Different Types Of Genes

Question

[deepthithomaskannan]

Hi all,

I need to find gene names from some Rnor5.0 rat genome assembly locations. When I tried to download genes and their locations from the following link http://hgdownload.soe.ucsc.edu/goldenPath/rn5/database/

I found different types of genes like ensGene, mgcGenes, xenoRefGenes, refGenes etc.

What are the difference between all these genes? Which database I should use? EDIT: I downloaded the assembly from NCBI site

Thanks, Deepthi

Answer 1

[Jordan]

They are different genes in different databases:

1. refGenes are from RefSeq, you can take a look at the link here: format
2. ensGens are from the database Ensembl.
3. As per UCSC xenoRefGenes means that it has information about other organisms but not your organism. This definition I'm not sure though!
4. And mgcGenes represent Mammalian Gene Collection database

All these are different formats to represent gene names or ids. Which one to choose depends on which one you need.

[deepthithomaskannan]

I am still confused!

For example the location I need for say gene Ncam2 is Location :11q11 Chromosome: 11; NC_005110.3 (23856942..24353041) in Rnor5.0 genome assembly based on the following NCBI link http://www.ncbi.nlm.nih.gov/gene/288280

I can not find this location in any of these Gene info files. I got an entry in refGene.txt. But the starting location seems different. 11 NM_203409 chr11 + 23870312 24353041 23870446 24351531 18 23870312,24122739,24125886,24128606,24131948,24143419,24149921,24152741,24179785,24215355,24218345,24226006,24282876,24286650,24298228,24336988,24348733,24351419, 23870501,24122814,24126093,24128750,24132086,24143537,24150082,24152887,24179936,24215543,24218442,24226180,24282996,24286772,24298409,24337193,24348853,24353041, 0 Ncam2 cmpl cmpl0,1,1,1,1,1,2,1,0,1,0,1,1,1,0,1,2,2,

Do you have any idea from where I can download gene locations for Rnor5.0 rat genome assembly?

[tgrbrb]

The difference between NCBI's Gene definition vs the RefSeq is the level of support. The gene extents are currently defined by all the mRNA/EST evidence at that locus, which extends out to 23856942 based on accession AY495696.1. But those 5'-most 'exons' have no second line of support from the current transcript evidence. Based on the lack of support, RefSeq is conservative and doesn't extend NM_203409.1 out that far, so you end up with the 5' end defined at 23870312.

[deepthithomaskannan]

In that case I think I have to rely on refseq genes. Thank you tgrbrb.

EDIT: I was wrong. I downloaded my genome assembly from genbank not from refseq. For Rnor5.0 refseq and Genbank assemblies are not the same. Do you have any idea where can I find NCBI genes and locations?

How can I determine which Gene info I have to use?ensemble of NCBI?

[Jordan]

I have written down the answer below. Take a look, and see if helps.

Answer 2

[Jordan]

For downloading the genes and it's locations, do the following:

1. Go to UCSC Table browser: Link
2. Under clade: choose Mammal.
3. For genome: choose Rat
4. assembly: choose Rn5
5. Under group: choose Genes and Gene Prediction Tracks
6. track: RefSeq Genes if you prefer so
7. Under table: refGene
8. For region: select genome
9. For output: select BED - browser extendible data
10. Under file type returned: plain text
11. Click get ouput

This returns a list of genes in bed format. Hope this helps.

About which genome information to use - NCBI or Ensembl, that's a never ending debate. Usually I ask the people who request the information regarding which format they need. Some labs are used to certain format. Based on the needs just give which they need.

If you need Ensembl, then in step6 above, select Ensembl genes and step7, select ensGene. Rest remains the same.

[deepthithomaskannan]

Thank you. I really appreciate this help!