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

XP_013635325.1

Organism

Brassica oleracea

Taxonomic ID

3712

Taxonomic Lineage

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

Family

TALE

Protein Properties

Length: 237aa MW: 27331 Da PI: 5.9726

Description

TALE family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
XP_013635325.1	genome	NCBI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	Homeobox	28.7	2.2e-09	164	197	22	55
SSS--HHHHHHHHHHCTS-HHHHHHHHHHHHHHH CS Homeobox 22 nrypsaeereeLAkklgLterqVkvWFqNrRake 55 +yp ++++ LA+++gL+++q+ +WF N+R ++ XP_013635325.1 164 WPYPPEQQKLALAESTGLDQKQINNWFINQRXRH 197 58*****************************986 PP
2	ELK	35.8	1.7e-12	117	138	1	22
ELK 1 ELKhqLlrKYsgyLgsLkqEFs 22 ELK qLlrKYsgy gsLkqEF+ XP_013635325.1 117 ELKGQLLRKYSGYXGSLKQEFM 138 9********************8 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SMART	SM01256	9.5E-4	39	76	IPR005541	KNOX2
PROSITE profile	PS51213	10.336	117	137	IPR005539	ELK domain
Pfam	PF03789	3.3E-9	117	138	IPR005539	ELK domain
SMART	SM01188	6.4E-7	117	138	IPR005539	ELK domain
PROSITE profile	PS50071	12.017	137	200	IPR001356	Homeobox domain
SMART	SM00389	6.7E-9	139	204	IPR001356	Homeobox domain
SuperFamily	SSF46689	7.27E-18	139	215	IPR009057	Homeodomain-like
Gene3D	G3DSA:1.10.10.60	3.9E-25	142	200	IPR009057	Homeodomain-like
Pfam	PF05920	1.0E-15	157	196	IPR008422	Homeobox KN domain
CDD	cd00086	1.62E-9	163	199	No hit	No description
PROSITE pattern	PS00027	0	175	198	IPR017970	Homeobox, conserved site

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: 237 aa Download sequence Send to blast
MLFMYINYKF IKVEAPPEVQ ARQEETCSSA AAAAASXGPT ESLGEDPGLD QELSKPFKEA 60 LVFLQRVECQ FKSLSLSSPS SFSGYGETAI DRNNNGSSEE EVDMNNEFID PQAEDRELKG 120 QLLRKYSGYX GSLKQEFMKK RKKGKLPKEA RQQVLDWWSR HYKWPYPPEQ QKLALAESTG 180 LDQKQINNWF INQRXRHWKL SEDMQFVVMD ATHPHHYFMD NVLGNPFPTD HITSTML

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	132	141	LKQEFMKKRK
2	138	142	KKRKK

Expression -- Description ? help Back to Top
Source	Description
Uniprot	DEVELOPMENTAL STAGE: First expressed in early to mid-globular-stage embryos. In late globular stage, detected as a stripe running medially across the top of the embryo. In heart stage embryo, expression is restricted to a notch between the cotyledons, in both hypodermal and protoderm cells. In the bending-cotyledon stage, localized in the SAM, but disappears from the boundary region of cotyledon margins (BCM). In seedlings and adult plants found in all shoot apical meristems. In the inflorescence meristem, expression disappears as floral buds are initiated and reappears in the later floral meristem where it is found in the central portion of the developing gyneocium. Also detected in the L1 layer of embryo. {ECO:0000269\|PubMed:10079219}.
Uniprot	TISSUE SPECIFICITY: Expressed in all four types of shoot apical meristems (SAM) i.e. in vegetative, axillary, inflorescence and floral.

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	XP_013635325.1

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	AB971253	0.0	AB971253.1 Rorippa aquatica RaSTM mRNA for class I knotted1-like homeobox protein, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_013635325.1	1e-177	PREDICTED: LOW QUALITY PROTEIN: homeobox protein SHOOT MERISTEMLESS, partial
Swissprot	Q38874	1e-127	STM_ARATH; Homeobox protein SHOOT MERISTEMLESS
TrEMBL	D4NZH6	1e-135	D4NZH6_BRANA; SHOOT MERISTEMLESS
STRING	Bra027050.1-P	1e-128	(Brassica rapa)

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	1e-127	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]