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_013606085.1

Organism

Brassica oleracea

Taxonomic ID

3712

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: 484aa MW: 50902 Da PI: 7.2931

Description

C2H2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
XP_013606085.1	genome	NCBI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-C2H2	16.7	2e-05	54	76	1	23
EEETTTTEEESSHHHHHHHHHHT CS zf-C2H2 1 ykCpdCgksFsrksnLkrHirtH 23 ++C++C+k F r nL+ H r H XP_013606085.1 54 FVCEICSKGFQRDQNLQLHRRGH 76 89*******************88 PP
2	zf-C2H2	15.7	4.4e-05	130	152	1	23
EEETTTTEEESSHHHHHHHHHHT CS zf-C2H2 1 ykCpdCgksFsrksnLkrHirtH 23 ykC++C+ks+ +s+ k H + + XP_013606085.1 130 YKCEKCSKSYAVQSDWKAHSKIC 152 9******************9876 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Gene3D	G3DSA:3.30.160.60	5.7E-5	53	76	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamily	SSF57667	2.74E-7	53	76	No hit	No description
SMART	SM00355	0.036	54	76	IPR015880	Zinc finger, C2H2-like
PROSITE profile	PS50157	10.887	54	76	IPR007087	Zinc finger, C2H2
PROSITE pattern	PS00028	0	56	76	IPR007087	Zinc finger, C2H2
SMART	SM00355	81	95	125	IPR015880	Zinc finger, C2H2-like
Gene3D	G3DSA:3.30.160.60	5.7E-5	118	151	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamily	SSF57667	2.74E-7	125	150	No hit	No description
SMART	SM00355	65	130	150	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: 484 aa Download sequence Send to blast
MPVDLDDSST VSGDASVSST GNQNPPPQSA VKKKHPDSEV IALSPKTLMT TNRFVCEICS 60 KGFQRDQNLQ LHRRGHNLPW KLRQRSSKEV RKKVYVCPVS GCVHHDPSRA LGDLTGIKKH 120 FCRKHGEKKY KCEKCSKSYA VQSDWKAHSK ICGSKEYRCD CGTLFSRRDS FITHRAFCDV 180 LAEESAKNHT QSKKLYPETV SESQQKSPAA VESPPPSPSP PPVAPSVSVS VESETEPEPA 240 NIASSLVLPI QDSSDDPENN TLEVIMEEAP GTIGLNGSND HSNNSKSVYA ALFASSSSSS 300 PSLYAASSTP SPSLFPPSSS MEPISLCLST TGPSLFGATI QDPPPPHFLT PLLPPPQPAI 360 SATALLQKAA QMGSTGSGGS LLRGLGIVST TSSPMELSSH DAGFGLGLGL PCSSGPGLKE 420 LMMGNSSVFD PKQTTLDFLG LGRAVGNGGN NTGGGLSALF GGGGGMDVFG SGELSDNDTG 480 RRSS

Sequence ? help Back to Top

Protein Sequence Length: 484 aa Download sequence Send to blast

MPVDLDDSST VSGDASVSST GNQNPPPQSA VKKKHPDSEV IALSPKTLMT TNRFVCEICS  60
KGFQRDQNLQ LHRRGHNLPW KLRQRSSKEV RKKVYVCPVS GCVHHDPSRA LGDLTGIKKH  120
FCRKHGEKKY KCEKCSKSYA VQSDWKAHSK ICGSKEYRCD CGTLFSRRDS FITHRAFCDV  180
LAEESAKNHT QSKKLYPETV SESQQKSPAA VESPPPSPSP PPVAPSVSVS VESETEPEPA  240
NIASSLVLPI QDSSDDPENN TLEVIMEEAP GTIGLNGSND HSNNSKSVYA ALFASSSSSS  300
PSLYAASSTP SPSLFPPSSS MEPISLCLST TGPSLFGATI QDPPPPHFLT PLLPPPQPAI  360
SATALLQKAA QMGSTGSGGS LLRGLGIVST TSSPMELSSH DAGFGLGLGL PCSSGPGLKE  420
LMMGNSSVFD PKQTTLDFLG LGRAVGNGGN NTGGGLSALF GGGGGMDVFG SGELSDNDTG  480
RRSS

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5b3h_C	2e-31	126	192	3	69	Zinc finger protein JACKDAW
5b3h_F	2e-31	126	192	3	69	Zinc finger protein JACKDAW
Search in ModeBase

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	80	92	KLRQRSSKEVRKK

Expression -- Description ? help Back to Top
Source	Description
Uniprot	DEVELOPMENTAL STAGE: Strongly up-regulated during seed development. {ECO:0000269\|PubMed:21571950}.
Uniprot	TISSUE SPECIFICITY: At 3 days post anthesis (DPA), expressed in the chalazal endosperm region. By 6 DPA, expressed in the endosperm and embryo. In fully germinated seed, strongest expression in the root tip and not detected in the cotyledons. In 4-days old seedlings, restricted to the vasculature of the cotyledons, the shoot apical meristem region, and the root tip. By 8 days, restricted to newly emerged leaves. {ECO:0000269\|PubMed:21571950}.

Functional Description ? help Back to Top
Source	Description
UniProt	Transcription factor promoting the transition to germination by regulating light and hormonal signaling during seed maturation (PubMed:21571950). Acts as a positive regulator of phytochrome and/or gibberellin action (PubMed:21571950, PubMed:25035403). {ECO:0000269\|PubMed:21571950, ECO:0000269\|PubMed:25035403}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	XP_013606085.1

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

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AC189225	0.0	AC189225.2 Brassica rapa subsp. pekinensis cultivar Inbred line 'Chiifu' clone KBrB011P07, complete sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_013606085.1	0.0	PREDICTED: protein indeterminate-domain 1-like isoform X2
Swissprot	Q9LVQ7	0.0	IDD1_ARATH; Zinc finger protein ENHYDROUS
TrEMBL	M4F7U0	0.0	M4F7U0_BRARP; Uncharacterized protein
STRING	Bra037151.1-P	0.0	(Brassica rapa)

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT5G66730.1	1e-157	C2H2-like zinc finger protein

Publications ? help Back to Top
Fukazawa J, et al. DELLAs function as coactivators of GAI-ASSOCIATED FACTOR1 in regulation of gibberellin homeostasis and signaling in Arabidopsis. Plant Cell, 2014. 26(7): p. 2920-38 [PMID:25035403] Moreno-Risueno MA, et al. Transcriptional control of tissue formation throughout root development. Science, 2015. 350(6259): p. 426-30 [PMID:26494755]