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

MELO3C020907P1

Organism

Cucumis melo

Taxonomic ID

3656

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Cucurbitales; Cucurbitaceae; Benincaseae; Cucumis

Family

GRAS

Protein Properties

Length: 503aa MW: 56656.9 Da PI: 6.7937

Description

GRAS family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
MELO3C020907P1	genome	MELONOMICS	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	GRAS	295.7	1.2e-90	110	490	3	373
GRAS 3 elLlecAeavssgdlelaqalLarlselaspdgdpmqRlaayfteALaarlarsvselykalppsetseknsseelaalklfsevsPilkfshlt 97 ++Ll+ A a+ +++++++q+l++ l+el sp+gd q+la+yf++++ +r+++s+ ++y++l++ ++++ + ++ f evsP+++f+h++ MELO3C020907P1 110 TVLLQTAIAIVNKNTTRIQHLMWVLNELGSPYGDIDQKLAFYFLQGMFSRVTDSGAKCYRTLAAALEKQSCFGSMRRMVLKFEEVSPWMRFGHVA 204 689*********************************************************9999986554444444455********** PP GRAS 98 aNqaIleavegeervHiiDfd...isqGlQWpaLlqaLasRpegppslRiTgvgspesg.....skeeleetgerLakfAeelgvpfefnvlvak 184 N ++ea+ ge+++HiiD+ s ++QWp++++aLa++++++p+l +T++++++s+ +k+ ++e+ +rL+kfA+ +g++f+f+++ + MELO3C020907P1 205 SNGSLMEALRGEKKLHIIDIPgsySSFCTQWPTFIEALATQSDQTPHLTLTTLVAAKSEgtlraHKKLMKEISRRLEKFARLMGISFKFKPIFHY 299 ****************63336789*********************998888999999**********************9555 PP GRAS 185 .rledleleeLrvkpgEalaVnlvlqlhrlldesvsleserdevLklvkslsPkvvvvveqeadhnse....sFlerflealeyysalfdsleak 274 +++ +++ +L +k++Ea+aVn++ +l ++ +l+++rd +++l++sl+Pk+++vve+ead+n+ +F++++ e+l+++ fdsl+ + MELO3C020907P1 300 gDVSHFDFTHLPLKHDEAVAVNCSGALRSVA----PLHNRRDFLISLFRSLRPKIITVVEEEADLNADggadDFFKHLQECLRWFRLYFDSLDGS 390 5**********************9997....999999*****************99987767779****************** PP GRAS 275 lpreseerikvErellgreivnvvacegaerrerhetlekWrerleeaGFkpvplsekaakqaklllrkvksdgyrveee...sgslvlgWkdrp 366 +p ++er ++Er+ gr++v+++ac ae++er+et+ +W +rl++ GFkpv++se++++++++llr++k dg++v + + ++l Wk++p MELO3C020907P1 391 FPIVTDERLMLERA-AGRSVVDLLACGLAESVERRETAVRWTRRLHDGGFKPVSFSEDVNDDVRALLRRYK-DGWTVMDGdgaGAGMFLAWKGQP 483 **********.****************************************************.9999996623245678*** PP GRAS 367 LvsvSaW 373 +v++ aW MELO3C020907P1 484 VVWAAAW 490 ***** PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50985	44.669	82	469	IPR005202	Transcription factor GRAS
Pfam	PF03514	4.1E-88	110	490	IPR005202	Transcription factor GRAS

Sequence ? help Back to Top
Protein Sequence Length: 503 aa Download sequence Send to blast
MDTLLRLVND LGSSDQYSYN NNSSSSSKNS SDRNHYNYYL QNPQSQECFN NSFMEDEDHF 60 SASSSSSHHH HHQLRQLQCS TTTTSTTSTG AAAPVDHDLN FELSEEWAST VLLQTAIAIV 120 NKNTTRIQHL MWVLNELGSP YGDIDQKLAF YFLQGMFSRV TDSGAKCYRT LAAALEKQSC 180 FGSMRRMVLK FEEVSPWMRF GHVASNGSLM EALRGEKKLH IIDIPGSYSS FCTQWPTFIE 240 ALATQSDQTP HLTLTTLVAA KSEGTLRAHK KLMKEISRRL EKFARLMGIS FKFKPIFHYG 300 DVSHFDFTHL PLKHDEAVAV NCSGALRSVA PLHNRRDFLI SLFRSLRPKI ITVVEEEADL 360 NADGGADDFF KHLQECLRWF RLYFDSLDGS FPIVTDERLM LERAAGRSVV DLLACGLAES 420 VERRETAVRW TRRLHDGGFK PVSFSEDVND DVRALLRRYK DGWTVMDGDG AGAGMFLAWK 480 GQPVVWAAAW VPGQVDGEKT HV*

