PlantTFDB - Plant Transcription Factor Database @ CBI, PKU

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; lamiids; Solanales; Solanaceae; Solanoideae; Solaneae; Solanum; Lycopersicon

Family

MYB

Protein Properties

Length: 361aa MW: 41179.9 Da PI: 9.7548

Description

MYB family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Solyc09g010840.1.1	genome	ITAG	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	Myb_DNA-binding	47.9	3.1e-15	4	53	1	48
TSSS-HHHHHHHHHHHHHTTTT-HHHHHHHHT..TTS-HHHHHHHHHHHT CS Myb_DNA-binding 1 rgrWTteEdellvdavkqlGggtWktIartmg..kgRtlkqcksrwqkyl 48 r+rW +eEd ll +v+q+G++ W++++++m+ ++R +k+c +rw +yl Solyc09g010840.1.1 4 RQRWRAEEDALLRAYVRQYGPKEWHLVSQRMNtpLNRDAKSCLERWKNYL 53 89**********************************************97 PP
2	Myb_DNA-binding	35.8	1.8e-11	59	103	1	47
TSSS-HHHHHHHHHHHHHTTTT-HHHHHHHHTTTS-HHHHHHHHHHH CS Myb_DNA-binding 1 rgrWTteEdellvdavkqlGggtWktIartmgkgRtlkqcksrwqky 47 +g+ T++E+ l +++ +++G++ Wk+Ia++++ gRt+k + +w + Solyc09g010840.1.1 59 KGSLTEDEQRLVIQLQAKHGNK-WKKIAAEVP-GRTAKRLGKWWEVF 103 6788****************.*****.***999999766 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS51294	16.492	1	53	IPR017930	Myb domain
SMART	SM00717	1.4E-13	3	55	IPR001005	SANT/Myb domain
SuperFamily	SSF46689	2.98E-21	4	98	IPR009057	Homeodomain-like
CDD	cd00167	9.92E-9	6	53	No hit	No description
Gene3D	G3DSA:1.10.10.60	7.4E-20	6	60	IPR009057	Homeodomain-like
Pfam	PF13921	3.6E-13	7	68	No hit	No description
PROSITE profile	PS51294	23.061	54	108	IPR017930	Myb domain
SMART	SM00717	4.6E-10	58	106	IPR001005	SANT/Myb domain
Gene3D	G3DSA:1.10.10.60	6.4E-15	61	102	IPR009057	Homeodomain-like
CDD	cd00167	8.63E-7	63	104	No hit	No description

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0003677	Molecular Function	DNA binding

Sequence ? help Back to Top
Protein Sequence Length: 361 aa Download sequence Send to blast
MRERQRWRAE EDALLRAYVR QYGPKEWHLV SQRMNTPLNR DAKSCLERWK NYLKPGIKKG 60 SLTEDEQRLV IQLQAKHGNK WKKIAAEVPG RTAKRLGKWW EVFKEKQQRE QKENNKVVDP 120 VDEGKYDHIL ETFAEKIVKE RSVPGLLMAT SNGGFLHADA STPTPQTLLP PWLSNSSAPS 180 TVRSSSPSVT LSLSPSTVPP TPTPGIPWLQ TDRGPDNAPL ILSSFPHHSV APCGENPFIT 240 ELAECCKDLD EGHRTWTAHK KEAAWRLRRV ELQLESEKAS KVREKMEEIE AKMKALREEQ 300 KATLDRIEAE YKEQLAGLRR DAEAKEQKLA EQWTSKHMRL AKFLEQMGCQ SRLAEPNGGR 360 *

Sequence ? help Back to Top

Protein Sequence Length: 361 aa Download sequence Send to blast

MRERQRWRAE EDALLRAYVR QYGPKEWHLV SQRMNTPLNR DAKSCLERWK NYLKPGIKKG  60
SLTEDEQRLV IQLQAKHGNK WKKIAAEVPG RTAKRLGKWW EVFKEKQQRE QKENNKVVDP  120
VDEGKYDHIL ETFAEKIVKE RSVPGLLMAT SNGGFLHADA STPTPQTLLP PWLSNSSAPS  180
TVRSSSPSVT LSLSPSTVPP TPTPGIPWLQ TDRGPDNAPL ILSSFPHHSV APCGENPFIT  240
ELAECCKDLD EGHRTWTAHK KEAAWRLRRV ELQLESEKAS KVREKMEEIE AKMKALREEQ  300
KATLDRIEAE YKEQLAGLRR DAEAKEQKLA EQWTSKHMRL AKFLEQMGCQ SRLAEPNGGR  360
*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
1gv2_A	9e-16	7	92	7	89	MYB PROTO-ONCOGENE PROTEIN
1mse_C	9e-16	7	92	7	89	C-Myb DNA-Binding Domain
1msf_C	9e-16	7	92	7	89	C-Myb DNA-Binding Domain
Search in ModeBase

