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

GSBRNA2T00040747001

Common Name

GSBRNA2T00040747001

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: 452aa MW: 50412.9 Da PI: 8.8698

Description

C2H2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
GSBRNA2T00040747001	genome	Genoscope	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-C2H2	17.5	1.1e-05	81	103	1	23
EEETTTTEEESSHHHHHHHHHHT CS zf-C2H2 1 ykCpdCgksFsrksnLkrHirtH 23 y C++C++ F r nL+ H r+H GSBRNA2T00040747001 81 YICEICNQGFQRDQNLQMHRRRH 103 89********************9 PP
2	zf-C2H2	14.5	0.0001	159	181	1	23
EEETTTTEEESSHHHHHHHHHHT CS zf-C2H2 1 ykCpdCgksFsrksnLkrHirtH 23 ++C+ C+k + +s++k H++t+ GSBRNA2T00040747001 159 WVCERCSKGYAVQSDYKAHLKTC 181 58*******************98 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF57667	5.97E-5	78	104	No hit	No description
Gene3D	G3DSA:3.30.160.60	1.3E-5	80	103	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profile	PS50157	10.866	81	103	IPR007087	Zinc finger, C2H2
SMART	SM00355	0.0065	81	103	IPR015880	Zinc finger, C2H2-like
PROSITE pattern	PS00028	0	83	103	IPR007087	Zinc finger, C2H2
SMART	SM00355	160	123	153	IPR015880	Zinc finger, C2H2-like
Gene3D	G3DSA:3.30.160.60	6.6E-4	150	180	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SMART	SM00355	100	159	186	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: 452 aa Download sequence Send to blast
MRTDQGAVVM LDDDASNKNT SNPCCVVSSS SSDPFLTSSE NGVTTTNTST KKRKRRPAGT 60 PDPDAEVVSL SPRTLLESDR YICEICNQGF QRDQNLQMHR RRHKVPWKLL KRDNNIEVKK 120 RVYVCPEPTC LHHSPCHALG DLVGIKKHFR RKHSNHKQWV CERCSKGYAV QSDYKAHLKT 180 CGTRGHSCDC GRVFSRVESF IEHQDNCSVR KVNRKPPPPQ TAVAVPACSS ITASTASTPS 240 SEGNNCGAVA VATPIPLEGR PIHLRNSCFT PSILTNSSSL NLELQLLPLT SNQNPNQENH 300 QHKVNEPSHH HHHHDTTNLN LSIAPSSSSY HRPYNNFDRI KEIMASEQMM KIAMKEKAYA 360 EEAKREAKRQ REMAENEFMN AKKIRQQAQA ELERAKLLKE QSMKKISSTI MQVTCQTCKG 420 QFQAVAVPAA ADETSLVVSY MSSANTDGEE S*

Sequence ? help Back to Top

Protein Sequence Length: 452 aa Download sequence Send to blast

MRTDQGAVVM LDDDASNKNT SNPCCVVSSS SSDPFLTSSE NGVTTTNTST KKRKRRPAGT  60
PDPDAEVVSL SPRTLLESDR YICEICNQGF QRDQNLQMHR RRHKVPWKLL KRDNNIEVKK  120
RVYVCPEPTC LHHSPCHALG DLVGIKKHFR RKHSNHKQWV CERCSKGYAV QSDYKAHLKT  180
CGTRGHSCDC GRVFSRVESF IEHQDNCSVR KVNRKPPPPQ TAVAVPACSS ITASTASTPS  240
SEGNNCGAVA VATPIPLEGR PIHLRNSCFT PSILTNSSSL NLELQLLPLT SNQNPNQENH  300
QHKVNEPSHH HHHHDTTNLN LSIAPSSSSY HRPYNNFDRI KEIMASEQMM KIAMKEKAYA  360
EEAKREAKRQ REMAENEFMN AKKIRQQAQA ELERAKLLKE QSMKKISSTI MQVTCQTCKG  420
QFQAVAVPAA ADETSLVVSY MSSANTDGEE S*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5b3h_C	1e-17	155	207	3	55	Zinc finger protein JACKDAW
5b3h_F	1e-17	155	207	3	55	Zinc finger protein JACKDAW
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Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	50	55	KKRKRR

Expression -- Description ? help Back to Top
Source	Description
Uniprot	DEVELOPMENTAL STAGE: Expression levels gradually decrease with aging in both the shoot and root vasculature. {ECO:0000269\|PubMed:16813575}.
Uniprot	TISSUE SPECIFICITY: Mainly expressed in the endodermis, the gravity-sensing tissue in inflorescence stems. Mostly present in stems and flowers, and, to a lower extent, in seedlings, hypocotyls, roots and the shoot apical meristem (SAM). {ECO:0000269\|PubMed:16813575}.

Functional Description ? help Back to Top
Source	Description
UniProt	Transcription factor involved in inflorescence stems gravitropism, probably by regulating starch accumulation in amyloplasts of graviperceptive cells. Required for stem circumnutation movements. Regulates lateral organ morphogenesis and gravitropic responses (PubMed:24039602). Acts cooperatively with IDD16 to control silique and branche orientation (PubMed:24039602). Involved in the establishment of auxin gradients through the regulation of auxin biosynthesis and transport (PubMed:24039602). {ECO:0000269\|PubMed:16813575, ECO:0000269\|PubMed:18259878, ECO:0000269\|PubMed:24039602, ECO:0000269\|PubMed:9210330}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	GSBRNA2T00040747001

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	AK226703	0.0	AK226703.1 Arabidopsis thaliana mRNA for putative C2H2-type zinc finger protein, complete cds, clone: RAFL07-61-I21.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_013607262.1	0.0	PREDICTED: protein SHOOT GRAVITROPISM 5-like
Swissprot	F4IPE3	0.0	IDD15_ARATH; Zinc finger protein SHOOT GRAVITROPISM 5
TrEMBL	A0A078JCY5	0.0	A0A078JCY5_BRANA; BnaC09g52310D protein
STRING	Bo9g070370.1	0.0	(Brassica oleracea)

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
AT2G01940.1	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] 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] Kim JY,Ryu JY,Baek K,Park CM High temperature attenuates the gravitropism of inflorescence stems by inducing SHOOT GRAVITROPISM 5 alternative splicing in Arabidopsis. New Phytol., 2016. 209(1): p. 265-79 [PMID:26256266] Ryu JY,Kim JY,Park CM Adaptive thermal control of stem gravitropism through alternative RNA splicing in Arabidopsis. Plant Signal Behav, 2015. 10(11): p. e1093715 [PMID:26452406] 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] Shi H, et al. Zinc finger of Arabidopsis thaliana 6 is involved in melatonin-mediated auxin signaling through interacting INDETERMINATE DOMAIN15 and INDOLE-3-ACETIC ACID 17. J. Pineal Res., 2018. 65(2): p. e12494 [PMID:29607541]