Sequence ? help Back to Top

Protein Sequence Length: 503 aa Download sequence Send to blast

MDTLLRLVND LGSSDQYSYN NNSSSSSKNS SDRNHYNYYL QNPQSQECFN NSFMEDEDHF  60
SASSSSSHHH HHQLRQLQCS TTTTSTTSTG AAAPVDHDLN FELSEEWAST VLLQTAIAIV  120
NKNTTRIQHL MWVLNELGSP YGDIDQKLAF YFLQGMFSRV TDSGAKCYRT LAAALEKQSC  180
FGSMRRMVLK FEEVSPWMRF GHVASNGSLM EALRGEKKLH IIDIPGSYSS FCTQWPTFIE  240
ALATQSDQTP HLTLTTLVAA KSEGTLRAHK KLMKEISRRL EKFARLMGIS FKFKPIFHYG  300
DVSHFDFTHL PLKHDEAVAV NCSGALRSVA PLHNRRDFLI SLFRSLRPKI ITVVEEEADL  360
NADGGADDFF KHLQECLRWF RLYFDSLDGS FPIVTDERLM LERAAGRSVV DLLACGLAES  420
VERRETAVRW TRRLHDGGFK PVSFSEDVND DVRALLRRYK DGWTVMDGDG AGAGMFLAWK  480
GQPVVWAAAW VPGQVDGEKT HV*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5b3h_B	1e-156	99	492	24	420	Protein SHORT-ROOT
5b3h_E	1e-156	99	492	24	420	Protein SHORT-ROOT
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Functional Description ? help Back to Top
Source	Description
UniProt	Transcription factor required for quiescent center cells specification and maintenance of surrounding stem cells, and for the asymmetric cell division involved in radial pattern formation in roots. Essential for both cell division and cell specification. Regulates the radial organization of the shoot axial organs and is required for normal shoot gravitropism. Directly controls the transcription of SCR, and when associated with SCR, of MGP, RLK, TRI, NUC and SCL3. {ECO:0000269\|PubMed:10850497, ECO:0000269\|PubMed:12569126, ECO:0000269\|PubMed:15314023, ECO:0000269\|PubMed:16640459, ECO:0000269\|PubMed:17446396, ECO:0000269\|PubMed:9670559}.

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	LN681913	0.0	LN681913.1 Cucumis melo genomic scaffold, anchoredscaffold00045.
GenBank	LN713265	0.0	LN713265.1 Cucumis melo genomic chromosome, chr_11.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_008457838.1	0.0	PREDICTED: protein SHORT-ROOT-like isoform X1
Refseq	XP_008457842.1	0.0	PREDICTED: protein SHORT-ROOT-like isoform X1
Refseq	XP_008457843.1	0.0	PREDICTED: protein SHORT-ROOT-like isoform X1
Refseq	XP_016902150.1	0.0	PREDICTED: protein SHORT-ROOT-like isoform X1
Swissprot	Q9SZF7	1e-157	SHR_ARATH; Protein SHORT-ROOT
TrEMBL	A0A1S3C604	0.0	A0A1S3C604_CUCME; protein SHORT-ROOT-like isoform X1
STRING	XP_008457838.1	0.0	(Cucumis melo)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Fabids	OGEF1297	34	106

