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How One Can Separate Noncoding From Coding Ucsc And Ensembl Transcripts

Dear biostars,

Do you know how one can separate noncoding from coding UCSC and ENSEMBL transcripts ? In general I use NR_* to identify noncoding and NM_* to identify protein coding genes in Refseq database.

Thanx in advance

code ucsc ensembl refseq
• 9,004 views • link
updated by Ram Ram • written by biorepine biorepine

what is your input ? a list of knownGene identifiers ? a list of ENSGxxxxxxx ?

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written by Pierre Lindenbaum Pierre Lindenbaum

yes ENS* in case of ENSEMBL and ucsc.* in case of UCSC.

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written by biorepine biorepine

2 answers

for the ucsc/knownGene, you can select the transcripts having cdsStart==cdsEnd

$ mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -D hg19 -e 'select name,chrom,cdsStart,cdsEnd from knownGene where cdsStart=cdsEnd limit 10'
+------------+-------+----------+--------+
| name       | chrom | cdsStart | cdsEnd |
+------------+-------+----------+--------+
| uc001aaa.3 | chr1  |    11873 |  11873 |
| uc010nxr.1 | chr1  |    11873 |  11873 |
| uc009vis.3 | chr1  |    14361 |  14361 |
| uc009vit.3 | chr1  |    14361 |  14361 |
| uc009viu.3 | chr1  |    14361 |  14361 |
| uc001aae.4 | chr1  |    14361 |  14361 |
| uc001aah.4 | chr1  |    14361 |  14361 |
| uc009vir.3 | chr1  |    14361 |  14361 |
| uc009viq.3 | chr1  |    14361 |  14361 |
| uc001aac.4 | chr1  |    14361 |  14361 |
+------------+-------+----------+--------+
• 141 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

So if I change cdsStart!=cdsEnd, does it print only coding genes ? Thanks

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written by biorepine biorepine

You can download ENSEMBL annotation from Biomart (http://useast.ensembl.org/biomart/martview/) , you can select Gene Biotype information that will tell you if a given transcript is protein-coding or non-coding.

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written by Ashutosh Pandey Ashutosh Pandey

Thanx but any idea regarding UCSC transcripts ?

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written by biorepine biorepine

You can input UCSC IDs into BioMart.

There's a help video on BioMart here:

• 199 views • link
updated by Ram Ram • written by Emily Emily

Using Ensembl biomart, is it possible to find gene biotype on the opposite(antisense) strands, especially if it is coding and non-coding.

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written by hbr721 • hbr721

I'm afraid I don't understand your question. Are you looking to find out if there's a gene on the opposite strand of your gene of interest and find out what its biotype is? If so, there isn't a way to do that using BioMart. That would be a job for the Perl API.

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written by Emily Emily

I am sorry that my question was not clear. But still you got it right - yes I am indeed interesting in looking on the non coding genes on the opposite strand of my gene of interest. I will look into Perl API. Thanks again.

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written by hbr721 • hbr721

Great !!! thanks so much. Currently i am trying to see the reverse strand information from the Blat output, if i can't then i have to switch to perl api.

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written by hbr721 • hbr721

I think hundreds of ENSEMBL lincRNAs annotations were wrong. (They should be intergenic and in principle they should not overlap with any known coding transcript irrespective of strand direction)

ex: 

chr8    33998976    34060498    NM_001177589_Gm3985    0    -    chr8    33998977    34060498    lincRNA_ENSMUSG00000079070_ENSMUST00000132101_Gm3985    0    -
chr8    33998976    34060498    NM_001177589_Gm3985    0    -    chr8    34000947    34052954    lincRNA_ENSMUSG00000079070_ENSMUST00000180220_Gm3985    0    -
chr8    48265402    48437702    proteinCoding_ENSMUSG00000038143_8_Stox2    0    -    chr8    48379626    48531716    lincRNA_ENSMUSG00000097922_ENSMUST00000181417_AC102862.2    0    -
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written by biorepine biorepine

I'm afraid you've got that wrong. lincRNAs can be anywhere in the genome and can overlap coding genes in both directions.

See the wikipedia article on lincRNAs.

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written by Emily Emily

Please see the wiki again.

Long intergenic non-coding RNAs (lincRNA) : "Intergenic" refers to long non-coding RNAs that are transcribed from non-coding DNA sequences between protein-coding genes"

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written by biorepine biorepine

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