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

KHN09491.1

Organism

Glycine soja

Taxonomic ID

3848

Taxonomic Lineage

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

Family

C2H2

Protein Properties

Length: 514aa MW: 55810.4 Da PI: 9.807

Description

C2H2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
KHN09491.1	genome	TCUHK	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-C2H2	16.1	3.1e-05	67	89	1	23
EEETTTTEEESSHHHHHHHHHHT CS zf-C2H2 1 ykCpdCgksFsrksnLkrHirtH 23 + C++C+k F r nL+ H r H KHN09491.1 67 FICEICNKGFQRDQNLQLHRRGH 89 89*******************88 PP
2	zf-C2H2	13.9	0.00016	143	165	1	23
EEETTTTEEESSHHHHHHHHHHT CS zf-C2H2 1 ykCpdCgksFsrksnLkrHirtH 23 +kC++C+k + +s+ k H +t+ KHN09491.1 143 WKCEKCSKKYAVQSDWKAHTKTC 165 58*******************98 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF57667	4.07E-7	66	89	No hit	No description
Gene3D	G3DSA:3.30.160.60	1.4E-5	66	89	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profile	PS50157	10.845	67	89	IPR007087	Zinc finger, C2H2
SMART	SM00355	0.022	67	89	IPR015880	Zinc finger, C2H2-like
Pfam	PF12171	6.2E-5	67	89	IPR022755	Zinc finger, double-stranded RNA binding
PROSITE pattern	PS00028	0	69	89	IPR007087	Zinc finger, C2H2
SMART	SM00355	98	108	138	IPR015880	Zinc finger, C2H2-like
Gene3D	G3DSA:3.30.160.60	4.6E-5	131	164	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamily	SSF57667	4.07E-7	138	163	No hit	No description
SMART	SM00355	130	143	163	IPR015880	Zinc finger, C2H2-like

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0010075	Biological Process	regulation of meristem growth
GO:0045604	Biological Process	regulation of epidermal cell differentiation
GO:0048364	Biological Process	root development
GO:0051302	Biological Process	regulation of cell division
GO:0003676	Molecular Function	nucleic acid binding
GO:0042803	Molecular Function	protein homodimerization activity
GO:0046872	Molecular Function	metal ion binding

Sequence ? help Back to Top
Protein Sequence Length: 514 aa Download sequence Send to blast
MQMIPGDPFS LSTSLPAGLP NEQSTNTNPN PNPPPPNKKK RNLPGTPDPD AEVIALSPKT 60 LMATNRFICE ICNKGFQRDQ NLQLHRRGHN LPWKLRQRSN KEVRKKVYIC PEKTCVHHDA 120 ARALGDLTGI KKHYSRKHGE KKWKCEKCSK KYAVQSDWKA HTKTCGTREY KCDCGNLFSR 180 KDSFITHRAF CDALADESSR LTSVASTSLN FKNEDATMIN TQASLSTRGL ITGHGMQNVS 240 QFGPHGFRLM NMGTDQQRPN LSLWLNQGNH HINNPLDVAL SSSSSGLPEV VHMAQANINN 300 NALIGSSSVF SNFGMPASSN SSNPNLMGKK GDGGASDLAS MYSESQNKNS NSTSPMSATA 360 LLQKAAQMGS TRSTNPSIFS GSFGVMSSSS TQSTSLNSNI ANQSCDQLNQ AFQNFNATSS 420 SSATMLGSST NFSSLTHSSN GFDQFMMQNK VEPTQLKLHH PGSNSVEHNL TRDFLGVSGN 480 GGGHVHHAFL PQELAKFASL GSSMGLNQFT VGHQ

Sequence ? help Back to Top

Protein Sequence Length: 514 aa Download sequence Send to blast

MQMIPGDPFS LSTSLPAGLP NEQSTNTNPN PNPPPPNKKK RNLPGTPDPD AEVIALSPKT  60
LMATNRFICE ICNKGFQRDQ NLQLHRRGHN LPWKLRQRSN KEVRKKVYIC PEKTCVHHDA  120
ARALGDLTGI KKHYSRKHGE KKWKCEKCSK KYAVQSDWKA HTKTCGTREY KCDCGNLFSR  180
KDSFITHRAF CDALADESSR LTSVASTSLN FKNEDATMIN TQASLSTRGL ITGHGMQNVS  240
QFGPHGFRLM NMGTDQQRPN LSLWLNQGNH HINNPLDVAL SSSSSGLPEV VHMAQANINN  300
NALIGSSSVF SNFGMPASSN SSNPNLMGKK GDGGASDLAS MYSESQNKNS NSTSPMSATA  360
LLQKAAQMGS TRSTNPSIFS GSFGVMSSSS TQSTSLNSNI ANQSCDQLNQ AFQNFNATSS  420
SSATMLGSST NFSSLTHSSN GFDQFMMQNK VEPTQLKLHH PGSNSVEHNL TRDFLGVSGN  480
GGGHVHHAFL PQELAKFASL GSSMGLNQFT VGHQ

