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

KN538794.1_FGP036

Organism

Oryza longistaminata

Taxonomic ID

4528

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: 860aa MW: 94598.3 Da PI: 5.5757

Description

GATA family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
KN538794.1_FGP036	genome	BGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	GATA	47.3	2.8e-15	209	243	1	33
GATA 1 CsnCgttk..TplWRrgpdgnktLCnaCGlyyrkk 33 C++Cg Tp++Rrgpdg++tLCnaCGl+++ k KN538794.1_FGP036 209 CHHCGINAkaTPMMRRGPDGPRTLCNACGLMWANK 243 **977777********************986 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SMART	SM00979	5.9E-11	73	108	IPR010399	Tify domain
PROSITE profile	PS51320	14.975	73	108	IPR010399	Tify domain
Pfam	PF06200	1.2E-12	76	107	IPR010399	Tify domain
PROSITE profile	PS51017	13.404	134	176	IPR010402	CCT domain
Pfam	PF06203	2.6E-15	134	176	IPR010402	CCT domain
SMART	SM00401	1.5E-8	203	255	IPR000679	Zinc finger, GATA-type
SuperFamily	SSF57716	1.76E-9	207	248	No hit	No description
CDD	cd00202	3.63E-11	208	249	No hit	No description
Gene3D	G3DSA:3.30.50.10	2.5E-13	208	244	IPR013088	Zinc finger, NHR/GATA-type
PROSITE pattern	PS00344	0	209	236	IPR000679	Zinc finger, GATA-type
Pfam	PF00320	5.3E-13	209	243	IPR000679	Zinc finger, GATA-type
Pfam	PF12066	1.6E-11	358	414	IPR021933	Protein of unknown function DUF3546
Pfam	PF04959	1.8E-35	567	754	IPR007042	Arsenite-resistance protein 2
PROSITE pattern	PS00028	0	636	659	IPR007087	Zinc finger, C2H2

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0006355	Biological Process	regulation of transcription, DNA-templated
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: 860 aa Download sequence Send to blast
MARFEEEHRA LGAEEEDEEE EDELEEEEEE MEEDEDAQHH EGVGGEVAVP MDAEAAAQLD 60 PHGGMLAAAG AVQPMASNQL TLSFQGEVYV FDSVSPDKVQ AVLLLLGGRE LNPGLGSGAS 120 SSAPYSKRLN FPHRVASLMR FREKRKERNF DKKIRYSVRK EVALRMQRNR GQFTSSKPKG 180 DEATSELTAS DGSPNWGSVE GRPPSAAECH HCGINAKATP MMRRGPDGPR TLCNACGLMW 240 ANKVKMPSSR CHANLGMLRD LSKAPPTPIQ VVASVNDGNG SAAAPTTEQE IPAPATANGH 300 ESSTYGYDHE RGGGRGGYDD DRYHGRYQNR AADWADSGFG ASNDGPGITQ REGLMTYKQF 360 IQVLEDDISP AEAEKRYQEY RTEYITTQKR AYFDLNKNDD RLKDKYHPTN LSSVIDSGPG 420 ITAAAASGSD GNSDDDGDSD KRRKHGRGSS KETDPLSGAP VAHPVSSESR RVQVDIEQAL 480 ALVRKLDTEK GIVGNILSSG DHDKSDVDKS HIGSMGPIII IRGLTTVKGL EGVELLDTLL 540 TYLWRIHGVD YYGMSETNEA KGSRHVRADN KASNTTNINA ADWEKKVDTF WQERLRGQDP 600 MVILAAKDKI DAAAVEVLEP YVRKIRDEKY GWKYGCGAKG CTKLFHAPEF VHKHLRLKHP 660 ELVLELTSKV REDLYFQNYM NDPNAPGGTP VMQQSAPDKS RQRPGMDNRL RYDRANRREY 720 DRAERDGGRY GRGDRSPSRD GADDQMFDAF RGRGPNAPFV PELPAPPILM PVPGAGPLGP 780 FVPAPPEIAM HMLREQGPPP PFEPNGPPHA NAGVLGPMMG GPAPIITMPP SFRQDPRRLR 840 SYNDLDAPDE EVTVLDYRSL

Sequence ? help Back to Top

Protein Sequence Length: 860 aa Download sequence Send to blast

MARFEEEHRA LGAEEEDEEE EDELEEEEEE MEEDEDAQHH EGVGGEVAVP MDAEAAAQLD  60
PHGGMLAAAG AVQPMASNQL TLSFQGEVYV FDSVSPDKVQ AVLLLLGGRE LNPGLGSGAS  120
SSAPYSKRLN FPHRVASLMR FREKRKERNF DKKIRYSVRK EVALRMQRNR GQFTSSKPKG  180
DEATSELTAS DGSPNWGSVE GRPPSAAECH HCGINAKATP MMRRGPDGPR TLCNACGLMW  240
ANKVKMPSSR CHANLGMLRD LSKAPPTPIQ VVASVNDGNG SAAAPTTEQE IPAPATANGH  300
ESSTYGYDHE RGGGRGGYDD DRYHGRYQNR AADWADSGFG ASNDGPGITQ REGLMTYKQF  360
IQVLEDDISP AEAEKRYQEY RTEYITTQKR AYFDLNKNDD RLKDKYHPTN LSSVIDSGPG  420
ITAAAASGSD GNSDDDGDSD KRRKHGRGSS KETDPLSGAP VAHPVSSESR RVQVDIEQAL  480
ALVRKLDTEK GIVGNILSSG DHDKSDVDKS HIGSMGPIII IRGLTTVKGL EGVELLDTLL  540
TYLWRIHGVD YYGMSETNEA KGSRHVRADN KASNTTNINA ADWEKKVDTF WQERLRGQDP  600
MVILAAKDKI DAAAVEVLEP YVRKIRDEKY GWKYGCGAKG CTKLFHAPEF VHKHLRLKHP  660
ELVLELTSKV REDLYFQNYM NDPNAPGGTP VMQQSAPDKS RQRPGMDNRL RYDRANRREY  720
DRAERDGGRY GRGDRSPSRD GADDQMFDAF RGRGPNAPFV PELPAPPILM PVPGAGPLGP  780
FVPAPPEIAM HMLREQGPPP PFEPNGPPHA NAGVLGPMMG GPAPIITMPP SFRQDPRRLR  840
SYNDLDAPDE EVTVLDYRSL

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
3ax1_A	1e-143	353	680	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	KN538794.1_FGP036

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_025882281.1	0.0	serrate RNA effector molecule
Swissprot	Q9ZVD0	0.0	SRRT_ARATH; Serrate RNA effector molecule
TrEMBL	A0A0E0HUV9	0.0	A0A0E0HUV9_ORYNI; Uncharacterized protein
STRING	ONIVA06G28780.1	0.0	(Oryza nivara)

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-66	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]