Nucleotides coding sequence

Transfer RNA (tRNA) RNA with a triplet nucleotide sequence that is complementary to the triplet nucleotide coding sequences of mRNA. tRNAs in protein synthesis bond with amino acids and transfer them to the ribosomes, where proteins are assembled according to the genetic code carried by mRNA... 

Swiss-Prot, TrEMBL Annotated non-redundant protein sequence database, TrEMBL is a computer-annotated supplement to Swiss-Prot. TrEMBL contains the translations of all coding sequences present in the EMBL Nucleotide Sequence Database which are no yet integrated into Swiss-Prot... 

DNA from a gene contains hundreds to thousands of nucleotide units for which the sequence is needed in order to interpret its code. Sequencing methods require only small amounts (5 (tg) of purified DNA, which can be produced by cloning. Automated sequencers are available that can daily sequence DNA containing hundreds of nucleotide units. 

SNPs, or single nucleotide polymorphims, are the subtle changes in the genome sequence that can lead to alterations either within single proteins by altering the protein coding sequence, or whole pathways, if the mutation affects... 

Genetic code Sequence of nucleotides along the DNA and coded in triplets (codons) along the mRNA that determines the sequence of amino acids in protein synthesis. The DNA sequence of a gene can be used to predict the mRNA sequence, and subsequently to predict the amino acid sequence. 

Various verification steps have been introduced to ensure that SPTR is comprehensive and contains all relevant data sources. The main source of new protein sequences is the translations of CDS in the nucleotide sequence databases. The up-to-date inclusion of new protein sequence entries is ensured by the weekly translation of EMBL-NEW (the updates to the EMBL nucleotide sequence database). The three collaborating nucleotide sequence databases DDBJ, EMBL, and GenBank exchange their data on a daily basis. Therefore any protein coding sequence submitted to DDBJ/EMBL/GenBank will appear in SPTR within 2 weeks in the worst case and within less than 1 week in the average case. 

Codon A set of three nucleotides in a protein coding sequence that specifies individual amino acids or a termination signal (codon, terminator). Most codons are universal, but some organisms do not produce the transfer RNAs (RNA, transfer) complementary to all codons. These codons are referred to as unassigned codons (codons, nonsense). [NIH]... 

Frameshift Mutation A type of mutation in which a number of nucleotides not divisible by three is deleted from or inserted into a coding sequence, thereby causing an alteration in the reading frame of the entire sequence downstream of the mutation. These mutations may be induced by certain types of mutagens or may occur spontaneously. [NIH]... 

Translation of the information encoded in DNA, expressed as a particular nucleotide sequence, into a protein, expressed as an amino acid sequence, depends on the genetic code. In this code, sequences of three nucleotides (termed a codon) represent one of the 20 amino acids that compose the protein molecule. Because there are 64 codons which can be constructed for the four different bases, and only 20 different amino acids that are coded for, several amino acids may be coded for by more than one codon. There are also three codons, called stop codons, that terminate the transfer of information. Furthermore, although all cells contain the same complement of genes, certain cells (for example, the neurons) have specialized genes that encode specific proteins for the synthesis of specific transmitters. The expression of such genes is under the control of regulatory proteins called transcription factors which control the transcription of mRNAs from the genes they control. 

Okazaki N, Kikimo R, Ohara R, et al. (2002) Prediction of the coding sequences of mouse homologues of KIAA gene I. The complete nucleotide sequences of 100 mouse KIAA-homologous cDNAs identified by screening of terminal sequences of cDNA clones randomly sampled from size-fractionated libraries DNA Res 9, 179-188. 

The triplets of nucleotide units in DNA determine the amino acids in a protein through the intermediary mRNA. One of the DNA strands serves as a template for synthesis of mRNA, which has nucleotide triplets (codons) complementary to those of the DNA. In some bacterial and many eukaryotic genes, coding sequences are interrupted at intervals by regions of noncoding sequences (called introns). 

The sequences of the amino acids in the chains from which proteins are constructed are encoded in the nucleotide sequences of DNA (deoxyribonucleic acid). The coding sequence for a protein in the DNA is found in the structural gene for that protein. The RNA enzymes are also encoded by DNA genes. A fourth major theme of the book deals with the nature of the genetic code used in DNA and with the processes by which cells read and interpret the code. It also includes study of the methods by which thousands of genes have been mapped to specific positions in chromosomes, isolated, cloned, and sequenced. 

Fig. 6. Nucleotide sequence of a genomic clone (eth 1) for the pTOM 13 cDNA. The translation start site (V) and termination codon ( ) are indicated. Coding sequences are shown in capitals and introns in lower case (after Kock et al., 1991).

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