allele expression check

[ValWood]

uniquename	name	allele_type	sessions
SPBC216.05:allele-2	rad3-136	unknown	e6d26db4caf74ac5,e6d26db4caf74ac5,69403b8ceb819841,38560610372534b4,93ca4cadd1ff6a75,52e0036cabf3303e,40024707aa700ccb,84d34826e72c8725,c16d1f65344ac5bf,45d907cccb67195b,e0f7d8e22ba14953,c106524e4c73575e,0bcb6b33a1bdb4ea,335eb22b9fc8a7c1
SPNCRNA.103:allele-7	sme2-m	nucleotide_mutation	45395a087bd927e5,e3c8313e9bd1dabc
SPBC32C12.02:allele-12	ste11-mutant	unknown	ef2da839886aa260,b5aa547b2e76978f,133b9a4cefba1a78
SPNCRNA.9001:allele-5	prt2delta-2	partial_nucleotide_deletion	a93df4140a4b1e4c
SPAC2F7.03c:allele-3	pom1-as1	amino_acid_mutation	c6be22ca31f0e630,a475a61f06526c04,e223a3074a0b59fa,3d43cf9a14d68a43,0fa0811aad33bde1,1de58f8a4e93861a,e58982138a6526c3,bbe966c7c31d9042,bbe966c7c31d9042
SPNCRNA.9001:allele-4	prt2delta-1	partial_nucleotide_deletion	a93df4140a4b1e4c
SPBC14F5.13c:allele-4	pho8-m1	amino_acid_mutation	2c0b3f9b052bea9e
SPAC6B12.15:allele-3	cpc2-W43*	partial_amino_acid_deletion	a9ee2fb1cb19f385
SPBC14F5.13c:allele-5	pho8-m2	amino_acid_mutation	2c0b3f9b052bea9e
SPNCRNA.103:allele-9	sme2deltaC	partial_nucleotide_deletion	e3c8313e9bd1dabc
SPCC18B5.03:allele-2	wee1+	wild_type	acb154d034f85813,d8cd69d2eda564a7,50a497b4c268664e,3d43cf9a14d68a43,890568af6939d0d6,890568af6939d0d6,cac62efc496fffc5,18a27420dc89982d,20d4154e6b32a4f3,ef61ac1ac91c951e,6a1cd0660cdba7fd,20c200984ffb7421,697b0dd703952f05,91da8e4c4e7b6d48,37651048e44cc918,c7dfdbd8467f6d60,6c335a4e1d1a262d
SPNCRNA.214:allele-30	ter1-delta(25-1135)::ura4+-tk	partial_nucleotide_deletion	72c1277f6497035f
SPAC25B8.19c:allele-7	loz1-23	amino_acid_mutation	bf037075feb20f28
SPCC285.09c:allele-2	cgs2-2	nucleotide_insertion	219e86a87274fe5f,0d638c12aef4db07,0d638c12aef4db07

[ValWood]

• [x] rad3-136 "not assayed"
• [x] sme2-m (knockdown -promoter deletion)
• [x] sme2deltaC (knockdown -promoter deletion)
• [x] ~ste11-mutant DELETED~
• [x] prt2delta-2 (knockdown -promoter deletion)
• [x] pom1-as1 This has a mixture of WT, NULL and knockdown. I think these should all be WT. The activity is knocked down, but not the expression level as far as I'm aware?
• [x] prt2delta-1 (knockdown -promoter deletion)
• [x] pho8-m1 not asssayed (protein level checked, not RNA and this will be a phenotype)
• [x] pho8-m2 not asssayed (protein level checked and this will be a phenotype)
• [x] cpc2-W43* has "[decreased RNA level during vegetative growth] phenotype so this can be "knockdown" (it's only a tiny N-term fragment anyway so not much can be inferred - it is probably equivalent. to NULL, but it isn't really
• [x] ~wee1+ deleted, no annotations in session~
• [x] ter1-delta(25-1135)::ura4+-tk can be knockdown, almost entirely deleted
• [x] loz1-23 since the single phenotype annotation is "increased RNA level during cellular response to zinc ion change to "not assayed"
• [x] ~cgs2-2~ DELETED, no annotations in this session

[ValWood]

• [ ] pho8-m1 & ms check phenotypes As a complementary approach to examine the effects of zinc binding on the stability of Pho8, we generated derivatives of Pho8-HA containing amino acid substitutions that prevented zinc from binding to the first zinc-binding site (Pho8-m1), the second zinc-binding site (Pho8-m2), or both sites (Pho8-m1/2). No alkaline phosphatase activity was detected in pho2Δ pho8Δ cells expressing these zinc-binding mutants, consistent with zinc binding to both sites being critical for function (Fig. 5B). When the effects of these mutations on Pho8 protein levels were analyzed by immunoblot analysis, slightly lower levels of the mature forms of Pho8-m1 and Pho8-m1/2 accumulated to lower levels in zinc-limited cells, whereas the levels of the mature Pho8-HA-m2 were not significantly altered by zinc levels (Fig. 5D). These results suggest that apo and holo forms of Pho8 accumulate in cells and that loss of zinc from site 1 may interfere with the processing or stability of the mature Pho8 protein under low-zinc conditions.

[kimrutherford]

Sorry the list of sessions in incorrect. In includes all sessions with the allele whatever the expression level. Where there is one session listed, that will be correct and will have the Null allele. I'll make a new table.

[kimrutherford]

Here's a better table:

uniquename	name	allele_type	session
- [x]	SPAC25B8.19c:allele-7	loz1-23	amino_acid_mutation	bf037075feb20f28
- [x]	SPAC2F7.03c:allele-3	pom1-as1	amino_acid_mutation	bbe966c7c31d9042
- [x]	SPAC6B12.15:allele-3	cpc2-W43*	partial_amino_acid_deletion	a9ee2fb1cb19f385
- [x]	SPBC14F5.13c:allele-4	pho8-m1	amino_acid_mutation	2c0b3f9b052bea9e
- [x]	SPBC14F5.13c:allele-5	pho8-m2	amino_acid_mutation	2c0b3f9b052bea9e
- [x]	SPBC216.05:allele-2	rad3-136	unknown	e6d26db4caf74ac5
- [x]	SPBC32C12.02:allele-12	ste11-mutant	unknown	133b9a4cefba1a78
- [x]	SPCC18B5.03:allele-2	wee1+	wild_type	ef61ac1ac91c951e
- [x]	SPCC285.09c:allele-2	cgs2-2	nucleotide_insertion	0d638c12aef4db07
- [x]	SPNCRNA.103:allele-7	sme2-m	nucleotide_mutation	45395a087bd927e5
- [x]	SPNCRNA.103:allele-7	sme2-m	nucleotide_mutation	e3c8313e9bd1dabc
- [x]	SPNCRNA.103:allele-9	sme2deltaC	partial_nucleotide_deletion	e3c8313e9bd1dabc
- [x]	SPNCRNA.214:allele-30	ter1-delta(25-1135)::ura4+-tk	partial_nucleotide_deletion	72c1277f6497035f
- [x]	SPNCRNA.9001:allele-4	prt2delta-1	partial_nucleotide_deletion	a93df4140a4b1e4c
- [x]	SPNCRNA.9001:allele-5	prt2delta-2	partial_nucleotide_deletion	a93df4140a4b1e4c