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

Csa09g096980.1

Organism

Camelina sativa

Taxonomic ID

90675

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Camelina

Family

TALE

Protein Properties

Length: 405aa MW: 45736.6 Da PI: 6.9509

Description

TALE family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Csa09g096980.1	genome	CSGP	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	Homeobox	28.9	2e-09	308	342	21	55
HSSS--HHHHHHHHHHCTS-HHHHHHHHHHHHHHH CS Homeobox 21 knrypsaeereeLAkklgLterqVkvWFqNrRake 55 k +yps++++ LA+++gL+++q+ +WF N+R ++ Csa09g096980.1 308 KWPYPSEQQKLALAESTGLDQKQINNWFINQRKRH 342 569*****************************885 PP
2	ELK	40.9	4.2e-14	262	283	1	22
ELK 1 ELKhqLlrKYsgyLgsLkqEFs 22 ELK qLlrKYsgyLgsLkqEF+ Csa09g096980.1 262 ELKGQLLRKYSGYLGSLKQEFM 283 9********************8 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SMART	SM01255	6.1E-20	119	163	IPR005540	KNOX1
Pfam	PF03790	2.0E-22	121	159	IPR005540	KNOX1
SMART	SM01256	8.8E-27	170	221	IPR005541	KNOX2
Pfam	PF03791	1.1E-20	174	219	IPR005541	KNOX2
SMART	SM01188	2.8E-8	262	283	IPR005539	ELK domain
PROSITE profile	PS51213	11.174	262	282	IPR005539	ELK domain
Pfam	PF03789	6.9E-11	262	283	IPR005539	ELK domain
PROSITE profile	PS50071	13.151	282	345	IPR001356	Homeobox domain
SMART	SM00389	5.3E-13	284	349	IPR001356	Homeobox domain
SuperFamily	SSF46689	2.31E-18	284	349	IPR009057	Homeodomain-like
Gene3D	G3DSA:1.10.10.60	4.4E-28	287	347	IPR009057	Homeodomain-like
CDD	cd00086	6.10E-12	294	346	No hit	No description
Pfam	PF05920	3.7E-17	302	341	IPR008422	Homeobox KN domain
PROSITE pattern	PS00027	0	320	343	IPR017970	Homeobox, conserved site
Gene3D	G3DSA:1.10.10.60	4.8E-5	353	369	IPR009057	Homeodomain-like

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0006355	Biological Process	regulation of transcription, DNA-templated
GO:0005634	Cellular Component	nucleus
GO:0043565	Molecular Function	sequence-specific DNA binding

Sequence ? help Back to Top
Protein Sequence Length: 405 aa Download sequence Send to blast
MESGSNSTSC PMAFAGDNSD GPMCPMMMMM PPIMTSHQHR GHDHQHQQQE HDGYAYQSHH 60 QQSSSLFLQS LPPPPQATKN KVVSSSPSSC VPAYSLMEIH HNDVVAGGIN PCSSSSSSAS 120 VKAKIMAHPH YHRLLAAYVN CQKVGAPPEV VARLEEACSS AAAAAASMGP TSCLGEDPGL 180 DQFMEAYCEM LVKYEQELSK PFKEAMVFLQ RVECQFKSLS LSSPSSFSGY GETAIDRNNN 240 GSSEEEVDMN NEFVDPQAED RELKGQLLRK YSGYLGSLKQ EFMKKRKKGK LPKEARQQLL 300 DWWSRHYKWP YPSEQQKLAL AESTGLDQKQ INNWFINQRK RHWKPSEDMQ FVINNWFINQ 360 RKRHWKPSED MQFVVMDATH PHHYFMDNVL GNPFPMDHIS STML*

Sequence ? help Back to Top

Protein Sequence Length: 405 aa Download sequence Send to blast

MESGSNSTSC PMAFAGDNSD GPMCPMMMMM PPIMTSHQHR GHDHQHQQQE HDGYAYQSHH  60
QQSSSLFLQS LPPPPQATKN KVVSSSPSSC VPAYSLMEIH HNDVVAGGIN PCSSSSSSAS  120
VKAKIMAHPH YHRLLAAYVN CQKVGAPPEV VARLEEACSS AAAAAASMGP TSCLGEDPGL  180
DQFMEAYCEM LVKYEQELSK PFKEAMVFLQ RVECQFKSLS LSSPSSFSGY GETAIDRNNN  240
GSSEEEVDMN NEFVDPQAED RELKGQLLRK YSGYLGSLKQ EFMKKRKKGK LPKEARQQLL  300
DWWSRHYKWP YPSEQQKLAL AESTGLDQKQ INNWFINQRK RHWKPSEDMQ FVINNWFINQ  360
RKRHWKPSED MQFVVMDATH PHHYFMDNVL GNPFPMDHIS STML*

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	277	286	LKQEFMKKRK
2	283	287	KKRKK

Functional Description ? help Back to Top
Source	Description
UniProt	Required for shoot apical meristem (SAM) formation during embryogenesis. Negatively regulates ASYMMETRIC LEAVES1 (AS1) and ASYMMETRIC LEAVES2 (AS2 or LBD6). Probably binds to the DNA sequence 5'-TGAC-3'. Binds to RNA (By similarity). {ECO:0000250\|UniProtKB:P24345, ECO:0000269\|PubMed:10079219, ECO:0000269\|PubMed:11934861}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Csa09g096980.1