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
Les.33	0.0	callus\| fruit\| leaf

Expression -- Description ? help Back to Top
Source	Description
Uniprot	DEVELOPMENTAL STAGE: Preferential expression in young and immature plant tissues. In embryos, expressed from the late globular stage onwards. After germination, detected in leaf founder cells and on flowering, in primordia of all floral organs.
Uniprot	TISSUE SPECIFICITY: Expressed in roots, stems, leaves, flowers, siliques and in lateral organ promordia (PubMed:17559509). Found in the inner domain between the adaxial and abaxial domains of leaves (PubMed:17559509). Expressed in the phloem tissues of leaves, cotyledons, hypocotyls, and roots (PubMed:21950734). {ECO:0000269\|PubMed:17559509, ECO:0000269\|PubMed:21950734}.

Functional Description ? help Back to Top
Source	Description
UniProt	Transcription factor required for normal cell differentiation. Positively regulates LATERAL ORGAN BOUNDARIES (LOB) within the shoot apex, and the class III HD-ZIP genes REV, PHB, and PHV. Interacts directly with ASYMMETRIC LEAVES 2 (LBD6/AS2) to repress the knox homeobox genes BP/KNAT1, KNAT2, and KNAT6 and the abaxial determinants ARF3/ETT, KAN2 and YAB5. May act in parallel with the RDR6-SGS3-AGO7 pathway, an endogenous RNA silencing pathway, to regulate the leaf morphogenesis (PubMed:11076771, PubMed:11140682, PubMed:11882937, PubMed:12750468, PubMed:16006579, PubMed:16699177, PubMed:17395603, PubMed:17559509, PubMed:23271976). Binds directly to KNAT1, KNAT2, and KNATM chromatin, regulating leaf development (PubMed:23271976). LBD6 is required for this binding (PubMed:23271976). Positive regulator of flowering that binds to the promoter of FT (PubMed:21950734). Regulates FT expression by forming a functional complex with CO (PubMed:21950734). Involved in leaf polarity establishment by functioning cooperatively with NUCL1 to repress abaxial genes ARF3, ARF4, KAN1, KAN2, YAB1 and YAB5, and the knox homeobox genes KNAT1, KNAT2, KNAT6, and STM to promote adaxial development in leaf primordia at shoot apical meristems at high temperatures (PubMed:27334696). {ECO:0000269\|PubMed:11076771, ECO:0000269\|PubMed:11140682, ECO:0000269\|PubMed:11882937, ECO:0000269\|PubMed:12750468, ECO:0000269\|PubMed:16006579, ECO:0000269\|PubMed:16699177, ECO:0000269\|PubMed:17395603, ECO:0000269\|PubMed:17559509, ECO:0000269\|PubMed:23271976, ECO:0000269\|PubMed:27334696}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Solyc09g010840.1.1

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: Circadian-regulation with an afternoon peak in long days and with a broad night peak in short days (PubMed:21950734). Expression of AS1 in stem cells of the shoot apical meristem is prevented by SHOOT MERISTEMLESS (STM). Expression is activated by GTE6 during leaf morphogenesis (PubMed:16166385). {ECO:0000269\|PubMed:16166385, ECO:0000269\|PubMed:21950734}.

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	AF148934	0.0	Lycopersicon esculentum phantastica mRNA, complete cds

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	NP_001234276.2	0.0	phantastica
Refseq	XP_025888480.1	0.0	phantastica isoform X1
Swissprot	O80931	1e-167	AS1_ARATH; Transcription factor AS1
TrEMBL	A0A3Q7HZZ1	0.0	A0A3Q7HZZ1_SOLLC; Uncharacterized protein
STRING	Solyc09g010840.1.1	0.0	(Solanum lycopersicum)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Asterids	OGEA2933	24	45
Representative plant	OGRP5096	14	21

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT2G37630.1	1e-138	MYB family protein

