Lecture 18

Question 1

The ____is evolving faster than the___

Answer 1

intron
exon

Question 2

They learned that the Zebrafish gene was very old so maybe the genome duplication was a trait shared by all fish?

Question 3

Photo 16 where are the duplication and speciation events?

Question 4

How old the the genome duplication in fishes?

Answer 4

older then 300 million years and younger then 450

Question 5

De novo genes are?

Answer 5

new genes from non-coding DNA, vary rare

Question 6

Knowles and Mclysaght found multi-gene regions that were_____in_____.

They did this by?

Answer 6

homologous in different species(synteny blocks)

by usig reciprocal best hit pairs…..gnes in human that did have hits in chimp

Question 7

____is the way most new genes evolve….but there is another way

Answer 7

Duplication

de novo genes

Question 8

How many genes in humans have originated from de novo?

Answer 8

0.075%
18 out of 24,000 protien coding genes

Question 9

In photo 17 explain what is happening?
644 human proteins with no BLASTp
425 had gap….why did they exclude them?

150 ortholog

Answer 9

1.Human genes with no BLASTp hit in chimps are sequenced in chimps to find a gap
2.If no gap is found then they look for sequence similarity
3. If found the sequence then we exclude it but if no ORF is seen then its a candidate gene
2. If gap is found then we exclude it

excluded b/c can’t be positive since the genome is not sequenced yet

Question 10

Photo 18
explain

Answer 10

gap in human sequence leads to a bigger ORF and a frame shift not creating a stop codon. Without the 1bp deletion chimp and macaque hit a stop codon

Question 11

There are no___in CLLU1.

What is CLLU1, C22orf45 and DNAH10Os

Answer 11

introns
filtering genes

Question 12

Photo 19.
All three genes(green)…
Range
The gene is going____

Answer 12

overlap with the known gene on the complementary strand
range-121-163 AA long

the gene is going the oppiste way for the complementay gene…so the change in the silent site could be significant in the opposite direction since it would actually be the first codon.

Question 13

Photo 20.
Explain the process?
4. None of the de novo gnes were found in____

Answer 13

1.6 pop. of drophila had the mRNA sequenced, then found on that was transcribed( hard since the genome has been avaialbe of 14 years)
2. Found 142 de novo genes
3.are alignable to unique orthologous regions in the Droshilia refernce genome sequences(DNA)
4.IN the RNA sequnces

Question 14

For the de novo genes in Drosophila…. it looks like the ___

Answer 14

ORF comes first(enhancer) then a cis-acting mutation that starts transciption

Not trans since they produced only one strand/allele with it

Question 15

Photo 21
What was the path of the Drosophila and chimp papers?

Answer 15

Drososphila had the ORF first
Chimp have transcription first

Question 16

Photo 22
This shows that most de novo genes are

Answer 16

Most de novo genes are young in hominoids

Question 17

When using the exoncapture step the study went from 1% of the genome is coding to ___% of the reads obtained by the sequenceinf step, mapped by exons_____

Answer 17

37%

the targeted bases

Question 18

Each of the five people in the study ahs ____coding single nucleotide variants(cSNVs) and _____have never been seen before

Answer 18

12,000
600-700

Question 19

Did these cSNVs change AA sequences?
Photo 23 explain

Among the missense novel variaents ___per exom introduced…..

Answer 19

Synonymous means it doesnt have an affect
missense-change AA
second # is mutation never seen before

147 exomes introduced AA sub at positions where the human ref is the same as other vertebrates

so it could be the subs dont matter

Question 20

____missence mutation per exome occur at positions where the human ref AA can also be found in fly and worm

Answer 20

40

could be bad….or dont matter if your hetero

Question 21

What did they do to test of Bartter syndrome?
What happende?

Answer 21

they determined 5.3 Mb of his exome was homozygous within those were 2459 genes

He was homo at a position that is highly conserved

Question 22

Explain photo 24

Answer 22

We can say that the protien need D to work since it is found in most animals. Are patient GIT 264-1 had a N

The patient had CLD not Bartter syndrome