Difference between revisions of "Time of bloom"

From GcatWiki
Jump to: navigation, search
Line 62: Line 62:
 
|-
 
|-
 
! <i>Arabidopsis</i> Locus !! Other Names !! AA Sequence !! Pathway !! Potential Ortholog
 
! <i>Arabidopsis</i> Locus !! Other Names !! AA Sequence !! Pathway !! Potential Ortholog
 +
|-
 +
| AGL14||||[http://arabidopsis.org/servlets/TairObject?id=129748&type=locus TAIR]||V||
 +
|-
 +
| AGL19||||[http://arabidopsis.org/servlets/TairObject?id=128336&type=locus TAIR]||V||
 +
|-
 +
| AGL24||||[http://arabidopsis.org/servlets/TairObject?id=127586&type=locus TAIR]||V||
 +
|-
 +
| AGL31||||[http://arabidopsis.org/servlets/TairObject?id=135154&type=locus TAIR]||Am, FPI, V||
 +
|-
 +
| APRR3||||[http://arabidopsis.org/servlets/TairObject?id=133317&type=locus TAIR]||L||
 +
|-
 +
| APRR5||||[http://arabidopsis.org/servlets/TairObject?id=135985&type=locus TAIR]||L||
 +
|-
 +
| APRR9||||[http://arabidopsis.org/servlets/TairObject?id=32227&type=locus TAIR]||L||
 +
|-
 +
| AT1G26790||||[http://arabidopsis.org/servlets/TairObject?id=137136&type=locus TAIR]||L||
 +
|-
 +
| AT1G29160||||[http://arabidopsis.org/servlets/TairObject?id=29883&type=locus TAIR]||L||
 +
|-
 +
| AT2G34140||||[http://arabidopsis.org/servlets/TairObject?id=33865&type=locus TAIR]||L||
 +
|-
 +
| AT2G46670*||||[http://arabidopsis.org/servlets/TairObject?id=35019&type=locus TAIR]||L||
 +
|-
 +
| AT3G21320||||[http://arabidopsis.org/servlets/TairObject?id=39170&type=locus TAIR]||L||
 +
|-
 +
| AT3G25730||||[http://arabidopsis.org/servlets/TairObject?id=37641&type=locus TAIR]||L||
 +
|-
 +
| AT5G08230*||||[http://arabidopsis.org/servlets/TairObject?id=135669&type=locus TAIR]||V||
 +
|-
 +
| AT5G23280*||||[http://arabidopsis.org/servlets/TairObject?id=133661&type=locus TAIR]||L||
 +
|-
 +
| AT5G48250*||||[http://arabidopsis.org/servlets/TairObject?id=133393&type=locus TAIR]||L||
 +
|-
 +
| AT5G59570*||||[http://arabidopsis.org/servlets/TairObject?id=131156&type=locus TAIR]||L||
 +
|-
 +
| ATARP6||||[http://arabidopsis.org/servlets/TairObject?id=40458&type=locus TAIR]||Am, V||
 +
|-
 +
| ATBZIP27||||[http://arabidopsis.org/servlets/TairObject?id=227228&type=locus TAIR]||Am, MI||
 
|-
 
|-
 
| ATCOL4||||[http://arabidopsis.org/servlets/TairObject?id=131285&type=locus TAIR]||L||
 
| ATCOL4||||[http://arabidopsis.org/servlets/TairObject?id=131285&type=locus TAIR]||L||
Line 68: Line 106:
 
|-
 
|-
 
| ATSWC6||||[http://arabidopsis.org/servlets/TairObject?id=500231974&type=locus TAIR]||V||
 
| ATSWC6||||[http://arabidopsis.org/servlets/TairObject?id=500231974&type=locus TAIR]||V||
 +
|-
 +
| CCA1||||[http://arabidopsis.org/servlets/TairObject?id=32221&type=locus TAIR]||L||
 +
|-
 +
| CDF1||||[http://arabidopsis.org/servlets/TairObject?id=131911&type=locus TAIR]||L||
 +
|-
 +
| CDF2||||[http://arabidopsis.org/servlets/TairObject?id=133414&type=locus TAIR]||L||
 +
|-
 +
| CDF3||||[http://arabidopsis.org/servlets/TairObject?id=36439&type=locus TAIR]||L||
 +
|-
 +
| CHE||||[http://www.uniprot.org/uniprot/Q9FTA2 UniProtKB]||L||
 
|-
 
|-
 
| CIB1||||[http://arabidopsis.org/servlets/TairObject?id=130033&type=locus TAIR]||L||
 
| CIB1||||[http://arabidopsis.org/servlets/TairObject?id=130033&type=locus TAIR]||L||
Line 152: Line 200:
 
|-
 
|-
 
| MSI1||||[http://arabidopsis.org/servlets/TairObject?id=132921&type=locus TAIR]||Au, V||
 
