PlantTFDB - Plant Transcription Factor Database @ CBI, PKU

PlantRegMap/PlantTFDB v5.0

Plant Transcription Factor Database

Transcription Factor Information

Basic Information | Signature Domain | Sequence |

Basic Information? help Back to Top

TF ID

AT4G16780.1

Common Name

ATHB2, ATHB-2, dl4415w, FCAALL.101, HAT4, HB-2

Organism

Arabidopsis thaliana

Taxonomic ID

3702

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis

Family

HD-ZIP

Protein Properties

Length: 284aa MW: 31852.5 Da PI: 9.0241

Description

homeobox protein 2

Gene Model

Gene Model ID	Type	Source	Coding Sequence
AT4G16780.1	genome	TAIR	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	Homeobox	61	1.9e-19	128	182	2	56
T--SS--HHHHHHHHHHHHHSSS--HHHHHHHHHHCTS-HHHHHHHHHHHHHHHH CS Homeobox 2 rkRttftkeqleeLeelFeknrypsaeereeLAkklgLterqVkvWFqNrRakek 56 rk+ +++k+q +Lee F+ +++++ ++++ LAk+lgL rqV vWFqNrRa+ k AT4G16780.1 128 RKKLRLSKDQSAILEETFKDHSTLNPKQKQALAKQLGLRARQVEVWFQNRRARTK 182 788899***********************************************98 PP
2	HD-ZIP_I/II	124.3	5.5e-40	128	217	1	91
HD-ZIP_I/II 1 ekkrrlskeqvklLEesFeeeekLeperKvelareLglqprqvavWFqnrRARtktkqlEkdyeaLkraydalkeenerLekeveeLreel 91 +kk+rlsk+q+++LEe+F+ +++L+p++K++la++Lgl++rqv+vWFqnrRARtk+kq+E+d+e+L+r++++l+een+rL+kev+eLr +l AT4G16780.1 128 RKKLRLSKDQSAILEETFKDHSTLNPKQKQALAKQLGLRARQVEVWFQNRRARTKLKQTEVDCEFLRRCCENLTEENRRLQKEVTELR-AL 217 69*************************************************************************************9.55 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Pfam	PF04618	5.0E-30	2	107	IPR006712	HD-ZIP protein, N-terminal
Gene3D	G3DSA:1.10.10.60	4.2E-18	115	178	IPR009057	Homeodomain-like
PROSITE profile	PS50071	17.427	124	184	IPR001356	Homeobox domain
SuperFamily	SSF46689	4.28E-18	126	193	IPR009057	Homeodomain-like
SMART	SM00389	5.2E-16	126	188	IPR001356	Homeobox domain
Pfam	PF00046	7.7E-17	128	182	IPR001356	Homeobox domain
CDD	cd00086	5.70E-15	128	185	No hit	No description
PRINTS	PR00031	1.1E-5	155	164	IPR000047	Helix-turn-helix motif
PROSITE pattern	PS00027	0	159	182	IPR017970	Homeobox, conserved site
PRINTS	PR00031	1.1E-5	164	180	IPR000047	Helix-turn-helix motif
Pfam	PF02183	8.3E-11	184	218	IPR003106	Leucine zipper, homeobox-associated
SMART	SM00340	3.8E-26	184	227	IPR003106	Leucine zipper, homeobox-associated

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0008283	Biological Process	cell proliferation
GO:0009585	Biological Process	red, far-red light phototransduction
GO:0009641	Biological Process	shade avoidance
GO:0009733	Biological Process	response to auxin
GO:0009735	Biological Process	response to cytokinin
GO:0009826	Biological Process	unidimensional cell growth
GO:0010016	Biological Process	shoot system morphogenesis
GO:0010017	Biological Process	red or far-red light signaling pathway
GO:0010218	Biological Process	response to far red light
GO:0045892	Biological Process	negative regulation of transcription, DNA-templated
GO:0048364	Biological Process	root development
GO:0005634	Cellular Component	nucleus
GO:0003700	Molecular Function	transcription factor activity, sequence-specific DNA binding
GO:0042803	Molecular Function	protein homodimerization activity
GO:0043565	Molecular Function	sequence-specific DNA binding

Plant Ontology ? help Back to Top
PO Term	PO Category	PO Description
PO:0000013	anatomy	cauline leaf
PO:0000230	anatomy	inflorescence meristem
PO:0000293	anatomy	guard cell
PO:0009005	anatomy	root
PO:0009025	anatomy	vascular leaf
PO:0009030	anatomy	carpel
PO:0009046	anatomy	flower
PO:0009047	anatomy	stem
PO:0020137	anatomy	leaf apex
PO:0025022	anatomy	collective leaf structure
PO:0001054	developmental stage	vascular leaf senescent stage
PO:0007095	developmental stage	LP.08 eight leaves visible stage
PO:0007098	developmental stage	LP.02 two leaves visible stage
PO:0007103	developmental stage	LP.10 ten leaves visible stage
PO:0007115	developmental stage	LP.04 four leaves visible stage
PO:0007123	developmental stage	LP.06 six leaves visible stage
PO:0007611	developmental stage	petal differentiation and expansion stage

