Lecture 24

Question 1

how can we predict the presence of an exon/gene using ORFs?

Answer 1

find the predicted translation in all 6 reading frames –> if ORF is above a specified minimum length (i.e. not interrupted by stop codon) it may be an exon

Question 2

what is an ORF?

Answer 2

stretches of codons that are not stop codons

Question 3

once we have a predicted ORF, 3 ways to look for evidence it is part of an exon

Answer 3

1. conservation across species
2. if cDNAs contain the sequence
3. codon bias

Question 4

how can we use conservation as evidence a predicted ORF is part of an exon?

Answer 4

if there are stretches of conservation across species that match up to an exon, it must be an exon

Question 5

what is the gold standard method for finding an exon?

Answer 5

looking for cDNAs that map to the gene

Question 6

describe the use of cDNAs to find an exon

Answer 6

if cDNA has same sequence as predicted exon –> it was once mRNA –> it was transcribed –> it’s a coding gene

Question 7

what is an EST?

Answer 7

“Expressed Sequences Tag”

cDNA that only sequences 5’ and 3’ ends

Question 8

describe the use of codon bias to find a predicted exon

Answer 8

most aa can be coded for by >1 codon (redundancy) but these codons are not equally utilized in diff organism –> this can be a signature of an ORF that’s a gene

ex. 1% of arginine in E. coli is made by AGA –> if you see AGA, unlikely to be coding bc so rare in E. coli

Question 9

what % of genome is exons of protein-encoding genes?

Answer 9

3%

Question 10

what % of genome is exons + introns + regulatory sequences?

Answer 10

28%

Question 11

what % of genome encodes protein sequences?

Answer 11

1%

Question 12

what % of genome is repetitive sequence?

Answer 12

45%

Question 13

why is the cDNA method not always helpful?

Answer 13

3% of genome is exons of protein-encoding genes but only 1% of genome encodes protein sequences

therefore, not all genes encode

Question 14

if 3% is exons, why does only 1% encode protein?

Answer 14

start codon is not always at start of exon and stop codon is not always at end of exon

Question 15

3 ways to conduct comparative genomics

Answer 15

1. within an organism
2. btwn individuals in a species
3. btwn organisms

Question 16

purpose of doing comparative genomics within an organism

Answer 16

to identify gene families and gene duplications

Question 17

purpose of doing comparative genomics btwn individuals in a species

Answer 17

to identify differences associated with phenotype or disease

Question 18

what is a paralog?

Answer 18

related genes within an organism that encode proteins with similar aa sequence

Question 19

function of genes that are paralogs

Answer 19

may be functionally redundant or have independent function

Question 20

what is a possible origin of paralogs?

Answer 20

Gene duplication during evolution

Question 21

why do we sequence the exome?

Answer 21

compare the exomes of ppl with disease and without disease to identify disease-associated gene

Question 22

benefits of sequencing the exome compared to whole-genome sequencing

Answer 22

effective and cost-effective

Question 23

similarities btwn human and mouse genome?

Answer 23

99% of mouse genes have human paralog and vice verse

genome organization (order of genes and non-coding regions) is the same

Question 24

what is synteny?

Answer 24

conserved order of genes btwn 2 species

Question 25

why do we use phylogenetic inference?

Answer 25

to see how genes evolved over time

Question 26

what is an ortholog?

Answer 26

homologous genes at same genetic locus in diff species

Question 27

describe the evolution of the Vitellogenin gene in platypus

Answer 27

platypus has 1 vitellogenin gene but other mammals don’t have at all

chickens have 3 vitellogenin genes and share common ancestor with platypus so ancestor had 3 vitellogenin genes, then were lost in mammals

Question 28

what is uniparental disomy?

Answer 28

correct number of chromosomes but both came from same parent

Question 29

what causes uniparental disomy?

Answer 29

non-disjunction

Question 30

why does non-disjunction in UPD not cause trisomy?

Answer 30

there is trisomy rescue, so randomly an extra chromosome will get lost