I have a list of Genes (Ensemble ids). I need to find their locations in the human chromosomes. Information that I need- Start location Stop Location Length
I have tried ShinyGo but got only a graph with the location of genes on the chromosome but not exact locations.
2 answers
If your list of Ensembl IDs isn't too long (500 max), probably the eaiest way to get the starts and the stop is from biomart. Select the "Ensembl Genes" database, and the "Human genes" dataset. Enter your gene ids under Filters>Gene>Input external references ID list and under Attributes>Gene select Gene ID, Chromosome, Gene Start and Gene End.
Note that because "Gene start" is the earliest start coordinate of any transcript associated with that gene, and gene end is the last end coordinate of any transcript, then the "Length" of the gene will almost certainly be longer than the length of any individual transcript.
Gene location information can be found in the GTF or GFF files on the Ensembl FTP site. You just need to make sure that the version of the GTF/GFF file you use is the same as the annotation of the gene list you received. Older versions of Ensembl can be found at the archive.
Here is the first few lines of a GTF file. You can see lines that have "gene" in the 3rd column, show the coordinates in column 4 and 5
#!genome-build GRCh38.p5
#!genome-version GRCh38
#!genome-date 2013-12
#!genome-build-accession NCBI:GCA_000001405.20
#!genebuild-last-updated 2015-10
1 havana gene 11869 14409 . + . gene_id "ENSG00000223972"; gene_version "5"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; havana_gene "OTTHUMG00000000961"; havana_gene_version "2";
1 havana transcript 11869 14409 . + . gene_id "ENSG00000223972"; gene_version "5"; transcript_id "ENST00000456328"; transcript_version "2"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; havana_gene "OTTHUMG00000000961"; havana_gene_version "2"; transcript_name "DDX11L1-002"; transcript_source "havana"; transcript_biotype "processed_transcript"; havana_transcript "OTTHUMT00000362751"; havana_transcript_version "1"; tag "basic"; transcript_support_level "1";
1 havana exon 11869 12227 . + . gene_id "ENSG00000223972"; gene_version "5"; transcript_id "ENST00000456328"; transcript_version "2"; exon_number "1"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; havana_gene "OTTHUMG00000000961"; havana_gene_version "2"; transcript_name "DDX11L1-002"; transcript_source "havana"; transcript_biotype "processed_transcript"; havana_transcript "OTTHUMT00000362751"; havana_transcript_version "1"; exon_id "ENSE00002234944"; exon_version "1"; tag "basic"; transcript_support_level "1";
1 havana exon 12613 12721 . + . gene_id "ENSG00000223972"; gene_version "5"; transcript_id "ENST00000456328"; transcript_version "2"; exon_number "2"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; havana_gene "OTTHUMG00000000961"; havana_gene_version "2"; transcript_name "DDX11L1-002"; transcript_source "havana"; transcript_biotype "processed_transcript"; havana_transcript "OTTHUMT00000362751"; havana_transcript_version "1"; exon_id "ENSE00003582793"; exon_version "1"; tag "basic"; transcript_support_level "1";
1 havana exon 13221 14409 . + . gene_id "ENSG00000223972"; gene_version "5"; transcript_id "ENST00000456328"; transcript_version "2"; exon_number "3"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; havana_gene "OTTHUMG00000000961"; havana_gene_version "2"; transcript_name "DDX11L1-002"; transcript_source "havana"; transcript_biotype "processed_transcript"; havana_transcript "OTTHUMT00000362751"; havana_transcript_version "1"; exon_id "ENSE00002312635"; exon_version "1"; tag "basic"; transcript_support_level "1";
You can use your favorite scripting language to extract the coordinate information for your genes of interest.
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