Sequence ? help Back to Top
Protein Sequence Length: 284 aa Download sequence Send to blast
MMFEKDDLGL SLGLNFPKKQ INLKSNPSVS VTPSSSSFGL FRRSSWNESF TSSVPNSDSS 60 QKETRTFIRG IDVNRPPSTA EYGDEDAGVS SPNSTVSSST GKRSEREEDT DPQGSRGISD 120 DEDGDNSRKK LRLSKDQSAI LEETFKDHST LNPKQKQALA KQLGLRARQV EVWFQNRRAR 180 TKLKQTEVDC EFLRRCCENL TEENRRLQKE VTELRALKLS PQFYMHMSPP TTLTMCPSCE 240 HVSVPPPQPQ AATSAHHRSL PVNAWAPATR ISHGLTFDAL RPRS

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	126	132	SRKKLRL
2	176	184	RRARTKLKQ

Expression -- Microarray ? help Back to Top
Source	ID	E-value
GEO	166751	0.0
Genevisible	245276_at	0.0
Expression Atlas	AT4G16780	-
AtGenExpress	AT4G16780	-
ATTED-II	AT4G16780	-

Expression -- Description ? help Back to Top
Source	Description
Uniprot	TISSUE SPECIFICITY: Predominantly expressed in leaves and stems. {ECO:0000269\|PubMed:8106086}.

Functional Description ? help Back to Top
Source	Description
TAIR	Encodes a homeodomain-leucine zipper protein that is rapidly and strongly induced by changes in the ratio of red to far-red light. It is also involved in cell expansion and cell proliferation and in the response to auxin.
UniProt	Probable transcription factor involved in the negative regulation of cell elongation and specific cell proliferation processes such as lateral root formation and secondary growth of the vascular system. Acts as mediator of the red/far-red light effects on leaf cell expansion in the shading response. Binds to the DNA sequence 5'-CAAT[GC]ATTG-3'. Negatively regulates its own expression. {ECO:0000269\|PubMed:10477292, ECO:0000269\|PubMed:11260495, ECO:0000269\|PubMed:8449400}.

Function -- GeneRIF ? help Back to Top
Arabidopsis thaliana homeobox protein2 (ATHB2)together with auxin-inducible IAA29, is diurnally expressed with a peak at dawn under the control of PHYTOCHROME-INTERACTING FACTOR4 (PIF4) and PIF5. [AtHB2] [PMID: 21666227] a genetic system consisting of HD-Zip II and HD-Zip III genes (ATHB2, ATHB4) cooperates in establishing bilateral symmetry and patterning along the adaxial-abaxial axis in the embryo as well as in controlling SAM activity [PMID: 23578926]

Cis-element ? help Back to Top
Source	Link
PlantRegMap	AT4G16780.1

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: Rapidly and strongly induced by lowering the ratio of red to far-red light. {ECO:0000269\|PubMed:8106086}.

Regulation -- PlantRegMap ? help Back to Top
Source	Upstream Regulator	Target Gene
PlantRegMap	Retrieve	Retrieve

Regulation -- ATRM (Manually Curated Upstream Regulators) ? help Back to Top
Source	Upstream Regulator (A: Activate/R: Repress)
ATRM	AT1G02340 (R)

Regulation -- ATRM (Manually Curated Target Genes) ? help Back to Top
Source	Target Gene (A: Activate/R: Repress)
ATRM	AT1G02340(A)

Regulation -- Hormone ? help Back to Top
Source	Hormone
AHD	cytokinin

Interaction ? help Back to Top
Source	Intact With
BioGRID	AT4G16780, AT4G37790, AT5G06710, AT5G47370
IntAct	Search Q05466

Phenotype -- Mutation ? help Back to Top
Source	ID
T-DNA Express	AT4G16780

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AF375453	0.0	AF375453.1 Arabidopsis thaliana AT4g16780/dl4415w mRNA, complete cds.
GenBank	AY081747	0.0	AY081747.1 Arabidopsis thaliana AT4g16780/dl4415w mRNA, complete cds.
GenBank	X68145	0.0	X68145.1 A.thaliana Athb-2 mRNA.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	NP_193411.1	0.0	homeobox protein 2
Swissprot	Q05466	0.0	HAT4_ARATH; Homeobox-leucine zipper protein HAT4
TrEMBL	A0A178V3W8	0.0	A0A178V3W8_ARATH; HB-2
STRING	AT4G16780.1	0.0	(Arabidopsis thaliana)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM1563	26	90
Representative plant	OGRP196	16	156

