Lecture 18 Flashcards
The ____is evolving faster than the___
intron
exon
They learned that the Zebrafish gene was very old so maybe the genome duplication was a trait shared by all fish?
Photo 16 where are the duplication and speciation events?
How old the the genome duplication in fishes?
older then 300 million years and younger then 450
De novo genes are?
new genes from non-coding DNA, vary rare
Knowles and Mclysaght found multi-gene regions that were_____in_____.
They did this by?
homologous in different species(synteny blocks)
by usig reciprocal best hit pairs…..gnes in human that did have hits in chimp
____is the way most new genes evolve….but there is another way
Duplication
de novo genes
How many genes in humans have originated from de novo?
0.075%
18 out of 24,000 protien coding genes
In photo 17 explain what is happening?
644 human proteins with no BLASTp
425 had gap….why did they exclude them?
150 ortholog
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
Photo 18
explain
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
There are no___in CLLU1.
What is CLLU1, C22orf45 and DNAH10Os
introns
filtering genes
Photo 19.
All three genes(green)…
Range
The gene is going____
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.
Photo 20.
Explain the process?
4. None of the de novo gnes were found in____
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
For the de novo genes in Drosophila…. it looks like the ___
ORF comes first(enhancer) then a cis-acting mutation that starts transciption
Not trans since they produced only one strand/allele with it
Photo 21
What was the path of the Drosophila and chimp papers?
Drososphila had the ORF first
Chimp have transcription first
Photo 22
This shows that most de novo genes are
Most de novo genes are young in hominoids
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_____
37%
the targeted bases
Each of the five people in the study ahs ____coding single nucleotide variants(cSNVs) and _____have never been seen before
12,000
600-700
Did these cSNVs change AA sequences?
Photo 23 explain
Among the missense novel variaents ___per exom introduced…..
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
____missence mutation per exome occur at positions where the human ref AA can also be found in fly and worm
40
could be bad….or dont matter if your hetero
What did they do to test of Bartter syndrome?
What happende?
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
Explain photo 24
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
