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

AT1G62990.1

Common Name

F16P17.16, IRX11, IXR11, KNAT7

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

TALE

Protein Properties

Length: 291aa MW: 32908.1 Da PI: 6.5649

Description

KNOTTED-like homeobox of Arabidopsis thaliana 7

Gene Model

Gene Model ID	Type	Source	Coding Sequence
AT1G62990.1	genome	TAIR	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	Homeobox	22.7	1.7e-07	241	273	22	54
SSS--HHHHHHHHHHCTS-HHHHHHHHHHHHHH CS Homeobox 22 nrypsaeereeLAkklgLterqVkvWFqNrRak 54 +yp+++++++L +++gL+ +q+ +WF N+R + AT1G62990.1 241 WPYPTEDDKAKLVEETGLQLKQINNWFINQRKR 273 58*****************************87 PP
2	ELK	22.7	2.3e-08	194	215	1	22
ELK 1 ELKhqLlrKYsgyLgsLkqEFs 22 ELK +L++++++++ ++++E++ AT1G62990.1 194 ELKLELKQGFKSRIEDVREEIM 215 9********************8 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SMART	SM01255	8.1E-19	27	71	IPR005540	KNOX1
Pfam	PF03790	2.9E-16	29	70	IPR005540	KNOX1
SMART	SM01256	1.5E-26	80	135	IPR005541	KNOX2
Pfam	PF03791	6.0E-19	84	134	IPR005541	KNOX2
PROSITE profile	PS51213	9.202	194	214	IPR005539	ELK domain
PROSITE profile	PS50071	11.823	214	277	IPR001356	Homeobox domain
SuperFamily	SSF46689	2.44E-16	216	280	IPR009057	Homeodomain-like
SMART	SM00389	6.3E-11	216	281	IPR001356	Homeobox domain
CDD	cd00086	2.96E-12	217	278	No hit	No description
Gene3D	G3DSA:1.10.10.60	4.9E-25	221	279	IPR009057	Homeodomain-like
Pfam	PF05920	3.2E-18	234	273	IPR008422	Homeobox KN domain

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0010089	Biological Process	xylem development
GO:0010192	Biological Process	mucilage biosynthetic process
GO:0045892	Biological Process	negative regulation of transcription, DNA-templated
GO:2000652	Biological Process	regulation of secondary cell wall biogenesis
GO:0005634	Cellular Component	nucleus
GO:0003677	Molecular Function	DNA binding
GO:0003700	Molecular Function	transcription factor activity, sequence-specific DNA binding

Plant Ontology ? help Back to Top
PO Term	PO Category	PO Description
PO:0000013	anatomy	cauline leaf
PO:0000037	anatomy	shoot apex
PO:0000230	anatomy	inflorescence meristem
PO:0000272	anatomy	protoxylem
PO:0000293	anatomy	guard cell
PO:0005352	anatomy	xylem
PO:0005848	anatomy	secondary xylem
PO:0009005	anatomy	root
PO:0009006	anatomy	shoot system
PO:0009009	anatomy	plant embryo
PO:0009025	anatomy	vascular leaf
PO:0009029	anatomy	stamen
PO:0009030	anatomy	carpel
PO:0009031	anatomy	sepal
PO:0009032	anatomy	petal
PO:0009046	anatomy	flower
PO:0009047	anatomy	stem
PO:0020038	anatomy	petiole
PO:0020100	anatomy	hypocotyl
PO:0025022	anatomy	collective leaf structure
PO:0025281	anatomy	pollen
PO:0001185	developmental stage	plant embryo globular stage
PO:0007064	developmental stage	LP.12 twelve leaves visible stage
PO:0007095	developmental stage	LP.08 eight leaves visible stage
PO:0007115	developmental stage	LP.04 four leaves visible stage
PO:0007611	developmental stage	petal differentiation and expansion stage
PO:0007616	developmental stage	flowering stage

Sequence ? help Back to Top
Protein Sequence Length: 291 aa Download sequence Send to blast
MQEAALGMMG ATVGGDGDTA VVAEQNRQLK GEIATHPMYE QLLAAHVACL RVATPIDQLP 60 IIEAQLSQSH HLLRSYASTA VGYHHDRHEL DNFLAQYVMV LCSFKEQLQQ HVRVHAVEAV 120 MACREIENNL HSLTGATLGE GSGATMSEDE DDLPMDFSSD NSGVDFSGGH DMTGFGPLLP 180 TESERSLMER VRQELKLELK QGFKSRIEDV REEIMRKRRA GKLPGDTTTV LKNWWQQHCK 240 WPYPTEDDKA KLVEETGLQL KQINNWFINQ RKRNWHNNSH SLTSLKSKRK H

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
At.70104	0.0	root\| seed\| silique

Expression -- Microarray ? help Back to Top
Source	ID	E-value
GEO	11878229	0.0
Genevisible	261106_at	0.0
Expression Atlas	AT1G62990	-
AtGenExpress	AT1G62990	-
ATTED-II	AT1G62990	-

Functional Description ? help Back to Top
Source	Description
TAIR	Encodes a homeodomain transcription factor of the Knotted family. May be involved in secondary cell wall biosynthesis. Mutants have moderately irregular xylem development. Expression of this gene is upregulated by SND1 and MYB46.
UniProt	May be involved in secondary cell wall biosynthesis. {ECO:0000269\|PubMed:15980264}.

