How to find the gene chromosome in the mysql table of Ensembl Database

Question

[xidianbill]

Hi,

I want to download the genome coordination of some transcripts and genes from ensembl database. Because these transcripts and genes are found only in some specific version of ensembl, biomart and ensembl api can't connect to that. I have to download these information by connecting to the mysql server directly and search data with mysql statements. But I find there isn't any colnum in any table representing the chromosome of a gene or a transcript. Dose anyone know how can I get the chromosome information of a gene or a transcript from ensembl mysql server directly?

The schema description of mysql is in this page https://asia.ensembl.org/info/docs/api/core/core_schema.html

[Emily]

Please do not send identical posts to BioStars and the Ensembl helpdesk, as it can create duplicate work.

Answer 1

[Pierre Lindenbaum]

But I find there isn't any colnum in any table representing the chromosome of a gene or a transcript.

https://www.ensembl.org/info/docs/api/core/core_schema.html#seq_region

seq_region Stores information about sequence regions. The primary key is used as a pointer into the dna table so that actual sequence can be obtained, and the coord_system_id allows sequence regions of multiple types to be stored. Clones, contigs and chromosomes are all now stored in the seq_region table. Contigs are stored with the co-ordinate system 'contig'. The relationship between contigs and clones is stored in the assembly table. The relationships between contigs and chromosomes, and between contigs and supercontigs, are stored in the assembly table.

[xidianbill]

Thanks for your reply. But actually I want to know the chromosome that the transcript or gene locates on. seq_region may not be able to supply this kind of information.

[Emily]

seq_region (which is in both the gene and transcript tables) contains a primary key which links to the seq_region table. The name column in the seq_region table gives the name of the chromosome.

[xidianbill]

OK，thanks a lot. The problem is solved~

[Pierre Lindenbaum]

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