I am trying to make clear one confusion regarding complete cds (sequence) that is given for some genes. This sequence is the extension of 5' and 3' end of the original encoding sequence (ORF).
Does it include total 5'UTR and 3'UTR regions or it is just given for the cloning purpose.
I would be thankful if anyone would clarify me about complete cds, whether it does include complete 5' and 3' UTR or not.
Regards,
Naveen
From my understanding, cds refers to the coding sequencing, which means the translated region. Therefore no, the UTRs and introns are not included. This might help.
CDS is a sequence of nucleotides that corresponds with the sequence of amino acids in a protein. A typical CDS starts with ATG and ends with a stop codon. As mentioned in the above reply, it doesn't have any introns, 5'- and 3'-UTR. CDS can be a subset of an open reading frame (ORF).
Attached a pdf with picture for better understanding.
The figure sent by Brijesh Kumar is very explainative, the only thing I disaggree is that if a gene is transcribed it don't have to code for a protein, because there are many genes that give a RNA and the RNA itself have a function and it doesn't code for a protein.
I have similar question. Even though cds is known as coding sequence which doesn't include intron like in Brijesh Kumar's pdf, There are "complete cds" in NCBI which has intron. For example,
https://www.ncbi.nlm.nih.gov/nucleotide/AH001475.2?report=genbank&log$=nuclalign&blast_rank=1&RID=K0YFW5M5014
This sequence is called 'Homo sapiens beta-globin gene, complete cds', and it has exon, and intron too.
I think it looks like pre-mRNA sequence in DNA format (Or ORF + 5',3' UTR).
as a reference:
https://github.com/PacificBiosciences/ANGEL/issues/9
The reason to have complete and partial CDS descriptions is because in many cases the sequences are not covering the complete region encoding the protein sequence from start to stop codon. This could be due to many causes, biological, as for a natural pseudogene that is having in the middle of the CDS a disruption due to deletion, insertion or recombination events, or due to technical issues, i.e. the sequence is at the end of genomic contigs that can not be further assembled, thus a fraction of the gene is detected but not the start or stop codons. Even more common, sequences deposited in GenBank that are coming from PCR amplifications are usually producing a gene fragment if the primers anneal in sites inside the CDS, so it will be a partial CDS.
That was very very helpful. Thank you all for such descriptive replies. Also, thanks to the one who asked the question.
Some of the answers here seem in conflict with what I observe at NCBI.
For example, JQ811934.1 is described as "complete cds" (of human SRY gene). It is an 824 nt sequence and a 204 aa translation is given. 204x3 is only 612, so the fasta sequence is too long -- it MUST include either introns or UTRs.
JQ811934.1 does have a subsequence ATGCAA ... CTGTAG that has length 612+3 and which corresponds to the aa sequence (probably, I haven't checked).
Am I missing something? I'd be interested to know how the two answerers that said UTRs and introns are not included explain this.
I recently encountered this challenge on NCBI portal and the answers here have been very helpful.
Thanks Howard Junca
- Badges
- Science method