d	a or g or t	not c
b	c or g or t	not a
n	a or c or g or t	any

Amino Acid Codes

The amino acid code that is used with the International Nucleotide Sequence Database is as follows. These amino acids are described with one letter abbreviation in /translation qualifier of CDS feature. The listed amino acid abbreviations are legal values for qualifiers /transl_except and /anticodon. Those that are not included in “Amino acid codes”, please refer to Modified and unusual Amino Acids.

Abbreviation	1 letter abbreviation	Amino acid name
Ala	A	Alanine
Arg	R	Arginine
Asn	N	Asparagine
Asp	D	Aspartic acid
Cys	C	Cysteine
Gln	Q	Glutamine
Glu	E	Glutamic acid
Gly	G	Glycine
His	H	Histidine
Ile	I	Isoleucine
Leu	L	Leucine
Lys	K	Lysine
Met	M	Methionine
Phe	F	Phenylalanine
Pro	P	Proline

Abbreviation	1 letter abbreviation	Amino acid name
Pyl	O	Pyrrolysine
Ser	S	Serine
Sec	U	Selenocysteine
Thr	T	Threonine
Trp	W	Tryptophan
Tyr	Y	Tyrosine
Val	V	Valine
Asx	B	Aspartic acid or Asparagine
Glx	Z	Glutamic acid or Glutamine
Xaa	X	Any amino acid
Xle	J	Leucine or Isoleucine
TERM		termination codon

