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

GSBRNA2T00102083001

Common Name

GSBRNA2T00102083001

Organism

Brassica napus

Taxonomic ID

3708

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: 234aa MW: 26757.2 Da PI: 9.6736

Description

C2H2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
GSBRNA2T00102083001	genome	Genoscope	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-C2H2	19.7	2.3e-06	68	90	1	23
EEETTTTEEESSHHHHHHHHHHT CS zf-C2H2 1 ykCpdCgksFsrksnLkrHirtH 23 y+C++C++ F r nL+ H r+H GSBRNA2T00102083001 68 YVCEICNQGFQRDQNLQMHRRRH 90 9*********************9 PP
2	zf-C2H2	14.8	8.5e-05	147	168	2	23
EETTTTEEESSHHHHHHHHHHT CS zf-C2H2 2 kCpdCgksFsrksnLkrHirtH 23 C+ C+k + +s++k H++t+ GSBRNA2T00102083001 147 ICERCSKGYAVQSDYKAHLKTC 168 7*******************98 PP
3	zf-C2H2	11.3	0.0011	176	194	5	23
TTTEEESSHHHHHHHHHHT CS zf-C2H2 5 dCgksFsrksnLkrHirtH 23 dCg++Fsr +++ H+ ++ GSBRNA2T00102083001 176 DCGRVFSRVESFIEHQDNC 194 9**************9877 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF57667	2.02E-5	65	91	No hit	No description
Gene3D	G3DSA:3.30.160.60	7.9E-6	67	90	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SMART	SM00355	0.0052	68	90	IPR015880	Zinc finger, C2H2-like
PROSITE profile	PS50157	10.97	68	90	IPR007087	Zinc finger, C2H2
Pfam	PF12874	0.0097	68	86	No hit	No description
PROSITE pattern	PS00028	0	70	90	IPR007087	Zinc finger, C2H2
SMART	SM00355	160	110	140	IPR015880	Zinc finger, C2H2-like
Gene3D	G3DSA:3.30.160.60	4.6E-4	137	167	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SMART	SM00355	110	146	173	IPR015880	Zinc finger, C2H2-like
Pfam	PF09596	2.2E-4	183	218	IPR019082	Neurogenic mastermind-like, N-terminal

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0007219	Biological Process	Notch signaling pathway
GO:0045944	Biological Process	positive regulation of transcription from RNA polymerase II promoter
GO:0016607	Cellular Component	nuclear speck
GO:0003676	Molecular Function	nucleic acid binding
GO:0003713	Molecular Function	transcription coactivator activity
GO:0046872	Molecular Function	metal ion binding

Sequence ? help Back to Top
Protein Sequence Length: 234 aa Download sequence Send to blast
MINYERSKNT KNINHHRNPP SSSSSDLLPD GNGAAVTQKR KRRPAGTPDP EAEVVALSPR 60 TLLESDRYVC EICNQGFQRD QNLQMHRRRH KVPWKLLKRE TTEEVKKRVY VCPEPTCLHH 120 NPCHALGDLV GIKKHFRRKH SNHKQWICER CSKGYAVQSD YKAHLKTCGT RGHSCDCGRV 180 FSRVESFIEH QDNCTMRQSQ PSSHRVQQQQ QHTANAAQTA STAENIDLYT VII*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5b3h_C	5e-18	142	194	3	55	Zinc finger protein JACKDAW
5b3h_F	5e-18	142	194	3	55	Zinc finger protein JACKDAW
Search in ModeBase

Expression -- Description ? help Back to Top
Source	Description
Uniprot	TISSUE SPECIFICITY: Expressed in cotyledons and the vasculature of reosette leaves. Weak expression in hypocotyls and floral organs, but not detected in roots and inflorescence stems. {ECO:0000269\|PubMed:24039602}.

Functional Description ? help Back to Top
Source	Description
UniProt	Transcription factor regulating starch metabolism by binding directly to the promoter of QQS (PubMed:21556057). The IDD14beta isoform attenuates the transcription factor activity by competitively forming heterodimers with reduced DNA-binding capacity(PubMed:21556057). Regulates lateral organ morphogenesis and gravitropic responses (PubMed:24039602). Has a redundant role with IDD16 in directing leaf and floral organ morphogenesis (PubMed:24039602). Involved in the establishment of auxin gradients through the regulation of auxin biosynthesis and transport (PubMed:24039602). {ECO:0000269\|PubMed:21556057, ECO:0000269\|PubMed:24039602}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	GSBRNA2T00102083001

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: Not regulated by auxin. {ECO:0000269\|PubMed:24039602}.

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	AC189489	0.0	AC189489.2 Brassica rapa subsp. pekinensis cultivar Inbred line 'Chiifu' clone KBrB084K02, complete sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_018445099.1	1e-158	PREDICTED: protein indeterminate-domain 14-like
Swissprot	Q9C9X7	1e-145	IDD14_ARATH; Protein indeterminate-domain 14
TrEMBL	A0A397YWV0	1e-155	A0A397YWV0_BRACM; Uncharacterized protein
TrEMBL	A0A3P6BWK8	1e-155	A0A3P6BWK8_BRACM; Uncharacterized protein
STRING	Bra004283.1-P	1e-155	(Brassica rapa)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM693	28	131

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT1G68130.1	1e-130	indeterminate(ID)-domain 14

Publications ? help Back to Top
Chalhoub B, et al. Plant genetics. Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome. Science, 2014. 345(6199): p. 950-3 [PMID:25146293] Arendsee ZW,Li L,Wurtele ES Coming of age: orphan genes in plants. Trends Plant Sci., 2014. 19(11): p. 698-708 [PMID:25151064] Qu Y, et al. Peroxisomal CuAOζ and its product H2O2 regulate the distribution of auxin and IBA-dependent lateral root development in Arabidopsis. J. Exp. Bot., 2017. 68(17): p. 4851-4867 [PMID:28992128]