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

PGSC0003DMP400026962

Common Name

LOC102578818

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

TCP

Protein Properties

Length: 422aa MW: 45806.8 Da PI: 7.3179

Description

TCP family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
PGSC0003DMP400026962	genome	PGSC	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	TCP	112.9	4.3e-35	54	168	3	85
TCP 3 gkkdrhskihTkvggRdRRvRlsaecaarfFdLqdeLGfdkdsktieWLlqqakpaikeltgt.......................... 65 g+kdrhsk++T++g+RdRRvRl a++a++f+d+qd+LG+d++sk+++WL+++ak++i+el+++ PGSC0003DMP400026962 54 GRKDRHSKVCTAKGPRDRRVRLAAHTAIQFYDVQDRLGYDRPSKAVDWLIKKAKASIDELAELppwkpttgvttfdqekdvedddnngh 142 89*************************************************************88887777776666655555555555 PP TCP 66 ..ssssasec....eaesssssasns 85 +++s+s++ +++s sss++n PGSC0003DMP400026962 143 fvGTTSKSSMimlgQNNSASSSGENA 168 55222222222343222222222222 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Pfam	PF03634	1.4E-29	54	196	IPR005333	Transcription factor, TCP
PROSITE profile	PS51369	32.855	55	113	IPR017887	Transcription factor TCP subgroup

Sequence ? help Back to Top
Protein Sequence Length: 422 aa Download sequence Send to blast
MYQDLDKIKQ QAQSKKRSYV PPLPRPKQKV GTSSRFGGGE IVEVQGGHII RSIGRKDRHS 60 KVCTAKGPRD RRVRLAAHTA IQFYDVQDRL GYDRPSKAVD WLIKKAKASI DELAELPPWK 120 PTTGVTTFDQ EKDVEDDDNN GHFVGTTSKS SMIMLGQNNS ASSSGENANG SNFLPHSLDS 180 DAISDTIKSF FPMGGGSTEG NSSGMQFQSF QEHNLLSTTS SQSQDLKLSL QSFQDPVLLH 240 NHQIEQSQAQ FQASNFFTGS TPLIGFDASV WPQPQTQHQQ QPVELGRLAA ARGAGGYTGM 300 AFGGGAIAGA NSYLFNSQPA PPLLQQLFSQ NQFLSQRGPL QSSYSPSIRA WIDPSAIAIA 360 TADPIHHHQH HVLPMYSTSV SGIGFASEVG GFSGFRIPTR IQGEIEEHDG TSDKPSSDSR 420 H*

Sequence ? help Back to Top

Protein Sequence Length: 422 aa Download sequence Send to blast

MYQDLDKIKQ QAQSKKRSYV PPLPRPKQKV GTSSRFGGGE IVEVQGGHII RSIGRKDRHS  60
KVCTAKGPRD RRVRLAAHTA IQFYDVQDRL GYDRPSKAVD WLIKKAKASI DELAELPPWK  120
PTTGVTTFDQ EKDVEDDDNN GHFVGTTSKS SMIMLGQNNS ASSSGENANG SNFLPHSLDS  180
DAISDTIKSF FPMGGGSTEG NSSGMQFQSF QEHNLLSTTS SQSQDLKLSL QSFQDPVLLH  240
NHQIEQSQAQ FQASNFFTGS TPLIGFDASV WPQPQTQHQQ QPVELGRLAA ARGAGGYTGM  300
AFGGGAIAGA NSYLFNSQPA PPLLQQLFSQ NQFLSQRGPL QSSYSPSIRA WIDPSAIAIA  360
TADPIHHHQH HVLPMYSTSV SGIGFASEVG GFSGFRIPTR IQGEIEEHDG TSDKPSSDSR  420
H*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5zkt_A	1e-19	60	113	1	54	Putative transcription factor PCF6
5zkt_B	1e-19	60	113	1	54	Putative transcription factor PCF6
Search in ModeBase