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	ATU32344	0.0	U32344.1 Arabidopsis thaliana Shootmeristemless (STM) mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_010430288.1	0.0	PREDICTED: homeobox protein SHOOT MERISTEMLESS-like isoform X1
Refseq	XP_010430289.1	0.0	PREDICTED: homeobox protein SHOOT MERISTEMLESS-like isoform X2
Swissprot	Q38874	0.0	STM_ARATH; Homeobox protein SHOOT MERISTEMLESS
TrEMBL	D4NZH6	0.0	D4NZH6_BRANA; SHOOT MERISTEMLESS
STRING	XP_010430289.1	0.0	(Camelina sativa)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM6473	26	44

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT1G62360.1	0.0	KNOX/ELK homeobox transcription factor

Publications ? help Back to Top
Zhang XL,Yang ZP,Zhang J,Zhang LG Ectopic expression of BraYAB1-702, a member of YABBY gene family in Chinese cabbage, causes leaf curling, inhibition of development of shoot apical meristem and flowering stage delaying in Arabidopsis thaliana. Int J Mol Sci, 2013. 14(7): p. 14872-91 [PMID:23863694] Liu C, et al. Phosphatidylserine synthase 1 is required for inflorescence meristem and organ development in Arabidopsis. J Integr Plant Biol, 2013. 55(8): p. 682-95 [PMID:23931744] Simonini S,Kater MM Class I BASIC PENTACYSTEINE factors regulate HOMEOBOX genes involved in meristem size maintenance. J. Exp. Bot., 2014. 65(6): p. 1455-65 [PMID:24482368] 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] Kamiuchi Y,Yamamoto K,Furutani M,Tasaka M,Aida M The CUC1 and CUC2 genes promote carpel margin meristem formation during Arabidopsis gynoecium development. Front Plant Sci, 2014. 5: p. 165 [PMID:24817871] Chen C, et al. Transcriptome profiling reveals roles of meristem regulators and polarity genes during fruit trichome development in cucumber (Cucumis sativus L.). J. Exp. Bot., 2014. 65(17): p. 4943-58 [PMID:24962999] Lee JE,Lampugnani ER,Bacic A,Golz JF SEUSS and SEUSS-LIKE 2 coordinate auxin distribution and KNOXI activity during embryogenesis. Plant J., 2014. 80(1): p. 122-35 [PMID:25060324] Ckurshumova W,Berleth T Overcoming recalcitrance - Auxin response factor functions in plant regeneration. Plant Signal Behav, 2015. 10(7): p. e993293 [PMID:26098229] Liang Z,Brown RC,Fletcher JC,Opsahl-Sorteberg HG Calpain-Mediated Positional Information Directs Cell Wall Orientation to Sustain Plant Stem Cell Activity, Growth and Development. Plant Cell Physiol., 2015. 56(9): p. 1855-66 [PMID:26220906] 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] Landrein B, et al. Mechanical stress contributes to the expression of the STM homeobox gene in Arabidopsis shoot meristems. Elife, 2015. 4: p. e07811 [PMID:26623515] 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] Shi B, et al. Two-Step Regulation of a Meristematic Cell Population Acting in Shoot Branching in Arabidopsis. PLoS Genet., 2016. 12(7): p. e1006168 [PMID:27398935] Lee HG,Choi YR,Seo PJ Increased STM expression is associated with drought tolerance in Arabidopsis. J. Plant Physiol., 2016. 201: p. 79-84 [PMID:27448723] Balkunde R,Kitagawa M,Xu XM,Wang J,Jackson D SHOOT MERISTEMLESS trafficking controls axillary meristem formation, meristem size and organ boundaries in Arabidopsis. Plant J., 2017. 90(3): p. 435-446 [PMID:28161901] Singh S, et al. Sirtinol, a Sir2 protein inhibitor, affects stem cell maintenance and root development in Arabidopsis thaliana by modulating auxin-cytokinin signaling components. Sci Rep, 2017. 7: p. 42450 [PMID:28195159] Lee HG,Choi YR,Seo PJ Erratum to "Increased STM expression is associated with drought tolerance in Arabidopsis" [J. Plant Physiol. 201 (2016) 79-84]. J. Plant Physiol., 2018. 228: p. 218 [PMID:28456397] Xue T, et al. ARGONAUTE10 Inhibits In Vitro Shoot Regeneration Via Repression of miR165/166 in Arabidopsis thaliana. Plant Cell Physiol., 2017. 58(10): p. 1789-1800 [PMID:29016889] Dolzblasz A, et al. Impairment of Meristem Proliferation in Plants Lacking the Mitochondrial Protease AtFTSH4. Int J Mol Sci, 2018. [PMID:29538317] Scofield S, et al. Coordination of meristem and boundary functions by transcription factors in the SHOOT MERISTEMLESS regulatory network. Development, 2018. [PMID:29650590] Liu L, et al. FTIP-Dependent STM Trafficking Regulates Shoot Meristem Development in Arabidopsis. Cell Rep, 2018. 23(6): p. 1879-1890 [PMID:29742441] Chung Y, et al. Auxin Response Factors promote organogenesis by chromatin-mediated repression of the pluripotency gene SHOOTMERISTEMLESS. Nat Commun, 2019. 10(1): p. 886 [PMID:30792395]