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

Lj3g3v1074990.2

Organism

Lotus japonicus

Taxonomic ID

34305

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Fabales; Fabaceae; Papilionoideae; Loteae; Lotus

Family

HD-ZIP

Protein Properties

Length: 841aa MW: 92039.8 Da PI: 6.3127

Description

HD-ZIP family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Lj3g3v1074990.2	genome	Kazusa	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	Homeobox	53.1	5.4e-17	23	80	4	57
-SS--HHHHHHHHHHHHHSSS--HHHHHHHHHHC....TS-HHHHHHHHHHHHHHHHC CS Homeobox 4 RttftkeqleeLeelFeknrypsaeereeLAkkl....gLterqVkvWFqNrRakekk 57 ++t+ q+e+Le+++ ++++ps +r++L +++ +++ +q+kvWFqNrR +ek+ Lj3g3v1074990.2 23 YVRYTAGQVEALERVYTECPKPSSLRRQQLIRECpvlaNVEPKQIKVWFQNRRCREKQ 80 6789****************************************************97 PP
2	START	159.6	2.5e-50	162	370	2	205
HHHHHHHHHHHHHHHC-TT-EEEEEXCCTTEEEEEEESSS.SCEEEEEEEECCSCHHHHHHHHHCCCGGCT-TT-SEEEEEEEECTT..EEEEE CS START 2 laeeaaqelvkkalaeepgWvkssesengdevlqkfeeskvdsgealrasgvvdmvlallveellddkeqWdetlakaetlevissg..galql 93 +aee+++e+++ka+ ++ Wv+++ +++g++++ +f+ s+++sg a+ra+g+v ++ v+e+l+d++ W +++++ e+ g g+++l Lj3g3v1074990.2 162 IAEETLAEFLSKATGTAVDWVQLPGMKPGPDSVGIFTISQSCSGVAARACGLVSLEPN-KVAEILKDRLSWFRDCRSLEVFTMFPAGngGTIEL 254 7899****************************************************.9999999999*******999999999* PP EEEXXTTXX-SSX.EEEEEEEEEEE.TTS-EEEEEEEEE-TTS--....-TTSEE-EESSEEEEEEEECTCEEEEEEEE-EE--SSXXHHHHHH CS START 94 mvaelqalsplvp.RdfvfvRyirqlgagdwvivdvSvdseqkppe...sssvvRaellpSgiliepksnghskvtwvehvdlkgrlphwllrs 183 +++++a+ +l+p Rdf+++Ry+ +l+ g++v++++S++ p+ +++vRae+lpSg+li+p+++g+s +++v+h +l++++++++lr+ Lj3g3v1074990.2 255 VYTQTYAPMTLSPaRDFWTLRYTTTLENGSLVVCERSLSGSGAGPNaaaAHQFVRAEMLPSGYLIRPCEGGGSIIHIVDHLNLQAWSVPEVLRP 348 ***********************************99999999999**************************************** PP HHHHHHHHHHHHHHHHTXXXXX CS START 184 lvksglaegaktwvatlqrqce 205 l++s+ + +++++ a+l++ ++ Lj3g3v1074990.2 349 LYESSKVVAQRMTIAALRYVRQ 370 ***************98765 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50071	14.803	17	81	IPR001356	Homeobox domain
SuperFamily	SSF46689	8.13E-16	18	85	IPR009057	Homeodomain-like
SMART	SM00389	2.8E-13	19	85	IPR001356	Homeobox domain
CDD	cd00086	2.71E-14	22	82	No hit	No description
Pfam	PF00046	1.4E-14	23	80	IPR001356	Homeobox domain
Gene3D	G3DSA:1.10.10.60	1.4E-17	24	80	IPR009057	Homeodomain-like
CDD	cd14686	5.29E-6	74	113	No hit	No description
PROSITE profile	PS50848	26.147	152	380	IPR002913	START domain
CDD	cd08875	5.56E-66	156	372	No hit	No description
Gene3D	G3DSA:3.30.530.20	1.6E-20	161	348	IPR023393	START-like domain
SMART	SM00234	4.7E-44	161	371	IPR002913	START domain
SuperFamily	SSF55961	4.53E-34	161	373	No hit	No description
Pfam	PF01852	1.1E-47	162	370	IPR002913	START domain
Pfam	PF08670	5.6E-47	697	840	IPR013978	MEKHLA

