Difference between revisions of "RiceWiki:GeneFamilies"

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* http://rice.plantbiology.msu.edu/annotation_community_families.shtml
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The curation of '''Rice Gene Families''' for both '''''Japonica''''' and '''''Indica''''' group is one of the objectives of RiceWiki, we cordially invite you to make it with us! You can either enrich the information of existed gene family pages, or create a new gene family page. We are also very glad if you can identify any new memebers of specific gene family or delete the redundant ones.
 +
=='''Gene Families under Curation'''==
 +
 
 +
{|class="wikitable  sortable" style="width:90%;text-align:center" 
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|-
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!Gene Family
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!Number
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!Pfam & InterPro
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!Last update
 +
|-
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|[[AP2/ERF|'''AP2/ERF''']]
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|''Japnoica'' ('''111''') '''&'''  ''Indica'' ('''156''')
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|'''Pfam: [http://pfam.janelia.org/family/PF00847 PF00847]'''    &    '''InterPro: [http://www.ebi.ac.uk/interpro/entry/IPR001471 IPR001471]'''
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|2013-07-13
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|-
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|[[ARF|'''ARF''']] 
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|''Japnoica'' ('''24''') '''&'''  ''Indica'' ('''24''')
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|'''Pfam: [http://pfam.janelia.org/family/PF06507 PF06507]'''    &    '''InterPro: [http://www.ebi.ac.uk/interpro/entry/IPR010525 IPR010525]'''
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|2013-07-21
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|-
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|[[BHLH|'''bHLH''']]
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|''Japnoica'' ('''101''') '''&'''  ''Indica'' ('''107''')
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|'''Pfam: [http://pfam.janelia.org/family/PF00010 PF00010]'''  &  '''InterPro: [http://www.ebi.ac.uk/interpro/entry/IPR011598 IPR011598]'''
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|2013-07-21
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|-
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|[[BZIP|'''bZIP''']]
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|''Japnoica'' ('''72''') '''&'''  ''Indica'' ('''84''')
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|'''Pfam: [http://pfam.janelia.org/family/PF00170 PF00170]'''  &  '''InterPro:[http://www.ebi.ac.uk/interpro/entry/IPR004827 IPR004827]'''
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|2013-06-10
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|-
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|[[Sucrose synthase|'''Sucrose synthase''']]
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|''Japnoica'' ('''9''') '''&'''  ''Indica'' ('''13''')
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|'''Pfam: [http://pfam.janelia.org/family/PF00862 PF00862]'''  &  '''InterPro: [http://www.ebi.ac.uk/interpro/entry/IPR000368 IPR000368]'''
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|2013-07-17
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|-
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|[[HSF|'''HSF''']]
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|''Japnoica'' ('''23''') '''&'''  ''Indica'' ('''28''')
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|'''Pfam: [http://pfam.janelia.org/family/PF00447 PF00447]'''  &  '''InterPro: [http://www.ebi.ac.uk/interpro/entry/IPR000232 IPR000232]'''
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|2013-07-12
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|-
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|[[MADS|'''MADS-box''']]
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|''Japnoica'' ('''42''') '''&'''  ''Indica'' ('''67''')
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||'''Pfam: [http://pfam.janelia.org/family/PF00319 PF00319]'''  &  '''InterPro: [http://www.ebi.ac.uk/interpro/entry/IPR002100 IPR002100]'''
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|2012-05-14
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|-
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|[[MYB|'''MYB''']]
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|''Japnoica'' ('''195''') '''&'''  ''Indica'' ('''264''')
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||'''Pfam: [http://pfam.janelia.org/family/PF00249 PF00249]'''  &  '''InterPro: [http://www.ebi.ac.uk/interpro/entry/IPR001005 IPR001005]'''
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|2013-07-16
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|-
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|[[NAC|'''NAC''']]
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|''Japnoica'' ('''91''') '''&'''  ''Indica'' ('''124''')
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||'''Pfam: [http://pfam.janelia.org/family/PF02365 PF02365]'''  &  '''InterPro: [http://www.ebi.ac.uk/interpro/entry/IPR003441 IPR003441]'''
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|2013-07-15
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|-
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|[[SBP|'''SBP''']]
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|''Japnoica'' ('''17''') '''&'''  ''Indica'' ('''20''')
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||'''Pfam: [http://pfam.janelia.org/family/PF03110 PF03110]'''  &  '''InterPro: [http://www.ebi.ac.uk/interpro/entry/IPR004333 IPR004333]'''
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|2013-07-21
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|-
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|[[WRKY|'''WRKY''']]
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|''Japnoica'' ('''79''') '''&'''  ''Indica'' ('''109''')
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||'''Pfam: [http://pfam.janelia.org/family/PF03106 PF03106]'''  &  '''InterPro: [http://www.ebi.ac.uk/interpro/entry/IPR003657 IPR003657]'''
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|2013-06-12
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|}
 +
 
