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

AT4G02560.1

Common Name

LD, T10P11.15

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

HB-other

Protein Properties

Length: 953aa MW: 105415 Da PI: 9.1457

Description

HB-other family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
AT4G02560.1	genome	TAIR	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	Homeobox	18.1	4.7e-06	66	122	1	57
TT--SS--HHHHHHHHHHHHHSSS--HHHHHHHHHHCTS-HHHHHHHHHHHHHHHHC CS Homeobox 1 rrkRttftkeqleeLeelFeknrypsaeereeLAkklgLterqVkvWFqNrRakekk 57 +r+R ++++ ++ L+++F+ + +s++e +e+++ g+t +qV+ +F ++++ +k AT4G02560.1 66 KRPRDLLNPKAVKYLQAVFAIKDAISKRESREISALFGITVAQVREFFVTQKTRVRK 122 799*********************************************999999886 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50071	9.572	63	123	IPR001356	Homeobox domain
SMART	SM00389	5.9E-5	65	127	IPR001356	Homeobox domain
CDD	cd00086	6.55E-4	66	123	No hit	No description
Gene3D	G3DSA:1.10.10.60	7.5E-5	66	125	IPR009057	Homeodomain-like
SuperFamily	SSF46689	6.84E-6	66	129	IPR009057	Homeodomain-like
Gene3D	G3DSA:1.20.930.10	6.1E-5	228	323	IPR017923	Transcription factor IIS, N-terminal
SuperFamily	SSF47676	1.18E-5	231	324	IPR017923	Transcription factor IIS, N-terminal

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0006355	Biological Process	regulation of transcription, DNA-templated
GO:0009911	Biological Process	positive regulation of flower development
GO:0010228	Biological Process	vegetative to reproductive phase transition of meristem
GO:0030154	Biological Process	cell differentiation
GO:0005634	Cellular Component	nucleus
GO:0003677	Molecular Function	DNA binding
GO:0003700	Molecular Function	transcription factor activity, sequence-specific DNA binding
GO:0005515	Molecular Function	protein binding

Plant Ontology ? help Back to Top
PO Term	PO Category	PO Description
PO:0000013	anatomy	cauline leaf
PO:0000037	anatomy	shoot apex
PO:0000084	anatomy	plant sperm cell
PO:0000230	anatomy	inflorescence meristem
PO:0000293	anatomy	guard cell
PO:0008019	anatomy	leaf lamina base
PO:0009005	anatomy	root
PO:0009006	anatomy	shoot system
PO:0009009	anatomy	plant embryo
PO:0009010	anatomy	seed
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:0009052	anatomy	flower pedicel
PO:0020030	anatomy	cotyledon
PO:0020038	anatomy	petiole
PO:0020100	anatomy	hypocotyl
PO:0020137	anatomy	leaf apex
PO:0025022	anatomy	collective leaf structure
PO:0025195	anatomy	pollen tube cell
PO:0025281	anatomy	pollen
PO:0001016	developmental stage	L mature pollen stage
PO:0001017	developmental stage	M germinated pollen stage
PO:0001054	developmental stage	vascular leaf senescent stage
PO:0001078	developmental stage	plant embryo cotyledonary stage
PO:0001081	developmental stage	mature plant embryo stage
PO:0001185	developmental stage	plant embryo globular stage
PO:0004507	developmental stage	plant embryo bilateral stage
PO:0007064	developmental stage	LP.12 twelve leaves visible 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
PO:0007616	developmental stage	flowering stage

