Difference between revisions of "Time of bloom"

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! <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||
+
| AT1G04400||AT-PHH1, ATCRY2, CRY2, CRYPTOCHROME 2, FHA, PHH1||[http://arabidopsis.org/servlets/TairObject?id=28374&type=locus TAIR]||L||
 
|-
 
|-
−
| AGL19||||[http://arabidopsis.org/servlets/TairObject?id=128336&type=locus TAIR]||V||
+
| AT1G26790||||[http://arabidopsis.org/servlets/TairObject?id=137136&type=locus TAIR]||L||
 
|-
 
|-
−
| AGL24||||[http://arabidopsis.org/servlets/TairObject?id=127586&type=locus TAIR]||V||
+
| AT1G29160||||[http://arabidopsis.org/servlets/TairObject?id=29883&type=locus TAIR]||L||
 
|-
 
|-
−
| AGL31||||[http://arabidopsis.org/servlets/TairObject?id=135154&type=locus TAIR]||Am, FPI, V||
+
| AT2G17770||ATBZIP27, BASIC REGION/LEUCINE ZIPPER MOTIF 27, BZIP27, FD PARALOG, FDP||[http://arabidopsis.org/servlets/TairObject?id=227228&type=locus TAIR]||Am, MI||
 
|-
 
|-
−
| APRR3||||[http://arabidopsis.org/servlets/TairObject?id=133317&type=locus TAIR]||L||
+
| AT2G23380||CLF, CURLY LEAF, ICU1, INCURVATA 1, SDG1, SET1, SETDOMAIN 1, SETDOMAIN GROUP 1||[http://arabidopsis.org/servlets/TairObject?id=26534&type=locus TAIR]||Au, V||
 
|-
 
|-
−
| APRR5||||[http://arabidopsis.org/servlets/TairObject?id=135985&type=locus TAIR]||L||
+
| AT2G32950||ARABIDOPSIS THALIANA CONSTITUTIVE PHOTOMORPHOGENIC 1, ATCOP1, CONSTITUTIVE PHOTOMORPHOGENIC 1, COP1, DEETIOLATED MUTANT 340, DET340, EMB168, EMBRYO DEFECTIVE 168, FUS1, FUSCA 1||[http://arabidopsis.org/servlets/TairObject?id=34462&type=locus TAIR]||L||
 
|-
 
|-
−
| APRR9||||[http://arabidopsis.org/servlets/TairObject?id=32227&type=locus TAIR]||L||
+
| AT2G34140||||[http://arabidopsis.org/servlets/TairObject?id=33865&type=locus TAIR]||L||
 
|-
 
|-
−
| AT1G26790||||[http://arabidopsis.org/servlets/TairObject?id=137136&type=locus TAIR]||L||
+
| AT2G46670*||||[http://arabidopsis.org/servlets/TairObject?id=35019&type=locus TAIR]||L||
 +
|-
 +
| AT2G46790||APRR9, ARABIDOPSIS PSEUDO-RESPONSE REGULATOR 9, PRR9, PSEUDO-RESPONSE REGULATOR 9, TL1, TOC1-LIKE PROTEIN 1||[http://arabidopsis.org/servlets/TairObject?id=32227&type=locus TAIR]||L||
 
|-
 
|-
−
| AT1G29160||||[http://arabidopsis.org/servlets/TairObject?id=29883&type=locus TAIR]||L||
+
| AT2G46830||ATCCA1, CCA1, CIRCADIAN CLOCK ASSOCIATED 1||[http://arabidopsis.org/servlets/TairObject?id=32221&type=locus TAIR]||L||
 
|-
 
|-
−
| AT2G34140||||[http://arabidopsis.org/servlets/TairObject?id=33865&type=locus TAIR]||L||
+
| AT3G02380||ATCOL2, B-BOX DOMAIN PROTEIN 3, BBX3, COL2, CONSTANS-LIKE 2||[http://arabidopsis.org/servlets/TairObject?id=35635&type=locus TAIR]||FPI, L||
 
|-
 
|-
−
| AT2G46670*||||[http://arabidopsis.org/servlets/TairObject?id=35019&type=locus TAIR]||L||
+
| AT3G07650||B-BOX DOMAIN PROTEIN 7, BBX7, COL9, CONSTANS-LIKE 9||[http://arabidopsis.org/servlets/TairObject?id=38550&type=locus TAIR]||L||
 
