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_009794508.1

Organism

Nicotiana sylvestris

Taxonomic ID

4096

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; lamiids; Solanales; Solanaceae; Nicotianoideae; Nicotianeae; Nicotiana

Family

GRF

Protein Properties

Length: 329aa MW: 36347.2 Da PI: 8.868

Description

GRF family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
XP_009794508.1	genome	NCBI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	WRC	77	1.9e-24	92	136	1	45
WRC 1 daepgrCrRtDGKkWRCsrrvlegkklCErHlhrgrsrsrkskee 45 d+epgrCrRtDGKkWRCs+++ +++k+CErH+hrgr+rsrk++e+ XP_009794508.1 92 DPEPGRCRRTDGKKWRCSKDAHPDSKYCERHMHRGRNRSRKPVES 136 79****************************************986 PP
2	QLQ	65.6	1.2e-22	31	66	2	37
QLQ 2 aFTaaQlqlLksQilAyKyLaanqPvPpeLlqaiqk 37 +FTa Q+q+L++Q+++yKyL+a++PvPp+L+++i++ XP_009794508.1 31 PFTAVQWQELEHQAMIYKYLVAGLPVPPDLVVPIRR 66 9*********************************86 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SMART	SM00951	7.9E-13	30	66	IPR014978	Glutamine-Leucine-Glutamine, QLQ
Pfam	PF08880	3.9E-17	31	65	IPR014978	Glutamine-Leucine-Glutamine, QLQ
PROSITE profile	PS51666	24.343	31	66	IPR014978	Glutamine-Leucine-Glutamine, QLQ
PROSITE profile	PS51667	25.831	92	136	IPR014977	WRC domain
Pfam	PF08879	5.9E-21	93	135	IPR014977	WRC domain

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0006355	Biological Process	regulation of transcription, DNA-templated
GO:0005634	Cellular Component	nucleus
GO:0005524	Molecular Function	ATP binding

Sequence ? help Back to Top
Protein Sequence Length: 329 aa Download sequence Send to blast
MSGTSTSLGV GVGGGGGEGG VLSYDYGFRP PFTAVQWQEL EHQAMIYKYL VAGLPVPPDL 60 VVPIRRSFDA ISARFFNHPS LSYCSYYGKK FDPEPGRCRR TDGKKWRCSK DAHPDSKYCE 120 RHMHRGRNRS RKPVESQSTS QSLSTSMSHI TTGSSNRSGS FQSNSSGNFH NMPLYSVANS 180 DGLSYGSTAT KLQMEPVSYG INNKEYRYLQ GMVPDAEGSS EVSASVRNLG MGSNTDNIWR 240 PPHPFEPVTN ATIAKQQPQH CFFGNDIDPP VKQEPHPMRS FFDEWPTSKE SWSNLDDGSS 300 KNNFSTTQLS ISIPNVHSGF SSTSTRSPK

Functional Description ? help Back to Top
Source	Description
UniProt	Transcription activator that plays a role in the regulation of meristematic function in leaves, stems and inflorescences (PubMed:24532604). Transcription activator that plays a regulatory role in grain development (PubMed:26187814, PubMed:27250747, PubMed:27250749, PubMed:26936408, PubMed:27107174). Positively regulates grain size by promoting cell division and expansion, leading to increased grain length and width (PubMed:26187814, PubMed:27250747, PubMed:27250749, PubMed:26936408, PubMed:27107174). Positively regulates the expression of genes promoting cell proliferation (PubMed:26187814, PubMed:26936408). Activates the expression of expansin genes to promote cell expansion and grain size (PubMed:27250747). May promote grain size by activating brassinosteroid responses (PubMed:27250747). Component of a network formed by the microRNA396 (miRNA396), the GRFs and their interacting factors (GIFs) acting in the regulation of meristem function, at least partially through the control of cell proliferation (Probable). Component of the miRNA396c-GRF4-GIF1 regulatory module that plays an important role in grain size determination (Probable) (PubMed:27250747, PubMed:27250749, PubMed:27107174). {ECO:0000269\|PubMed:24532604, ECO:0000269\|PubMed:26187814, ECO:0000269\|PubMed:26936408, ECO:0000269\|PubMed:27107174, ECO:0000269\|PubMed:27250747, ECO:0000269\|PubMed:27250749, ECO:0000305\|PubMed:26187814, ECO:0000305\|PubMed:27107174, ECO:0000305\|PubMed:27250747, ECO:0000305\|PubMed:27250749}.

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: The microRNA396c negatively regulates GRF4 at the transcriptional level. {ECO:0000269\|PubMed:26187814, ECO:0000269\|PubMed:26936408, ECO:0000269\|PubMed:27107174, ECO:0000269\|PubMed:27250747}.

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	AY303171	1e-122	AY303171.1 Solanum bulbocastanum chromosome 8 clone UW177O13, complete sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_009794508.1	0.0	PREDICTED: growth-regulating factor 4-like isoform X1
Refseq	XP_009794509.1	0.0	PREDICTED: growth-regulating factor 4-like isoform X1
Refseq	XP_009794510.1	0.0	PREDICTED: growth-regulating factor 4-like isoform X1
Swissprot	Q6ZIK5	7e-79	GRF4_ORYSJ; Growth-regulating factor 4
TrEMBL	A0A1U7Y5J5	0.0	A0A1U7Y5J5_NICSY; growth-regulating factor 4-like isoform X1
STRING	XP_009794508.1	0.0	(Nicotiana sylvestris)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Asterids	OGEA743	23	84

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT3G13960.1	2e-48	growth-regulating factor 5

Publications ? help Back to Top
Kikuchi S, et al. Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice. Science, 2003. 301(5631): p. 376-9 [PMID:12869764] Kuijt SJ, et al. Interaction between the GROWTH-REGULATING FACTOR and KNOTTED1-LIKE HOMEOBOX families of transcription factors. Plant Physiol., 2014. 164(4): p. 1952-66 [PMID:24532604] Hu J, et al. A Rare Allele of GS2 Enhances Grain Size and Grain Yield in Rice. Mol Plant, 2015. 8(10): p. 1455-65 [PMID:26187814] Sun P, et al. OsGRF4 controls grain shape, panicle length and seed shattering in rice. J Integr Plant Biol, 2016. 58(10): p. 836-847 [PMID:26936408] Li S, et al. The OsmiR396c-OsGRF4-OsGIF1 regulatory module determines grain size and yield in rice. Plant Biotechnol. J., 2016. 14(11): p. 2134-2146 [PMID:27107174] Che R, et al. Control of grain size and rice yield by GL2-mediated brassinosteroid responses. Nat Plants, 2015. 2: p. 15195 [PMID:27250747] Duan P, et al. Regulation of OsGRF4 by OsmiR396 controls grain size and yield in rice. Nat Plants, 2015. 2: p. 15203 [PMID:27250749]