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

Sobic.003G417500.1.p

Common Name

Sb03g045120, SORBIDRAFT_03g045120

Organism

Sorghum bicolor

Taxonomic ID

4558

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; PACMAD clade; Panicoideae; Andropogonodae; Andropogoneae; Sorghinae; Sorghum

Family

C2H2

Protein Properties

Length: 521aa MW: 54699.9 Da PI: 8.1222

Description

C2H2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Sobic.003G417500.1.p	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-C2H2	16.3	2.7e-05	96	118	1	23
EEETTTTEEESSHHHHHHHHHHT CS zf-C2H2 1 ykCpdCgksFsrksnLkrHirtH 23 ++C++C+k F r nL+ H r H Sobic.003G417500.1.p 96 FVCEICHKGFQRDQNLQLHRRGH 118 89*******************88 PP
2	zf-C2H2	12.3	0.00051	210	228	5	23
TTTEEESSHHHHHHHHHHT CS zf-C2H2 5 dCgksFsrksnLkrHirtH 23 dCg++Fsr++++++H + Sobic.003G417500.1.p 210 DCGTVFSRRDSFVTHRAFC 228 9**************8765 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF57667	6.88E-6	95	118	No hit	No description
Gene3D	G3DSA:3.30.160.60	7.9E-5	95	118	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profile	PS50157	10.637	96	118	IPR007087	Zinc finger, C2H2
PROSITE pattern	PS00028	0	98	118	IPR007087	Zinc finger, C2H2
Gene3D	G3DSA:3.30.160.60	9.0E-4	168	200	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamily	SSF57667	6.88E-6	175	200	No hit	No description

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0003676	Molecular Function	nucleic acid binding
GO:0046872	Molecular Function	metal ion binding

Sequence ? help Back to Top
Protein Sequence Length: 521 aa Download sequence Send to blast
MSGGSSSLSS VSNTPREVEE KFLQYHIQPL LGGPMEMQNG GGGGDLQHVI GGPSEPLPPA 60 PPPPTVKKKR SLPGTPDPSA EVIALSPRTL MATNRFVCEI CHKGFQRDQN LQLHRRGHNL 120 PWKLRQRGGA GADGPGGGPP RKRVYVCPEA SCVHHNPARA LGDLTGIKKH YCRKHGEKKW 180 KCERCAKRYA VHSDWKAHAK VCGTREYKCD CGTVFSRRDS FVTHRAFCDA LAQENNKLSQ 240 PMNMATVASA LQGQAAPHHL APPSSSSQPE DDLDAAAGED NDDDFALDTK SPKLRMLPTM 300 SDADATAANQ LLLPPLSMAG CMLSSLQHGA ARPAPPTPPS PATFFSGVKA GLDGPSSSCD 360 PSMGGAFSPP GASASMSATA LLQKAAEMGA TAGGYGVGAG FSTVGFGPMI GGPPVMGPFG 420 PLKTPAVLEP FDGLPFGQTH LVGLDVGRLL PGQHFYGSSH GHGHGVGSMT RAIGSLMHGG 480 QQMDHRRPDD VRVVDYLGVD DQRSCFSGVS PFGPDLGPWS *

Sequence ? help Back to Top

Protein Sequence Length: 521 aa Download sequence Send to blast

MSGGSSSLSS VSNTPREVEE KFLQYHIQPL LGGPMEMQNG GGGGDLQHVI GGPSEPLPPA  60
PPPPTVKKKR SLPGTPDPSA EVIALSPRTL MATNRFVCEI CHKGFQRDQN LQLHRRGHNL  120
PWKLRQRGGA GADGPGGGPP RKRVYVCPEA SCVHHNPARA LGDLTGIKKH YCRKHGEKKW  180
KCERCAKRYA VHSDWKAHAK VCGTREYKCD CGTVFSRRDS FVTHRAFCDA LAQENNKLSQ  240
PMNMATVASA LQGQAAPHHL APPSSSSQPE DDLDAAAGED NDDDFALDTK SPKLRMLPTM  300
SDADATAANQ LLLPPLSMAG CMLSSLQHGA ARPAPPTPPS PATFFSGVKA GLDGPSSSCD  360
PSMGGAFSPP GASASMSATA LLQKAAEMGA TAGGYGVGAG FSTVGFGPMI GGPPVMGPFG  420
PLKTPAVLEP FDGLPFGQTH LVGLDVGRLL PGQHFYGSSH GHGHGVGSMT RAIGSLMHGG  480
QQMDHRRPDD VRVVDYLGVD DQRSCFSGVS PFGPDLGPWS *

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5b3h_C	2e-34	176	243	3	70	Zinc finger protein JACKDAW
5b3h_F	2e-34	176	243	3	70	Zinc finger protein JACKDAW
Search in ModeBase

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
Sbi.17158	3e-76	root

Expression -- Description ? help Back to Top
Source	Description
Uniprot	TISSUE SPECIFICITY: Observed in vegetative tissues. Mainly expressed in hypocotyls, petioles, shoot apices, root tips, and trichomes, and, at low levels, in leaves, stems and flowers. {ECO:0000269\|PubMed:25035403}.

Functional Description ? help Back to Top
Source	Description
UniProt	Transcription factor that acts as a positive regulator of gibberellin (GA) action, homeostasis and signaling. GA converts the GAF1 complex from transcriptional activator to repressor via the degradation of DELLA proteins. {ECO:0000269\|PubMed:25035403}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Sobic.003G417500.1.p

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	BT066652	0.0	BT066652.1 Zea mays full-length cDNA clone ZM_BFb0043G06 mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_002459052.1	0.0	protein indeterminate-domain 2
Swissprot	Q9SCQ6	1e-104	IDD2_ARATH; Zinc finger protein GAI-ASSOCIATED FACTOR 1
TrEMBL	C5XH47	0.0	C5XH47_SORBI; Uncharacterized protein
STRING	Sb03g045120.1	0.0	(Sorghum bicolor)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Monocots	OGMP12554	25	34
Representative plant	OGRP95	16	242

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT1G03840.1	1e-102	C2H2 family protein

Link Out ? help Back to Top
Phytozome	Sobic.003G417500.1.p
Entrez Gene	8059423

Publications ? help Back to Top
Fukazawa J, et al. DELLAs function as coactivators of GAI-ASSOCIATED FACTOR1 in regulation of gibberellin homeostasis and signaling in Arabidopsis. Plant Cell, 2014. 26(7): p. 2920-38 [PMID:25035403] Moreno-Risueno MA, et al. Transcriptional control of tissue formation throughout root development. Science, 2015. 350(6259): p. 426-30 [PMID:26494755] Khare D, et al. Root avoidance of toxic metals requires the GeBP-LIKE 4 transcription factor in Arabidopsis thaliana. New Phytol., 2017. 213(3): p. 1257-1273 [PMID:27768815]