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

XP_009129174.1

Organism

Brassica rapa

Taxonomic ID

3711

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Brassica

Family

C2H2

Protein Properties

Length: 492aa MW: 53634.2 Da PI: 9.3266

Description

C2H2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
XP_009129174.1	genome	NCBI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-C2H2	14.9	7.4e-05	82	104	1	23
EEETTTTEEESSHHHHHHHHHHT CS zf-C2H2 1 ykCpdCgksFsrksnLkrHirtH 23 + C C+k F r nL+ H r H XP_009129174.1 82 FICDVCKKGFQREQNLQLHRRGH 104 89*******************88 PP
2	zf-C2H2	13.4	0.00023	158	180	1	23
EEETTTTEEESSHHHHHHHHHHT CS zf-C2H2 1 ykCpdCgksFsrksnLkrHirtH 23 +kC++C+k++ +s+ k H +t+ XP_009129174.1 158 WKCEKCSKRYAVQSDWKAHSKTC 180 58*****************9998 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF57667	1.02E-6	81	104	No hit	No description
Gene3D	G3DSA:3.30.160.60	6.0E-5	81	104	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profile	PS50157	10.616	82	104	IPR007087	Zinc finger, C2H2
SMART	SM00355	0.014	82	104	IPR015880	Zinc finger, C2H2-like
PROSITE pattern	PS00028	0	84	104	IPR007087	Zinc finger, C2H2
SMART	SM00355	170	123	153	IPR015880	Zinc finger, C2H2-like
Gene3D	G3DSA:3.30.160.60	2.2E-5	146	179	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamily	SSF57667	1.02E-6	153	178	No hit	No description
SMART	SM00355	130	158	178	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: 492 aa Download sequence Send to blast
MSSSSYNASV APSSSSAEPF FLTGSGVGDN EFDRKDTFIS MIQEPNSSAQ PPKKRRNQPG 60 NPNPDAEVVA LSPKTLMATN RFICDVCKKG FQREQNLQLH RRGHNLPWKL KQKSTKDVKR 120 KVYLCPEPTC VHHDHSRALG DLTGIKKHYY RKHGEKKWKC EKCSKRYAVQ SDWKAHSKTC 180 GTKEYRCDCG TIFSRRDSYI THRAFCDALI QETARNSTVS FTSMASASSG AVSGGFYRRL 240 DGGNALAHRN LNDHHNSGFS TIPGYNLNIA SSENSRDYVQ QTSDPNFLNQ ISSSQRVLTV 300 PNNNDQSFMN EHGMIQFDPV NNTNLKSNTN NSFFNLGFFH ENTKNSETSL PSLYSTDVHT 360 RSSNVSATAL LQKATQMGSV TSNDPSAFFR GLASSSNSSS VVGNDFGGGQ IMGNNNNGSL 420 QGLVSSLVAV NGGGAGGSGG NIFDVHFGNI ENMSGSDKLT LDFLGVGGLV RNVNRGGGHG 480 DVPEQNHTFG RP

Sequence ? help Back to Top

Protein Sequence Length: 492 aa Download sequence Send to blast

MSSSSYNASV APSSSSAEPF FLTGSGVGDN EFDRKDTFIS MIQEPNSSAQ PPKKRRNQPG  60
NPNPDAEVVA LSPKTLMATN RFICDVCKKG FQREQNLQLH RRGHNLPWKL KQKSTKDVKR  120
KVYLCPEPTC VHHDHSRALG DLTGIKKHYY RKHGEKKWKC EKCSKRYAVQ SDWKAHSKTC  180
GTKEYRCDCG TIFSRRDSYI THRAFCDALI QETARNSTVS FTSMASASSG AVSGGFYRRL  240
DGGNALAHRN LNDHHNSGFS TIPGYNLNIA SSENSRDYVQ QTSDPNFLNQ ISSSQRVLTV  300
PNNNDQSFMN EHGMIQFDPV NNTNLKSNTN NSFFNLGFFH ENTKNSETSL PSLYSTDVHT  360
RSSNVSATAL LQKATQMGSV TSNDPSAFFR GLASSSNSSS VVGNDFGGGQ IMGNNNNGSL  420
QGLVSSLVAV NGGGAGGSGG NIFDVHFGNI ENMSGSDKLT LDFLGVGGLV RNVNRGGGHG  480
DVPEQNHTFG RP

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5b3h_C	7e-35	154	220	3	69	Zinc finger protein JACKDAW
5b3h_F	7e-35	154	220	3	69	Zinc finger protein JACKDAW
Search in ModeBase

Functional Description ? help Back to Top
Source	Description
UniProt	Transcription factor that may act a transcriptional activator of nuclear-encoded photosynthetic gene expression (Probable). 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:0000305\|PubMed:19726569}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	XP_009129174.1

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: Down-regulated by gibberellin. {ECO:0000305\|PubMed:17933900}.

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_009129169.1	0.0	PREDICTED: protein indeterminate-domain 4, chloroplastic-like
Refseq	XP_009129170.1	0.0	PREDICTED: protein indeterminate-domain 4, chloroplastic-like
Refseq	XP_009129171.1	0.0	PREDICTED: protein indeterminate-domain 4, chloroplastic-like
Refseq	XP_009129173.1	0.0	PREDICTED: protein indeterminate-domain 4, chloroplastic-like
Refseq	XP_009129174.1	0.0	PREDICTED: protein indeterminate-domain 4, chloroplastic-like
Swissprot	Q8GYC1	0.0	IDD4_ARATH; Protein indeterminate-domain 4, chloroplastic
TrEMBL	A0A398ALH0	0.0	A0A398ALH0_BRACM; Uncharacterized protein
STRING	Bra026616.1-P	0.0	(Brassica rapa)

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT2G02080.1	0.0	indeterminate(ID)-domain 4

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]