|-
 
|-
 
| AT3G21320||||[http://arabidopsis.org/servlets/TairObject?id=39170&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||
+
| AT3G25730||EDF3, ETHYLENE RESPONSE DNA BINDING FACTOR 3||[http://arabidopsis.org/servlets/TairObject?id=37641&type=locus TAIR]||L||
 
|-
 
|-
−
| AT5G08230*||||[http://arabidopsis.org/servlets/TairObject?id=135669&type=locus TAIR]||V||
+
| AT3G33520||ACTIN-RELATED PROTEIN 6, ARP6, ATARP6, EARLY IN SHORT DAYS 1, ESD1, SUF3, SUPPRESSOR OF FRI 3||[http://arabidopsis.org/servlets/TairObject?id=40458&type=locus TAIR]||Am, V||
 
|-
 
|-
−
| AT5G23280*||||[http://arabidopsis.org/servlets/TairObject?id=133661&type=locus TAIR]||L||
+
| AT3G47500||CDF3, CYCLING DOF FACTOR 3||[http://arabidopsis.org/servlets/TairObject?id=36439&type=locus TAIR]||L||
 
|-
 
|-
−
| AT5G48250*||||[http://arabidopsis.org/servlets/TairObject?id=133393&type=locus TAIR]||L||
+
| AT4G08920||ATCRY1, BLU1, BLUE LIGHT UNINHIBITED 1, CRY1, CRYPTOCHROME 1, ELONGATED HYPOCOTYL 4, HY4, OOP2, OUT OF PHASE 2||[http://arabidopsis.org/servlets/TairObject?id=129943&type=locus TAIR]||L||[http://www.uniprot.org/uniprot/B6REW9 Grape]
 
|-
 
|-
−
| AT5G59570*||||[http://arabidopsis.org/servlets/TairObject?id=131156&type=locus TAIR]||L||
+
| AT4G11880||AGAMOUS-LIKE 14, AGL14||[http://arabidopsis.org/servlets/TairObject?id=129748&type=locus TAIR]||V||
 
|-
 
|-
−
| ATARP6||||[http://arabidopsis.org/servlets/TairObject?id=40458&type=locus TAIR]||Am, V||
+
| AT4G22950||"AGAMOUS-LIKE 19, AGL19, GL19
 
|-
 
|-
−
| ATBZIP27||||[http://arabidopsis.org/servlets/TairObject?id=227228&type=locus TAIR]||Am, MI||
+
| "||[http://arabidopsis.org/servlets/TairObject?id=128336&type=locus TAIR]||V||
 
|-
 
|-
−
| ATCOL4||||[http://arabidopsis.org/servlets/TairObject?id=131285&type=locus TAIR]||L||
+
| AT4G24540||AGAMOUS-LIKE 24, AGL24||[http://arabidopsis.org/servlets/TairObject?id=127586&type=locus TAIR]||V||
 
|-
 
|-
−
| ATCOL5||||[http://arabidopsis.org/servlets/TairObject?id=134422&type=locus TAIR]||L||
+
| AT4G34530||CIB1, CRYPTOCHROME-INTERACTING BASIC-HELIX-LOOP-HELIX 1||[http://arabidopsis.org/servlets/TairObject?id=130033&type=locus TAIR]||L||
 
|-
 
|-
−
| ATSWC6||||[http://arabidopsis.org/servlets/TairObject?id=500231974&type=locus TAIR]||V||
+
| AT5G08230*||||[http://arabidopsis.org/servlets/TairObject?id=135669&type=locus TAIR]||V||
 
|-
 
|-
−
| CCA1||||[http://arabidopsis.org/servlets/TairObject?id=32221&type=locus TAIR]||L||
+
| AT5G08330||CCA1 HIKING EXPEDITION, CHE, TRANSCRIPTION FACTOR TCP21, TCP21||[http://www.uniprot.org/uniprot/Q9FTA2 UniProtKB]||L||
 
|-
 
|-
−
| CDF1||||[http://arabidopsis.org/servlets/TairObject?id=131911&type=locus TAIR]||L||
+
| AT5G15840||B-BOX DOMAIN PROTEIN 1, BBX1, CO, CONSTANS, FG||[http://arabidopsis.org/servlets/TairObject?id=130492&type=locus TAIR]||FPI, L||
 
|-
 
|-
−
| CDF2||||[http://arabidopsis.org/servlets/TairObject?id=133414&type=locus TAIR]||L||
+
| AT5G15850||ATCOL1, B-BOX DOMAIN PROTEIN 2, BBX2, COL1, CONSTANS-LIKE 1||[http://arabidopsis.org/servlets/TairObject?id=130495&type=locus TAIR]||FPI, L||
 
