PlantTFDB - Plant Transcription Factor Database @ CBI, PKU

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

Family

HB-PHD

Protein Properties

Length: 821aa MW: 90166.6 Da PI: 4.7067

Description

HB-PHD family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Glyma.10G260400.1.p	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	Homeobox	43.9	3.9e-14	686	731	11	56
HHHHHHHHHHHSSS--HHHHHHHHHHCTS-HHHHHHHHHHHHHHHH CS Homeobox 11 qleeLeelFeknrypsaeereeLAkklgLterqVkvWFqNrRakek 56 +++L + F++n+yp+++++e LA++lgLt +qV WF N R + Glyma.10G260400.1.p 686 VVQRLHKSFKENQYPDRTTKESLAQELGLTYQQVAKWFGNTRWSFR 731 6799**************************************8766 PP
2	PHD	37.2	6.8e-13	343	398	1	51
SBTTTSS..TCTTSSEEEBSS.SSSEEETTTSTSSSSHHSHHSS..TBSSHHHHTT CS PHD 1 rCkvCgk..sdeegelvlCdg.CkewfHlkClglkleseekpeg..ewlCeeCkek 51 +C+ C++ ++++++lCdg C++ fH+ Cl+++ +e++p g wlC+ C++k Glyma.10G260400.1.p 343 FCAKCQSkeLSTNNDIILCDGvCDRGFHQLCLDPPMLTEDIPPGdeGWLCPGCDCK 398 699*977777****77****************9999*****985 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF57903	3.1E-13	333	401	IPR011011	Zinc finger, FYVE/PHD-type
Gene3D	G3DSA:3.30.40.10	1.5E-12	340	397	IPR013083	Zinc finger, RING/FYVE/PHD-type
PROSITE profile	PS50016	10.798	341	398	IPR019787	Zinc finger, PHD-finger
Pfam	PF00628	2.0E-10	343	398	IPR019787	Zinc finger, PHD-finger
CDD	cd15504	1.15E-28	343	395	No hit	No description
SMART	SM00249	6.9E-10	343	396	IPR001965	Zinc finger, PHD-type
PROSITE pattern	PS01359	0	344	395	IPR019786	Zinc finger, PHD-type, conserved site
PROSITE profile	PS50071	13.604	673	733	IPR001356	Homeobox domain
SMART	SM00389	5.0E-13	675	737	IPR001356	Homeobox domain
SuperFamily	SSF46689	1.33E-13	676	736	IPR009057	Homeodomain-like
Pfam	PF00046	1.1E-11	686	731	IPR001356	Homeobox domain
CDD	cd00086	6.53E-13	687	734	No hit	No description
Gene3D	G3DSA:1.10.10.60	2.7E-14	687	736	IPR009057	Homeodomain-like

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0005634	Cellular Component	nucleus
GO:0003677	Molecular Function	DNA binding
GO:0005515	Molecular Function	protein binding
GO:0008270	Molecular Function	zinc ion binding

Sequence ? help Back to Top
Protein Sequence Length: 821 aa Download sequence Send to blast
MASPTGELTS HNDGTTDRMG TEQCELSEKT PQIGSEGLEN EQKELGTELT SSVIEEKSNQ 60 VSAIVTENAV IQLPEPLQHD LQKNCQTVEG SCLEQSTVEQ VTVDLSNDKP ENKCKPLSEN 120 VQSEPVESIP AVVVEGQMQS NPSQANMSSV NELLDQPSGD AVNNISSNCS EKMSNSPTHS 180 QSRRKGKKNS KLLKKYMLRS LGSSDRALRS RTKEKPKEPE PTSNLVDGNN NGVKRKSGRK 240 KKKRKEEGIT NQFSRIRSHL RYLLNRISYE NSLIDAYSGE GWKGYSIEKL KPEKELQRAK 300 SEILRRKLKI RDLFQNLDSL CAEGKFPESL FDSAGEIDSE DIFCAKCQSK ELSTNNDIIL 360 CDGVCDRGFH QLCLDPPMLT EDIPPGDEGW LCPGCDCKDD CMDLVNDSFG TSLSISDTWE 420 RVFPEAASFA GNNMDNNSGV PSDDSDDDDY NPNGPDDVKV EGDESSSDES EYASASEKLE 480 GGSHEDQYLG LPSEDSDDGD YDPDAPDVEC KVNEESSSSD FTSDSEDLAA AIEDNTSPGQ 540 DGGISSSKKK GKVGKKLSLP DELSSLLEPD SGQEAPTPVS GKRHVERLDY KKLYEETYHS 600 DTSDDEDWND TAAPSGKKKL TGNVTPVSPN GNASNNSIHT PKRNAHQNNV ENTNNSPTKS 660 LEGCSKSGSR DKKSGSSAHK RLGEAVVQRL HKSFKENQYP DRTTKESLAQ ELGLTYQQVA 720 KWFGNTRWSF RHSSQMETNS GINASQQVTD GRAENEGEKE CELISLEFSG EKSKTPNSRK 780 RKHLSEPLSE AQLDINGSAA SSPNVHLTQI GNKMKTRKRK *

