How to look up the mRNA transcript (no introns) and putative promoter sequence for a target human gene.
Пікірлер: 99
@ahmadniazrahman7446 ай бұрын
This video has been a life-changer for me. I think every view of this video resulted in a scientific paper. You deserve credit for each one of them. This is a prime example of how science grow. Thankyou.
@yeny71943 жыл бұрын
I feel like crying from how happy I am for coming across this amazing video. I wish I could subscribe to your channel a million times. Thank you so very much.
@ayeshaarshad954393 жыл бұрын
mutual feelings!
@sergioruiz97033 жыл бұрын
I totally agree
@radhikap24372 жыл бұрын
Couldn’t agree more.
@mominamalik13044 жыл бұрын
For the very first time someone made these complicated things easy for me.. thank you sooo much for such a detailed video. I really really appreciate your effort n skills. Please also make a video on primer designing for different PCR like Qpcr simple pcr thank you
@marianaschlesinger33584 жыл бұрын
So true! I feel the same.
@jonathanhaber22772 жыл бұрын
I have never commented on a youtube video in my life, but I have to make an exception. This is an amazing explanation and tutorial on finding an unknown gene sequence of a known protein. This helped me so much. Thank you!!
@juliablaszczyk8036 Жыл бұрын
You do not even know how helpful is that for me right now!!!! Very grateful for this tutorial! :) Create such videos more often
@mahshidpooladvand8502 Жыл бұрын
The best tutorial in the history of tutorials!
@Viraj_2305Ай бұрын
I cantvthank you enough for teaching it in wonderful way...love from India❤
@muhammadwaqasluqman29772 жыл бұрын
Wow. This is amazing Video. I have been looking for such videos for years. Uploaded in 2019, I wonder why it didn't show up in my search earlier. This is what I actually needed to see. Thank you so much for this.
@hassanelsaid95212 жыл бұрын
The best explanation I have came across so far
@yourlifeonpowerАй бұрын
Very helpful and clear! Thank you so much
@Fitriananr11072 ай бұрын
Your videos are life saving! Thank you
@wamiqfarooq74013 жыл бұрын
I want to give you a hug, thank you so much. You are helping people.
@Kalyanraj955 жыл бұрын
These videos are extremely useful for me as a Biology student. I have recently binge watched all of your educational videos especially the Primer design, gene cloning videos. So thank you so much. Please do not stop making these videos. Would love to learn more about laboratory techniques, molecular and cell biology from your channel.
@mnzubyk Жыл бұрын
Thank you so much for taking the time to do this. Wonderful video. Really quick, around 21:34, when you are pasting the 1500bp promoter region into Word, you pasted an extra "A" I believe before the beginning of the gene. There are two A's and I think there should be just one. When setting the EPD sequence retrieval tool from -1485 to 0, the 0 is the first base of the gene. So it doubles the last base, which is an "A". Awesome video though, really wonderful teaching.
@akshu2512 жыл бұрын
Your videos are a life saver. I am about to join a lab working on CRISPR CAS9 technique. I have done my PhD in Mechanobiology, an area very different from this. Your videos helped me to brush-up my Masters in Biotech knowledge. Thank you for the videos 🙏🏻
@ashwinshukla99903 жыл бұрын
very helpful video...keep uploading such contents.
@Alasdair003 ай бұрын
Very usuful and exhaustive for me. Thank you
@sukrishnatk17824 жыл бұрын
Very useful video. Thank you sir. Please keep uploading more informative videos like this.
@dipanwitapaul78332 жыл бұрын
Very much informative but easily explained video! thank you very much
@dkumar40242 жыл бұрын
Hey Jacob, Just awesome man...Just Awesome such a great video after a long time I watched!!
@biomelogus67202 жыл бұрын
Thank you very much for such useful & helpful video! You save me!
@tahirsuhail3 жыл бұрын
wonderful explanations Jacob. Please make more
@user-wx7dm5jz3u18 күн бұрын
cool video! so useful it is!
@zhanglu36003 жыл бұрын
Many thanks for such a well-explained video.
@user-yz1lq1rv8f5 ай бұрын
Everyone who learned from this video should always be awared, especially those who are designing experiments related to DNA, genome or chromatin... NOT ALL the transcription start sites are in the first exon of the gene and also MOST of the genes contain intron in DNA level...
@user-rl8dz4tj6b3 жыл бұрын
Such a great video! It helps a lot. Thanks very much.