|-
 
|-
−
| CDF3||||[http://arabidopsis.org/servlets/TairObject?id=36439&type=locus TAIR]||L||
+
| AT5G23280*||||[http://arabidopsis.org/servlets/TairObject?id=133661&type=locus TAIR]||L||
 
|-
 
|-
−
| CHE||||[http://www.uniprot.org/uniprot/Q9FTA2 UniProtKB]||L||
+
| AT5G24470||APRR5, PRR5, PSEUDO-RESPONSE REGULATOR 5||[http://arabidopsis.org/servlets/TairObject?id=135985&type=locus TAIR]||L||
 
|-
 
|-
−
| CIB1||||[http://arabidopsis.org/servlets/TairObject?id=130033&type=locus TAIR]||L||
+
| AT5G24930||ATCOL4, B-BOX DOMAIN PROTEIN 5, BBX5, COL4, CONSTANS-LIKE 4||[http://arabidopsis.org/servlets/TairObject?id=131285&type=locus TAIR]||L||
 
|-
 
|-
−
| CLF||||[http://arabidopsis.org/servlets/TairObject?id=26534&type=locus TAIR]||Au, V||
+
| AT5G37055||ATSWC6, SEF, SERRATED LEAVES AND EARLY FLOWERING||[http://arabidopsis.org/servlets/TairObject?id=500231974&type=locus TAIR]||V||
 
|-
 
|-
−
| CO||||[http://arabidopsis.org/servlets/TairObject?id=130492&type=locus TAIR]||FPI, L||
+
| AT5G39660||CDF2, CYCLING DOF FACTOR 2||[http://arabidopsis.org/servlets/TairObject?id=133414&type=locus TAIR]||L||
 
|-
 
|-
−
| COL1||||[http://arabidopsis.org/servlets/TairObject?id=130495&type=locus TAIR]||FPI, L||
+
| AT5G48250*||B-BOX DOMAIN PROTEIN 8, BBX8||[http://arabidopsis.org/servlets/TairObject?id=133393&type=locus TAIR]||L||
 
|-
 
|-
−
| COL2||||[http://arabidopsis.org/servlets/TairObject?id=35635&type=locus TAIR]||FPI, L||
+
| AT5G57660||ATCOL5, B-BOX DOMAIN PROTEIN 6, BBX6, COL5, CONSTANS-LIKE 5||[http://arabidopsis.org/servlets/TairObject?id=134422&type=locus TAIR]||L||
 
|-
 
|-
−
| COL9||||[http://arabidopsis.org/servlets/TairObject?id=38550&type=locus TAIR]||L||
+
| AT5G59570*||BOA, BROTHER OF LUX ARRHYTHMO||[http://arabidopsis.org/servlets/TairObject?id=131156&type=locus TAIR]||L||
 
|-
 
|-
−
| COP1||||[http://arabidopsis.org/servlets/TairObject?id=34462&type=locus TAIR]||L||
+
| AT5G60100||APRR3, PRR3, PSEUDO-RESPONSE REGULATOR 3||[http://arabidopsis.org/servlets/TairObject?id=133317&type=locus TAIR]||L||
 
|-
 
|-
−
| CRY1||||[http://arabidopsis.org/servlets/TairObject?id=129943&type=locus TAIR]||L||[http://www.uniprot.org/uniprot/B6REW9 Grape]
+
| AT5G62430||CDF1, CYCLING DOF FACTOR 1||[http://arabidopsis.org/servlets/TairObject?id=131911&type=locus TAIR]||L||
 
|-
 
|-
−
| CRY2||||[http://arabidopsis.org/servlets/TairObject?id=28374&type=locus TAIR]||L||
+
| AT5G65050||AGAMOUS-LIKE 31, AGL31, MADS AFFECTING FLOWERING 2, MAF2||[http://arabidopsis.org/servlets/TairObject?id=135154&type=locus TAIR]||Am, FPI, V||
 
|-
 
|-
 
| EFS||||[http://arabidopsis.org/servlets/TairObject?id=136429&type=locus TAIR]||V||
 
| EFS||||[http://arabidopsis.org/servlets/TairObject?id=136429&type=locus TAIR]||V||