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0005634	Cellular Component	nucleus
GO:0003677	Molecular Function	DNA binding
GO:0008289	Molecular Function	lipid binding

Sequence ? help Back to Top
Protein Sequence Length: 841 aa Download sequence Send to blast
MAMAFVQDRE SSIDRHLDSS GKYVRYTAGQ VEALERVYTE CPKPSSLRRQ QLIRECPVLA 60 NVEPKQIKVW FQNRRCREKQ RKEASRLQAV NRKLNAMNKL LMEENDRLQK QVSQLVCENG 120 FMRQQLQAPS AAGTTDGNGD SVATTSRNSM RDANSPAGFL SIAEETLAEF LSKATGTAVD 180 WVQLPGMKPG PDSVGIFTIS QSCSGVAARA CGLVSLEPNK VAEILKDRLS WFRDCRSLEV 240 FTMFPAGNGG TIELVYTQTY APMTLSPARD FWTLRYTTTL ENGSLVVCER SLSGSGAGPN 300 AAAAHQFVRA EMLPSGYLIR PCEGGGSIIH IVDHLNLQAW SVPEVLRPLY ESSKVVAQRM 360 TIAALRYVRQ IAQETSGEVV YGLGRQPAVL RTFSQRLSRG FNDAVNGFND DGWSVLNCDG 420 AEDVIISVNS TKNLSGTSNP ASSLTFAGGV LCAKASMLLQ NIPPAVLVRF LREHRSEWAD 480 FNVDAYSAAS LKAGSYAYPG MRPMRFTGNQ IIMPLGHTIE HEEMLEVIRL EGHSLAQEDA 540 FASRDVHLLQ LCSGIDEDAV GACCELIFAP IDEMFPDDAP LVPSGFRIIP LDSKPGDKKD 600 TMTTNKTLNL TSGLEVGAST NHTAGDASSC HNNRSVLTIA FQFPFESSLQ DNVAVMARQY 660 VRSVISSVQT VSMAISPSGT NPAAGAKLSV GSPEALTLAR WVCQSYSYYL GTGLLRSDSL 720 VGDLVLKHLW HHQDAILCCS LKSVPMFIFA NQAGLDMLET TLVALQDITL DKIFDESGRK 780 ALFADFAKLM QQGFAYLPAG ICMSTMGRHV SYEQVIAWKV LAEEDNSVHC LAFSFINWSF 840 V

Sequence ? help Back to Top

Protein Sequence Length: 841 aa Download sequence Send to blast

MAMAFVQDRE SSIDRHLDSS GKYVRYTAGQ VEALERVYTE CPKPSSLRRQ QLIRECPVLA  60
NVEPKQIKVW FQNRRCREKQ RKEASRLQAV NRKLNAMNKL LMEENDRLQK QVSQLVCENG  120
FMRQQLQAPS AAGTTDGNGD SVATTSRNSM RDANSPAGFL SIAEETLAEF LSKATGTAVD  180
WVQLPGMKPG PDSVGIFTIS QSCSGVAARA CGLVSLEPNK VAEILKDRLS WFRDCRSLEV  240
FTMFPAGNGG TIELVYTQTY APMTLSPARD FWTLRYTTTL ENGSLVVCER SLSGSGAGPN  300
AAAAHQFVRA EMLPSGYLIR PCEGGGSIIH IVDHLNLQAW SVPEVLRPLY ESSKVVAQRM  360
TIAALRYVRQ IAQETSGEVV YGLGRQPAVL RTFSQRLSRG FNDAVNGFND DGWSVLNCDG  420
AEDVIISVNS TKNLSGTSNP ASSLTFAGGV LCAKASMLLQ NIPPAVLVRF LREHRSEWAD  480
FNVDAYSAAS LKAGSYAYPG MRPMRFTGNQ IIMPLGHTIE HEEMLEVIRL EGHSLAQEDA  540
FASRDVHLLQ LCSGIDEDAV GACCELIFAP IDEMFPDDAP LVPSGFRIIP LDSKPGDKKD  600
TMTTNKTLNL TSGLEVGAST NHTAGDASSC HNNRSVLTIA FQFPFESSLQ DNVAVMARQY  660
VRSVISSVQT VSMAISPSGT NPAAGAKLSV GSPEALTLAR WVCQSYSYYL GTGLLRSDSL  720
VGDLVLKHLW HHQDAILCCS LKSVPMFIFA NQAGLDMLET TLVALQDITL DKIFDESGRK  780
ALFADFAKLM QQGFAYLPAG ICMSTMGRHV SYEQVIAWKV LAEEDNSVHC LAFSFINWSF  840
V

