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

OB06G33840.1

Organism

Oryza brachyantha

Taxonomic ID

4533

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; BOP clade; Oryzoideae; Oryzeae; Oryzinae; Oryza

Family

GATA

Protein Properties

Length: 898aa MW: 98702.8 Da PI: 5.752

Description

GATA family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
OB06G33840.1	genome	OGE	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	GATA	49.7	4.9e-16	216	252	1	35
GATA 1 CsnCgttk..TplWRrgpdgnktLCnaCGlyyrkkgl 35 C++Cg + Tp++Rrgpdg++tLCnaCGl+++ kg+ OB06G33840.1 216 CHHCGISAkaTPMMRRGPDGPRTLCNACGLMWANKGM 252 ***88889*********************9996 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS51320	15.114	80	115	IPR010399	Tify domain
SMART	SM00979	8.9E-12	80	115	IPR010399	Tify domain
Pfam	PF06200	1.4E-12	83	114	IPR010399	Tify domain
Pfam	PF06203	2.7E-15	141	183	IPR010402	CCT domain
PROSITE profile	PS51017	13.404	141	183	IPR010402	CCT domain
SMART	SM00401	1.3E-11	210	263	IPR000679	Zinc finger, GATA-type
PROSITE profile	PS50114	9.091	210	258	IPR000679	Zinc finger, GATA-type
SuperFamily	SSF57716	8.55E-12	214	266	No hit	No description
Gene3D	G3DSA:3.30.50.10	1.7E-15	215	257	IPR013088	Zinc finger, NHR/GATA-type
CDD	cd00202	2.15E-13	215	266	No hit	No description
Pfam	PF00320	1.3E-13	216	251	IPR000679	Zinc finger, GATA-type
PROSITE pattern	PS00344	0	216	243	IPR000679	Zinc finger, GATA-type
Pfam	PF12066	7.1E-18	369	450	IPR021933	Protein of unknown function DUF3546
Pfam	PF04959	7.7E-35	605	792	IPR007042	Arsenite-resistance protein 2
PROSITE pattern	PS00028	0	674	697	IPR007087	Zinc finger, C2H2

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0000381	Biological Process	regulation of alternative mRNA splicing, via spliceosome
GO:0006355	Biological Process	regulation of transcription, DNA-templated
GO:0010267	Biological Process	production of ta-siRNAs involved in RNA interference
GO:0031053	Biological Process	primary miRNA processing
GO:0048367	Biological Process	shoot system development
GO:0048509	Biological Process	regulation of meristem development
GO:2000011	Biological Process	regulation of adaxial/abaxial pattern formation
GO:0005730	Cellular Component	nucleolus
GO:0005829	Cellular Component	cytosol
GO:0005846	Cellular Component	nuclear cap binding complex
GO:0009507	Cellular Component	chloroplast
GO:0010445	Cellular Component	nuclear dicing body
GO:0016607	Cellular Component	nuclear speck
GO:0003700	Molecular Function	transcription factor activity, sequence-specific DNA binding
GO:0005515	Molecular Function	protein binding
GO:0008270	Molecular Function	zinc ion binding
GO:0043565	Molecular Function	sequence-specific DNA binding

Sequence ? help Back to Top
Protein Sequence Length: 898 aa Download sequence Send to blast
MARYEEHAHG HGHGHEAEDE DDEEEDEEEV EMEEDEDGEG RHHEGGGSAE EGVPMDADAA 60 AATLGAQMDQ HGAMVAAAVP AMASNQLTLS FQGEVYVFDS VSPDKVQAVL LLLGGRELNP 120 GLGSGASSSA PYSKRLNFPH RVASLMRFRE KRKERNFDKK IRYSVRKEVA LRMQRNRGQF 180 TSSKPKGDEA TSELTAPDGS PNWGSVEGRP PSAAECHHCG ISAKATPMMR RGPDGPRTLC 240 NACGLMWANK GMLRDLSKAP PTPIQAIPSA NDGNGSAGAP TTEQEIPTPA TANGHESSTL 300 DIVDRNCTLD QMVNTYGYDY ERGGGRGGYD DDRYHGRYQN RAADWPDSGF GASNDGPGIT 360 QREGLMTYKQ FMQVLEDDIL PAEAERRYQE YRTEYITTQK RAYFDIHKND ELLKNKYHPT 420 NLSSVIDSRN ARCKGVASNF FHDLQNGTLD LGPGITAAAA SKAASGSDGN TDDDGDNDKR 480 RKHGRISSKE TDPLSGAPVA HPVSSESRRV QVDIEQALAL VRKLDTEKGI VGNILSSGDH 540 DKSDVDKSHI GSMGPIIIIR GLTTVKGLEG VELLDTLLTY LWRIHGVDYY GMSEANEPKG 600 IRHVRADSKA SNTTNINAAD WEKKLDTFWQ ERLIGQDPMV ILAAKDKIDA AAVEVLEPYV 660 RKIRDEKYGW KYGCGAKGCT KLFHAPEFVH KHLRLKHPEL VIELTSKVRE DLYFQNYMND 720 PNAPGGTPVM QQSAPDKSRQ RPGMDNRLRY DRANRREYDR AERDGGRYSR GDRSPSRDGA 780 DDQMFDAFRG RGPNAPFVPE IPAPPILMPV PGAGPLGPFV PAPPEIAMHM LREQGPPPPF 840 EPNGPAHGNA GVLGPMMGGP APIITMPPSF RHDPRRLRSY NDLDAPDEEV TVLDYRSL