| MSI1||||[http://arabidopsis.org/servlets/TairObject?id=132921&type=locus TAIR]||Au, V||
 +
|-
 +
| MSI2*||||[http://arabidopsis.org/servlets/TairObject?id=34537&type=locus TAIR]||Au, V||
 +
|-
 +
| MSI3*||||[http://arabidopsis.org/servlets/TairObject?id=129003&type=locus TAIR]||Au, V||
 
|-
 
|-
 
| NFC5*||||[http://arabidopsis.org/servlets/TairObject?id=129407&type=locus TAIR]||Am, Au||
 
| NFC5*||||[http://arabidopsis.org/servlets/TairObject?id=129407&type=locus TAIR]||Am, Au||
Line 220: Line 272:
 
|-
 
|-
 
| ZTL||||[http://arabidopsis.org/servlets/TairObject?id=134481&type=locus TAIR]||L||
 
| ZTL||||[http://arabidopsis.org/servlets/TairObject?id=134481&type=locus TAIR]||L||
−
|-
 
−
| AGL14||||[http://arabidopsis.org/servlets/TairObject?id=129748&type=locus UniProtKB]||V||
 
−
|-
 
−
| AGL19||||[http://arabidopsis.org/servlets/TairObject?id=128336&type=locus UniProtKB]||V||
 
−
|-
 
−
| AGL24||||[http://arabidopsis.org/servlets/TairObject?id=127586&type=locus UniProtKB]||V||
 
−
|-
 
−
| AGL31||||[http://arabidopsis.org/servlets/TairObject?id=135154&type=locus UniProtKB]||Am, FPI, V||
 
−
|-
 
−
| APRR3||||[http://arabidopsis.org/servlets/TairObject?id=133317&type=locus UniProtKB]||L||
 
−
|-
 
−
| APRR5||||[http://arabidopsis.org/servlets/TairObject?id=135985&type=locus UniProtKB]||L||
 
−
|-
 
−
| APRR9||||[http://arabidopsis.org/servlets/TairObject?id=32227&type=locus UniProtKB]||L||
 
−
|-
 
−
| AT1G26790||||[http://arabidopsis.org/servlets/TairObject?id=137136&type=locus UniProtKB]||L||
 
−
|-
 
−
| AT1G29160||||[http://arabidopsis.org/servlets/TairObject?id=29883&type=locus UniProtKB]||L||
 
−
|-
 
−
| AT2G34140||||[http://arabidopsis.org/servlets/TairObject?id=33865&type=locus UniProtKB]||L||
 
−
|-
 
−
| AT2G46670*||||[http://arabidopsis.org/servlets/TairObject?id=35019&type=locus UniProtKB]||L||
 
−
|-
 
−
| AT3G21320||||[http://arabidopsis.org/servlets/TairObject?id=39170&type=locus UniProtKB]||L||
 
−
|-
 
−
| AT3G25730||||[http://arabidopsis.org/servlets/TairObject?id=37641&type=locus UniProtKB]||L||
 
−
|-
 
−
| AT5G08230*||||[http://arabidopsis.org/servlets/TairObject?id=135669&type=locus UniProtKB]||V||
 
−
|-
 
−
| AT5G23280*||||[http://arabidopsis.org/servlets/TairObject?id=133661&type=locus UniProtKB]||L||
 
−
|-
 
−
| AT5G48250*||||[http://arabidopsis.org/servlets/TairObject?id=133393&type=locus UniProtKB]||L||
 
−
|-
 
−
| AT5G59570*||||[http://arabidopsis.org/servlets/TairObject?id=131156&type=locus UniProtKB]||L||
 
−
|-
 
−
| ATARP6||||[http://arabidopsis.org/servlets/TairObject?id=40458&type=locus UniProtKB]||Am, V||
 
−
|-
 
−
| ATBZIP27||||[http://arabidopsis.org/servlets/TairObject?id=227228&type=locus UniProtKB]||Am, MI||
 
−
|-
 
−
| CCA1||||[http://arabidopsis.org/servlets/TairObject?id=32221&type=locus UniProtKB]||L||
 
−
|-
 
−
| CDF1||||[http://arabidopsis.org/servlets/TairObject?id=131911&type=locus UniProtKB]||L||
 
−
|-
 
−
| CDF2||||[http://arabidopsis.org/servlets/TairObject?id=133414&type=locus UniProtKB]||L||
 
−
|-
 
−
| CDF3||||[http://arabidopsis.org/servlets/TairObject?id=36439&type=locus UniProtKB]||L||
 
−
|-
 
−
| CHE||||[http://www.uniprot.org/uniprot/Q9FTA2 UniProtKB]||L||
 
−
|-
 
−
| MSI2*||||[http://arabidopsis.org/servlets/TairObject?id=34537&type=locus UniProtKB]||Au, V||
 