Link Out ? help Back to Top
Phytozome	AT4G16780.1
Entrez Gene	827384
iHOP	AT4G16780
wikigenes	AT4G16780

Publications ? help Back to Top
Steindler C, et al. Shade avoidance responses are mediated by the ATHB-2 HD-zip protein, a negative regulator of gene expression. Development, 1999. 126(19): p. 4235-45 [PMID:10477292] Riechmann JL, et al. Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes. Science, 2000. 290(5499): p. 2105-10 [PMID:11118137] Ohgishi M,Oka A,Morelli G,Ruberti I,Aoyama T Negative autoregulation of the Arabidopsis homeobox gene ATHB-2. Plant J., 2001. 25(4): p. 389-98 [PMID:11260495] Morelli G,Ruberti I Light and shade in the photocontrol of Arabidopsis growth. Trends Plant Sci., 2002. 7(9): p. 399-404 [PMID:12234731] Franklin KA, et al. Phytochromes B, D, and E act redundantly to control multiple physiological responses in Arabidopsis. Plant Physiol., 2003. 131(3): p. 1340-6 [PMID:12644683] Wright SI,Lauga B,Charlesworth D Subdivision and haplotype structure in natural populations of Arabidopsis lyrata. Mol. Ecol., 2003. 12(5): p. 1247-63 [PMID:12694288] Schena M,Davis RW HD-Zip proteins: members of an Arabidopsis homeodomain protein superfamily. Proc. Natl. Acad. Sci. U.S.A., 1992. 89(9): p. 3894-8 [PMID:1349174] Yamada K, et al. Empirical analysis of transcriptional activity in the Arabidopsis genome. Science, 2003. 302(5646): p. 842-6 [PMID:14593172] Jiao Y, et al. A genome-wide analysis of blue-light regulation of Arabidopsis transcription factor gene expression during seedling development. Plant Physiol., 2003. 133(4): p. 1480-93 [PMID:14605227] Koroleva OA,Tomlinson ML,Leader D,Shaw P,Doonan JH High-throughput protein localization in Arabidopsis using Agrobacterium-mediated transient expression of GFP-ORF fusions. Plant J., 2005. 41(1): p. 162-74 [PMID:15610358] Henriksson E, et al. Homeodomain leucine zipper class I genes in Arabidopsis. Expression patterns and phylogenetic relationships. Plant Physiol., 2005. 139(1): p. 509-18 [PMID:16055682] Brenner WG,Romanov GA,K Immediate-early and delayed cytokinin response genes of Arabidopsis thaliana identified by genome-wide expression profiling reveal novel cytokinin-sensitive processes and suggest cytokinin action through transcriptional cascades. Plant J., 2005. 44(2): p. 314-33 [PMID:16212609] Sessa G, et al. A dynamic balance between gene activation and repression regulates the shade avoidance response in Arabidopsis. Genes Dev., 2005. 19(23): p. 2811-5 [PMID:16322556] Roig-Villanova I,Bou J,Sorin C,Devlin PF,Martínez-García JF Identification of primary target genes of phytochrome signaling. Early transcriptional control during shade avoidance responses in Arabidopsis. Plant Physiol., 2006. 141(1): p. 85-96 [PMID:16565297] Ruberti I,Sessa G,Lucchetti S,Morelli G A novel class of plant proteins containing a homeodomain with a closely linked leucine zipper motif. EMBO J., 1991. 10(7): p. 1787-91 [PMID:1675603] Brock MT,Tiffin P,Weinig C Sequence diversity and haplotype associations with phenotypic responses to crowding: GIGANTEA affects fruit set in Arabidopsis thaliana. Mol. Ecol., 2007. 16(14): p. 3050-62 [PMID:17614917] Franklin KA,Whitelam GC Light-quality regulation of freezing tolerance in Arabidopsis thaliana. Nat. Genet., 2007. 39(11): p. 1410-3 [PMID:17965713] Ciarbelli AR, et al. The Arabidopsis homeodomain-leucine zipper II gene family: diversity and redundancy. Plant Mol. Biol., 2008. 68(4-5): p. 465-78 [PMID:18758690] Finlayson SA,Krishnareddy SR,Kebrom TH,Casal JJ Phytochrome regulation of branching in Arabidopsis. Plant Physiol., 2010. 152(4): p. 1914-27 [PMID:20154098] K Ectopic expression of different cytokinin-regulated transcription factor genes of Arabidopsis thaliana alters plant growth and development. J. Plant Physiol., 2011. 168(12): p. 1320-7 [PMID:21453984] Kunihiro A, et al. Phytochrome-interacting factor 4 and 5 (PIF4 and PIF5) activate the homeobox ATHB2 and auxin-inducible IAA29 genes in the coincidence mechanism underlying photoperiodic control of plant growth of Arabidopsis thaliana. Plant Cell Physiol., 2011. 