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

Zpz_sc00174.1.g00120.1.am.mkhc

Organism

Zoysia pacifica

Taxonomic ID

1070856

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; PACMAD clade; Chloridoideae; Zoysieae; Zoysiinae; Zoysia

Family

GATA

Protein Properties

Length: 1119aa MW: 122826 Da PI: 7.7473

Description

GATA family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Zpz_sc00174.1.g00120.1.am.mkhc	genome	ZGD	View Nucleic Acid

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	GATA	50.2	3.5e-16	202	238	1	35
GATA 1 CsnCg..ttkTplWRrgpdgnktLCnaCGlyyrkkgl 35 C++Cg +t+Tp++Rrgpdg++tLCnaCGl+++ kgl Zpz_sc00174.1.g00120.1.am.mkhc 202 CHHCGisATNTPMMRRGPDGPRTLCNACGLMWANKGL 238 **955777*********************9996 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS51320	15.123	66	101	IPR010399	Tify domain
SMART	SM00979	9.2E-13	66	101	IPR010399	Tify domain
Pfam	PF06200	3.0E-12	70	100	IPR010399	Tify domain
Pfam	PF06203	1.3E-15	127	169	IPR010402	CCT domain
PROSITE profile	PS51017	13.334	127	169	IPR010402	CCT domain
PROSITE profile	PS50114	10.607	196	252	IPR000679	Zinc finger, GATA-type
SMART	SM00401	2.4E-13	196	249	IPR000679	Zinc finger, GATA-type
SuperFamily	SSF57716	9.5E-12	200	253	No hit	No description
CDD	cd00202	8.09E-14	201	244	No hit	No description
Gene3D	G3DSA:3.30.50.10	2.1E-15	201	243	IPR013088	Zinc finger, NHR/GATA-type
PROSITE pattern	PS00344	0	202	229	IPR000679	Zinc finger, GATA-type
Pfam	PF00320	3.2E-14	202	238	IPR000679	Zinc finger, GATA-type
Pfam	PF12066	1.6E-19	513	594	IPR021933	Protein of unknown function DUF3546
Pfam	PF04959	1.4E-33	745	929	IPR007042	Arsenite-resistance protein 2
PROSITE pattern	PS00028	0	814	837	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: 1119 aa Download sequence Send to blast
EEVGEEEEEE DEDMEDEEDD GAEGDGQEGG VTGEHVPMDS EAAAAAAAAS GMQMDPHGAM 60 VPMTVPPISS NQLTLSFQGE VYVFDSVSPD KVQAVLLLLG GRELNPGLGA SASSSTPYSK 120 RLNYPHRVAS LMRFREKRKE RNFDKKIRYT VRKEVALRMQ RNKGQFTSSK PKPDEAASEL 180 TTADGSPNWG ALEGRPPSAS ECHHCGISAT NTPMMRRGPD GPRTLCNACG LMWANKGLLR 240 DLSKSPQVVQ STPAVDDGQN GGVTQVVVAP GAEQENPAPD TTNGHKLSTR FSLSLSLSLS 300 PAPLLPPPSR PPVRCGLLLL DSTPNPRAGA SMADLLDPSS EAPRARRPPP PPPDSPEDPS 360 QDLPPPPPGG PPPSRKRSRS PPSSALPPPP PPPVGSSRPQ RYRDHHHRGS RGGSSPSPPP 420 YRGGRRHSPS RRSPSPPFKR SRRDDGYDRR GGRSPPRYGY NDRRRGYDYE RGGGRGGYDD 480 DRYQGRYPNR AQGYGASTDG PGNTQREGLM TYKQFIQVLE DDISPTEAER RYQEYRTEYI 540 TTQKRAYFDL HKNEDWLKDK YHPTNLLSVI ERRNERCKVT AKDFFLDLQN GTLDLGPGVT 600 AGAVSKSGNG SDGNSEDEED TDKRRKNSKD SSKGTDCPKA HPVSAESRRI QIDIEQTLSL 660 VRKLDAEKGI EGNILSSGDH DKSDVDKSHI GSMGPIIIIR GLTTVKGLEG VELLDTVLTY 720 LWRIHGVDYY GTSESLEAKG LRHVRADNKT SSTSDINAAD WEKKLDSFWQ ERLSGQDPMI 780 LLTAKDKIDA AAVEVLEPYV RKIRDEKYGW KYGCGAKGCT KLFHAPEFVH KHLRLKHPDL 840 VLELTSKVRE DLYFQNYMND PNAPGGTPVM QQPALDKTRG RSGMDGRLRF DDSRSEAERD 900 GGRYGRGDRS PSGDGPDDQM FDTFRGRGSN APFVAEFPPP PILMPVPGAG PLGPFVPAPP 960 EIAMHMMREQ GGPAPFEPNG VPHGNTGVLG PMLGGPAPII TMPPNFRHDP RRLRSYNDLD 1020 APDEEVTVLD YRKRKSLSLV LVILLVNGLR FDSQFARVNF FAPVGYLCCS RKTQTPLPFG 1080 HSGSNAGGLK HAFVSCSSCV LRTPACFRRL SLLLRLLFM