Sequence ? help Back to Top

Protein Sequence Length: 898 aa Download sequence Send to blast

MARYEEHAHG HGHGHEAEDE DDEEEDEEEV EMEEDEDGEG RHHEGGGSAE EGVPMDADAA  60
AATLGAQMDQ HGAMVAAAVP AMASNQLTLS FQGEVYVFDS VSPDKVQAVL LLLGGRELNP  120
GLGSGASSSA PYSKRLNFPH RVASLMRFRE KRKERNFDKK IRYSVRKEVA LRMQRNRGQF  180
TSSKPKGDEA TSELTAPDGS PNWGSVEGRP PSAAECHHCG ISAKATPMMR RGPDGPRTLC  240
NACGLMWANK GMLRDLSKAP PTPIQAIPSA NDGNGSAGAP TTEQEIPTPA TANGHESSTL  300
DIVDRNCTLD QMVNTYGYDY ERGGGRGGYD DDRYHGRYQN RAADWPDSGF GASNDGPGIT  360
QREGLMTYKQ FMQVLEDDIL PAEAERRYQE YRTEYITTQK RAYFDIHKND ELLKNKYHPT  420
NLSSVIDSRN ARCKGVASNF FHDLQNGTLD LGPGITAAAA SKAASGSDGN TDDDGDNDKR  480
RKHGRISSKE TDPLSGAPVA HPVSSESRRV QVDIEQALAL VRKLDTEKGI VGNILSSGDH  540
DKSDVDKSHI GSMGPIIIIR GLTTVKGLEG VELLDTLLTY LWRIHGVDYY GMSEANEPKG  600
IRHVRADSKA SNTTNINAAD WEKKLDTFWQ ERLIGQDPMV ILAAKDKIDA AAVEVLEPYV  660
RKIRDEKYGW KYGCGAKGCT KLFHAPEFVH KHLRLKHPEL VIELTSKVRE DLYFQNYMND  720
PNAPGGTPVM QQSAPDKSRQ RPGMDNRLRY DRANRREYDR AERDGGRYSR GDRSPSRDGA  780
DDQMFDAFRG RGPNAPFVPE IPAPPILMPV PGAGPLGPFV PAPPEIAMHM LREQGPPPPF  840
EPNGPAHGNA GVLGPMMGGP APIITMPPSF RHDPRRLRSY NDLDAPDEEV TVLDYRSL

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
3ax1_A	1e-156	364	718	1	351	Serrate RNA effector molecule
Search in ModeBase

Functional Description ? help Back to Top
Source	Description
UniProt	Acts as a mediator between the cap-binding complex (CBC) and both the pre-mRNA splicing and primary microRNAs (miRNAs) processing machinery. Required for proper processing of primary miRNAs to miRNAs, thereby playing a role in RNA-mediated gene silencing (RNAi) by miRNAs. Does not participate in sense post-transcriptional gene silencing. Acts as a regulator of meristem activity and adaxial leaf fate via the miRNA gene-silencing pathway by regulating the expression of PHB and by limiting the competence of shoot tissue to respond to KNOX expression. Its function is however not limited to miRNA-mediated repression of leaf polarity genes, but rather acts as a general regulator of primary microRNAs processing. Also critical for the accumulation of the trans-acting small interfering RNA (ta-siRNA). Required for pre-mRNA splicing. {ECO:0000269\|PubMed:16222298, ECO:0000269\|PubMed:16889646, ECO:0000269\|PubMed:16977334, ECO:0000269\|PubMed:18550839, ECO:0000269\|PubMed:18632569}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	OB06G33840.1