@MrRamaeri2 жыл бұрын
thank you for such a great presentation
@sayankundu29789 ай бұрын
Very helpful Video. Thank you
@arimene37483 жыл бұрын
Thank you so much , this was amazing , well explained and in all details
@avikchattopadhyay14833 жыл бұрын
IT IS EXTREMELY HELPFUL.
@taitopotato2 жыл бұрын
Thank you for the video! Extremely helpful
@adhirajgoel304 Жыл бұрын
Hi Jacob, great video, thanks!
@hammedtukur2 жыл бұрын
Many thanks for this. Really helpful
@dr.weamelbezanti53522 жыл бұрын
Thank you so much. That is really helpful!
@neelimak86734 жыл бұрын
Your videos are awesome! Thank you.
@yishun36714 жыл бұрын
thank you so much for your wonderful video, it really helps!!!
@masumakhatun29824 жыл бұрын
Thank you so much for this well explained vedio. I would like to see tutorials related to how to find similar motif to some known steoird receptor binding sites for example PGR, ESR, AR etc.
@ThiagoBenazziMaia2 жыл бұрын
Amazing, really helpful
@liangzhao39993 жыл бұрын
Such a great lecture!
@ZOMBIE2LIFE3 жыл бұрын
Great video. Much help!!!
@CancerSleuth4 жыл бұрын
A great video Jacob. Keep publishing more. Subscribed with thanks :)
@xiuteng87163 жыл бұрын
Much help! Thanks a lot!
@eftychiamarkopoulou6314 Жыл бұрын
You are amazing Sir! Thank you so so so much!!! I am a PhD student in Molecular Biology and I found that video terrific! Can I do a donation to support your work?
@nancyanderson54133 жыл бұрын
Thank you very much.
@zaidalsaialy65882 жыл бұрын
Thanks
@younesabuelayyan4520 Жыл бұрын
thanks a lot, very useful. pls do more vids about genome brousers platforms.
@alphaconceptinc3 жыл бұрын
Thanks...very useful
@Cdictator2 жыл бұрын
Thank you so much
@seowshirui3 жыл бұрын
Thank you so much !
@amandagong35182 жыл бұрын
Hi, I found when we set "0 to TSS" in EPD, the last latter was the 0 position of the TSS, which is the first letter of TSS, here in your video was "A", so I think when we copy it, it should be deleted. :)
@cerentosun73273 жыл бұрын
you saved my life. i wish i could make u some cookies. thanks a lot for this amazing video.
@Ichiban_in_Japan4 жыл бұрын
thanks so much i really need it
@_rj_sarma_4 жыл бұрын
What was the reason for choosing 1500 bases ? Could you please explain?
@jakelmer19854 жыл бұрын
1500 bases is the average size of a promoter. Some are definitely smaller and some are definitely larger while others cover tens of thousands of bases when you include topologically associated domains. So in short, 1500 is really just a "best guess" to start, then you would have to truncate the promoter from there to determine the actual size of the promoter.
@_rj_sarma_4 жыл бұрын
@@jakelmer1985 Thank you. And yes.... I also have seen people choosing more than 2000 . It's a great tutorial.
@pujathacker38794 жыл бұрын
@@jakelmer1985 the 5'UTR sequence before the start codon , is that also called as promoter?
@mominamalik13044 жыл бұрын
Puja thacker no 5’UTR is not the part of promoter
@ayeshawadood36352 жыл бұрын
@@pujathacker3879 No, it's the part of gene.
@guihuajia7696 Жыл бұрын
Hey Jacob Elmer, I don't quite clear in exon junctions as you explained.
@09olia8 ай бұрын
Thank you very much! I would appreciate if you might add a comment on how to proceed if for my gene of interest I see - strand in the EPD? Should I invert the sequence to get the correct promoter?
@nici79043 жыл бұрын
If the gene is on the reverse strand, should I then convert the sequence to its reverse complement in Entrez before doing any further analyses?
@designerguy62575 ай бұрын
3:20 Promoter active , recruiting r n a polimerates to transcribe genes, encourages binding
@designerguy62575 ай бұрын
9:30 the entire transcript sequence.
@user-dx5il5ww8x9 ай бұрын
After obtaining the designed gRNA from CHOPCHOP, why is it necessary to have upstream and downstream primers? Can't we directly synthesize the gRNA and then add an oligo? What is the purpose of designing upstream and downstream primers?
@tahirsuhail3 жыл бұрын
how did you decide 1500bp upstream of TSS?
