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

Lus10018633

Organism

Linum usitatissimum

Taxonomic ID

4006

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Malpighiales; Linaceae; Linum

Family

C2H2

Protein Properties

Length: 446aa MW: 49955.6 Da PI: 8.1988

Description

C2H2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Lus10018633	genome	BGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-C2H2	15.8	3.9e-05	8	28	3	23
ETTTTEEESSHHHHHHHHHHT CS zf-C2H2 3 CpdCgksFsrksnLkrHirtH 23 C++Cgk F r nL+ H r H Lus10018633 8 CEICGKGFQRDQNLQLHRRGH 28 *******************88 PP
2	zf-C2H2	11.1	0.0012	82	104	1	23
EEETTTTEEESSHHHHHHHHHHT CS zf-C2H2 1 ykCpdCgksFsrksnLkrHirtH 23 +kC++C k++ +s+ k H +t+ Lus10018633 82 WKCEKCAKRYAVQSDWKAHSKTC 104 58*****************9998 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF57667	4.23E-6	5	28	No hit	No description
Gene3D	G3DSA:3.30.160.60	3.8E-5	5	28	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profile	PS50157	11.489	6	28	IPR007087	Zinc finger, C2H2
PROSITE pattern	PS00028	0	8	28	IPR007087	Zinc finger, C2H2
Gene3D	G3DSA:3.30.160.60	2.1E-4	70	103	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamily	SSF57667	4.23E-6	77	102	No hit	No description

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0005634	Cellular Component	nucleus
GO:0044212	Molecular Function	transcription regulatory region DNA binding
GO:0046872	Molecular Function	metal ion binding

Sequence ? help Back to Top
Protein Sequence Length: 446 aa Download sequence Send to blast
MATNRFLCEI CGKGFQRDQN LQLHRRGHNL PWKLKQRTSK EIRKRVYVCP EKSCVHHHPS 60 RALGDLTGIK KHFCRKHGEK KWKCEKCAKR YAVQSDWKAH SKTCGTREYK CDCGTLFSRR 120 DSFITHRAFC DALAEETARM NAASSITSFS TLSNYNNLMG GQHHHNNNIM NPHNFSSMFK 180 PMISSSNTNE HQHQHQHQHP EEEEAELVLN NQHHHHQDRS GSLAFWMNQG LHQPQHQQEV 240 IVHVMPNGTS TNTSHQDHHQ IQQLGGSITS GEMFVPCTSS NPQSDHQHQH FDLSWPIVGL 300 NNVKELGHGS TELQSVPSLH QQASANMSAT ALLQKAAQMG ATSSSDNHHQ SKLCGLYGTS 360 TNSNCTSTSS LLFGSLHELE SLNSSTHMDQ LEQMQVMYPP LKRQRTFQSS DQDCGGGGQT 420 RDFLGVGAVQ AAAALCHPSS INGWI*

Sequence ? help Back to Top

Protein Sequence Length: 446 aa Download sequence Send to blast

MATNRFLCEI CGKGFQRDQN LQLHRRGHNL PWKLKQRTSK EIRKRVYVCP EKSCVHHHPS  60
RALGDLTGIK KHFCRKHGEK KWKCEKCAKR YAVQSDWKAH SKTCGTREYK CDCGTLFSRR  120
DSFITHRAFC DALAEETARM NAASSITSFS TLSNYNNLMG GQHHHNNNIM NPHNFSSMFK  180
PMISSSNTNE HQHQHQHQHP EEEEAELVLN NQHHHHQDRS GSLAFWMNQG LHQPQHQQEV  240
IVHVMPNGTS TNTSHQDHHQ IQQLGGSITS GEMFVPCTSS NPQSDHQHQH FDLSWPIVGL  300
NNVKELGHGS TELQSVPSLH QQASANMSAT ALLQKAAQMG ATSSSDNHHQ SKLCGLYGTS  360
TNSNCTSTSS LLFGSLHELE SLNSSTHMDQ LEQMQVMYPP LKRQRTFQSS DQDCGGGGQT  420
RDFLGVGAVQ AAAALCHPSS INGWI*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5b3h_C	1e-36	78	144	3	69	Zinc finger protein JACKDAW
5b3h_F	1e-36	78	144	3	69	Zinc finger protein JACKDAW
Search in ModeBase

Functional Description ? help Back to Top
Source	Description
UniProt	Transcription factor that regulates tissue boundaries and asymmetric cell division (PubMed:17785527, PubMed:25829440). Contributes to the sequestration of 'SHORT-ROOT' to the nucleus (PubMed:17785527, PubMed:25829440). Interacts with the SCR and MGP promoters (PubMed:21935722). Does not show transcription activity by itself, but regulates the transcription of downstream genes through interaction with other transcription factors (PubMed:21935722). 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). Positively involved in gibberellic acid (GA) signaling (PubMed:24821766). {ECO:0000269\|PubMed:17785527, ECO:0000269\|PubMed:21935722, ECO:0000269\|PubMed:24821766, ECO:0000269\|PubMed:25829440}.

Binding Motif ? help Back to Top
Motif ID	Method	Source	Motif file
MP00125	DAP	Transfer from AT1G03840	Download

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Lus10018633

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: Up-regulated by the transcription factor JKD, and down-regulated by SHR, SCR and itself. {ECO:0000269\|PubMed:21935722}.

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

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_021630010.1	1e-150	zinc finger protein MAGPIE-like
Swissprot	Q9ZWA6	1e-121	IDD3_ARATH; Zinc finger protein MAGPIE
TrEMBL	A0A2C9UUT0	1e-149	A0A2C9UUT0_MANES; Uncharacterized protein
STRING	Lus10018633	0.0	(Linum usitatissimum)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Fabids	OGEF4626	29	51

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT1G03840.2	1e-112	C2H2 family protein

Link Out ? help Back to Top
Phytozome	Lus10018633

Publications ? help Back to Top
Muñoz-Strale D,León G Identification of two highly specific pollen promoters using transcriptomic data. Plant Physiol. Biochem., 2014. 83: p. 292-9 [PMID:25208507] Moreno-Risueno MA, et al. Transcriptional control of tissue formation throughout root development. Science, 2015. 350(6259): p. 426-30 [PMID:26494755]