User:Nkuldell/SAGA vs Swi/Snf: Difference between revisions

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most strains listed in Martens, Wu, Winston G&D paper 2005 [[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=16291644&query_hl=10&itool=pubmed_docsum]]
most strains listed in Martens, Wu, Winston G&D paper 2005 [[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=16291644&query_hl=10&itool=pubmed_docsum]]
<br>link to FW yeast strain collection [[http://genepath.med.harvard.edu/strainfinder/yeast.php]] <br>
<br>link to FW yeast strain collection [[http://genepath.med.harvard.edu/strainfinder/yeast.php]] <br>
Parent strain for 109 deletion analysis:  
Parent strain for 109 deletion analysis: FY2068 = MAT(alpha) ura3-52 his3D200 leu2D1 lys2-128d
{| border="1"   
{| border="1"   
! Ada subunits   
! Ada subunits   
Line 12: Line 12:
|-     
|-     
| Ada1 (aka HFI1, SUP110, SRM12, GAN1) [[http://db.yeastgenome.org/cgi-bin/locus.pl?locus=ADA1]]   
| Ada1 (aka HFI1, SUP110, SRM12, GAN1) [[http://db.yeastgenome.org/cgi-bin/locus.pl?locus=ADA1]]   
| 1.467 kb/489 aa, <br> Chr. XVI, viable
| 1.467 kb/489 aa, Chr. XVI, <br>viable
|
| FY1560<br> aka NY383
|
| MAT(A) ura3-52 his3D200 lys2-173R2 <br> <b>ada1::HIS3</b>
|-     
|-     
| Ada2 (aka SWI8) [[http://db.yeastgenome.org/cgi-bin/locus.pl?locus=ADA2]]   
| Ada2 (aka SWI8) [[http://db.yeastgenome.org/cgi-bin/locus.pl?locus=ADA2]]   
| 1.305 kb/434aa, <br> Chr. IV, viable  
| 1.305 kb/434aa, Chr. IV, <br>viable  
|
| FY1548<br> aka NY384
|
| MAT(A) ura3-52 his3D200 leu2D1 lys2-128d <br> <b> ada2::HIS3 </b>
|-     
|-     
| Ada3 (aka NGG1, SWI7) [[http://db.yeastgenome.org/cgi-bin/locus.pl?locus=ADA3]]   
| Ada3 (aka NGG1, SWI7) [[http://db.yeastgenome.org/cgi-bin/locus.pl?locus=ADA3]]   
| 2.109 kb/702aa, <br> Chr. IV, viable   
| 2.109 kb/702aa, Chr. IV, <br>viable   
|
| FY1596<br> aka NY385
|
| MAT(A) ura3-52 his3D200 his4-912d lys2-173R2 <br> <b> ada3::HIS3 </b>
|-   
|-   
| Gcn5 (aka ADA4, SWI9) [[http://db.yeastgenome.org/cgi-bin/locus.pl?locus=GCN5]]   
| Gcn5 (aka ADA4, SWI9) [[http://db.yeastgenome.org/cgi-bin/locus.pl?locus=GCN5]]   
| 1.32 kb/439aa, <br> Chr. VII, viable
| 1.32 kb/439aa, Chr. VII, <br>viable
|
| FY1600<br> aka NY386
|
| MAT(A) ura3-52 leu2D1 his3D200 his4-917d <br> <b> gcn5::HIS3 </b>
|-   
|-   
| Ada5 (aka SPT20) [[http://db.yeastgenome.org/cgi-bin/locus.pl?locus=Ada5]]   
| Ada5 (aka SPT20) [[http://db.yeastgenome.org/cgi-bin/locus.pl?locus=Ada5]]   
| 1.815 kb/604aa, <br> Chr. XV, viable