Function -- GeneRIF ? help Back to Top
KNAT7 forms a functional complex with OFP proteins to regulate aspects of secondary cell wall formation. [PMID: 21457372] KNAT7 is a negative regulator of secondary wall biosynthesis. [PMID: 22236040] BLH6 and KNAT7 bind to the REV promoter and repress REV expression. [PMID: 25490916] This study shows that OFP1 and OFP4 enhance the repression activity of BLH6, supporting a role for these OFPs as components of a putative multi-protein transcription regulatory complex containing BLH6 and KNAT7. [PMID: 26107719] KNAT7 activates the promoters of the xylan biosynthetic genes, IRREGULAR XYLEM 9 (IRX9), IRX10, IRREGULAR XYLEM 14-LIKE (IRX14L), and FRAGILE FIBER 8 (FRA8). [PMID: 29393579]

Cis-element ? help Back to Top
Source	Link
PlantRegMap	AT1G62990.1

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

Regulation -- ATRM (Manually Curated Upstream Regulators) ? help Back to Top
Source	Upstream Regulator (A: Activate/R: Repress)
ATRM	AT1G32770 (A), AT1G71930 (A), AT2G46770 (A), AT3G61910 (A), AT5G12870 (A), AT5G62380 (A)

Interaction ? help Back to Top
Source	Intact With
BioGRID	AT1G62990
IntAct	Search Q9FPQ8

Phenotype -- Mutation ? help Back to Top
Source	ID
T-DNA Express	AT1G62990

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AF308451	0.0	AF308451.1 Arabidopsis thaliana homeodomain transcription factor KNAT7 (KNAT7) mRNA, complete cds.
GenBank	BT026059	0.0	BT026059.1 Arabidopsis thaliana At1g62990 mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	NP_564805.1	0.0	homeobox knotted-like protein
Swissprot	Q9FPQ8	0.0	KNAT7_ARATH; Homeobox protein knotted-1-like 7
TrEMBL	A0A1J3GZ74	0.0	A0A1J3GZ74_NOCCA; Homeobox protein HD1
STRING	AT1G62990.1	0.0	(Arabidopsis thaliana)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM444	28	158
Representative plant	OGRP167	17	148

Link Out ? help Back to Top
Phytozome	AT1G62990.1
Entrez Gene	842602
iHOP	AT1G62990
wikigenes	AT1G62990

