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_009117891.1

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: 467aa MW: 51305.9 Da PI: 9.1066

Description

C2H2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
XP_009117891.1	genome	NCBI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-C2H2	14.4	0.00011	83	103	3	23
ETTTTEEESSHHHHHHHHHHT CS zf-C2H2 3 CpdCgksFsrksnLkrHirtH 23 C+ C+k F r nL+ H r H XP_009117891.1 83 CEVCNKGFQREQNLQLHRRGH 103 *******************88 PP
2	zf-C2H2	11.5	0.00095	158	179	2	23
EETTTTEEESSHHHHHHHHHHT CS zf-C2H2 2 kCpdCgksFsrksnLkrHirtH 23 C++C+k++ +s+ k H + + XP_009117891.1 158 NCEKCSKRYAVQSDWKAHSKIC 179 6*****************9876 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF57667	9.16E-7	80	103	No hit	No description
Gene3D	G3DSA:3.30.160.60	8.7E-6	80	103	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profile	PS50157	10.97	81	103	IPR007087	Zinc finger, C2H2
SMART	SM00355	0.025	81	103	IPR015880	Zinc finger, C2H2-like
PROSITE pattern	PS00028	0	83	103	IPR007087	Zinc finger, C2H2
SMART	SM00355	58	122	152	IPR015880	Zinc finger, C2H2-like
Gene3D	G3DSA:3.30.160.60	7.6E-5	145	178	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamily	SSF57667	9.16E-7	152	177	No hit	No description
SMART	SM00355	220	157	177	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: 467 aa Download sequence Send to blast
MSSSYNNTIS SSSTQSFLLS SAATGSNNFN REETAMTMIQ QPNSVAPPPP PKKRRNQPGN 60 SYPDAEVIAL SPKTIMATNR FLCEVCNKGF QREQNLQLHR RGHNLPWKLK QKSNKEVRRK 120 VYICPEPTCV HHDPSRALGD LTGIKKHYYR KHGEKKWNCE KCSKRYAVQS DWKAHSKICG 180 TKEYRCDCGT IFSRRDSYIT HRAFCDALIQ ESARNPTVSF TAIAAASGGG GRHGFYDGAS 240 SALSHNHFGN NSNTGFTPLA AGYNLNRSSS EKFEDFIPQP TNPYHGPNNF LMQCSSNQGL 300 LAHNDQSLLN QHGMISLGDT ISNNNNNLFN LGNFQLNIKN SDQISAPSLF ADGAENNDPS 360 ALLRGLTSSS SSSAVVNEFG DNVNGNLHGL MNSLATTTDQ QGRSGSSIFD LHFGNNLSMG 420 GSDRLTLDFL GVNGRVMSNV NGRGGRNQAP LDTEMKFSQP NHPFERA

Sequence ? help Back to Top

Protein Sequence Length: 467 aa Download sequence Send to blast

MSSSYNNTIS SSSTQSFLLS SAATGSNNFN REETAMTMIQ QPNSVAPPPP PKKRRNQPGN  60
SYPDAEVIAL SPKTIMATNR FLCEVCNKGF QREQNLQLHR RGHNLPWKLK QKSNKEVRRK  120
VYICPEPTCV HHDPSRALGD LTGIKKHYYR KHGEKKWNCE KCSKRYAVQS DWKAHSKICG  180
TKEYRCDCGT IFSRRDSYIT HRAFCDALIQ ESARNPTVSF TAIAAASGGG GRHGFYDGAS  240
SALSHNHFGN NSNTGFTPLA AGYNLNRSSS EKFEDFIPQP TNPYHGPNNF LMQCSSNQGL  300
LAHNDQSLLN QHGMISLGDT ISNNNNNLFN LGNFQLNIKN SDQISAPSLF ADGAENNDPS  360
ALLRGLTSSS SSSAVVNEFG DNVNGNLHGL MNSLATTTDQ QGRSGSSIFD LHFGNNLSMG  420
GSDRLTLDFL GVNGRVMSNV NGRGGRNQAP LDTEMKFSQP NHPFERA

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5b3h_C	2e-32	153	219	3	69	Zinc finger protein JACKDAW
5b3h_F	2e-32	153	219	3	69	Zinc finger protein JACKDAW
Search in ModeBase

Functional Description ? help Back to Top
Source	Description
UniProt	Probable transcription factor. {ECO:0000305}.

Binding Motif ? help Back to Top
Motif ID	Method	Source	Motif file
MP00142	DAP	Transfer from AT1G14580	Download

Cis-element ? help Back to Top
Source	Link
PlantRegMap	XP_009117891.1

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	AK353183	0.0	AK353183.1 Thellungiella halophila mRNA, complete cds, clone: RTFL01-38-E19.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_018510654.1	0.0	PREDICTED: LOW QUALITY PROTEIN: protein indeterminate-domain 6, chloroplastic-like
Swissprot	Q8RWX7	0.0	IDD6_ARATH; Protein indeterminate-domain 6, chloroplastic
TrEMBL	M4EDF9	0.0	M4EDF9_BRARP; Uncharacterized protein
STRING	Bra026819.1-P	0.0	(Brassica rapa)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM3678	17	59

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT1G14580.2	0.0	C2H2-like zinc finger protein

Publications ? help Back to Top
Ding Y, et al. Four distinct types of dehydration stress memory genes in Arabidopsis thaliana. BMC Plant Biol., 2013. 13: p. 229 [PMID:24377444] Moreno-Risueno MA, et al. Transcriptional control of tissue formation throughout root development. Science, 2015. 350(6259): p. 426-30 [PMID:26494755] 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]