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Because their shape reminded researchers of rolls of Sushi (Ichinose et al, 1990): These repeats were initially called GP-I structures because they were first identified in $\beta_2$-glycoprotein I. More recently, they have been called short consensus repeats or sushi structures because of their shape.


23

The short answer is that corn genome is large and has a huge amount of duplication events. Around 80% of the genome are repeated. It's hard to assemble genomes with large amount of duplications because our sequencing technology, practically, at best can give ~500 base pairs. Figuring out the ordering of duplicated regions relies on scaffold sequences or ...


11

What a timely question. Does DNA contain information beyond protein synthesis? Yes. In fact, protein-coding genes only constitute a tiny part – less than 2% – of the whole DNA. There are of course many other genes which aren’t protein coding: there are genes for ribosomal RNA and we find more and more genes which code for small RNAs, such as tRNA. But ...


11

Here is a short summary of the sequencing technologies you listed. Illumina is the most frequently used one. Roche/454 FLX Pyrosequencer technology is based on pyrosequencing method, which utilizes the use of the enzymes ATP sulfurylase and luciferase. After the incorporation of each nucleotide by DNA polymerase, a pyrophosphate is released, which further ...


11

The difference boils down to UnTranslated Regions. A CDS or coding sequence is the part of a transcript that is actually translated into protein. Therefore a CDS will (almost) always start with an AUG codon and stop at one of the three STOP codons (UAA,UGA,UAG). The transcript however (note that I am referring to mature transcripts that have already been ...


10

The sequencing technologies that were developed in the last 20 years have a range of optimal use at an average A+T/G+C rate. Both highly AT-rich and GC-rich regions are complicated to process by the different sequencing technologies. Each technology has different ranges of usage, but to name one, Illumina technology prefers sequences in the middle range. If ...


10

You're asking about the C-value enigma, in particular this kind of diagram:1 The quick answer is that there is no "why" in evolution; things happen and if they're beneficial they tend to stick around more than the deleterious things. The longer, (slightly) more satisfying answer is non-coding DNA. Thanks to non-coding DNA the size of a genome doesn't even ...


10

The MIT synthetic chemist Gobind Khorana won the 1968 Nobel Prize in Chemistry for his work which successfully was able to make chains of Ribonucleic acids. The chemistry was difficult at the time but he won the prize for making specific sequences of RNA bases which were then fed to cells, resulting in specific amino acid chains, which ultimately deciphered ...


10

Welcome to Biology.SE. if I take an X-chromosome from two random humans would I count exactly 155,270,560 base pairs in both cases No, you would probably not find the exact same number of base pairs because mutations do no only change one nucleotide to another (what we call a substitution) but sometimes add or delete few (or sometimes many) nucleotides. ...


9

A human genome sequence can uncover large deletions and insertions in the genome and would give the genotypes of both common and private (rare to very rare) small polymorphisms (e.g. SNPs) and SSRs (simple sequence repeats). From this information, one can learn about some curiosity traits (say, sensing asparagus metabolites in the urine, slow or fast twitch ...


9

Okay, I'll take this out of the comments and put in an answer for all of us to work on. To directly answer your question: "Is there an estimate for the percentage of these genes whose primary function is related to regulation of gene expression?" It depends on how you define "gene expression." And what cellular processes you want to include in that ...


9

You might be interested in the INK4A locus (chromosome 9p), encoding both p19 and p16 genes, very close to p15. You can read a description here. All three proteins are known experimentally to exist. Now, whether these are two different genes or the same gene with alternative splicing and start sites leading to different reading frames it's up to discussion....


9

Why was decoding the genome so significant? Because decoding the genome gives us a complete picture of the genetic makeup of an organism. What made it so difficult? The repetitive sequences as mentioned by other people is a main problem. Imaging you are trying to complete a big puzzle with millions of pieces. Each piece represents a sequencing reads that we ...


9

Top 10 long processed transcripts in humans (with multiple isoforms), from gencode 19 annotations: Transcript Length(bases) ------------------------ TTN-018 108861 <-- Titin TTN-019 103988 TTN-002 101206 KCNQ1OT1-001 91666 TTN-201 82413 TTN-202 82212 TTN-003 81838 MUC16-001 43732 ...


