity was identified. Only alignments having a base identity level within 0.5% of the best and at least 25% base identity with the genomic sequence were kept.

These sequences, either the RNA used or the aligning Rhesus genomic sequence, can be downloaded using the Table Browser. To get your sequence, I used the following Table Browser settings:

clade: Mammal
genome: Human
assembly: Nov. 2015 (BCM Mmul_8.0.1/rheMac8)
group: Genes and Gene Predictions
track: Other RefSeq
table: xenoRefGene
region: chr12:48876322-48885844
output format: sequence

Once you have configured the Table Browser's settings, click get output.

You will be redirected to a new page where you can select either genomic, protein, or mRNA for the sequence output.

Select the output that you want and click submit. If you select genomic for sequence output, you will be taken to an additional page where you can specify regions of the genomic sequence that you are interested in, such as introns, or configure the formatting of the sequence output.

You can also search our mailing list archives for previously answered questions. For example, you may find the following questions useful:

Question about Other Refseq tracks - parameters used for blat alignment generation

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu.
All messages sent to that address are archived on a publicly-accessible Google Groups forum.
If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Jairo Navarro 
UCSC Genomics Institute

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