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

PGSC0003DMP400032217

Organism

Solanum tuberosum

Taxonomic ID

4113

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; lamiids; Solanales; Solanaceae; Solanoideae; Solaneae; Solanum

Family

GRF

Protein Properties

Length: 354aa MW: 38776.8 Da PI: 8.8617

Description

GRF family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
PGSC0003DMP400032217	genome	PGSC	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	WRC	76.9	2.1e-24	92	136	1	45
WRC 1 daepgrCrRtDGKkWRCsrrvlegkklCErHlhrgrsrsrkskee 45 d+epgrCrRtDGKkWRCs+++ +++k+CErH+hrgr+rsrk++e+ PGSC0003DMP400032217 92 DPEPGRCRRTDGKKWRCSKDAHPDSKYCERHMHRGRNRSRKPVES 136 79****************************************986 PP
2	QLQ	65.5	1.3e-22	31	66	2	37
QLQ 2 aFTaaQlqlLksQilAyKyLaanqPvPpeLlqaiqk 37 +FTa Q+q+L++Q+++yKyL+a++PvPp+L+++i++ PGSC0003DMP400032217 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
PROSITE profile	PS51666	24.343	31	66	IPR014978	Glutamine-Leucine-Glutamine, QLQ
Pfam	PF08880	4.3E-17	31	65	IPR014978	Glutamine-Leucine-Glutamine, QLQ
PROSITE profile	PS51667	25.831	92	136	IPR014977	WRC domain
Pfam	PF08879	6.5E-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:0048366	Biological Process	leaf development
GO:0005634	Cellular Component	nucleus
GO:0005524	Molecular Function	ATP binding

Sequence ? help Back to Top
Protein Sequence Length: 354 aa Download sequence Send to blast
MSGTSTTSVV GVGLVGGGGE VGYNDYGFRP PFTAVQWQEL EHQAMIYKYL VAGLPVPPDL 60 VVPIRRSFDA ISARFFNHPS LGYCSYYGKK FDPEPGRCRR TDGKKWRCSK DAHPDSKYCE 120 RHMHRGRNRS RKPVESQTTS QSLSTSISHT ATGSSNRSGS FQSNSSGSFQ NMPLYSVANS 180 DGISYGSTTT KLQMEPASYG INNKEYRYGM APDADDHNFL PVASASVRGL GGTGSNTDNM 240 WRLMPSQVPS KPNLKNDSQL LGSSPNPFEP VIESKQQPQH CFFSSDIDSP GTVKQETQHP 300 MRSFFDEWPT SKESWSNLDE GSGKNNFSTT QLSISIPNAP SGFSSRSASS PKW*

Sequence ? help Back to Top

Protein Sequence Length: 354 aa Download sequence Send to blast

MSGTSTTSVV GVGLVGGGGE VGYNDYGFRP PFTAVQWQEL EHQAMIYKYL VAGLPVPPDL  60
VVPIRRSFDA ISARFFNHPS LGYCSYYGKK FDPEPGRCRR TDGKKWRCSK DAHPDSKYCE  120
RHMHRGRNRS RKPVESQTTS QSLSTSISHT ATGSSNRSGS FQSNSSGSFQ NMPLYSVANS  180
DGISYGSTTT KLQMEPASYG INNKEYRYGM APDADDHNFL PVASASVRGL GGTGSNTDNM  240
WRLMPSQVPS KPNLKNDSQL LGSSPNPFEP VIESKQQPQH CFFSSDIDSP GTVKQETQHP  300
MRSFFDEWPT SKESWSNLDE GSGKNNFSTT QLSISIPNAP SGFSSRSASS PKW*

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}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	PGSC0003DMP400032217

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	AP009594	0.0	AP009594.1 Solanum lycopersicum DNA, chromosome 8, clone: C08HBa0022E13, complete sequence.
GenBank	HG975447	0.0	HG975447.1 Solanum pennellii chromosome ch08, complete genome.
GenBank	HG975520	0.0	HG975520.1 Solanum lycopersicum chromosome ch08, complete genome.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_006361251.1	0.0	PREDICTED: growth-regulating factor 4-like
Refseq	XP_015170685.1	0.0	PREDICTED: growth-regulating factor 4-like
Refseq	XP_015170686.1	0.0	PREDICTED: growth-regulating factor 4-like
Swissprot	Q6ZIK5	8e-86	GRF4_ORYSJ; Growth-regulating factor 4
TrEMBL	M1BL14	0.0	M1BL14_SOLTU; Uncharacterized protein
STRING	PGSC0003DMT400047580	0.0	(Solanum tuberosum)

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	6e-49	growth-regulating factor 5

Link Out ? help Back to Top
Phytozome	PGSC0003DMP400032217

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] Xu X, et al. Genome sequence and analysis of the tuber crop potato. Nature, 2011. 475(7355): p. 189-95 [PMID:21743474] 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]