Link Out ? help Back to Top
Phytozome	Solyc09g010840.1.1
Entrez Gene	543604

Publications ? help Back to Top
Koltai H,Bird DM Epistatic repression of PHANTASTICA and class 1 KNOTTED genes is uncoupled in tomato. Plant J., 2000. 22(5): p. 455-9 [PMID:10849361] Kim M,McCormick S,Timmermans M,Sinha N The expression domain of PHANTASTICA determines leaflet placement in compound leaves. Nature, 2003. 424(6947): p. 438-43 [PMID:12879073] Hazen SP, et al. Rapid array mapping of circadian clock and developmental mutations in Arabidopsis. Plant Physiol., 2005. 138(2): p. 990-7 [PMID:15908595] Wang Y,van der Hoeven RS,Nielsen R,Mueller LA,Tanksley SD Characteristics of the tomato nuclear genome as determined by sequencing undermethylated EcoRI digested fragments. Theor. Appl. Genet., 2005. 112(1): p. 72-84 [PMID:16208505] Pinon V, et al. Three PIGGYBACK genes that specifically influence leaf patterning encode ribosomal proteins. Development, 2008. 135(7): p. 1315-24 [PMID:18305008] Zoulias N,Koenig D,Hamidi A,McCormick S,Kim M A role for PHANTASTICA in medio-lateral regulation of adaxial domain development in tomato and tobacco leaves. Ann. Bot., 2012. 109(2): p. 407-18 [PMID:22184618] Ding Y, et al. Four distinct types of dehydration stress memory genes in Arabidopsis thaliana. BMC Plant Biol., 2013. 13: p. 229 [PMID:24377444] Zhou F,Roy B,Dunlap JR,Enganti R,von Arnim AG Translational control of Arabidopsis meristem stability and organogenesis by the eukaryotic translation factor eIF3h. PLoS ONE, 2014. 9(4): p. e95396 [PMID:24736281] Scofield S,Dewitte W,Murray JA STM sustains stem cell function in the Arabidopsis shoot apical meristem and controls KNOX gene expression independently of the transcriptional repressor AS1. Plant Signal Behav, 2018. [PMID:24776954] Ivanova A, et al. A Functional Antagonistic Relationship between Auxin and Mitochondrial Retrograde Signaling Regulates Alternative Oxidase1a Expression in Arabidopsis. Plant Physiol., 2014. 165(3): p. 1233-1254 [PMID:24820025] Machida C,Nakagawa A,Kojima S,Takahashi H,Machida Y The complex of ASYMMETRIC LEAVES (AS) proteins plays a central role in antagonistic interactions of genes for leaf polarity specification in Arabidopsis. Wiley Interdiscip Rev Dev Biol, 2015 Nov-Dec. 4(6): p. 655-71 [PMID:26108442] Kaurilind E,Xu E,Brosché M A genetic framework for H2O2 induced cell death in Arabidopsis thaliana. BMC Genomics, 2015. 16: p. 837 [PMID:26493993] Mateo-Bonmatí E, et al. Plastid control of abaxial-adaxial patterning. Sci Rep, 2015. 5: p. 15975 [PMID:26522839] Rast-Somssich MI, et al. Alternate wiring of a KNOXI genetic network underlies differences in leaf development of A. thaliana and C. hirsuta. Genes Dev., 2015. 29(22): p. 2391-404 [PMID:26588991] Guzmán-López JA,Abraham-Juárez MJ,Lozano-Sotomayor P,de Folter S,Simpson J Arabidopsis thaliana gonidialess A/Zuotin related factors (GlsA/ZRF) are essential for maintenance of meristem integrity. Plant Mol. Biol., 2016. 91(1-2): p. 37-51 [PMID:26826012] Li Z, et al. Transcription factors AS1 and AS2 interact with LHP1 to repress KNOX genes in Arabidopsis. J Integr Plant Biol, 2016. 58(12): p. 959-970 [PMID:27273574] Matsumura Y, et al. A genetic link between epigenetic repressor AS1-AS2 and a putative small subunit processome in leaf polarity establishment of Arabidopsis. Biol Open, 2016. 5(7): p. 942-54 [PMID:27334696] Silverblatt-Buser EW,Frick MA,Rabeler C,Kaplinsky NJ Genetic Interactions Between BOB1 and Multiple 26S Proteasome Subunits Suggest a Role for Proteostasis in Regulating Arabidopsis Development. G3 (Bethesda), 2018. 8(4): p. 1379-1390 [PMID:29487187] Bird DM,Wilson MA DNA sequence and expression analysis of root-knot nematode-elicited giant cell transcripts. Mol. Plant Microbe Interact., 1994 May-Jun. 7(3): p. 419-24 [PMID:8012051] Tsukaya H,Uchimiya H Genetic analyses of the formation of the serrated margin of leaf blades in Arabidopsis: combination of a mutational analysis of leaf morphogenesis with the characterization of a specific marker gene expressed in hydathodes and stipules. Mol. Gen. Genet., 1997. 256(3): p. 231-8 [PMID:9393447]