Sequence ? help Back to Top
Protein Sequence Length: 953 aa Download sequence Send to blast
MDAFKEEIEI GSSVESLMEL LDSQKVLFHS QIDQLQDVVV AQCKLTGVNP LAQEMAAGAL 60 SIKIGKRPRD LLNPKAVKYL QAVFAIKDAI SKRESREISA LFGITVAQVR EFFVTQKTRV 120 RKQVRLSREK VVMSNTHALQ DDGVPENNNA TNHVEPVPLN SIHPEACSIS WGEGETVALI 180 PPEDIPPDIS DSDKYFVENI FSLLRKEETF SGQVKLMEWI MQIQDASVLI WFLSKGGVLI 240 LTTWLSQAAS EEQTSVLLLI LKVLCHLPLH KASPENMSAI LQSVNGLRFY RISDISNRAK 300 GLLSRWTKLF AKIQAMKKQN RNSSQIDSQS QLLLKQSIAE IMGDSSNPED ILSLSNGKSE 360 NVRRIESSQG PKLLLTSADD STKKHMLGSN PSYNKERRKV QMVEQPGQKA AGKSPQTVRI 420 GTSGRSRPMS ADDIQKAKMR ALYMQSKNSK KDPLPSAIGD SKIVAPEKPL ALHSAKDSPP 480 IQNNEAKTED TPVLSTVQPV NGFSTIQPVN GPSAVQPVNG PLAVQPVNGP SALQPVNGPS 540 AVIVPVQADE IKKPSTPPKS ISSKVGVMMK MSSQTILKNC KRKQIDWHVP PGMELDELWR 600 VAAGGNSKEA DVQRNRNRRE RETTYQSLQT IPLNPKEPWD REMDYDDSLT PEIPSQQPPE 660 ESLTEPQDSL DERRIAAGAA TTSSSLSSPE PDLELLAALL KNPDLVYALT SGKPSNLAGQ 720 DMVKLLDVIK TGAPNSSSSS NKQVEERVEV SLPSPTPSTN PGMSGWGQEG IRNPFSRQNQ 780 VGTAVARSGT QLRVGSMQWH QTNEQSIPRH APSAYSNSIT LAHTEREQQQ YMQPKLHHNL 840 HFQQQQQQPI STTSYAVREP VGQMGTGTSS SWRSQQSQNS YYSHQENEIA SASQVTSYQG 900 NSQYMSSNPG YESWSPDNSP SRNQLNMRGQ QQQASRKHDS STHPYWNQNK RWR

Sequence ? help Back to Top

Protein Sequence Length: 953 aa Download sequence Send to blast

MDAFKEEIEI GSSVESLMEL LDSQKVLFHS QIDQLQDVVV AQCKLTGVNP LAQEMAAGAL  60
SIKIGKRPRD LLNPKAVKYL QAVFAIKDAI SKRESREISA LFGITVAQVR EFFVTQKTRV  120
RKQVRLSREK VVMSNTHALQ DDGVPENNNA TNHVEPVPLN SIHPEACSIS WGEGETVALI  180
PPEDIPPDIS DSDKYFVENI FSLLRKEETF SGQVKLMEWI MQIQDASVLI WFLSKGGVLI  240
LTTWLSQAAS EEQTSVLLLI LKVLCHLPLH KASPENMSAI LQSVNGLRFY RISDISNRAK  300
GLLSRWTKLF AKIQAMKKQN RNSSQIDSQS QLLLKQSIAE IMGDSSNPED ILSLSNGKSE  360
NVRRIESSQG PKLLLTSADD STKKHMLGSN PSYNKERRKV QMVEQPGQKA AGKSPQTVRI  420
GTSGRSRPMS ADDIQKAKMR ALYMQSKNSK KDPLPSAIGD SKIVAPEKPL ALHSAKDSPP  480
IQNNEAKTED TPVLSTVQPV NGFSTIQPVN GPSAVQPVNG PLAVQPVNGP SALQPVNGPS  540
AVIVPVQADE IKKPSTPPKS ISSKVGVMMK MSSQTILKNC KRKQIDWHVP PGMELDELWR  600
VAAGGNSKEA DVQRNRNRRE RETTYQSLQT IPLNPKEPWD REMDYDDSLT PEIPSQQPPE  660
ESLTEPQDSL DERRIAAGAA TTSSSLSSPE PDLELLAALL KNPDLVYALT SGKPSNLAGQ  720
DMVKLLDVIK TGAPNSSSSS NKQVEERVEV SLPSPTPSTN PGMSGWGQEG IRNPFSRQNQ  780
VGTAVARSGT QLRVGSMQWH QTNEQSIPRH APSAYSNSIT LAHTEREQQQ YMQPKLHHNL  840
HFQQQQQQPI STTSYAVREP VGQMGTGTSS SWRSQQSQNS YYSHQENEIA SASQVTSYQG  900
NSQYMSSNPG YESWSPDNSP SRNQLNMRGQ QQQASRKHDS STHPYWNQNK RWR

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
At.240	0.0	flower

Expression -- Microarray ? help Back to Top
Source	ID	E-value
GEO	145339932	0.0
Genevisible	255444_at	0.0
Expression Atlas	AT4G02560	-
AtGenExpress	AT4G02560	-
ATTED-II	AT4G02560	-

Expression -- Description ? help Back to Top
Source	Description
Uniprot	DEVELOPMENTAL STAGE: Accumulates prior to flowering in the vegetative shoot apical meristem and after flowering in floral meristems.
Uniprot	TISSUE SPECIFICITY: Expressed in shoot apex, root apex, leaf primordia and floral buds.

