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17 Cards in this Set

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How are genes from the human genome found?

- Identifying DNA corresponding to known human proteins and/or mRNAs, or to sequenced but uncharacterised mRNAs ESTs




- identifying DNA corresponding to genes from other species




- using computer analysis to detect previously unknown genes (ab initio prediction)

What is ab initio prediction?

- using computer to detect previously unknown genes




- comparatively easy in prokaryotes - just got to look for long ORFs




- but long ORFs in eukaryotes are interrupted by introns => gene prediction is way more difficult

What are the questions that should be asked about the investigated DNA before doing ab initio prediciton?

- is there evidence that DNA is transcribed




- does DNA show evolutionary conservation




- does DNA have predicted exons




- does combining these exons generate potential ORF

How do you distinguish conserved non-coding DNA from conserved protein-coding DNA.

- Protein-coding DNA - base substitutions (SNPs) separated by three nucleotides




- e.g. SOX9 gene from human and 3 fish - substitution on every 3rd nucleotide




- each of the DNA seq - encode same AA seq

How many genes are there in the human genome?

20 000 - 22 000? BUT many more proteins!

Why are there more proteins than genes discovered?

- alternative splicing - 20-90% of genes show it




- each alternatively spliced gene produces an average of 4 different mRNAs




=> human genome may encode over 60 000 proteins

Average human gene - numbers

- exons - 11




- median exon size - 140bp




- median intron size - 1700 bp




- average gene size - 54 000

What is the biggest known gene?

Dystrophin (DMD): 2400 kb - including a 250 000 intron


What is the biggest protein?

- Titin - 36 000 AAs encoded by a gene with 364 exons

Gene density and gene number varies between chromosomes. Which chromosome has highest gene density and which lowest?

- Highest - 19 - 22.5 genes per Mb




- Lowest - y 0.76 genes per Mb

There could be up to 20 000 genes that encode functional RNA that is not mRNA. What are they?

- tRNA and rRNA




- snRNA and snoRNA - involved in splicing




- miRNA - regulate stability and translation




- Long non-coding RNAs with regulatory enzymic or structural roles

Most genes occur in a single copy but genes have more. Why?

- if the genes encode proteins that are very abundant




- e.g. Histone - humans have approx 61 copies of each histone gene

Most human genes belong to a gene family. What is that?

- family of related genes all derived from a common ancestor




- members of gene families may be clustered or dispersed

What are homologues?

- Genes that share a common ancestor

What are orthologues?

- two homologous genes arising as a result of a species divergence

What are paralogues?

- two homologous genes arising as a result of a gene duplication

How can functional DNA be identified?

- Encodes a protein or known functional RNA




- more evolutionarily conserved




- genetic anal. - knock in knock out




- biochem function - transcribed, associated with histone, in open chromatin, bound by a TF