Revision as of 21:44, 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
AT1G04400 AT-PHH1, ATCRY2, CRY2, CRYPTOCHROME 2, FHA, PHH1 TAIR L
AT1G26790 TAIR L
AT1G29160 TAIR L
AT2G17770 ATBZIP27, BASIC REGION/LEUCINE ZIPPER MOTIF 27, BZIP27, FD PARALOG, FDP TAIR Am, MI
AT2G23380 CLF, CURLY LEAF, ICU1, INCURVATA 1, SDG1, SET1, SETDOMAIN 1, SETDOMAIN GROUP 1 TAIR Au, V
AT2G32950 ARABIDOPSIS THALIANA CONSTITUTIVE PHOTOMORPHOGENIC 1, ATCOP1, CONSTITUTIVE PHOTOMORPHOGENIC 1, COP1, DEETIOLATED MUTANT 340, DET340, EMB168, EMBRYO DEFECTIVE 168, FUS1, FUSCA 1 TAIR L
AT2G34140 TAIR L
AT2G46670* TAIR L
AT2G46790 APRR9, ARABIDOPSIS PSEUDO-RESPONSE REGULATOR 9, PRR9, PSEUDO-RESPONSE REGULATOR 9, TL1, TOC1-LIKE PROTEIN 1 TAIR L
AT2G46830 ATCCA1, CCA1, CIRCADIAN CLOCK ASSOCIATED 1 TAIR L
AT3G02380 ATCOL2, B-BOX DOMAIN PROTEIN 3, BBX3, COL2, CONSTANS-LIKE 2 TAIR FPI, L
AT3G07650 B-BOX DOMAIN PROTEIN 7, BBX7, COL9, CONSTANS-LIKE 9 TAIR L
AT3G21320 TAIR L
AT3G25730 EDF3, ETHYLENE RESPONSE DNA BINDING FACTOR 3 TAIR L
AT3G33520 ACTIN-RELATED PROTEIN 6, ARP6, ATARP6, EARLY IN SHORT DAYS 1, ESD1, SUF3, SUPPRESSOR OF FRI 3 TAIR Am, V
AT3G47500 CDF3, CYCLING DOF FACTOR 3 TAIR L
AT4G08920 ATCRY1, BLU1, BLUE LIGHT UNINHIBITED 1, CRY1, CRYPTOCHROME 1, ELONGATED HYPOCOTYL 4, HY4, OOP2, OUT OF PHASE 2 TAIR L Grape
AT4G11880 AGAMOUS-LIKE 14, AGL14 TAIR V
AT4G22950 "AGAMOUS-LIKE 19, AGL19, GL19
" TAIR V
AT4G24540 AGAMOUS-LIKE 24, AGL24 TAIR V
AT4G34530 CIB1, CRYPTOCHROME-INTERACTING BASIC-HELIX-LOOP-HELIX 1 TAIR L
AT5G08230* TAIR V
AT5G08330 CCA1 HIKING EXPEDITION, CHE, TRANSCRIPTION FACTOR TCP21, TCP21 UniProtKB L
AT5G15840 B-BOX DOMAIN PROTEIN 1, BBX1, CO, CONSTANS, FG TAIR FPI, L
AT5G15850 ATCOL1, B-BOX DOMAIN PROTEIN 2, BBX2, COL1, CONSTANS-LIKE 1 TAIR FPI, L
AT5G23280* TAIR L
AT5G24470 APRR5, PRR5, PSEUDO-RESPONSE REGULATOR 5 TAIR L
AT5G24930 ATCOL4, B-BOX DOMAIN PROTEIN 5, BBX5, COL4, CONSTANS-LIKE 4 TAIR L
AT5G37055 ATSWC6, SEF, SERRATED LEAVES AND EARLY FLOWERING TAIR V
AT5G39660 CDF2, CYCLING DOF FACTOR 2 TAIR L
AT5G48250* B-BOX DOMAIN PROTEIN 8, BBX8 TAIR L
AT5G57660 ATCOL5, B-BOX DOMAIN PROTEIN 6, BBX6, COL5, CONSTANS-LIKE 5 TAIR L
AT5G59570* BOA, BROTHER OF LUX ARRHYTHMO TAIR L
AT5G60100 APRR3, PRR3, PSEUDO-RESPONSE REGULATOR 3 TAIR L
AT5G62430 CDF1, CYCLING DOF FACTOR 1 TAIR L
AT5G65050 AGAMOUS-LIKE 31, AGL31, MADS AFFECTING FLOWERING 2, MAF2 TAIR Am, FPI, V
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
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