Sequence ? help Back to Top

Protein Sequence Length: 1119 aa Download sequence Send to blast

EEVGEEEEEE DEDMEDEEDD GAEGDGQEGG VTGEHVPMDS EAAAAAAAAS GMQMDPHGAM  60
VPMTVPPISS NQLTLSFQGE VYVFDSVSPD KVQAVLLLLG GRELNPGLGA SASSSTPYSK  120
RLNYPHRVAS LMRFREKRKE RNFDKKIRYT VRKEVALRMQ RNKGQFTSSK PKPDEAASEL  180
TTADGSPNWG ALEGRPPSAS ECHHCGISAT NTPMMRRGPD GPRTLCNACG LMWANKGLLR  240
DLSKSPQVVQ STPAVDDGQN GGVTQVVVAP GAEQENPAPD TTNGHKLSTR FSLSLSLSLS  300
PAPLLPPPSR PPVRCGLLLL DSTPNPRAGA SMADLLDPSS EAPRARRPPP PPPDSPEDPS  360
QDLPPPPPGG PPPSRKRSRS PPSSALPPPP PPPVGSSRPQ RYRDHHHRGS RGGSSPSPPP  420
YRGGRRHSPS RRSPSPPFKR SRRDDGYDRR GGRSPPRYGY NDRRRGYDYE RGGGRGGYDD  480
DRYQGRYPNR AQGYGASTDG PGNTQREGLM TYKQFIQVLE DDISPTEAER RYQEYRTEYI  540
TTQKRAYFDL HKNEDWLKDK YHPTNLLSVI ERRNERCKVT AKDFFLDLQN GTLDLGPGVT  600
AGAVSKSGNG SDGNSEDEED TDKRRKNSKD SSKGTDCPKA HPVSAESRRI QIDIEQTLSL  660
VRKLDAEKGI EGNILSSGDH DKSDVDKSHI GSMGPIIIIR GLTTVKGLEG VELLDTVLTY  720
LWRIHGVDYY GTSESLEAKG LRHVRADNKT SSTSDINAAD WEKKLDSFWQ ERLSGQDPMI  780
LLTAKDKIDA AAVEVLEPYV RKIRDEKYGW KYGCGAKGCT KLFHAPEFVH KHLRLKHPDL  840
VLELTSKVRE DLYFQNYMND PNAPGGTPVM QQPALDKTRG RSGMDGRLRF DDSRSEAERD  900
GGRYGRGDRS PSGDGPDDQM FDTFRGRGSN APFVAEFPPP PILMPVPGAG PLGPFVPAPP  960
EIAMHMMREQ GGPAPFEPNG VPHGNTGVLG PMLGGPAPII TMPPNFRHDP RRLRSYNDLD  1020
APDEEVTVLD YRKRKSLSLV LVILLVNGLR FDSQFARVNF FAPVGYLCCS RKTQTPLPFG  1080
HSGSNAGGLK HAFVSCSSCV LRTPACFRRL SLLLRLLFM

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
3ax1_A	1e-154	508	858	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	Zpz_sc00174.1.g00120.1.am.mkhc

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_025811396.1	0.0	serrate RNA effector molecule-like
Swissprot	Q9ZVD0	0.0	SRRT_ARATH; Serrate RNA effector molecule
TrEMBL	A0A2T8JBH9	0.0	A0A2T8JBH9_9POAL; Uncharacterized protein
STRING	Pavir.Da00165.1.p	0.0	(Panicum virgatum)

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	3e-71	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]