−
|-
 
−
| MSI3*||||[http://arabidopsis.org/servlets/TairObject?id=129003&type=locus UniProtKB]||Au, V||
 
 
|}
 
|}

Revision as of 21:26, 5 March 2013

By Austin Mudd - Spring 2013


To Do

  • Write introduction and procedure sections
  • Aggregate all sequences into a single document in proper FASTA format


Introduction

The factors affecting time of flowering from the Max Planck Institute for Plant Breeding Research


Procedure

  • Overall procedure for finding the genes, running with GenSAS, determining SSRs, etc


Gallery of Arabidopsis Flowering Pathways


105 Flowering Genes

The below table lists all of the genes involved in the ambient temperature, autonomous, light signaling, and vernalization pathways.

Note: All Arabidopsis genes are compiled from Jung et al., 2012. All potential orthologs are found via UniProt Grape or UniProt Strawberry nomenclature search. Formatting is the same as Jung et al., 2012 where a * indicates 1 of "24 Arabidopsis genes, which had not been previously investigated for their roles in flowering, [that] belong to [paralog groups] with known Arabidopsis flowering genes." Moreover, for pathways, "Am: Ambient temperature pathway, Au: Autonomous pathway, FPI: Flowering Pathway [Integrators], L: Light signaling pathway, MI: Meristem Identity, V: Vernalization pathway."

Arabidopsis Locus Other Names AA Sequence Pathway Potential Ortholog
AGL14 TAIR V
AGL19 TAIR V
AGL24 TAIR V
AGL31 TAIR Am, FPI, V
APRR3 TAIR L
APRR5 TAIR L
APRR9 TAIR L
AT1G26790 TAIR L
AT1G29160 TAIR L
AT2G34140 TAIR L
AT2G46670* TAIR L
AT3G21320 TAIR L
AT3G25730 TAIR L
AT5G08230* TAIR V
AT5G23280* TAIR L
AT5G48250* TAIR L
AT5G59570* TAIR L
ATARP6 TAIR Am, V
ATBZIP27 TAIR Am, MI
ATCOL4 TAIR L
ATCOL5 TAIR L
ATSWC6 TAIR V
CCA1 TAIR L
CDF1 TAIR L
CDF2 TAIR L
CDF3 TAIR L
CHE UniProtKB L
CIB1 TAIR L
CLF TAIR Au, V
CO TAIR FPI, L
COL1 TAIR FPI, L
COL2 TAIR FPI, L
COL9 TAIR L
COP1 TAIR L
CRY1 TAIR L Grape
CRY2 TAIR L
EFS TAIR V
ELF3 TAIR L
ELF4 TAIR L
ELF4-L3 TAIR L
FCA TAIR Am, Au Grape
FD TAIR Am, MI
FES1 TAIR V
FIE1 TAIR Au, V
FKF1 TAIR L
FLC TAIR Am, FPI, V Grape
FLD TAIR Am, Au
FLK TAIR Au
FPA TAIR Au
FRI TAIR V
FRL1 TAIR V
FRL2 TAIR V
FT TAIR Am, FPI Grape, Strawberry
FVE TAIR Am, Au
FY TAIR Au
GI TAIR L
HUA2 TAIR V
LD TAIR Au
LDL1* TAIR Am, Au
LDL2* TAIR Am, Au
LHY TAIR L
LKP2 TAIR L
LUX TAIR L
MAF1 TAIR Am, FPI, V
MAF3 TAIR Am, FPI, V
MAF4 TAIR Am, FPI, V
MAF5 TAIR Am, FPI, V
MEA* TAIR Au, V
MSI1 TAIR Au, V
MSI2* TAIR Au, V
MSI3* TAIR Au, V
NFC5* TAIR Am, Au
PAF1 TAIR V
PAF2 TAIR V
PEP TAIR V
PHYA TAIR L Grape
PHYB TAIR L Grape
PHYC TAIR L Grape
PHYD TAIR L
PHYE TAIR L Grape
PIE1 TAIR V
PRR7 TAIR L
RAV1 TAIR L
RFI2 TAIR L
SPA1 TAIR L
SPA2 TAIR L
SPA3 TAIR L
SPA4 TAIR L
SUF4 TAIR V
SVP TAIR Am, V Grape
SWN TAIR Au, V
TEM1 TAIR L
TEM2 TAIR L
TFL1 TAIR Am, FPI Grape, Strawberry
TOC1 TAIR L
TSF TAIR Am, FPI
UVR3* TAIR L
VEL1 TAIR Au, V
VEL2 TAIR Au
VEL3 TAIR Au
VIN3 TAIR Au, V
VRN1 TAIR V
VRN2 TAIR Au, V
VRN5 TAIR Au, V
ZTL TAIR L
Retrieved from "http://gcat.davidson.edu/GcatWiki/index.php?title=Time_of_bloom&oldid=16096"