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5b3h_C	2e-35	139	208	3	72	Zinc finger protein JACKDAW
5b3h_F	2e-35	139	208	3	72	Zinc finger protein JACKDAW
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Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	93	105	KLRQRSNKEVRKK

Functional Description ? help Back to Top
Source	Description
UniProt	Transcription factor that, together with BIB, regulates tissue boundaries and asymmetric cell division by a rapid up-regulation of 'SCARECROW' (SCR), thus controlling the nuclear localization of 'SHORT-ROOT' (SHR) and restricting its action (PubMed:17785527, PubMed:25829440). Binds DNA via its zinc fingers (PubMed:28211915, PubMed:24821766). Recognizes and binds to SCL3 promoter sequence 5'-AGACAA-3' to promotes its expression when in complex with RGA (PubMed:24821766). Confines CYCD6 expression to the cortex-endodermis initial/daughter (CEI/CEID) tissues (PubMed:25829440). Required for radial patterning and stem cell maintenance (PubMed:17785527). Counteracted by 'MAGPIE' (MGP) (PubMed:17785527). Binds to the SCR and MGP promoter sequences (PubMed:21935722). Controls position-dependent signals that regulate epidermal-cell-type patterning (PubMed:20356954). {ECO:0000269\|PubMed:17785527, ECO:0000269\|PubMed:20356954, ECO:0000269\|PubMed:21935722, ECO:0000269\|PubMed:24821766, ECO:0000269\|PubMed:25829440, ECO:0000269\|PubMed:28211915}.

Binding Motif ? help Back to Top
Motif ID	Method	Source	Motif file
MP00485	DAP	Transfer from AT5G03150	Download

Cis-element ? help Back to Top
Source	Link
PlantRegMap	KHN09491.1

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: Not regulated by SCR and SHR. {ECO:0000269\|PubMed:21935722}.

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

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AP015037	1e-165	AP015037.1 Vigna angularis var. angularis DNA, chromosome 4, almost complete sequence, cultivar: Shumari.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_028225828.1	0.0	zinc finger protein JACKDAW-like
Refseq	XP_028225830.1	0.0	zinc finger protein JACKDAW-like
Swissprot	Q700D2	1e-132	IDD10_ARATH; Zinc finger protein JACKDAW
TrEMBL	A0A445LE53	0.0	A0A445LE53_GLYSO; Zinc finger protein JACKDAW
STRING	GLYMA03G33700.1	0.0	(Glycine max)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Fabids	OGEF181	34	275

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT5G03150.1	1e-114	C2H2-like zinc finger protein

Publications ? help Back to Top
Qi X, et al. Identification of a novel salt tolerance gene in wild soybean by whole-genome sequencing. Nat Commun, 2014. 5: p. 4340 [PMID:25004933] Moreno-Risueno MA, et al. Transcriptional control of tissue formation throughout root development. Science, 2015. 350(6259): p. 426-30 [PMID:26494755] Hirano Y, et al. Structure of the SHR-SCR heterodimer bound to the BIRD/IDD transcriptional factor JKD. Nat Plants, 2017. 3: p. 17010 [PMID:28211915] Kobayashi A,Miura S,Kozaki A INDETERMINATE DOMAIN PROTEIN binding sequences in the 5'-untranslated region and promoter of the SCARECROW gene play crucial and distinct roles in regulating SCARECROW expression in roots and leaves. Plant Mol. Biol., 2017. 94(1-2): p. 1-13 [PMID:28324206] Long Y, et al. In vivo FRET-FLIM reveals cell-type-specific protein interactions in Arabidopsis roots. Nature, 2017. 548(7665): p. 97-102 [PMID:28746306] Bustillo-Avendaño E, et al. Regulation of Hormonal Control, Cell Reprogramming, and Patterning during De Novo Root Organogenesis. Plant Physiol., 2018. 176(2): p. 1709-1727 [PMID:29233938]