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	AK120947	0.0	AK120947.1 Oryza sativa Japonica Group cDNA clone:J023038B04, full insert sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_015693694.1	0.0	PREDICTED: serrate RNA effector molecule-like
Swissprot	Q9ZVD0	0.0	SRRT_ARATH; Serrate RNA effector molecule
TrEMBL	J3MH90	0.0	J3MH90_ORYBR; Uncharacterized protein
STRING	OB06G33840.1	0.0	(Oryza brachyantha)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Monocots	OGMP1734	4	4

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT1G51600.2	2e-70	ZIM-LIKE 2

Publications ? help Back to Top
Clarke JH,Tack D,Findlay K,Van Montagu M,Van Lijsebettens M The SERRATE locus controls the formation of the early juvenile leaves and phase length in Arabidopsis. Plant J., 1999. 20(4): p. 493-501 [PMID:10607301] Fang Y,Spector DL Identification of nuclear dicing bodies containing proteins for microRNA biogenesis in living Arabidopsis plants. Curr. Biol., 2007. 17(9): p. 818-23 [PMID:17442570] Chenu K,Franck N,Lecoeur J Simulations of virtual plants reveal a role for SERRATE in the response of leaf development to light in Arabidopsis thaliana. New Phytol., 2007. 175(3): p. 472-81 [PMID:17635222] Fujioka Y,Utsumi M,Ohba Y,Watanabe Y Location of a possible miRNA processing site in SmD3/SmB nuclear bodies in Arabidopsis. Plant Cell Physiol., 2007. 48(9): p. 1243-53 [PMID:17675322] Wilson MD, et al. ARS2 is a conserved eukaryotic gene essential for early mammalian development. Mol. Cell. Biol., 2008. 28(5): p. 1503-14 [PMID:18086880] Dong Z,Han MH,Fedoroff N The RNA-binding proteins HYL1 and SE promote accurate in vitro processing of pri-miRNA by DCL1. Proc. Natl. Acad. Sci. U.S.A., 2008. 105(29): p. 9970-5 [PMID:18632569] Yu B, et al. The FHA domain proteins DAWDLE in Arabidopsis and SNIP1 in humans act in small RNA biogenesis. Proc. Natl. Acad. Sci. U.S.A., 2008. 105(29): p. 10073-8 [PMID:18632581] Kim W, et al. Histone acetyltransferase GCN5 interferes with the miRNA pathway in Arabidopsis. Cell Res., 2009. 19(7): p. 899-909 [PMID:19436261] Voisin D, et al. Dissection of the complex phenotype in cuticular mutants of Arabidopsis reveals a role of SERRATE as a mediator. PLoS Genet., 2009. 5(10): p. e1000703 [PMID:19876373] Werner S,Wollmann H,Schneeberger K,Weigel D Structure determinants for accurate processing of miR172a in Arabidopsis thaliana. Curr. Biol., 2010. 20(1): p. 42-8 [PMID:20015654] Yang SW, et al. Structure of Arabidopsis HYPONASTIC LEAVES1 and its molecular implications for miRNA processing. Structure, 2010. 18(5): p. 594-605 [PMID:20462493] Furumizu C,Tsukaya H,Komeda Y Characterization of EMU, the Arabidopsis homolog of the yeast THO complex member HPR1. RNA, 2010. 16(9): p. 1809-17 [PMID:20668032] Wang M, et al. Molecular insights into plant cell proliferation disturbance by Agrobacterium protein 6b. Genes Dev., 2011. 25(1): p. 64-76 [PMID:21156810] Bassel GW, et al. Genome-wide network model capturing seed germination reveals coordinated regulation of plant cellular phase transitions. Proc. Natl. Acad. Sci. U.S.A., 2011. 108(23): p. 9709-14 [PMID:21593420] Machida S,Chen HY,Adam Yuan Y Molecular insights into miRNA processing by Arabidopsis thaliana SERRATE. Nucleic Acids Res., 2011. 39(17): p. 7828-36 [PMID:21685453] Wang W, et al. An importin β protein negatively regulates MicroRNA activity in Arabidopsis. Plant Cell, 2011. 23(10): p. 3565-76 [PMID:21984696] Christie M,Carroll BJ SERRATE is required for intron suppression of RNA silencing in Arabidopsis. Plant Signal Behav, 2011. 