| 1.815 kb/604aa, Chr. XV, <br>viable
|
| FY1098
|
| see spt20::URA3
|}
|}
{| border="1"   
{| border="1"   
Line 43: Line 43:
|-
|-
| Spt3 [[http://db.yeastgenome.org/cgi-bin/locus.pl?locus=spt3]]   
| Spt3 [[http://db.yeastgenome.org/cgi-bin/locus.pl?locus=spt3]]   
| 1.014 kb/337aa, <br> Chr. IV, viable
| 1.014 kb/337aa, Chr. IV, <br> viable
|
| FY2142<br> aka NY387
|
| MAT (alpha) <br> <b> spt3::KanMX </b>
|-     
|-     
| Spt7 (aka GIT2) [[http://db.yeastgenome.org/cgi-bin/locus.pl?locus=Spt7]]   
| Spt7 (aka GIT2) [[http://db.yeastgenome.org/cgi-bin/locus.pl?locus=Spt7]]   
| 3.999 kb/1332aa, <br> Chr. II, viable  
| 3.999 kb/1332aa, Chr. II, <br> viable  
|
| FY963<br> aka NY388
|  
| MAT(A)  ura3-52 his4-917d leu2d1 <br> <b> spt7::LEU2 </b>
|-
|-
| Spt8 [[http://db.yeastgenome.org/cgi-bin/locus.pl?locus=Spt8]]   
| Spt8 [[http://db.yeastgenome.org/cgi-bin/locus.pl?locus=Spt8]]   
| 1.809 kb/602aa, <br> Chr. XII, viable
| 1.809 kb/602aa, Chr. XII, <br> viable
|
| FY50<br> aka NY389
|
| MAT(A)  ura3-52 his4-917d leu2d1 trp1d63 <br> <b>spt8d-302::LEU2 </b>
|-   
|-   
| Spt20 (aka Ada5) [[http://db.yeastgenome.org/cgi-bin/locus.pl?locus=SPT20]]   
| Spt20 (aka Ada5) [[http://db.yeastgenome.org/cgi-bin/locus.pl?locus=SPT20]]   
| same as Ada5 <br> 1.815 kb/604aa, Chr. XV, viable
| 1.815 kb/604aa, Chr. XV, <br> viable
|
| FY1098<br> aka NY390
|
| MAT(A) ura3-52 his3d200 leu2d1 <br> <b>spt20d100::URA3 </b>
|}
|}
{| border="1"  
{| border="1"  
! TAF subunits, cerevisiae </i> 
! TAF subunits  
! size, chromosome, null p-type  
! size, chromosome, null p-type  
|-   
|-   
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|-   
|-   
| Sgf73 [[http://db.yeastgenome.org/cgi-bin/locus.pl?locus=sgf73]]   
| Sgf73 [[http://db.yeastgenome.org/cgi-bin/locus.pl?locus=sgf73]]   
| 1.974 kb/657aa, Chr. VII , viable  
| 1.974 kb/657aa, Chr. VII , <br> viable  
|
| NY350
|  
| MAT(A) ura3D0 his3D200 leu2D0 lys2-128d HAP1 DAN3:HIS3 <br> <b> sgf73::URA3</b>
|-
|-
| Sgf29 [[http://db.yeastgenome.org/cgi-bin/locus.pl?locus=sgf29]]   
| Sgf29 [[http://db.yeastgenome.org/cgi-bin/locus.pl?locus=sgf29]]   
| 0.779 kb/259aa, Chr. III, viable
| 0.779 kb/259aa, Chr. III, <br> viable
|
| FY2474
|
| MAT(A) ura3-52 his4-917d leu2D1 lys2-173R2 arg4-12 <br> <b> sgf29D0::KanMX </b>
|-
|-
| Sgf11 [[http://db.yeastgenome.org/cgi-bin/locus.pl?locus=sgf11]]   
| Sgf11 [[http://db.yeastgenome.org/cgi-bin/locus.pl?locus=sgf11]]   
| 0.3 kb/99aa, Chr.XVI, viable
| 0.3 kb/99aa, Chr.XVI, <br> viable
|
| NY391
|
