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

29643.m000323

Common Name

LOC8279905, RCOM_0550010

Organism

Ricinus communis

Taxonomic ID

3988

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Malpighiales; Euphorbiaceae; Acalyphoideae; Acalypheae; Ricinus

Family

C2H2

Protein Properties

Length: 543aa MW: 59791.9 Da PI: 9.1113

Description

C2H2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
29643.m000323	genome	JCVI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-C2H2	13.9	0.00016	66	86	3	23
ETTTTEEESSHHHHHHHHHHT CS zf-C2H2 3 CpdCgksFsrksnLkrHirtH 23 C++C+k F r nL+ H r H 29643.m000323 66 CEICNKGFQRDQNLQLHRRGH 86 *******************88 PP
2	zf-C2H2	11.7	0.00078	140	162	1	23
EEETTTTEEESSHHHHHHHHHHT CS zf-C2H2 1 ykCpdCgksFsrksnLkrHirtH 23 +kC++C+k + +s+ k H + + 29643.m000323 140 WKCEKCSKKYAVQSDWKAHSKIC 162 58*****************9876 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF57667	4.96E-7	63	86	No hit	No description
Gene3D	G3DSA:3.30.160.60	2.5E-5	63	86	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SMART	SM00355	0.11	64	86	IPR015880	Zinc finger, C2H2-like
PROSITE profile	PS50157	10.824	64	86	IPR007087	Zinc finger, C2H2
PROSITE pattern	PS00028	0	66	86	IPR007087	Zinc finger, C2H2
SMART	SM00355	110	105	135	IPR015880	Zinc finger, C2H2-like
Gene3D	G3DSA:3.30.160.60	1.7E-4	128	161	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamily	SSF57667	4.96E-7	135	160	No hit	No description
SMART	SM00355	140	140	160	IPR015880	Zinc finger, C2H2-like

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0003676	Molecular Function	nucleic acid binding
GO:0046872	Molecular Function	metal ion binding

Sequence ? help Back to Top
Protein Sequence Length: 543 aa Download sequence Send to blast
MMPEDGFSIP STIIGFVQEP TTNPNPNPTS NPVMKKKRNL PGTPDPDAEV VALSPKSLMA 60 TNRFLCEICN KGFQRDQNLQ LHRRGHNLPW KLKQRSTKEV KKKVYICPEK SCVHHDPSRA 120 LGDLTGIKKH FSRKHGEKKW KCEKCSKKYA VQSDWKAHSK ICGTREYRCD CGTLFSRKDS 180 FITHRAFCDA LAEESGRFTP VSAAINANLR NDLINGANSI NLPPPHHQTT VISQFSSVFR 240 PEFGTTTASE LLGSNNLGVD VQKPRLPIWL DNANPQLNPI GVGSNANSFL PHELVQTQQI 300 NMFGSGSSQL QWLSKYQEGL FTGSLPRGLK EEEGSKGDLT ESITSLYSSN HHHQQQRSSL 360 SSSSSAHMSA TALLQKAAQM GSTRSNNSIS LMSSSLSNVS NFNSYNQRKN NDETLKFLSS 420 RQPINQAENL NELANSISPS GTTPAATFTK ESTLLGDSNS SSVLTSTRNN TTKHWNHLIM 480 QQQANGDQQN HGFISSDEVV EGSLTRDFLG VGAAEAASRA PFLQHELVKF ASIGSGSHEF 540 EPI

Sequence ? help Back to Top

Protein Sequence Length: 543 aa Download sequence Send to blast

MMPEDGFSIP STIIGFVQEP TTNPNPNPTS NPVMKKKRNL PGTPDPDAEV VALSPKSLMA  60
TNRFLCEICN KGFQRDQNLQ LHRRGHNLPW KLKQRSTKEV KKKVYICPEK SCVHHDPSRA  120
LGDLTGIKKH FSRKHGEKKW KCEKCSKKYA VQSDWKAHSK ICGTREYRCD CGTLFSRKDS  180
FITHRAFCDA LAEESGRFTP VSAAINANLR NDLINGANSI NLPPPHHQTT VISQFSSVFR  240
PEFGTTTASE LLGSNNLGVD VQKPRLPIWL DNANPQLNPI GVGSNANSFL PHELVQTQQI  300
NMFGSGSSQL QWLSKYQEGL FTGSLPRGLK EEEGSKGDLT ESITSLYSSN HHHQQQRSSL  360
SSSSSAHMSA TALLQKAAQM GSTRSNNSIS LMSSSLSNVS NFNSYNQRKN NDETLKFLSS  420
RQPINQAENL NELANSISPS GTTPAATFTK ESTLLGDSNS SSVLTSTRNN TTKHWNHLIM  480
QQQANGDQQN HGFISSDEVV EGSLTRDFLG VGAAEAASRA PFLQHELVKF ASIGSGSHEF  540
EPI

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5b3h_C	3e-35	136	202	3	69	Zinc finger protein JACKDAW
5b3h_F	3e-35	136	202	3	69	Zinc finger protein JACKDAW
Search in ModeBase

Functional Description ? help Back to Top
Source	Description
UniProt	Transcription factor that, together with JKD, regulates tissue boundaries and asymmetric cell division in roots by a rapid up-regulation of 'SCARECROW' (SCR), thus controlling the nuclear localization of 'SHORT-ROOT' (SHR) and restricting its action (PubMed:25829440). Confines CYCD6 expression to the cortex-endodermis initial/daughter (CEI/CEID) tissues (PubMed:25829440). Binds DNA via its zinc fingers (PubMed:24821766). Recognizes and binds to SCL3 promoter sequence 5'-AGACAA-3' to promotes its expression when in complex with RGA (PubMed:24821766). {ECO:0000269\|PubMed:24821766, ECO:0000269\|PubMed:25829440}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	29643.m000323

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_002532599.1	0.0	protein indeterminate-domain 9
Refseq	XP_015582988.1	0.0	protein indeterminate-domain 9
Refseq	XP_015582989.1	0.0	protein indeterminate-domain 9
Refseq	XP_025015484.1	0.0	protein indeterminate-domain 9
Swissprot	Q944L3	1e-117	IDD9_ARATH; Zinc finger protein BALDIBIS
TrEMBL	B9T2Y0	0.0	B9T2Y0_RICCO; Nucleic acid binding protein, putative
STRING	XP_002532599.1	0.0	(Ricinus communis)

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
AT3G45260.1	1e-103	C2H2-like zinc finger protein

Link Out ? help Back to Top
Phytozome	29643.m000323
Entrez Gene	8279905

Publications ? help Back to Top
Moreno-Risueno MA, et al. Transcriptional control of tissue formation throughout root development. Science, 2015. 350(6259): p. 426-30 [PMID:26494755]