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT4G37650.1	1e-156	GRAS family 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] Muraro D, et al. Integration of hormonal signaling networks and mobile microRNAs is required for vascular patterning in Arabidopsis roots. Proc. Natl. Acad. Sci. U.S.A., 2014. 111(2): p. 857-62 [PMID:24381155] Tian H,Jia Y,Niu T,Yu Q,Ding Z The key players of the primary root growth and development also function in lateral roots in Arabidopsis. Plant Cell Rep., 2014. 33(5): p. 745-53 [PMID:24504658] Gao X,Wang C,Cui H Identification of bundle sheath cell fate factors provides new tools for C3-to-C4 engineering. Plant Signal Behav, 2018. [PMID:24819776] Ahrazem O, et al. Ectopic expression of a stress-inducible glycosyltransferase from saffron enhances salt and oxidative stress tolerance in Arabidopsis while alters anchor root formation. Plant Sci., 2015. 234: p. 60-73 [PMID:25804810] Jia Y, et al. The Arabidopsis thaliana elongator complex subunit 2 epigenetically affects root development. J. Exp. Bot., 2015. 66(15): p. 4631-42 [PMID:25998905] Zhang M, et al. A tetratricopeptide repeat domain-containing protein SSR1 located in mitochondria is involved in root development and auxin polar transport in Arabidopsis. Plant J., 2015. 83(4): p. 582-99 [PMID:26072661] Moreno-Risueno MA, et al. Transcriptional control of tissue formation throughout root development. Science, 2015. 350(6259): p. 426-30 [PMID:26494755] Miguel A,Milhinhos A,Novák O,Jones B,Miguel CM The SHORT-ROOT-like gene PtSHR2B is involved in Populus phellogen activity. J. Exp. Bot., 2016. 67(5): p. 1545-55 [PMID:26709311] Gong X, et al. SEUSS Integrates Gibberellin Signaling with Transcriptional Inputs from the SHR-SCR-SCL3 Module to Regulate Middle Cortex Formation in the Arabidopsis Root. Plant Physiol., 2016. 170(3): p. 1675-83 [PMID:26818732] Kim ES, et al. HAWAIIAN SKIRT regulates the quiescent center-independent meristem activity in Arabidopsis roots. Physiol Plant, 2016. 157(2): p. 221-33 [PMID:26968317] Lee SA, et al. Interplay between ABA and GA Modulates the Timing of Asymmetric Cell Divisions in the Arabidopsis Root Ground Tissue. Mol Plant, 2016. 9(6): p. 870-84 [PMID:26970019] Li Q,Zhao Y,Yue M,Xue Y,Bao S The Protein Arginine Methylase 5 (PRMT5/SKB1) Gene Is Required for the Maintenance of Root Stem Cells in Response to DNA Damage. J Genet Genomics, 2016. 43(4): p. 187-97 [PMID:27090604] Clark NM, et al. Tracking transcription factor mobility and interaction in Arabidopsis roots with fluorescence correlation spectroscopy. Elife, 2017. [PMID:27288545] Yoon EK, et al. Conservation and Diversification of the SHR-SCR-SCL23 Regulatory Network in the Development of the Functional Endodermis in Arabidopsis Shoots. Mol Plant, 2016. 9(8): p. 1197-1209 [PMID:27353361] Waszczak C, et al. SHORT-ROOT Deficiency Alleviates the Cell Death Phenotype of the Arabidopsis catalase2 Mutant under Photorespiration-Promoting Conditions. Plant Cell, 2016. 28(8): p. 1844-59 [PMID:27432873] Yu Q, et al. A P-Loop NTPase Regulates Quiescent Center Cell Division and Distal Stem Cell Identity through the Regulation of ROS Homeostasis in Arabidopsis Root. PLoS Genet., 2016. 12(9): p. e1006175 [PMID:27583367] Sparks EE, et al. Establishment of Expression in the SHORTROOT-SCARECROW Transcriptional Cascade through Opposing Activities of Both Activators and Repressors. Dev. Cell, 2016. 39(5): p. 585-596 [PMID:27923776] Hirano Y, et al. Structure of the SHR-SCR heterodimer bound to the BIRD/IDD transcriptional factor JKD. Nat Plants, 2017. 3: p. 17010 [PMID:28211915] Henry S, et al. SHR overexpression induces the formation of supernumerary cell layers with cortex cell identity in rice. Dev. Biol., 2017. 425(1): p. 1-7 [PMID:28263767] Möller BK, et al. Auxin response cell-autonomously controls ground tissue initiation in the early Arabidopsis embryo. Proc. Natl. Acad. Sci. U.S.A., 2017. 114(12): p. E2533-E2539 [PMID:28265057] Kobayashi A,Miura S,Kozaki A INDETERMINATE DOMAIN PROTEIN binding sequences in the 5'-untranslated region and promoter of the SCARECROW gene play crucial and distinct roles in regulating SCARECROW expression in roots and leaves. Plant Mol. Biol., 2017. 94(1-2): p. 1-13 [PMID:28324206] Díaz-Triviño S,Long Y,Scheres B,Blilou I Analysis of a Plant Transcriptional Regulatory Network Using Transient Expression Systems. Methods Mol. Biol., 2017. 1629: p. 83-103 [PMID:28623581] Long Y, et al. In vivo FRET-FLIM reveals cell-type-specific protein interactions in Arabidopsis roots. Nature, 2017. 548(7665): p. 97-102 [PMID:28746306] Yu Q, et al. Cell-Fate Specification in Arabidopsis Roots Requires Coordinative Action of Lineage Instruction and Positional Reprogramming. Plant Physiol., 2017. 175(2): p. 816-827 [PMID:28821591] Spiegelman Z,Lee CM,Gallagher KL KinG Is a Plant-Specific Kinesin That Regulates Both Intra- and Intercellular Movement of SHORT-ROOT. Plant Physiol., 2018. 176(1): p. 392-405 [PMID:29122988] Bustillo-Avendaño E, et al. Regulation of Hormonal Control, Cell Reprogramming, and Patterning during De Novo Root Organogenesis. Plant Physiol., 2018. 176(2): p. 1709-1727 [PMID:29233938]