Sequence ? help Back to Top

Protein Sequence Length: 821 aa Download sequence Send to blast

MASPTGELTS HNDGTTDRMG TEQCELSEKT PQIGSEGLEN EQKELGTELT SSVIEEKSNQ  60
VSAIVTENAV IQLPEPLQHD LQKNCQTVEG SCLEQSTVEQ VTVDLSNDKP ENKCKPLSEN  120
VQSEPVESIP AVVVEGQMQS NPSQANMSSV NELLDQPSGD AVNNISSNCS EKMSNSPTHS  180
QSRRKGKKNS KLLKKYMLRS LGSSDRALRS RTKEKPKEPE PTSNLVDGNN NGVKRKSGRK  240
KKKRKEEGIT NQFSRIRSHL RYLLNRISYE NSLIDAYSGE GWKGYSIEKL KPEKELQRAK  300
SEILRRKLKI RDLFQNLDSL CAEGKFPESL FDSAGEIDSE DIFCAKCQSK ELSTNNDIIL  360
CDGVCDRGFH QLCLDPPMLT EDIPPGDEGW LCPGCDCKDD CMDLVNDSFG TSLSISDTWE  420
RVFPEAASFA GNNMDNNSGV PSDDSDDDDY NPNGPDDVKV EGDESSSDES EYASASEKLE  480
GGSHEDQYLG LPSEDSDDGD YDPDAPDVEC KVNEESSSSD FTSDSEDLAA AIEDNTSPGQ  540
DGGISSSKKK GKVGKKLSLP DELSSLLEPD SGQEAPTPVS GKRHVERLDY KKLYEETYHS  600
DTSDDEDWND TAAPSGKKKL TGNVTPVSPN GNASNNSIHT PKRNAHQNNV ENTNNSPTKS  660
LEGCSKSGSR DKKSGSSAHK RLGEAVVQRL HKSFKENQYP DRTTKESLAQ ELGLTYQQVA  720
KWFGNTRWSF RHSSQMETNS GINASQQVTD GRAENEGEKE CELISLEFSG EKSKTPNSRK  780
RKHLSEPLSE AQLDINGSAA SSPNVHLTQI GNKMKTRKRK *

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	186	194	KKNSKLLKK
2	238	243	RKKKKR
3	238	244	RKKKKRK
4	238	245	RKKKKRKE
5	239	244	KKKKRK

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
Gma.42079	0.0	somatic embryo

Expression -- Description ? help Back to Top
Source	Description
Uniprot	DEVELOPMENTAL STAGE: Expressed in the outer layers of globular embryos. {ECO:0000269\|PubMed:15094187}.
Uniprot	TISSUE SPECIFICITY: Expressed in roots, leaves, stems, panicle and seeds. {ECO:0000269\|PubMed:21951842}.

Functional Description ? help Back to Top
Source	Description
UniProt	Transcriptional repressor involved in the regulation of gibberrelin (GA) signaling. Binds to the 5'-GATC-3' motif of HD16/EL1 promoter. Functions as a positive regulator of GA signaling by suppressing the expression of HD16/EL1, a negative regulator of GA signaling. {ECO:0000269\|PubMed:21951842}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Glyma.10G260400.1.p

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: Induced by gibberellin. {ECO:0000269\|PubMed:21951842}.

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

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	BT090955	0.0	BT090955.1 Soybean clone JCVI-FLGm-5D8 unknown mRNA.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_006589630.1	0.0	homeobox protein HAT3.1
Swissprot	Q8H991	1e-138	HAZ1_ORYSJ; Homeobox protein HAZ1
TrEMBL	K7LLH5	0.0	K7LLH5_SOYBN; Uncharacterized protein
STRING	GLYMA10G40641.1	0.0	(Glycine max)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Fabids	OGEF8437	31	41
Representative plant	OGRP1830	15	39

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT3G19510.1	9e-95	Homeodomain-like protein with RING/FYVE/PHD-type zinc finger domain

Link Out ? help Back to Top
Phytozome	Glyma.10G260400.1.p
Entrez Gene	100306715

Publications ? help Back to Top
Kikuchi S, et al. Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice. Science, 2003. 301(5631): p. 376-9 [PMID:12869764] Wen BQ,Xing MQ,Zhang H,Dai C,Xue HW Rice homeobox transcription factor HOX1a positively regulates gibberellin responses by directly suppressing EL1. J Integr Plant Biol, 2011. 53(11): p. 869-78 [PMID:21951842]