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Table 1 Classification of putative transcription factors of Medicago into families and sub-families

From: A community resource for high-throughput quantitative RT-PCR analysis of transcription factor gene expression in Medicago truncatula

TF Family No. of Genes Characteristic Domain (InterPro No.) Domain Function Domain Description
MYB/HD-like 76 IPR001005, IPR009057 D Myb, DNA-binding; homeodomain like
MYB 58 IPR001005 D Myb, DNA-binding
C2H2 (Zn) 64 IPR007087 NA Zn-finger, C2H2 type
AP2/EREBP 55 IPR001471 D Pathogenesis-related transcriptional factor and ethylene response factor
BHLH 49 IPR001092 D Basic helix-loop-helix dimerisation region bHLH
HD-like 50 IPR009057 D Homeodomain like
HD family   IPR001356 D Homeobox
HD 25    
HD-ZIP 5 IPR006712 P HD-ZIP protein, N terminus
HD-PHD finger 2 IPR001965 P Zn-finger like, PHD-finger
MADS 48 IPR002100 D TF, MADS-box
BZIP 41 IPR004827 D Basic Leu zipper (bZIP) TF
PHD 34 IPR001965 P Zn-finger like, PHD-finger
WRKY family   IPR003657 D DNA-binding WRKY
WRKY 29    
LLR WRKY 1 IPR001611   Leu-rich repeat
ABI3/VP1 29 IPR003340 D TF B3
NAC 29 IPR003441 D No apical meristem (NAM) protein
C3H-type1(Zn) 27 IPR000571 D Zn-finger, C-x8-C-x5-C-x3-H type
ARF 23 IPR003340, IPR010525, IPR011525 D  
JUMONJI 20 IPR003347 D TF jumonji, jmjC
GRAS 19 IPR005202 P GRAS TF
HMG 15 IPR000637 D HMG-I and HMG-Y, DNA binding
AS2 14 IPR004883 P Lateral organ boundaries
C2C2 (Zn)     
Dof 13 IPR003851 D Zn-finger, Dof type
GATA 7 IPR000679 D Zn-finger, GATA type
CO-like 6 IPR000315 D Zn-finger, B-box
YABBY 5 IPR006780 D YABBY protein
CCAAT-HAP3 type 12 IPR003958 D TF CBF/NF-Y/archaeal histone
GRF 8 IPR010666 D Zn-finger, GRF type
SBP 8 IPR004333 D SBP
EIL 7 IPR006957 D Ethylene insensitive 3
LIM 7 IPR001781 P Zn-binding protein, LIM
SNF2 6 IPR000330 D SNF2 family N-terminal domain
E2F/DP 5 IPR003316 D TF E2F/dimerisation partner (TDP)
TCP 5 IPR005333 D TCP TF
FHA 5 IPR000253 D Forkhead-associated
ARID 4 IPR001606 D AT-rich interaction region
HSF 4 IPR000232 D Heat shock factor (HSF)-type, DNA binding
AUX/IAA 3 IPR003311 D AUX/IAA protein
SRS 3 IPR006510 D Zn-finger, LRP1 type
TUB 3 IPR000007 D Tubby
ZIM 3 IPR010399 D ZIM
DDT 3 IPR004022 D DDT
ZF-HD 2 IPR006455 D Homeobox domain, ZF-HD class
MBF1 2 IPR001387 D Helix-turn-helix type 3
S1Fa-like 2 IPR006779 D DNA binding protein S1FA
CAMTA 2 IPR005559 D CG-1
LFY 1 IPR002910 D Floricaula/leafy protein
Nin-like 1 IPR003035 D Plant regulator RWP-RK
TAZ 1 IPR000197 P Zn-finger, TAZ-type
Potentially novel plant TFs and transcriptional regulators
CCHC (Zn) 112 IPR001878 NA Zn-finger, CCHC-type
RR 16 IPR001789, IPR011006 RD Response regulator receiver
DHHC (Zn) 14 IPR001594 D or P Zn-finger, DHHC-type
HTH     
FIS 11 IPR002197 D Helix-turn-helix, Fis-type
AraC 2 IPR000005 D Helix-turn-helix, AraC type
BTB/POZ 7 IPR000210 P BTB
TTF-type (Zn) 6 IPR006580 D Zn-finger, TTF-type
BD 6 IPR001487 P Bromodomain
Lambda-DB 3 IPR010982 D Lambda_DNA_bd
TrpR 3 IPR010921 D Trp repressor/replication initiator
TPR 3 IPR001440 P Tetratricopeptide TPR_1
KRAB-box 2 IPR001909 P KRAB box
NRs 2 IPR008946 LBD Steroid nuclear receptor, ligand binding
R3H 2 IPR001374 NA Single-stranded nucleic acid binding R3H
YEATS 2 IPR005033 TA YEATS
U1-type (Zn) 2 IPR003604 NA Zn-finger, U1-type
A20-like 2 IPR002653 P Zn-finger, A20-type
Euk_TF 1 IPR008917 D Euk_TF, DNA binding
NGN 1 IPR006645 D NGN
p53-like 1 IPR008967 D p53-like TF, DNA binding
SSB protein 1 IPR011344 D Single-strand binding protein
ssDB TR 1 IPR009044 D Single-strand DNA binding transcriptional regulator
TCoAp15 1 IPR003173 D Transcriptional coactivator p15
BED-type (Zn) 1 IPR003656 D Zn-finger, BED-type predicted
TCoA 1 IPR009255 TA Transcriptional coactivation
Tc/PD 1 IPR001533 TA Transcriptional coactivator
  1. IMGAG (International Medicago Gene Annotation Group)-proteins were classified as putative TFs if they contained characteristic DNA-binding or other characteristic TF domains and if annotations of matching proteins obtained by BLAST searches were consistent with such a classification. TF families previously identified in plants are presented in the first part of the table while potentially novel plant TF families, which were identified by the presence of domains associated with TFs and other transcriptional regulators outside the plant kingdom, are presented in the latter part of the table. D = DNA binding domain; P = protein-protein interaction domain; NA = nucleic acid (DNA and RNA) binding domain; RD = receiver domain; LBD = ligand binding; transcriptional co-activator. Plant-specific TF families and sub-families are indicated in bold (according to [12])