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
Lja.7460	0.0	pod\| root

Expression -- Description ? help Back to Top
Source	Description
Uniprot	DEVELOPMENTAL STAGE: Expressed at the earliest stages and throughout LSM initiation and development. In embryo development, expressed at the heart stage until the 'walking stick' stage in the adaxial portion of the cotyledon primordia, the shoot apical meristem (SAM) and the vascular precursor cells of the hypocotyl and root. In developing flowers, expressed first at stage 1 in the center of L3 layer and then expands to the center of L2 and L1 layers. Expressed in the center of flower meristem through stages 4 and 5. At stage 6, expressed in the adaxial side of the carpel primordia and then on the adaxial carpel face. {ECO:0000269\|PubMed:11169198}.
Uniprot	TISSUE SPECIFICITY: Expressed in the interfascicular regions of stem and vascular bundles of young roots and leaves. {ECO:0000269\|PubMed:10559440}.

Functional Description ? help Back to Top
Source	Description
UniProt	Probable transcription factor involved in the regulation of interfascicular fiber (cortical cells) and secondary xylem differentiation in the inflorescence stems. Required for lateral shoot meristems (LSMs) and flower meristems (FMs) initiation. May be involved in the determination of vascular patterning and organ polarity (PubMed:10559440, PubMed:11169198, PubMed:11402186, PubMed:15111711, PubMed:15598805, PubMed:7555701). Directly regulates the expression of AGO10, ZPR1, ZPR2, ZPR3 and ZPR4 (PubMed:22781836). Required to regulate adaxial-abaxial polarity and leaf axial patterning (PubMed:20807212). {ECO:0000269\|PubMed:10559440, ECO:0000269\|PubMed:11169198, ECO:0000269\|PubMed:11402186, ECO:0000269\|PubMed:15111711, ECO:0000269\|PubMed:15598805, ECO:0000269\|PubMed:20807212, ECO:0000269\|PubMed:22781836, ECO:0000269\|PubMed:7555701}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Lj3g3v1074990.2

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: By auxin. Repressed by ZPR and miR165. Induced by DOF5.1 (PubMed:20807212). {ECO:0000269\|PubMed:15111711, ECO:0000269\|PubMed:17237362, ECO:0000269\|PubMed:20807212}.

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_027348757.1	0.0	homeobox-leucine zipper protein REVOLUTA isoform X1
Swissprot	Q9SE43	0.0	REV_ARATH; Homeobox-leucine zipper protein REVOLUTA
TrEMBL	Q147T3	0.0	Q147T3_LOTJA; Class III HD-Zip protein REV1
STRING	XP_007132262.1	0.0	(Phaseolus vulgaris)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Fabids	OGEF6633	31	47

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT5G60690.1	0.0	HD-ZIP family protein

Publications ? help Back to Top
Prigge MJ,Clark SE Evolution of the class III HD-Zip gene family in land plants. Evol. Dev., 2006 Jul-Aug. 8(4): p. 350-61 [PMID:16805899] Lian H,Li X,Liu Z,He Y HYL1 is required for establishment of stamen architecture with four microsporangia in Arabidopsis. J. Exp. Bot., 2013. 64(11): p. 3397-410 [PMID:23918970] Ding Y, et al. Four distinct types of dehydration stress memory genes in Arabidopsis thaliana. BMC Plant Biol., 2013. 13: p. 229 [PMID:24377444] Baima S, et al. Negative feedback regulation of auxin signaling by ATHB8/ACL5-BUD2 transcription module. Mol Plant, 2014. 7(6): p. 1006-1025 [PMID:24777988] Jia X, et al. Functional plasticity of miR165/166 in plant development revealed by small tandem target mimic. Plant Sci., 2015. 233: p. 11-21 [PMID:25711809] Roodbarkelari F,Du F,Truernit E,Laux T ZLL/AGO10 maintains shoot meristem stem cells during Arabidopsis embryogenesis by down-regulating ARF2-mediated auxin response. BMC Biol., 2015. 13: p. 74 [PMID:26358077] Shi B, et al. Two-Step Regulation of a Meristematic Cell Population Acting in Shoot Branching in Arabidopsis. PLoS Genet., 2016. 12(7): p. e1006168 [PMID:27398935]