9

Lets state what a Mutation is first. Mutation: A mutation is any change in an organism's genetic sequence which varies from that of the wild-type reference sequence (hg19/GrCH37 from 2009 or hg38/GrCH38 from 2013, which are the most current genome assembly). Single Nucleotide Polymorphisms (SNPs): These are any single nucleotide base mutations which have ...


9

TADs were initially discovered by computing contact probabilities between regions of the genome using HiC (a chromosome conformation capture method, that try to provide an idea on how the genome is organized inside the nucleus by computing the probability of each contact to be located nearby another locus). People have found that instead of being random, ...


9

The read length has absolutely nothing to do with what you are sequencing. It is a characteristic of the sequencing technology you use. NGS sequencing techniques typically produce this sort of short read you're seeing. The read length does not change because you are sequencing a longer molecule. You would still get ~250nt reads even if you were sequencing an ...


8

The larger differences are most likely in epigenetic marks on the DNA. The environment is a lot different today than it was 2000 years ago and those differences are stronger determinants of epigenetic change than sequence change. 2000 years is only about 40 generations and that is not very much to see great differences in DNA sequence or allele frequencies -...


8

The human genome contains less than 416 base pairs, so, even after including a factor of 2 for the two strands and another to allow for some genetic variation, there must certainly exist some 17-base string not found in either strand of the genome. Now, 417 bits is two gigabytes, which fits easily within the memory of a typical desktop computer these days, ...


8

I don't know, whether the organism you are working with is diploid, but suspect it's an animal (or even a mammal), so the most parsimonious explanation would be that you have homozygotes and heterozygotes at this SNP-position.


8

Be careful when reading media as they tend to exaggerate. That Abzhanov paper is interesting; it will be better when it's published and the figures released. He does a lot of evo-devo work surrounding beak development. What they did in this paper was to inhibit in chick embryos two signalling pathways (which are actually conserved amongst all animals, not ...


7

In short, yes, it is possible. There are companies that sequence part of your genome and then can trace it back to your ancestors. All human family trees can be traced back to their African origin 200 000 years ago, but the companies that sequence your genes do not do that. For example, 23andMe sequences only 1 million of your base pairs (single nucleotide ...


7

Take a look at the strategies used to sequence the wheat genome. Wheat is hexaploid. The project is described at http://www.wheatgenome.org/. For early work on the maize genome, we employed methyl filtration in order to reduce genome complexity and size - transposons are filtered out and genes + promoters and such remain. The gene sequences are different ...


7

Yes, look at FANTOM and their work. There are about 2000 transcription factors and co-factors in the human genome. These are proteins, of course. If you add a couple (or few?) thousand microRNAs and a few dozen anti-sense transcripts, although small in size, you inch that percentage upwards. With some 70% of the human genome transcribed, by some estimates, ...


7

Insects and spiders have tremendous sexual dimorphism, with males often being much smaller than females. They are pretty much just sperm carriers and sometimes do not eat. Insects may have two or one sex chromosome, where males my have only one chromosome. As is pointed out in the comments, not all mantis' species display this dimorphism. Since such ...


7

You are correct in thinking that any sequence of bases corresponds, via the genetic code, to a sequence of amino acids. However not all stretches of DNA are actually transcribed into mRNA for translation into proteins. For this to happen the stretch of DNA requires (DNA-encoded) elements to promote and regulate the transcription and translation processes, ...


7

You bring up a good point. "Coding" is a term that obviously carries some historical baggage that is gradually becoming less and less relevant. "Coding DNA" has typically been used to refer to DNA that encodes one or more functional protein products, which are constructed from an mRNA intermediate. As we've been learning over the last several years (and as ...


7

Your question could be phrased more specifically to avoid ambiguity, but rephrasing it the way that I suspect you mean it, ("Is there any evidence showing that [the rate of] copy number variation changes over time?"), then yes, there is indeed. The rate depends on many factors including which mechanism and which organism and which region of the organism's ...


7

HLA-B*1502 is not a SNP ID but rather, a name of an allele of HLA-B. This allele is made up of multiple mutations which can be found here.


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