| MAT(A) ura3-52 his3D200 leu2D0 lys2-128d trp1-63 <br> <b> sgf11::KanMX </b>
|-
|-
| Ubp8 [[http://db.yeastgenome.org/cgi-bin/locus.pl?locus=ubp8]]   
| Ubp8 [[http://db.yeastgenome.org/cgi-bin/locus.pl?locus=ubp8]]   
| 1.416 kb/471aa, Chr. XIII, viable  
| 1.416 kb/471aa, Chr. XIII, <br> viable  
|
| FY2473 <br> aka NY392
|  
| MAT(alpha) ura3-52 leu2D1 lys2-173R2 arg4-12 <br> <b>ubp8D0::KanMX </b>
|-   
|-   
| Sus1 [[http://db.yeastgenome.org/cgi-bin/locus.pl?locus=Sus1]]   
| Sus1 [[http://db.yeastgenome.org/cgi-bin/locus.pl?locus=Sus1]]   
| gene with intron, Chr. II, viable   
| gene with intron, Chr. II, <br> viable   
|
|
|
|
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|-
|-
|SWII (aka ADR6, GAM3, LPA1)[[http://db.yeastgenome.org/cgi-bin/locus.pl?locus=swi1]]
|SWII (aka ADR6, GAM3, LPA1)[[http://db.yeastgenome.org/cgi-bin/locus.pl?locus=swi1]]
|3945bp/1315 aa, Chr. XVI, <font color =red> inviable </font color>  
|3945bp/1315 aa, Chr. XVI, <br> <font color =red> inviable </font color>  
|-
|-
|SWI2 (aka GAM1, HAF1, <font color = red> SNF2 </font color>, TYE3)[[http://db.yeastgenome.org/cgi-bin/locus.pl?locus=SWI2]]
|SWI2 (aka GAM1, HAF1, <font color = red> SNF2 </font color>, TYE3)[[http://db.yeastgenome.org/cgi-bin/locus.pl?locus=SWI2]]
|5112bp/1704aa, Chr. XV, viable
|5112bp/1704aa, Chr. XV, <br> viable
|-
|-
|SWI3 (aka TYE2) [[http://db.yeastgenome.org/cgi-bin/locus.pl?locus=swi3]]
|SWI3 (aka TYE2) [[http://db.yeastgenome.org/cgi-bin/locus.pl?locus=swi3]]
|2478bp/826aa, Chr. X, viable
|2478bp/826aa, Chr. X,<br> viable
|}
|}
{| border="1"
{| border="1"
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! size, chromosome, null p-type
! size, chromosome, null p-type
|-
|-
|SNF5
|SNF5 (aka HAF4, SWI10, TYE4)[[http://db.yeastgenome.org/cgi-bin/locus.pl?locus=SNF5]]
|
|2718 bp/906aa, Chr. II <br>viable
|-
|-
|SNF6
|SNF6 [[http://db.yeastgenome.org/cgi-bin/locus.pl?locus=SNF6]]
|
|999bp/333aa, Chr. VIII, <br> viable
|-
|-
|SNF11
|SNF11 [[http://db.yeastgenome.org/cgi-bin/locus.pl?locus=SNF11]]
|
|510 bp/170aa, Chr. IV <br> viable
|}
|}
{| border="1"
{| border="1"
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|
|
|}
|}
==Deletion Primers==
* sgf73_URA3_KO_fwd (NO99)
**5' TGAACACACAAGAGAAGCGCAAAAGAGTAAAGAGCTAAAatgtcgaaagctacatataa
* sgf73_URA3_KO_rev (NO100)
**5' CTCACTTCGTGAACATGCTGGATAACGTGCATGATTCAA ttagttttgctggccgcatc
* sgf29_URA3_KO_fwd (NO101)
**5' GACTTTTTCACAGCAAAACACACGGTCACCTTTCTTATTatgtcgaaagctacatataa
* sgf29_URA3_KO_rev (NO102)
**5' AGAAGATCTTATGATATGTAGTAAATGTTAACCACCATTttagttttgctggccgcatc