Functional Description ? help Back to Top
Source	Description
TAIR	Encodes a nuclear localized protein with similarity to transcriptional regulators. Recessive mutants are late flowering. Expression of LFY is reduced in LD mutants.
UniProt	Seems to play a role in the regulation of flowering time in the autonomous flowering pathway by repressing FLOWERING LOCUS C expression. {ECO:0000269\|PubMed:10363371}.

Function -- GeneRIF ? help Back to Top
Luminidependens (LD) is an Arabidopsis protein with prion behavior [PMID: 27114519]

Cis-element ? help Back to Top
Source	Link
PlantRegMap	AT4G02560.1

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	AT1G01530 (A)

Regulation -- ATRM (Manually Curated Target Genes) ? help Back to Top
Source	Target Gene (A: Activate/R: Repress)
ATRM	AT2G45660(A), AT5G10140(R), AT5G61850(A)

Interaction ? help Back to Top
Source	Intact With
BioGRID	AT1G30970
IntAct	Search Q38796

Phenotype -- Disruption Phenotype ? help Back to Top
Source	Description
UniProt	DISRUPTION PHENOTYPE: Plants show late flowering phenotype (mutants LD-1 and LD-3). {ECO:0000269\|PubMed:7907507}.

Phenotype -- Mutation ? help Back to Top
Source	ID
T-DNA Express	AT4G02560

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AK226746	0.0	AK226746.1 Arabidopsis thaliana mRNA for luminidependens protein, complete cds, clone: RAFL07-75-C15.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	NP_001190660.1	0.0	Homeodomain-like superfamily protein
Refseq	NP_192165.1	0.0	Homeodomain-like superfamily protein
Swissprot	Q38796	0.0	LUMI_ARATH; Homeobox protein LUMINIDEPENDENS
TrEMBL	A0A178V7C4	0.0	A0A178V7C4_ARATH; LD
STRING	AT4G02560.1	0.0	(Arabidopsis thaliana)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM10876	24	28
Representative plant	OGRP4121	13	15

Link Out ? help Back to Top
Phytozome	AT4G02560.1
Entrez Gene	827904
iHOP	AT4G02560
wikigenes	AT4G02560

