PlantTFDB - Plant Transcription Factor Database @ CBI, PKU

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Malvales; Malvaceae; Malvoideae; Gossypium

Family

HD-ZIP

Protein Properties

Length: 302aa MW: 33836.8 Da PI: 7.8555

Description

HD-ZIP family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Gorai.008G233200.1	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	Homeobox	58.6	1e-18	137	191	2	56
T--SS--HHHHHHHHHHHHHSSS--HHHHHHHHHHCTS-HHHHHHHHHHHHHHHH CS Homeobox 2 rkRttftkeqleeLeelFeknrypsaeereeLAkklgLterqVkvWFqNrRakek 56 rk+ +++k+q +Lee F+++++++ +++ LAk+lgL rqV vWFqNrRa+ k Gorai.008G233200.1 137 RKKLRLSKDQSAILEENFKEHNTLNPKQKLALAKQLGLRPRQVEVWFQNRRARTK 191 788899***********************************************98 PP
2	HD-ZIP_I/II	128.5	2.9e-41	137	226	1	91
HD-ZIP_I/II 1 ekkrrlskeqvklLEesFeeeekLeperKvelareLglqprqvavWFqnrRARtktkqlEkdyeaLkraydalkeenerLekeveeLreel 91 +kk+rlsk+q+++LEe+F+e+++L+p++K +la++Lgl+prqv+vWFqnrRARtk+kq+E+d+e+Lkr++++l+een+rL+kev+eLr +l Gorai.008G233200.1 137 RKKLRLSKDQSAILEENFKEHNTLNPKQKLALAKQLGLRPRQVEVWFQNRRARTKLKQTEVDCEFLKRCCENLTEENRRLQKEVQELR-AL 226 69*************************************************************************************9.55 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Pfam	PF04618	1.8E-29	1	111	IPR006712	HD-ZIP protein, N-terminal
Gene3D	G3DSA:1.10.10.60	5.4E-18	119	194	IPR009057	Homeodomain-like
SuperFamily	SSF46689	1.13E-18	126	194	IPR009057	Homeodomain-like
PROSITE profile	PS50071	17.329	133	193	IPR001356	Homeobox domain
SMART	SM00389	1.1E-15	135	197	IPR001356	Homeobox domain
Pfam	PF00046	3.4E-16	137	191	IPR001356	Homeobox domain
CDD	cd00086	4.20E-15	137	194	No hit	No description
PRINTS	PR00031	2.1E-5	164	173	IPR000047	Helix-turn-helix motif
PROSITE pattern	PS00027	0	168	191	IPR017970	Homeobox, conserved site
PRINTS	PR00031	2.1E-5	173	189	IPR000047	Helix-turn-helix motif
Pfam	PF02183	2.3E-11	193	227	IPR003106	Leucine zipper, homeobox-associated
SMART	SM00340	1.6E-24	193	237	IPR003106	Leucine zipper, homeobox-associated

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0006355	Biological Process	regulation of transcription, DNA-templated
GO:0005634	Cellular Component	nucleus
GO:0003700	Molecular Function	transcription factor activity, sequence-specific DNA binding
GO:0043565	Molecular Function	sequence-specific DNA binding

Sequence ? help Back to Top
Protein Sequence Length: 302 aa Download sequence Send to blast
MAEKEDLGLS LSLSFPQNHH SLQRNLRPSL VPSSANSCSS PSTLTLNKHS WNDSSPPSDH 60 NSESFRAEMG SIFRGIDMNI LPSTVDCEEE AGVSSPNSTI SSVSGKRSER EGNGDELEIE 120 KSSSRGISDE EDGDTSRKKL RLSKDQSAIL EENFKEHNTL NPKQKLALAK QLGLRPRQVE 180 VWFQNRRART KLKQTEVDCE FLKRCCENLT EENRRLQKEV QELRALKLSS TQFYMQMTPP 240 TTLTMCTSCE RVAVPPNPPS SATVDPRSHH QLAQTHHRAF HMNPWAPSAA HRPLDALRPR 300 S*

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	135	141	SRKKLRL
2	185	193	RRARTKLKQ

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
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}.

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	-

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_012439453.1	0.0	PREDICTED: homeobox-leucine zipper protein HAT4-like
Swissprot	Q05466	1e-105	HAT4_ARATH; Homeobox-leucine zipper protein HAT4
TrEMBL	A0A0D2U8C3	0.0	A0A0D2U8C3_GOSRA; Uncharacterized protein
STRING	Gorai.008G233200.1	0.0	(Gossypium raimondii)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM1563	26	90

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT4G16780.1	3e-99	homeobox protein 2

Link Out ? help Back to Top
Phytozome	Gorai.008G233200.1
Entrez Gene	105765083

Publications ? help Back to Top
Paterson AH, et al. Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres. Nature, 2012. 492(7429): p. 423-7 [PMID:23257886] 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] 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]