@Viraj_2305Ай бұрын
Please make more videos on base editing andcprime editing ❤❤❤plzzz
@user-xe5wo6tn8u Жыл бұрын
Can you please talk for hours on Chipseq Data? Believe me I am ready to listen to every detail. 😊 and thank you so much for this
@jeremyli433411 ай бұрын
Amazing lesson. Could you also give a lesson using Konck-in approach?
@nilanjanaghosh82883 ай бұрын
Hi, first of all its a very helpful video. Could you please explain why did you consider only 1500 bp while adding the sequence range in Eukaryotic Promoter Database?
@SSRaja-zj6ug2 ай бұрын
Hi Jacob ' you did a brilliant presentation ' however i'm a beginner and still confused.Although it's not my field specifically but i need to choose a short dsRNA sequence of 20 or 27' 28 nucleotide sequence for application in plant but i am not familiar the specificity of the sequence if we had a genome like choloroplast genome and split that sequence into primers can we choose the shortest sequence ? Wether it will work or not??
@Yogeshpatil-qi4ze3 ай бұрын
Hi. Do you have any information on the database for Transcription factors for Filamentous fungi such as Trichoderma, and Aspergillus as PROMO doesn't contain these species?
@satwiksharma272011 күн бұрын
How do we know the 618th position we can't just keep reading the entire sequence length?
@user-me8dx5dy7e2 жыл бұрын
19:22 Why you select 15 bp before ATG in '' mRNA '' sequence to get promoter region? After I tried this, the result sequence didn't fit with mRNA sequence from ncbi. After that, I realized that there are introns between TSS and ATG in my chosen gene's genome sequence. Promoter region is before TSS, and introns also are transcripted which will be cut off during transcription. So, I think if we should select -1500 to 0 bp relative to TSS in EPD website?
@omarm11724 жыл бұрын
Hey Jacob , thank you for such a great video ! I was wondering when designing guide rna from the mRNA transcript do we use the exact sequence or one which is complementary ? additionally is there a need to use U instead of the T as I have seen some strands using this base . Thank you
@nooristic3 жыл бұрын
this video helped me a lot. Thank you Sir!. How can we select antisense strand in EPD?
@sivasankari9294 ай бұрын
Hi Jacob why there is no signal peptide in the NCBI and no annotation available in UNIPROT too. In that case can I select the Exon 2 as a target?
@yupaphonphannarangsee45702 жыл бұрын
I m working on bacteria, and it's working on this to find the promoter in the bacteria?
@MrRamaeri10 ай бұрын
I would like to extract the promoter sequences for 50,000 genes. I have both the Gene GFF file and the genome file available. Among 50,000 genes, 25000 genes are - strand. Could you suggest some other tools?
@-nightcore-2559 Жыл бұрын
the coding sequence for my gene starts at 1bp to the end. so my entire gene is a coding sequence... im stumped trying to find the UTR 5' AND 3' please help
@salemsulimanbaldi2853 жыл бұрын
How to solve the problem in case that EPD give you three promoters for one gene, which one is preferred for study of TF.
@papridas89792 жыл бұрын
Thank you sir! Sir i want to check my primers is reverse or forward. For that i want to know the gene sequnce. Can you u please suggest me?
@harnisha912 жыл бұрын
Correlate with UCSC genome browser promoter retrieval
@oleksandraskorobohatko21252 жыл бұрын
Dear Jacob Elmer, could you, please, tell if gRNA can "cut off" some part of the mRNA? I mean if a gRNA cuts at i.e. 15nt after ATG can it lead not just to the frame shift, but also that these 15 nt would be cut off? And the corresponding domain of the protein would be knocked out?
@jakelmer19852 жыл бұрын
Cas9 cannot react with mRNA, but there are other types (III and IV) of Cas enzymes that can cut RNA. www.ncbi.nlm.nih.gov/pmc/articles/PMC6013697/
@sarahmlugo293 жыл бұрын
What do I do when I have to analyze a gene on the reverse strand??
@neethuaruvilakad19073 жыл бұрын
Did you get the answer?
@Stop-and-listen Жыл бұрын
I have a question. Can a mutation in an intron part of a gene convert the intron into an exon?
@kaicheang45153 жыл бұрын
My sequence from EPD (the capital after the promoter region at 16:42) does not match with the mRNA that I found on NCBI.... What can I do?
@sajidhanif7034 жыл бұрын
Please also upload the links you used in your lecture so that we can follow them properly. Thanks for the vedio
@karimiqbalsworld28094 жыл бұрын
what about the Xenopus tropicalis? please inform me.
@MrNamgay2 жыл бұрын
How can I get the transcription start site of ruminats?