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

Cc07_g07090

Common Name

GSCOC_T00040045001

Organism

Coffea canephora

Taxonomic ID

49390

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; lamiids; Gentianales; Rubiaceae; Ixoroideae; Coffeeae; Coffea

Family

GRAS

Protein Properties

Length: 507aa MW: 57006.5 Da PI: 5.2445

Description

GRAS family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Cc07_g07090	genome	CGSC	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	GRAS	359.5	5e-110	125	505	3	374
GRAS 3 elLlecAeavssgdlelaqalLarlselaspdgdpmqRlaayfteALaarlarsvselykalppsetseknsseelaalklfsevsPilkfshltaNq 100 + Lle A+a+++++ +++q+l++ l+el+sp+gd+ q+la+yf++AL +r+++s++++y++l + ++++ + +++ +++ f+evsP+ +f+h+++N Cc07_g07090 125 DILLETARAIADKNSSRVQQLMWMLNELSSPYGDTDQKLASYFLQALFSRMTDSGERCYRTLVSASENTCSFESTRKMVLKFQEVSPWTTFGHVACNG 222 679*********************************************************8888876665555555556************* PP GRAS 101 aIleavegeervHiiDfdisqGlQWpaLlqaLasRpegppslRiTgvgspesg........skeeleetgerLakfAeelgvpfefnvlvak.rledl 189 aIleavege ++HiiD++ + ++QWp+Ll+aLa+R++++p+lR+T+v+ +++g ++ ++e+g+r++kfA+ +gvpf+fnvl++ +l++l Cc07_g07090 223 AILEAVEGEPKLHIIDISNTFCTQWPTLLEALATRSDETPHLRLTTVVVSKAGgagggaagVQKVMKEIGSRMEKFARLMGVPFKFNVLHHAgDLSEL 320 ********************************************988889999999*********************7777* PP GRAS 190 eleeLrvkpgEalaVnlvlqlhrlldesvsleserdevLklvkslsPkvvvvveqeadhnse....sFlerflealeyysalfdsleaklpreseeri 283 +l+eL++k++Eala+n+v +lh++ +l ++rd ++++++sl+P+++ vve+ead++ + +F+++f e+l+++ + f+sl+ ++p++s+er Cc07_g07090 321 NLSELDIKEDEALAINCVGALHSVS----TLGNRRDFLISIFRSLQPRIIAVVEEEADLDVGfdgyDFVKGFQECLRWFRVYFESLDDSFPKTSNERL 414 ********************8....8999999****************99865555569*************************** PP GRAS 284 kvErellgreivnvvacegaerrerhetlekWrerleeaGFkpvplsekaakqaklllrkvksdgyrve..eesgslvlgWkdrpLvsvSaWr 374 ++Er+ gr+iv++vac ae++er+et+ +W++rl+++GF+pv++s+++ +++++llr++k dg+++ +es+ ++l Wkd+p+v++SaWr Cc07_g07090 415 MLERQ-AGRAIVDLVACPAAESIERRETATRWSHRLHASGFGPVSFSDEVCDDVRALLRRYK-DGWSMAqcNESAGIFLSWKDQPVVWASAWR 505 *.****************************************************.776666446778888************8 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50985	50.798	97	484	IPR005202	Transcription factor GRAS
Pfam	PF03514	1.7E-107	125	505	IPR005202	Transcription factor GRAS

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0006355	Biological Process	regulation of transcription, DNA-templated
GO:0008356	Biological Process	asymmetric cell division
GO:0009956	Biological Process	radial pattern formation
GO:0045930	Biological Process	negative regulation of mitotic cell cycle
GO:0048366	Biological Process	leaf development
GO:0055072	Biological Process	iron ion homeostasis
GO:0005634	Cellular Component	nucleus
GO:0043565	Molecular Function	sequence-specific DNA binding

Sequence ? help Back to Top
Protein Sequence Length: 507 aa Download sequence Send to blast
MDTLFRLVSL QQPSDQSFNS SRTSSSSRSS RQNHHYNQHQ QEEEEECFNF FMDDEDFSSS 60 SSRPHYNPYQ QHQQQQTSST PTPTTTNTSS TPTHHPYESA DFSFSPARDI NQEFASSFSG 120 KWASDILLET ARAIADKNSS RVQQLMWMLN ELSSPYGDTD QKLASYFLQA LFSRMTDSGE 180 RCYRTLVSAS ENTCSFESTR KMVLKFQEVS PWTTFGHVAC NGAILEAVEG EPKLHIIDIS 240 NTFCTQWPTL LEALATRSDE TPHLRLTTVV VSKAGGAGGG AAGVQKVMKE IGSRMEKFAR 300 LMGVPFKFNV LHHAGDLSEL NLSELDIKED EALAINCVGA LHSVSTLGNR RDFLISIFRS 360 LQPRIIAVVE EEADLDVGFD GYDFVKGFQE CLRWFRVYFE SLDDSFPKTS NERLMLERQA 420 GRAIVDLVAC PAAESIERRE TATRWSHRLH ASGFGPVSFS DEVCDDVRAL LRRYKDGWSM 480 AQCNESAGIF LSWKDQPVVW ASAWRA*

Sequence ? help Back to Top

Protein Sequence Length: 507 aa Download sequence Send to blast

MDTLFRLVSL QQPSDQSFNS SRTSSSSRSS RQNHHYNQHQ QEEEEECFNF FMDDEDFSSS  60
SSRPHYNPYQ QHQQQQTSST PTPTTTNTSS TPTHHPYESA DFSFSPARDI NQEFASSFSG  120
KWASDILLET ARAIADKNSS RVQQLMWMLN ELSSPYGDTD QKLASYFLQA LFSRMTDSGE  180
RCYRTLVSAS ENTCSFESTR KMVLKFQEVS PWTTFGHVAC NGAILEAVEG EPKLHIIDIS  240
NTFCTQWPTL LEALATRSDE TPHLRLTTVV VSKAGGAGGG AAGVQKVMKE IGSRMEKFAR  300
LMGVPFKFNV LHHAGDLSEL NLSELDIKED EALAINCVGA LHSVSTLGNR RDFLISIFRS  360
LQPRIIAVVE EEADLDVGFD GYDFVKGFQE CLRWFRVYFE SLDDSFPKTS NERLMLERQA  420
GRAIVDLVAC PAAESIERRE TATRWSHRLH ASGFGPVSFS DEVCDDVRAL LRRYKDGWSM  480
AQCNESAGIF LSWKDQPVVW ASAWRA*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5b3g_B	0.0	114	505	78	473	Protein SHORT-ROOT
5b3h_B	0.0	96	505	2	419	Protein SHORT-ROOT
5b3h_E	0.0	96	505	2	419	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 -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_027073607.1	0.0	protein SHORT-ROOT-like
Swissprot	Q9SZF7	0.0	SHR_ARATH; Protein SHORT-ROOT
TrEMBL	A0A068U370	0.0	A0A068U370_COFCA; Uncharacterized protein
STRING	VIT_07s0129g00030.t01	0.0	(Vitis vinifera)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Asterids	OGEA2031	24	64

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT4G37650.1	0.0	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]