 +
=='''Gene Families to Be Curated'''==
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{| style="background:#A1A3A6; width:90%;"
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|-style="background:white; color:black" align="center"
 +
!
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'''ABI3/VP1'''
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||
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'''Alfin'''
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||     
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'''ARID'''
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|| 
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'''Ascorbate Peroxidase'''                         
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|-style="background:white; color:black" align="center"
 +
!
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'''AUX/IAA'''
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||
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'''BBR/BPC'''
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||
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'''AS2'''
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||
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'''ATP-dependent metalloprotease'''
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|-style="background:white; color:black" align="center"
 +
! 
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'''BTB'''
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||
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'''C2C2-CO-like'''
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||
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'''BES1'''
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||
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'''C2C2-Dof'''
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|-style="background:white; color:black" align="center"
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!
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'''Calmodulin'''
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||
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'''Receptor-Like Kinase'''
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||
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'''Phytochelatins synthetase'''
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||
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'''Yellow stripe-like'''
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|-style="background:white; color:black" align="center"
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! 
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'''Core Replication Machinery'''
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||
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'''C2H2 zinc finger'''
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||
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'''C3H'''
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||
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'''Conserved peptide uORF'''
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|-style="background:white; color:black" align="center"
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!
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'''Cellulose Synthase'''
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||
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'''Endo-Beta-Mannanases'''
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||
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'''FHA'''
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||
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'''GRAS'''
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|-style="background:white; color:black" align="center"
 +
!
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'''FXYD'''
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||
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'''TRPM'''
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||
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'''TRP ion channel'''
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||
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'''Glutaredoxin'''
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|-style="background:white; color:black" align="center"
 +
!
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'''Glycosyl Hydrolase Family 1'''
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||
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'''Indole-3-acetic-acid synthetase'''
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||
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'''GRF'''
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||
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'''HKT transporters'''
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|-style="background:white; color:black" align="center"
 +
!
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'''Type-A Response Regulators'''
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||
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'''JUMONJI'''
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||
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'''MAPKs'''
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||
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'''PLATZ'''
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|-style="background:white; color:black" align="center"
 +
!
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'''TUB'''
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||
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'''Trihelix''' 
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||
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'''TCP'''
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||
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'''TAZ'''
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|-style="background:white; color:black" align="center"
 +
!
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'''ZF-HD'''
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||
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'''ZIM'''
 +
||
 +
 
 +
||
 +
 
 +
|}

Latest revision as of 17:58, 21 July 2013

The curation of Rice Gene Families for both Japonica and Indica group is one of the objectives of RiceWiki, we cordially invite you to make it with us! You can either enrich the information of existed gene family pages, or create a new gene family page. We are also very glad if you can identify any new memebers of specific gene family or delete the redundant ones.

Gene Families under Curation

Gene Family Number Pfam & InterPro Last update
AP2/ERF Japnoica (111) & Indica (156) Pfam: PF00847 & InterPro: IPR001471 2013-07-13
ARF Japnoica (24) & Indica (24) Pfam: PF06507 & InterPro: IPR010525 2013-07-21
bHLH Japnoica (101) & Indica (107) Pfam: PF00010 & InterPro: IPR011598 2013-07-21
bZIP Japnoica (72) & Indica (84) Pfam: PF00170 & InterPro:IPR004827 2013-06-10
Sucrose synthase Japnoica (9) & Indica (13) Pfam: PF00862 & InterPro: IPR000368 2013-07-17
HSF Japnoica (23) & Indica (28) Pfam: PF00447 & InterPro: IPR000232 2013-07-12
MADS-box Japnoica (42) & Indica (67) Pfam: PF00319 & InterPro: IPR002100 2012-05-14
MYB Japnoica (195) & Indica (264) Pfam: PF00249 & InterPro: IPR001005 2013-07-16
NAC Japnoica (91) & Indica (124) Pfam: PF02365 & InterPro: IPR003441 2013-07-15
SBP Japnoica (17) & Indica (20) Pfam: PF03110 & InterPro: IPR004333 2013-07-21
WRKY Japnoica (79) & Indica (109) Pfam: PF03106 & InterPro: IPR003657 2013-06-12

Gene Families to Be Curated

ABI3/VP1

Alfin

ARID

Ascorbate Peroxidase

AUX/IAA

BBR/BPC

AS2

ATP-dependent metalloprotease

BTB

C2C2-CO-like

BES1

C2C2-Dof

Calmodulin

Receptor-Like Kinase

Phytochelatins synthetase

Yellow stripe-like

Core Replication Machinery

C2H2 zinc finger

C3H

Conserved peptide uORF

Cellulose Synthase

Endo-Beta-Mannanases

FHA

GRAS

FXYD

TRPM

TRP ion channel

Glutaredoxin

Glycosyl Hydrolase Family 1

Indole-3-acetic-acid synthetase

GRF

HKT transporters

Type-A Response Regulators

JUMONJI

MAPKs

PLATZ

TUB

Trihelix

TCP

TAZ

ZF-HD

ZIM

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