52(8): p. 1315-29 [PMID:21666227] Arabidopsis Interactome Mapping Consortium Evidence for network evolution in an Arabidopsis interactome map. Science, 2011. 333(6042): p. 601-7 [PMID:21798944] Tiwari SB, et al. The EDLL motif: a potent plant transcriptional activation domain from AP2/ERF transcription factors. Plant J., 2012. 70(5): p. 855-65 [PMID:22321262] Bou-Torrent J, et al. ATHB4 and HAT3, two class II HD-ZIP transcription factors, control leaf development in Arabidopsis. Plant Signal Behav, 2012. 7(11): p. 1382-7 [PMID:22918502] Turchi L, et al. Arabidopsis HD-Zip II transcription factors control apical embryo development and meristem function. Development, 2013. 140(10): p. 2118-29 [PMID:23578926] Carabelli M,Turchi L,Ruzza V,Morelli G,Ruberti I Homeodomain-Leucine Zipper II family of transcription factors to the limelight: central regulators of plant development. Plant Signal Behav, 2014. [PMID:23838958] Ding Y, et al. Four distinct types of dehydration stress memory genes in Arabidopsis thaliana. BMC Plant Biol., 2013. 13: p. 229 [PMID:24377444] Jung CG, et al. Molecular characterization of the cold- and heat-induced Arabidopsis PXL1 gene and its potential role in transduction pathways under temperature fluctuations. J. Plant Physiol., 2015. 176: p. 138-46 [PMID:25602612] Jin J, et al. An Arabidopsis Transcriptional Regulatory Map Reveals Distinct Functional and Evolutionary Features of Novel Transcription Factors. Mol. Biol. Evol., 2015. 32(7): p. 1767-73 [PMID:25750178] Francisco M, et al. Genome Wide Association Mapping in Arabidopsis thaliana Identifies Novel Genes Involved in Linking Allyl Glucosinolate to Altered Biomass and Defense. Front Plant Sci, 2016. 7: p. 1010 [PMID:27462337] Müller-Moulé P, et al. YUCCA auxin biosynthetic genes are required for Arabidopsis shade avoidance. PeerJ, 2016. 4: p. e2574 [PMID:27761349] Ivarson E, et al. Effects of Overexpression of WRI1 and Hemoglobin Genes on the Seed Oil Content of Lepidium campestre. Front Plant Sci, 2016. 7: p. 2032 [PMID:28119714] Kasulin L, et al. A single haplotype hyposensitive to light and requiring strong vernalization dominates Arabidopsis thaliana populations in Patagonia, Argentina. Mol. Ecol., 2017. 26(13): p. 3389-3404 [PMID:28316114] Singh M,Gupta A,Singh D,Khurana JP,Laxmi A Arabidopsis RSS1 Mediates Cross-Talk Between Glucose and Light Signaling During Hypocotyl Elongation Growth. Sci Rep, 2017. 7(1): p. 16101 [PMID:29170398] Schena M,Davis RW Structure of homeobox-leucine zipper genes suggests a model for the evolution of gene families. Proc. Natl. Acad. Sci. U.S.A., 1994. 91(18): p. 8393-7 [PMID:7915839] S Expression patterns of novel genes encoding homeodomain leucine-zipper proteins in Arabidopsis thaliana. Plant Mol. Biol., 1994. 26(1): p. 145-54 [PMID:7948864] Carabelli M,Sessa G,Baima S,Morelli G,Ruberti I The Arabidopsis Athb-2 and -4 genes are strongly induced by far-red-rich light. Plant J., 1993. 4(3): p. 469-79 [PMID:8106086] Sessa G,Morelli G,Ruberti I The Athb-1 and -2 HD-Zip domains homodimerize forming complexes of different DNA binding specificities. EMBO J., 1993. 12(9): p. 3507-17 [PMID:8253077] Schena M,Lloyd AM,Davis RW The HAT4 gene of Arabidopsis encodes a developmental regulator. Genes Dev., 1993. 7(3): p. 367-79 [PMID:8449400] Di Cristina M, et al. The Arabidopsis Athb-10 (GLABRA2) is an HD-Zip protein required for regulation of root hair development. Plant J., 1996. 10(3): p. 393-402 [PMID:8811855] Sessa G,Morelli G,Ruberti I DNA-binding specificity of the homeodomain-leucine zipper domain. J. Mol. Biol., 1997. 274(3): p. 303-9 [PMID:9405140] Sessa G,Steindler C,Morelli G,Ruberti I The Arabidopsis Athb-8, -9 and -14 genes are members of a small gene family coding for highly related HD-ZIP proteins. Plant Mol. Biol., 1998. 38(4): p. 609-22 [PMID:9747806]