Latest revision as of 15:17, 8 November 2006

in progress...

SAGA subunits, S. cerevisiae

most strains listed in Martens, Wu, Winston G&D paper 2005 [[1]]
link to FW yeast strain collection [[2]]
Parent strain for 109 deletion analysis: FY2068 = MAT(alpha) ura3-52 his3D200 leu2D1 lys2-128d

Ada subunits size,chromosome,null p-type deletion strain genotype
Ada1 (aka HFI1, SUP110, SRM12, GAN1) [[3]] 1.467 kb/489 aa, Chr. XVI,
viable 		FY1560
aka NY383 		MAT(A) ura3-52 his3D200 lys2-173R2
ada1::HIS3
Ada2 (aka SWI8) [[4]] 1.305 kb/434aa, Chr. IV,
viable 		FY1548
aka NY384 		MAT(A) ura3-52 his3D200 leu2D1 lys2-128d
ada2::HIS3
Ada3 (aka NGG1, SWI7) [[5]] 2.109 kb/702aa, Chr. IV,
viable 		FY1596
aka NY385 		MAT(A) ura3-52 his3D200 his4-912d lys2-173R2
ada3::HIS3
Gcn5 (aka ADA4, SWI9) [[6]] 1.32 kb/439aa, Chr. VII,
viable 		FY1600
aka NY386 		MAT(A) ura3-52 leu2D1 his3D200 his4-917d
gcn5::HIS3
Ada5 (aka SPT20) [[7]] 1.815 kb/604aa, Chr. XV,
viable 		FY1098 see spt20::URA3
Spt subunits size, chromosome, null p-type deletion strain genotype
Spt3 [[8]] 1.014 kb/337aa, Chr. IV,
viable 		FY2142
aka NY387 		MAT (alpha)
spt3::KanMX
Spt7 (aka GIT2) [[9]] 3.999 kb/1332aa, Chr. II,
viable 		FY963
aka NY388 		MAT(A) ura3-52 his4-917d leu2d1
spt7::LEU2
Spt8 [[10]] 1.809 kb/602aa, Chr. XII,
viable 		FY50
aka NY389 		MAT(A) ura3-52 his4-917d leu2d1 trp1d63
spt8d-302::LEU2
Spt20 (aka Ada5) [[11]] 1.815 kb/604aa, Chr. XV,
viable 		FY1098
aka NY390 		MAT(A) ura3-52 his3d200 leu2d1
spt20d100::URA3
TAF subunits size, chromosome, null p-type
TAF5 (aka TAF90) [[12]] 2.397 kb/798aa, Chr. II, inviable
TAF6 (aka TAF60) [[13]] 1.551 kb/516aa, Chr. VII, inviable
TAF9 (aka TAF17) [[14]] 0.474 kb/157aa, Chr. XIII, inviable
TAF10 (aka TAF23, TAF25) [[15]] 0.621 kb/206aa, Chr. IV, inviable
TAF12 (aka TAF61, TAF68) [[16]] 1.620 kb/539aa, Chr. IV, inviable
Tra1 subunit size, chromosome, null p-type
Tra1 [[17]] 11.235 kb/3744aa, Chr. VIII, inviable
other subunits size, chromosome, null p-type deletion strain genotype
Sgf73 [[18]] 1.974 kb/657aa, Chr. VII ,
viable 		NY350 MAT(A) ura3D0 his3D200 leu2D0 lys2-128d HAP1 DAN3:HIS3
sgf73::URA3
Sgf29 [[19]] 0.779 kb/259aa, Chr. III,
viable 		FY2474 MAT(A) ura3-52 his4-917d leu2D1 lys2-173R2 arg4-12
sgf29D0::KanMX
Sgf11 [[20]] 0.3 kb/99aa, Chr.XVI,
viable 		NY391 MAT(A) ura3-52 his3D200 leu2D0 lys2-128d trp1-63
sgf11::KanMX
Ubp8 [[21]] 1.416 kb/471aa, Chr. XIII,
viable 		FY2473
aka NY392 		MAT(alpha) ura3-52 leu2D1 lys2-173R2 arg4-12
ubp8D0::KanMX
Sus1 [[22]] gene with intron, Chr. II,
viable

SWI/SNF subunits

SWI subunits size,chromosome,null p-type
SWII (aka ADR6, GAM3, LPA1)[[23]] 3945bp/1315 aa, Chr. XVI,
inviable
SWI2 (aka GAM1, HAF1, SNF2 , TYE3)[[24]] 5112bp/1704aa, Chr. XV,
viable
SWI3 (aka TYE2) [[25]] 2478bp/826aa, Chr. X,
viable
SNF subunits size, chromosome, null p-type
SNF5 (aka HAF4, SWI10, TYE4)[[26]] 2718 bp/906aa, Chr. II
viable
SNF6 [[27]] 999bp/333aa, Chr. VIII,
viable
SNF11 [[28]] 510 bp/170aa, Chr. IV
viable
SWP subunits size, chromosome, null p-type
SWP82
SWP73
SWP59
SWP61
SWP29


Deletion Primers

  • sgf73_URA3_KO_fwd (NO99)
    • 5' TGAACACACAAGAGAAGCGCAAAAGAGTAAAGAGCTAAAatgtcgaaagctacatataa
  • sgf73_URA3_KO_rev (NO100)
    • 5' CTCACTTCGTGAACATGCTGGATAACGTGCATGATTCAA ttagttttgctggccgcatc
  • sgf29_URA3_KO_fwd (NO101)
    • 5' GACTTTTTCACAGCAAAACACACGGTCACCTTTCTTATTatgtcgaaagctacatataa
  • sgf29_URA3_KO_rev (NO102)
    • 5' AGAAGATCTTATGATATGTAGTAAATGTTAACCACCATTttagttttgctggccgcatc
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