6(12): p. 2035-7 [PMID:22112452] Liu J, et al. Genome-wide analysis uncovers regulation of long intergenic noncoding RNAs in Arabidopsis. Plant Cell, 2012. 24(11): p. 4333-45 [PMID:23136377] Manavella PA, et al. Fast-forward genetics identifies plant CPL phosphatases as regulators of miRNA processing factor HYL1. Cell, 2012. 151(4): p. 859-870 [PMID:23141542] Ben Chaabane S, et al. STA1, an Arabidopsis pre-mRNA processing factor 6 homolog, is a new player involved in miRNA biogenesis. Nucleic Acids Res., 2013. 41(3): p. 1984-97 [PMID:23268445] Wu X, et al. A role for the RNA-binding protein MOS2 in microRNA maturation in Arabidopsis. Cell Res., 2013. 23(5): p. 645-57 [PMID:23399598] Wang L, et al. NOT2 proteins promote polymerase II-dependent transcription and interact with multiple MicroRNA biogenesis factors in Arabidopsis. Plant Cell, 2013. 25(2): p. 715-27 [PMID:23424246] Iwata Y,Takahashi M,Fedoroff NV,Hamdan SM Dissecting the interactions of SERRATE with RNA and DICER-LIKE 1 in Arabidopsis microRNA precursor processing. Nucleic Acids Res., 2013. 41(19): p. 9129-40 [PMID:23921632] Speth C,Willing EM,Rausch S,Schneeberger K,Laubinger S RACK1 scaffold proteins influence miRNA abundance in Arabidopsis. Plant J., 2013. 76(3): p. 433-45 [PMID:23941160] Raczynska KD, et al. The SERRATE protein is involved in alternative splicing in Arabidopsis thaliana. Nucleic Acids Res., 2014. 42(2): p. 1224-44 [PMID:24137006] Bulgakov VP,Veremeichik GN,Shkryl YN The rolB gene activates the expression of genes encoding microRNA processing machinery. Biotechnol. Lett., 2015. 37(4): p. 921-5 [PMID:25491479] Baranauskė S, et al. Functional mapping of the plant small RNA methyltransferase: HEN1 physically interacts with HYL1 and DICER-LIKE 1 proteins. Nucleic Acids Res., 2015. 43(5): p. 2802-12 [PMID:25680966] Chen T,Cui P,Xiong L The RNA-binding protein HOS5 and serine/arginine-rich proteins RS40 and RS41 participate in miRNA biogenesis in Arabidopsis. Nucleic Acids Res., 2015. 43(17): p. 8283-98 [PMID:26227967] Niu D, et al. miRNA863-3p sequentially targets negative immune regulator ARLPKs and positive regulator SERRATE upon bacterial infection. Nat Commun, 2016. 7: p. 11324 [PMID:27108563] Yoshikawa M Pre-microRNA processing activity in nuclear extracts from Arabidopsis suspension cells. J. Plant Res., 2017. 130(1): p. 75-82 [PMID:27885505] Cho SK, et al. HIGLE is a bifunctional homing endonuclease that directly interacts with HYL1 and SERRATE in Arabidopsis thaliana. FEBS Lett., 2017. 591(10): p. 1383-1393 [PMID:28321834] Yan J, et al. The SnRK2 kinases modulate miRNA accumulation in Arabidopsis. PLoS Genet., 2017. 13(4): p. e1006753 [PMID:28419088] Foley SW, et al. A Global View of RNA-Protein Interactions Identifies Post-transcriptional Regulators of Root Hair Cell Fate. Dev. Cell, 2017. 41(2): p. 204-220.e5 [PMID:28441533] Armenta-Medina A, et al. Arabidopsis thaliana miRNAs promote embryo pattern formation beginning in the zygote. Dev. Biol., 2017. 431(2): p. 145-151 [PMID:28912016] Lepe-Soltero D, et al. Annotating and quantifying pri-miRNA transcripts using RNA-Seq data of wild type and serrate-1 globular stage embryos of Arabidopsis thaliana. Data Brief, 2017. 15: p. 642-647 [PMID:29124087] Wang Z, et al. SWI2/SNF2 ATPase CHR2 remodels pri-miRNAs via Serrate to impede miRNA production. Nature, 2018. 557(7706): p. 516-521 [PMID:29769717] Speth C, et al. Arabidopsis RNA processing factor SERRATE regulates the transcription of intronless genes. Elife, 2019. [PMID:30152752]