Can an eukaryotic gene have slightly long 5' UTR than its 3' UTR? I have one case in my hand, where I found out an ORF containing slightly larger 5' UTR than 3' UTR. And the gene is I think not getting translated. Can it occur when the gene is poorly translated? And only transcriptionally active? or it can rarely occur normally?
What do you mean by slightly longer (absolutely spoken)? And yes, why not, I know no rule, that the 5' UTR has to be shorter than the 3' UTR.
I meant that the 5' UTR is of 184 bases and the 3' UTR is of 120 bases. I heard that usually 3' UTR are longer in size than that of 5' UTR. I may be wrong, that is why I asked, anyways, thanks for the answer and it helped me out of a lot of confusions. Thanks again.
This is not much of a difference, if any. If you say that your 5' is 3kb long and the 3' only 200, that would probably be different. If your gene is transcribed (or is a pseudogene) depends on a lot of factors. How does the promoter look like, are there binding sites for general transcription factors available? Have you checked the ENCODE project for transcripts?
No that is not a pseudogene, I have cloned and sequenced the whole gene by primer walking by doing RACE. And found out that the UTRs are like this. But the Coding part is ok and showing fungal superfamily in the BLAST search with all the domains conserved in it. Only the UTRs were like that. I also have seen another report like this. So, I was just checking whether it was normal or not. I dont have any idea about the promoter of it.
I think it is not a problem, it can occur as you said. And as I have already said that there are another report of the same gene as mine from different source having slightly longer 5' UTR that its 3'. I think its normal.
And also this is a first time finding of the gene from that source. No data is available of the gene till now from my source.
I have done RACE to amplify the total gene. So, I also have got the poly A tail from where the 3' UTR started. And have done 5' RACE to obtain the 5' end including the 5' UTR.
@Pradbddha: This souds like pretty hard evidence about your gene. You identified both 5' and 3' regions by sequencing, its novel, looks good for me.
Yes, I have got the total ORF alongwith the both UTR s. Then analyzed with NCBI orf finder, and got the UTR s and ORF identified, and then got the gene identified using BLAST. I couldn't get your first line, what did you mean by hard evidence? I was a bit worried about the 5' UTR being slightly bigger than the 3' as I have already mentioned. Is that normal?
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