• 한 chromosome 에 500-4,000 genes → 한 gene 에 27,000 base pairs
• 한 사람에 24,000 genes,
• 한 사람에 200,000-백만개의 proteins
• structure of a gene
  • Promotor
  • Exon
  • Intron
  • Exon
  • Intron
• Transcribe 되면서 intron 은 splice out 되므로 RNA 에는 Exon (에 해당하는 base pair) 만 있음.
• Chromosomes : where the DNA is distributed, 23 pairs, chromosome 하나에 Long molecule of DNA 가 하나, 핵 하나에 4 cm의 chromosome.
• Chromatin: 옴, protein, RNA 의 complex
• DNA : an enormously long molecule, 핵 하나에 2 m 의 DNA
• Exome: all of the exons within the genome, the sequences which, when transcribed, remain within the mature RNA after introns are removed by RNA splicing
  • This includes untranslated regions of mRNA, and coding sequence (or CDS).
  • The human exome consists of roughly 233,785 exons, about 80% of which are less than 200 base pairs in length, constituting a total of about 1.1% of the total genome, or about 30 megabases of DNA.[2][3][4]
  • Though composing a very small fraction of the genome (only 1.5% of the whole genome), mutations in the exome are thought to harbor 85% of mutations that have a large effect on disease.[5]
• Genes : coded messages written into DNA
• Endophenotype: biomarker 와 비슷한 의미인데 genetic link (component) 가 어느 정도 있는 것
• Genetic interaction
  • Definition (다양한 정의를 가지는 broad term임)
    • Phenotype level: A genetic interaction (GI) between two genes generally indicates that the phenotype of a double mutant differs from what is expected from each individual mutant
    • two genes share a functional relationship.
    • Expression level: When expression of one gene depends on the presence or absence of another gene in an individual, it is known as gene interaction
    • does not necessarily imply that these two genes code for interacting proteins or that the two genes are even expressed in the same cell.
    • 비슷한 위치에 두 gene 이 있다는 의미 아니네.
  • Mechanism
    • These two genes may be involved in the same biological process or pathway; or they may also be involved in compensatory pathways with unrelated apparent function
• Genome : the genetic information
• Cerebral amyloid angiopathy (CAA) : Aβ deposits in blood vessels of the brain → ↓ BBB, extravasations of plasma proteins, edema formation, release of inflammatory mediators and matrix metalloproteases → ↑ ROS, ↑ inflammation → degradation of the basal lamin → vessel weakens → blood to leak out → cause hemorrhagic (bleeding) strokes in the elderly.
• Nucleotide : base+sugar+phosphate 로 된 unit
• Allele (=대립유전자): 한 allele 은 one version of a gene, one of two or more forms of a gene or a genetic locus (generally a group of genes).[1][2] Sometimes, different alleles can result in different observable phenotypic traits, such as different pigmentation. However, many variations at the genetic level result in little or no observable variation. Each unique form of a single gene is called an allele.
  • 특정한 DNA 서열이 사람의 눈 색깔을 결정한다면, 눈 색깔이 파란색이 되도록 하는 DNA 서열을 Allele 1번, 검정색이 되도록 하는 DNA 서열 이런식으로 여러 Allele 가 있겠다. 아래 그림에서 T 와 t 가 각각 allele 임.
  • Minor allele: 위 그림에서 T 가 t 보다 빈도수가 적으므로 T 가 minor allele 임
    • Minor allele frequency (MAF): 위 그림에서 0.429 가 MAF 임.
      • 분모는 개체수 (물고기수)가 아님, 분모는 14 임.
      • low frequency: (minor allele frequency (MAF) of =1% but <5%)
• Genetic polymorphism : the ccurrence of multiple alleles at a locus, where at least two are at frequencies greater than 1%. Over 30% of the genes that code for proteins are polymorphic
• Genetic drift : is change in allele frequencies in a population from generation to generation that occurs due to chance events.
• Homozygotes : indiciduals with identical alleles
• Heterozygotes : individuals with different alleles.
• Hemizygous: Having only a single copy of a gene instead of the customary two copies. (e.g. xY)
• polygenic trait: A polygenic trait is one whose phenotype is influenced by more than one gene., most traits in humans, and in fact most traits in most organisms, are polygenic, (but not affected by the environment). Mendelian traits, although we spend a lot of time talking about them, are really the exception.
• Multigenic: involving, produced by, or controlled by two or more genes, along with the influence of environment.
• Genetic association : the appearance (in many patients with disease) of a second genetically determined character at a frequency higher than would be predicted on the basis of their independent frequencies.
• Genetic linkage : the tendency for alleles close together on the same chromosome to be transmitted together to offspring.
• If genetic variations are more frequent in people with the disease, the variations are said to be “associated” with the disease
• Oligonucleotides : single-stranded DNA fragments of up 40 base pairs
• Gene : a specific segment of DNA, the unit of inheritance
• Cell autonomous: A genetic trait in multicellular organisms in which only genotypically mutant Cells exhibit the mutant phenotype. Conversely, a nonautonomous trait is one in which genotypically mutant Cells cause other Cells (regardless of their genotype) to exhibit a mutant phenotype.

Homology refers to biological features including genes and their products that are descended from a feature present in a common ancestor. Homologous features such as homologous genes are referred to as homologs (or homologues if you follow British spelling).

Homologous genes become separated in evolution in two different ways: separation of two populations with the ancestral gene into two species or gene duplication of the ancestral gene within a lineage.

• Genes separated by speciation are called orthologs.
• Genes separated by gene duplication events are called paralogs.

The process is shown in the diagram below.

Gene 1 in the ancestral species undergoes a duplication event generating Gene 1a and Gene 1b. The ancestral species splits into two species, each with its own copy of Gene 1a and Gene 1b.

• Gene 1a in species one is the ortholog of Gene 1a in species two.
• Gene 1a and Gene 1b are paralogs.

Uncertain Spans

• (Glossary, Chromatin bullet) The first token after Chromatin: is rendered as 옴 (single Hangul character) in the source — likely an OCR-faithful capture of an idiosyncratic abbreviation; the surrounding context implies the intended reading is “DNA, protein, RNA 의 complex” but the visible glyph is preserved as is.
• (Trailing homology paragraph) The first letter of the opening word Homology is partially clipped at the left edge of the body crop on this photo (visible as …ology refers to biological features…); the word is restored from the immediately following sentence which uses homologs / homologues.