I work on E. coli genomes and while going through the various genes present it, I have seen that in the coordinates area of the description it is suggested to join different regions of genome.
join(1463416..1465928,1467265..1467317,1468541..1472037)
I was wondering why is this so? Isn't a gene sequence meant to be continuous.
Another thing that I am not clear about is the difference between a gene and CDS - I see cases in E. coli (based on NCBI annotation file in FTP site) where mutiple CDS are present with gene, some times they overlap also. And in most of the cases the gene and the corresponding CDS have the same coordinates.
Please somebody clarify me regarding these two things.
•
written
by
SRKR
2 answers
The gene in your link is only a pseudogene, that has been interrupted by transposases. (Gene on NCBI) In this (or similar) cases, also a procaryotic gene without introns can be joint from several locations.
I just looked up, what is in the space included. (In this case, transposes.) This often gives you an idea. Functional genes in procaryotes shouldn't be interrupted, though.
The CDS is the coding DNA sequence, meaning it's the part of the genetic sequence that gets directly translated into a protein. Since a single gene can code for multiple proteins, there can be multiple CDS regions. For genes, that contain introns which do not code for protein sequence, this means the CDS may not be continous.
AFAIK isn't a prokaryotic gene intron free ? http://www.emunix.emich.edu/~rwinning/genetics/transcr.htm
No, they can have introns and there can even be splicing (though much less and most/all of the splicosomal pathway is missing).
Thanks, I looked it up after your answer and even found a publication ~30 years old (http://www.pnas.org/content/80/11/3309.full.pdf) , but what I don't understand is why do some texts and webpages say there are no introns in prokaryotes.
To rephrase what Neilfws said, always remember that biology is messy :)
Log in to answer this question.
-
Download specific sequences from databases using a Ruby-Script
written by Theresa •
-
KEGG pathways and modules
written by amborella •
-
Simple questions on using KEGG as end user
written by fr
-
Extracting All Cds From A Embl File
written by Pappu
-
Sequencing By Hybridization Data Analysis
written by jack •
-
Should Regulatory Regions Be Included In The Intergenic Sequences?
written by SRKR
-
Getting Est Sequence Corresponding To Kegg Go Id
written by Thomasvangurp •
-
Get Ensembl Gene By Species/Strain For E. Coli
written by Jirapong •
-
How To Get Flybase Gene Id According To Kegg Gene Id?
written by Dejian
-
Is There Any Way To Retrieve Genes' Sequences In Fasta Format Using The Kegg Orthology Code?
written by Luke