Publications ? help Back to Top
Michaels SD,Amasino RM FLOWERING LOCUS C encodes a novel MADS domain protein that acts as a repressor of flowering. Plant Cell, 1999. 11(5): p. 949-56 [PMID:10330478] Aukerman MJ,Lee I,Weigel D,Amasino RM The Arabidopsis flowering-time gene LUMINIDEPENDENS is expressed primarily in regions of cell proliferation and encodes a nuclear protein that regulates LEAFY expression. Plant J., 1999. 18(2): p. 195-203 [PMID:10363371] Chou ML,Yang CH Late-flowering genes interact with early-flowering genes to regulate flowering time in Arabidopsis thaliana. Plant Cell Physiol., 1999. 40(7): p. 702-8 [PMID:10501030] Soppe WJ,Bentsink L,Koornneef M The early-flowering mutant efs is involved in the autonomous promotion pathway of Arabidopsis thaliana. Development, 1999. 126(21): p. 4763-70 [PMID:10518493] Lee H, et al. The AGAMOUS-LIKE 20 MADS domain protein integrates floral inductive pathways in Arabidopsis. Genes Dev., 2000. 14(18): p. 2366-76 [PMID:10995392] van Nocke S,Muszynski M,Briggs K,Amasino RM Characterization of a gene from Zea mays related to the Arabidopsis flowering-time gene LUMINIDEPENDENS. Plant Mol. Biol., 2000. 44(1): p. 107-22 [PMID:11094985] Michaels SD,Amasino RM Loss of FLOWERING LOCUS C activity eliminates the late-flowering phenotype of FRIGIDA and autonomous pathway mutations but not responsiveness to vernalization. Plant Cell, 2001. 13(4): p. 935-41 [PMID:11283346] Schomburg FM,Patton DA,Meinke DW,Amasino RM FPA, a gene involved in floral induction in Arabidopsis, encodes a protein containing RNA-recognition motifs. Plant Cell, 2001. 13(6): p. 1427-36 [PMID:11402170] Zhang H,van Nocker S The VERNALIZATION INDEPENDENCE 4 gene encodes a novel regulator of FLOWERING LOCUS C. Plant J., 2002. 31(5): p. 663-73 [PMID:12207655] Noh YS,Amasino RM PIE1, an ISWI family gene, is required for FLC activation and floral repression in Arabidopsis. Plant Cell, 2003. 15(7): p. 1671-82 [PMID:12837955] Tzeng TY,Hsiao CC,Chi PJ,Yang CH Two lily SEPALLATA-like genes cause different effects on floral formation and floral transition in Arabidopsis. Plant Physiol., 2003. 133(3): p. 1091-101 [PMID:14526112] Boss PK,Bastow RM,Mylne JS,Dean C Multiple pathways in the decision to flower: enabling, promoting, and resetting. Plant Cell, 2004. 16 Suppl: p. S18-31 [PMID:15037730] Lewandowska D, et al. Determinants of plant U12-dependent intron splicing efficiency. Plant Cell, 2004. 16(5): p. 1340-52 [PMID:15100401] Nakagawa M,Komeda Y Flowering of Arabidopsis cop1 mutants in darkness. Plant Cell Physiol., 2004. 45(4): p. 398-406 [PMID:15111714] Doyle MR, et al. HUA2 is required for the expression of floral repressors in Arabidopsis thaliana. Plant J., 2005. 41(3): p. 376-85 [PMID:15659097] Werner JD, et al. FRIGIDA-independent variation in flowering time of natural Arabidopsis thaliana accessions. Genetics, 2005. 170(3): p. 1197-207 [PMID:15911588] Salathia N, et al. FLOWERING LOCUS C-dependent and -independent regulation of the circadian clock by the autonomous and vernalization pathways. BMC Plant Biol., 2006. 6: p. 10 [PMID:16737527] Yoo SK,Lee JS,Ahn JH Overexpression of AGAMOUS-LIKE 28 (AGL28) promotes flowering by upregulating expression of floral promoters within the autonomous pathway. Biochem. Biophys. Res. Commun., 2006. 348(3): p. 929-36 [PMID:16899218] Kim S,Choi K,Park C,Hwang HJ,Lee I SUPPRESSOR OF FRIGIDA4, encoding a C2H2-Type zinc finger protein, represses flowering by transcriptional activation of Arabidopsis FLOWERING LOCUS C. Plant Cell, 2006. 18(11): p. 2985-98 [PMID:17138694] Domagalska MA, et al. Attenuation of brassinosteroid signaling enhances FLC expression and delays flowering. Development, 2007. 134(15): p. 2841-50 [PMID:17611230] Jin JB, et al. The SUMO E3 ligase, AtSIZ1, regulates flowering by controlling a salicylic acid-mediated floral promotion pathway and through affects on FLC chromatin structure. Plant J., 2008. 53(3): p. 530-40 [PMID:18069938] Manzano C,Abraham Z,L Identification of ubiquitinated proteins in Arabidopsis. Plant Mol. Biol., 2008. 68(1-2): p. 145-58 [PMID:18535787] Wang Y, et al. Transcriptome analyses show changes in gene expression to accompany pollen germination and tube growth in Arabidopsis. Plant Physiol., 2008. 148(3): p. 1201-11 [PMID:18775970] Chang IF, et al. Proteomic profiling of tandem affinity purified 14-3-3 protein complexes in Arabidopsis thaliana. Proteomics, 2009. 9(11): p. 2967-85 [PMID:19452453] Doyle MR,Amasino RM A single amino acid change in the enhancer of zeste ortholog CURLY LEAF results in vernalization-independent, rapid flowering in Arabidopsis. Plant Physiol., 2009. 151(3): p. 1688-97 [PMID:19755537] Nah G,Jeffrey Chen Z Tandem duplication of the FLC locus and the origin of a new gene in Arabidopsis related species and their functional implications in allopolyploids. New Phytol., 2010. 186(1): p. 228-38 [PMID:20100201] Tamura K,Fukao Y,Iwamoto M,Haraguchi T,Hara-Nishimura I Identification and characterization of nuclear pore complex components in Arabidopsis thaliana. Plant Cell, 2010. 22(12): p. 4084-97 [PMID:21189294] 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] Chakrabortee S, et al. Luminidependens (LD) is an Arabidopsis protein with prion behavior. Proc. Natl. Acad. Sci. U.S.A., 2016. 113(21): p. 6065-70 [PMID:27114519] Lee I, et al. Isolation of LUMINIDEPENDENS: a gene involved in the control of flowering time in Arabidopsis. Plant Cell, 1994. 6(1): p. 75-83 [PMID:7907507] Sanda SL,Amasino RM Interaction of FLC and late-flowering mutations in Arabidopsis thaliana. Mol. Gen. Genet., 1996. 251(1): p. 69-74 [PMID:8628249] Haung MD,Yang CH EMF genes interact with late-flowering genes to regulate Arabidopsis shoot development. Plant Cell Physiol., 1998. 39(4): p. 382-93 [PMID:9615462]