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

GSBRNA2T00143932001

Common Name

GSBRNA2T00143932001

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: 449aa MW: 50068.3 Da PI: 9.7134

Description

C2H2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
GSBRNA2T00143932001	genome	Genoscope	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-C2H2	19.8	2.1e-06	71	93	1	23
EEETTTTEEESSHHHHHHHHHHT CS zf-C2H2 1 ykCpdCgksFsrksnLkrHirtH 23 + C++C+k F+r nL+ H r H GSBRNA2T00143932001 71 FICEICNKGFKRDQNLQLHRRGH 93 89*******************88 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF57667	9.83E-8	70	93	No hit	No description
Gene3D	G3DSA:3.30.160.60	5.2E-6	70	93	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SMART	SM00355	0.011	71	93	IPR015880	Zinc finger, C2H2-like
PROSITE profile	PS50157	10.866	71	93	IPR007087	Zinc finger, C2H2
Pfam	PF12171	1.6E-5	71	93	IPR022755	Zinc finger, double-stranded RNA binding
PROSITE pattern	PS00028	0	73	93	IPR007087	Zinc finger, C2H2
SMART	SM00355	93	113	143	IPR015880	Zinc finger, C2H2-like
Gene3D	G3DSA:3.30.160.60	3.9E-4	136	169	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamily	SSF57667	9.83E-8	143	168	No hit	No description
SMART	SM00355	190	148	168	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: 449 aa Download sequence Send to blast
MIIPDDPHLL SFPSYVLHQE HITPNPNPNP NPTASKSNKR KRNLPGNPGM YNPDAEVIAL 60 SPNSLMTTNR FICEICNKGF KRDQNLQLHR RGHNLPWKLK QRTDKEQVKK KVYICPENTC 120 VHHDPGRALG DLTGIKKHFS RKHGEKKWKC DKCSKKYAVV SDWKAHSKIC GTREYRCDCG 180 TLFSRKDSFI THRAFCDALA EESARFASLP PAAAAYLNNS SDAEVNLGNI KPNHQQRLLD 240 CTSSQLDRHD FNVNRNNING FTGQSSTNQL PLAANVFASS SSPSPHSASA LLQNLWQLQG 300 QSYQQLLLNK NNNNIIQSGM PNNQEDHDTI KRELVINGSL FSSEARTSYN QNGGQEIASM 360 SATALLQMAA QMGSKRSSSS SNNGMAFGLM TSSIFNNKEM ENKIKTKEVD ERGFTRDFLG 420 EGSQNRPRPI LMVNHNLPTT TTAHQPPT*

Sequence ? help Back to Top

Protein Sequence Length: 449 aa Download sequence Send to blast

MIIPDDPHLL SFPSYVLHQE HITPNPNPNP NPTASKSNKR KRNLPGNPGM YNPDAEVIAL  60
SPNSLMTTNR FICEICNKGF KRDQNLQLHR RGHNLPWKLK QRTDKEQVKK KVYICPENTC  120
VHHDPGRALG DLTGIKKHFS RKHGEKKWKC DKCSKKYAVV SDWKAHSKIC GTREYRCDCG  180
TLFSRKDSFI THRAFCDALA EESARFASLP PAAAAYLNNS SDAEVNLGNI KPNHQQRLLD  240
CTSSQLDRHD FNVNRNNING FTGQSSTNQL PLAANVFASS SSPSPHSASA LLQNLWQLQG  300
QSYQQLLLNK NNNNIIQSGM PNNQEDHDTI KRELVINGSL FSSEARTSYN QNGGQEIASM  360
SATALLQMAA QMGSKRSSSS SNNGMAFGLM TSSIFNNKEM ENKIKTKEVD ERGFTRDFLG  420
EGSQNRPRPI LMVNHNLPTT TTAHQPPT*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5b3h_C	6e-36	144	209	3	68	Zinc finger protein JACKDAW
5b3h_F	6e-36	144	209	3	68	Zinc finger protein JACKDAW
Search in ModeBase

Expression -- Description ? help Back to Top
Source	Description
Uniprot	TISSUE SPECIFICITY: Expressed in roots, especially in vascular initials, cortex, endodermis, and quiescent center (QC). {ECO:0000269\|PubMed:25829440}.

Functional Description ? help Back to Top
Source	Description
UniProt	Transcription factor that, together with JKD, regulates tissue boundaries and asymmetric cell division in roots by a rapid up-regulation of 'SCARECROW' (SCR), thus controlling the nuclear localization of 'SHORT-ROOT' (SHR) and restricting its action (PubMed:25829440). Confines CYCD6 expression to the cortex-endodermis initial/daughter (CEI/CEID) tissues (PubMed:25829440). 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:0000269\|PubMed:25829440}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	GSBRNA2T00143932001

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_013641314.1	0.0	protein indeterminate-domain 9-like isoform X1
Swissprot	Q944L3	0.0	IDD9_ARATH; Zinc finger protein BALDIBIS
TrEMBL	A0A3P6BCG0	0.0	A0A3P6BCG0_BRAOL; Uncharacterized protein
STRING	Bra038293.1-P	0.0	(Brassica rapa)
STRING	Bo3g129830.1	0.0	(Brassica oleracea)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM155	28	306

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT3G45260.1	1e-174	C2H2-like zinc finger protein

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] Moreno-Risueno MA, et al. Transcriptional control of tissue formation throughout root development. Science, 2015. 350(6259): p. 426-30 [PMID:26494755]