Publications ? help Back to Top
Riechmann JL, et al. Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes. Science, 2000. 290(5499): p. 2105-10 [PMID:11118137] Bellaoui M, et al. The Arabidopsis BELL1 and KNOX TALE homeodomain proteins interact through a domain conserved between plants and animals. Plant Cell, 2001. 13(11): p. 2455-70 [PMID:11701881] Seki M, et al. Functional annotation of a full-length Arabidopsis cDNA collection. Science, 2002. 296(5565): p. 141-5 [PMID:11910074] Hackbusch J,Richter K,Müller J,Salamini F,Uhrig JF A central role of Arabidopsis thaliana ovate family proteins in networking and subcellular localization of 3-aa loop extension homeodomain proteins. Proc. Natl. Acad. Sci. U.S.A., 2005. 102(13): p. 4908-12 [PMID:15781858] Ehlting J, et al. Global transcript profiling of primary stems from Arabidopsis thaliana identifies candidate genes for missing links in lignin biosynthesis and transcriptional regulators of fiber differentiation. Plant J., 2005. 42(5): p. 618-40 [PMID:15918878] Brown DM,Zeef LA,Ellis J,Goodacre R,Turner SR Identification of novel genes in Arabidopsis involved in secondary cell wall formation using expression profiling and reverse genetics. Plant Cell, 2005. 17(8): p. 2281-95 [PMID:15980264] Andersson-Gunner Biosynthesis of cellulose-enriched tension wood in Populus: global analysis of transcripts and metabolites identifies biochemical and developmental regulators in secondary wall biosynthesis. Plant J., 2006. 45(2): p. 144-65 [PMID:16367961] Tan QK,Irish VF The Arabidopsis zinc finger-homeodomain genes encode proteins with unique biochemical properties that are coordinately expressed during floral development. Plant Physiol., 2006. 140(3): p. 1095-108 [PMID:16428600] Truernit E,Siemering KR,Hodge S,Grbic V,Haseloff J A map of KNAT gene expression in the Arabidopsis root. Plant Mol. Biol., 2006. 60(1): p. 1-20 [PMID:16463096] Mandaokar A, et al. Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling. Plant J., 2006. 46(6): p. 984-1008 [PMID:16805732] Cao D,Cheng H,Wu W,Soo HM,Peng J Gibberellin mobilizes distinct DELLA-dependent transcriptomes to regulate seed germination and floral development in Arabidopsis. Plant Physiol., 2006. 142(2): p. 509-25 [PMID:16920880] Zhong R,Richardson EA,Ye ZH The MYB46 transcription factor is a direct target of SND1 and regulates secondary wall biosynthesis in Arabidopsis. Plant Cell, 2007. 19(9): p. 2776-92 [PMID:17890373] Di Giacomo E, et al. Characterization of KNOX genes in Medicago truncatula. Plant Mol. Biol., 2008. 67(1-2): p. 135-50 [PMID:18274864] Srinivasasainagendra V,Page GP,Mehta T,Coulibaly I,Loraine AE CressExpress: a tool for large-scale mining of expression data from Arabidopsis. Plant Physiol., 2008. 147(3): p. 1004-16 [PMID:18467456] Jakoby MJ, et al. Transcriptional profiling of mature Arabidopsis trichomes reveals that NOECK encodes the MIXTA-like transcriptional regulator MYB106. Plant Physiol., 2008. 148(3): p. 1583-602 [PMID:18805951] Zhong R,Lee C,Zhou J,McCarthy RL,Ye ZH A battery of transcription factors involved in the regulation of secondary cell wall biosynthesis in Arabidopsis. Plant Cell, 2008. 20(10): p. 2763-82 [PMID:18952777] Bhargava A,Mansfield SD,Hall HC,Douglas CJ,Ellis BE MYB75 functions in regulation of secondary cell wall formation in the Arabidopsis inflorescence stem. Plant Physiol., 2010. 154(3): p. 1428-38 [PMID:20807862] Li E,Wang S,Liu Y,Chen JG,Douglas CJ OVATE FAMILY PROTEIN4 (OFP4) interaction with KNAT7 regulates secondary cell wall formation in Arabidopsis thaliana. Plant J., 2011. 67(2): p. 328-41 [PMID:21457372] Arabidopsis Interactome Mapping Consortium Evidence for network evolution in an Arabidopsis interactome map. Science, 2011. 333(6042): p. 601-7 [PMID:21798944] Wang S, et al. Arabidopsis ovate family proteins, a novel transcriptional repressor family, control multiple aspects of plant growth and development. PLoS ONE, 2011. 6(8): p. e23896 [PMID:21886836] Zhong R,Ye ZH MYB46 and MYB83 bind to the SMRE sites and directly activate a suite of transcription factors and secondary wall biosynthetic genes. Plant Cell Physiol., 2012. 53(2): p. 368-80 [PMID:22197883] Li E, et al. The Class II KNOX gene KNAT7 negatively regulates secondary wall formation in Arabidopsis and is functionally conserved in Populus. New Phytol., 2012. 194(1): p. 102-15 [PMID:22236040] Heyndrickx KS,Vandepoele K Systematic identification of functional plant modules through the integration of complementary data sources. Plant Physiol., 2012. 159(3): p. 884-901 [PMID:22589469] Bhargava A, et al. The interacting MYB75 and KNAT7 transcription factors modulate secondary cell wall deposition both in stems and seed coat in Arabidopsis. Planta, 2013. 237(5): p. 1199-211 [PMID:23328896] Ding Y, et al. Four distinct types of dehydration stress memory genes in Arabidopsis thaliana. BMC Plant Biol., 2013. 13: p. 229 [PMID:24377444] Liu Y, et al. BEL1-LIKE HOMEODOMAIN6 and KNOTTED ARABIDOPSIS THALIANA7 interact and regulate secondary cell wall formation via repression of REVOLUTA. Plant Cell, 2014. 26(12): p. 4843-61 [PMID:25490916] Voiniciuc C,Yang B,Schmidt MH,G Starting to gel: how Arabidopsis seed coat epidermal cells produce specialized secondary cell walls. Int J Mol Sci, 2015. 16(2): p. 3452-73 [PMID:25658798] 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] Liu Y,Douglas CJ A role for OVATE FAMILY PROTEIN1 (OFP1) and OFP4 in a BLH6-KNAT7 multi-protein complex regulating secondary cell wall formation in Arabidopsis thaliana. Plant Signal Behav, 2015. 10(7): p. e1033126 [PMID:26107719] He JB, et al. KNAT7 positively regulates xylan biosynthesis by directly activating IRX9 expression in Arabidopsis. J Integr Plant Biol, 2018. 60(6): p. 514-528 [PMID:29393579]