Why some nucleotides in NONCODE database are in capital letter and some are in lowercase letter?

13 November 2016 1 5K Report

When I was looking for some information about CCAT1 gene in NONCODE, I realised that some part of sequence is written with capital letters and some part with lowercase letters, eg:GGTCTTCTCTGCAATCCATCTGGAGCATTCACTGACaacatcgactttgaagttgcactgacctggccagccctgccacttaccaggttggCTCTGTATGG

Ahmet Sinan Yavuz

Hi Mahdi,

Commonly, repeats identified by Repeat Masker or Tandem Repeat Finder are written in lowercase letters. This convention is called "soft masking".

HTH,

Badges
Science method

More Mahdi Nohtani's questions See All

How to visualize stress in a coating defined by "Skin" in Abaqus?

Hello All! I'm trying to model a contact between a coated substrate and a tip in Abaqus. The coating is ultra-thin compared to the geometry of the substrate. So I defined the coating using the...

16 February 2021 1,594 3 View

Is a Strong correlation between the Moderator variable and the dependent variable an issue for moderation model (model 1) in Hayes PROCESS?

In a typical moderation model with one moderator, is it a problem if the moderator and the dependent variable show a strong correlation (say 0.85)? What if a strong correlation exists between the...

27 January 2021 4,937 4 View

Which syringe filters (e.g., PTFE, MCE, PVDF, CA, PES, etc.) are the best to filter TBS/PBS buffer (pH 7.5-8.5) and glycine buffer (pH 2-3) solutions?

I intend to purify antibodies from serum using the affinity procedure, and I need to filter the binding (TBS/PBS) and elution (Glycine) buffers before applying them to my solution.

06 January 2021 5,769 3 View

Gear reduction for back-drivability of a motor?

Hi everyone, Does anyone know up to what reduction ratio of gear does a motor remain back-drivable? I want my robot to have safe interactions with the environment and other humans. Can you give a...

26 December 2020 7,142 3 View

How to export DigSilent Plots with high quality?

Hi all; I've started using DigSilent these days. However, I'm wondering how can I export the results with high quality the same as MATLAB plots as I currently do. Thanks

19 December 2020 2,666 2 View

How to assign initial stress to a coating in Abaqus?

Hello! I am trying to define/assign initial stress to a coating I modeled on a substrate. I defined the coating using "skin" function. I have tried "predefine filed" in load section. But it only...

10 December 2020 2,921 8 View

How to model a multilayer coating in ABAQUS?

Hello! I'm trying to model a multi-layer coating on a substrate in abaqus. The layers are homogenous and isotropic. My question is how should I approach the modeling? WHAT I'VE TRIED SO FAR: I...

09 December 2020 1,235 3 View

How can I calculate Nusselt number by using this equation (Nu = ht.gradTx * nx + ht.gradTy * ny + ht.gradTz * nz) step by step in COMSOL?

Calculate the Nusselt number using the COMSOL Program

09 December 2020 3,354 3 View

How to calculate sulfur loading of lithium -sulfur batteries using Li2S8 catholyte?

I am gonna use Li2S8 catholyte to introduce active material to cathode instead of using sulfur. May anybody kindly guide me about the way I can calculate the amount of sulfur (g/cm2) loaded on the...

07 December 2020 7,556 2 View

How to great data visualization and what example for it ?

i need explain data visualization and what type it and how great it by excel or other program > paper attached for help

30 November 2020 1,159 2 View

Enhanced Yellow Fluorescent Protein (Aequorea victoria) DNA sequence?

I am on the lookout for the Enhanced Yellow Fluorescent Protein (Aequorea victoria) DNA sequence. Does anyone know where I can find it? Thank you in advance

03 March 2021 3,568 1 View

Is it possible for two human neuronal cell lines to have different gene sequence for the same protein?

I am looking at the ATP1A2 (Sodium/Potassium ATPase alpha subunit 2) in two human neuronal cell lines. Expression levels of this protein seems to be almost equal when detected by one antibody....

01 March 2021 3,607 3 View

Anybody with an idea on how do design specific primers for detecting tomato resistance genes tm-1, TM-2 and Tm2^2?

I am trying to identify these 3 genes among some tomato cultivar collections and after aligning some sequences from NCBI, I couldn't find unique sequences to target for specific primers. There...

28 February 2021 606 3 View

Runs of nucleotides in Sanger sequencing?

I performed site directed mutagenesis, transformation, and then I sent out plasmids for Sanger sequencing and found out that there is extension of DNA just before the stop codon. I am not sure...

27 February 2021 547 3 View

Has anyone used the Illumina ITS1 primer sets?

Hi everyone, Illumina provides a list of primers to amplify with high taxonomic coverage the ITS1 region for further fungal sequencing, but I cannot find the exact amount necessary of each...

25 February 2021 6,969 3 View

Errors in DNA sequences?

I am trying to better understand the scope of DNA replication and sequencing errors, e.g. 1. I have seen similar error rates of 10e4 to 10e5 for cell & instrumental DNA replication,...

24 February 2021 4,397 3 View

I can detect my protein but the encoding DNA sequence has stop codons within. Should I ignore the stop codons?

I constructed a synthetic DNA library (scFv, VH-VL orientation) with a 3' reporter and 8x histag. I cloned and expressed this gene following which I performed an ELISA. The ELISA results suggested...

19 February 2021 7,006 5 View

What is the significance of (isolated) high titers of IgG anti GD1a antibodies in an older patient with polyneuropathy?

Remote history of Campylobacter infection with reactive arthritis, and Spitz nevus (UMP). Arthropod exposure in Zika/ChikV endemic area prior to emergence of length dependent, sensory PN with...

18 February 2021 8,719 1 View

Repository for capture-seq raw reads?

I am a research tech in a wildlife genetics group and my PI and I are trying to figure out how/where to put raw reads in a repository. We have capture-seq NGS from Rapid Genomics. The post-doc who...

17 February 2021 7,575 2 View

Unable to detect a truncated protein variant, but I can observe a truncated cDNA from Sanger?

Hi, so basically... I am trying to mimic a clinically observed condition wherein a frame-shift mutation happens only at one allele of the patients, giving rise to a truncated variant which evades...

17 February 2021 1,130 6 View