Functional Description ? help Back to Top
Source	Description
UniProt	Transcription factor playing a pivotal role in the control of morphogenesis of shoot organs by negatively regulating the expression of boundary-specific genes such as CUC genes, probably through the induction of miRNA (e.g. miR164) (PubMed:12931144, PubMed:17307931). Required during early steps of embryogenesis (PubMed:15634699). Participates in ovule develpment (PubMed:25378179). Activates LOX2 expression by binding to the 5'-GGACCA-3' motif found in its promoter (PubMed:18816164). {ECO:0000269\|PubMed:12931144, ECO:0000269\|PubMed:15634699, ECO:0000269\|PubMed:17307931, ECO:0000269\|PubMed:18816164, ECO:0000269\|PubMed:25378179}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	PGSC0003DMP400026962

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: Repressed by the miRNA miR-JAW/miR319 (PubMed:12931144, PubMed:18816164). {ECO:0000269\|PubMed:12931144, ECO:0000269\|PubMed:18816164}.

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	HG975451	1e-129	HG975451.1 Solanum pennellii chromosome ch12, complete genome.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_006358953.1	0.0	PREDICTED: transcription factor TCP4-like
Swissprot	Q8LPR5	2e-96	TCP4_ARATH; Transcription factor TCP4
TrEMBL	M1B8S2	0.0	M1B8S2_SOLTU; Uncharacterized protein
STRING	PGSC0003DMT400039786	0.0	(Solanum tuberosum)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Asterids	OGEA3207	23	49

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT3G15030.3	1e-56	TCP family protein

Link Out ? help Back to Top
Phytozome	PGSC0003DMP400026962
Entrez Gene	102578818

Publications ? help Back to Top
Schommer C, et al. Control of jasmonate biosynthesis and senescence by miR319 targets. PLoS Biol., 2008. 6(9): p. e230 [PMID:18816164] Xu X, et al. Genome sequence and analysis of the tuber crop potato. Nature, 2011. 475(7355): p. 189-95 [PMID:21743474] Ju Y, et al. Arabidopsis JINGUBANG Is a Negative Regulator of Pollen Germination That Prevents Pollination in Moist Environments. Plant Cell, 2016. 28(9): p. 2131-2146 [PMID:27468890] Challa KR,Aggarwal P,Nath U Activation of YUCCA5 by the Transcription Factor TCP4 Integrates Developmental and Environmental Signals to Promote Hypocotyl Elongation in Arabidopsis. Plant Cell, 2016. 28(9): p. 2117-2130 [PMID:27597774] Alvarez JP,Furumizu C,Efroni I,Eshed Y,Bowman JL Active suppression of a leaf meristem orchestrates determinate leaf growth. Elife, 2017. [PMID:27710768] Li J, et al. RABBIT EARS regulates the transcription of TCP4 during petal development in Arabidopsis. J. Exp. Bot., 2016. 67(22): p. 6473-6480 [PMID:27838638] Sun X, et al. Activation of secondary cell wall biosynthesis by miR319-targeted TCP4 transcription factor. Plant Biotechnol. J., 2017. 15(10): p. 1284-1294 [PMID:28233945] Kubota A, et al. TCP4-dependent induction of CONSTANS transcription requires GIGANTEA in photoperiodic flowering in Arabidopsis. PLoS Genet., 2017. 13(6): p. e1006856 [PMID:28628608] Koyama T,Sato F,Ohme-Takagi M Roles of miR319 and TCP Transcription Factors in Leaf Development. Plant Physiol., 2017. 175(2): p. 874-885 [PMID:28842549] Bresso EG,Chorostecki U,Rodriguez RE,Palatnik JF,Schommer C Spatial Control of Gene Expression by miR319-Regulated TCP Transcription Factors in Leaf Development. Plant Physiol., 2018. 176(2): p. 1694-1708 [PMID:29133375] Vadde BVL,Challa KR,Nath U The TCP4 transcription factor regulates trichome cell differentiation by directly activating GLABROUS INFLORESCENCE STEMS in Arabidopsis thaliana. Plant J., 2018. 93(2): p. 259-269 [PMID:29165850] Challa KR,Rath M,Nath U The CIN-TCP transcription factors promote commitment to differentiation in Arabidopsis leaf pavement cells via both auxin-dependent and independent pathways. PLoS Genet., 2019. 15(2): p. e1007988 [PMID:30742619]