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

Carubv10023478m

Common Name

CARUB_v10023478mg

Organism

Capsella rubella

Taxonomic ID

81985

Taxonomic Lineage

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

Family

SBP

Protein Properties

Length: 368aa MW: 39835.8 Da PI: 7.9786

Description

SBP family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Carubv10023478m	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	SBP	137.3	4.4e-43	72	149	1	78
--SSTT-----TT--HHHHHTT--HHHHT-S-EEETTEEEEE-TTTSSEEETTT--SS--S-STTTT-------S--- CS SBP 1 lCqvegCeadlseakeyhrrhkvCevhskapvvlvsgleqrfCqqCsrfhelsefDeekrsCrrrLakhnerrrkkqa 78 +CqvegC +dl++ak y++rh+vC vhsk+p+v+v+gleqrfCqqCsrfh+l efD ekrsCrrrLa+hnerrrk+q+ Carubv10023478m 72 RCQVEGCGMDLTNAKGYYSRHRVCGVHSKTPKVIVAGLEQRFCQQCSRFHQLPEFDLEKRSCRRRLAGHNERRRKPQP 149 6**************************************************************************986 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Gene3D	G3DSA:4.10.1100.10	1.4E-34	65	134	IPR004333	Transcription factor, SBP-box
PROSITE profile	PS51141	32.017	70	147	IPR004333	Transcription factor, SBP-box
SuperFamily	SSF103612	1.19E-40	71	151	IPR004333	Transcription factor, SBP-box
Pfam	PF03110	4.5E-32	73	146	IPR004333	Transcription factor, SBP-box

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0010228	Biological Process	vegetative to reproductive phase transition of meristem
GO:0048653	Biological Process	anther development
GO:2000025	Biological Process	regulation of leaf formation
GO:0005634	Cellular Component	nucleus
GO:0003677	Molecular Function	DNA binding

Sequence ? help Back to Top
Protein Sequence Length: 368 aa Download sequence Send to blast
MEMGSNSGPG LGPGQAESGG SSTESSSFSG GLMFGQKIYF EDGGGGSGSS SSGGSNRRVR 60 GGGSGQSGQI PRCQVEGCGM DLTNAKGYYS RHRVCGVHSK TPKVIVAGLE QRFCQQCSRF 120 HQLPEFDLEK RSCRRRLAGH NERRRKPQPA SLSVLSSRYG RIAPSLYGNA DAGMNGSFLG 180 NQDMGWTSAR TLDTRVMRRP VSAPSWQISP MNVFSQGSVG GGGTSFSSPE IMDTKLESYK 240 GMGDSNCALS LLSNPHQPQD NNNNNNTWRA SSGFCPMTVT MAQPPPAPGQ HQYLNPPWVF 300 KDDDSDMSPV LNLGRFTEPD NCQISNGTTM GEFELSDHHH QSRRQYIEDE QNTRAYDSSS 360 HHNNWSL*

Sequence ? help Back to Top

Protein Sequence Length: 368 aa Download sequence Send to blast

MEMGSNSGPG LGPGQAESGG SSTESSSFSG GLMFGQKIYF EDGGGGSGSS SSGGSNRRVR  60
GGGSGQSGQI PRCQVEGCGM DLTNAKGYYS RHRVCGVHSK TPKVIVAGLE QRFCQQCSRF  120
HQLPEFDLEK RSCRRRLAGH NERRRKPQPA SLSVLSSRYG RIAPSLYGNA DAGMNGSFLG  180
NQDMGWTSAR TLDTRVMRRP VSAPSWQISP MNVFSQGSVG GGGTSFSSPE IMDTKLESYK  240
GMGDSNCALS LLSNPHQPQD NNNNNNTWRA SSGFCPMTVT MAQPPPAPGQ HQYLNPPWVF  300
KDDDSDMSPV LNLGRFTEPD NCQISNGTTM GEFELSDHHH QSRRQYIEDE QNTRAYDSSS  360
HHNNWSL*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
1ul4_A	7e-31	62	146	1	84	squamosa promoter binding protein-like 4
Search in ModeBase

Functional Description ? help Back to Top
Source	Description
UniProt	Trans-acting factor that binds specifically to the consensus nucleotide sequence 5'-TNCGTACAA-3'. {ECO:0000250}.

Binding Motif ? help Back to Top
Motif ID	Method	Source	Motif file
MP00307	DAP	Transfer from AT2G42200	Download

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Carubv10023478m

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: Negatively regulated by microRNAs miR156 and miR157. {ECO:0000305\|PubMed:12202040}.

Regulation -- PlantRegMap ? help Back to Top
Source	Upstream Regulator	Target Gene
PlantRegMap	Retrieve	Retrieve

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AK353538	0.0	AK353538.1 Thellungiella halophila mRNA, complete cds, clone: RTFL01-50-J24.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_006294465.1	0.0	squamosa promoter-binding-like protein 9
Swissprot	Q700W2	0.0	SPL9_ARATH; Squamosa promoter-binding-like protein 9
TrEMBL	R0HTJ6	0.0	R0HTJ6_9BRAS; Uncharacterized protein
STRING	XP_006294465.1	0.0	(Capsella rubella)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM2144	27	75

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT2G42200.1	0.0	squamosa promoter binding protein-like 9

Link Out ? help Back to Top
Phytozome	Carubv10023478m
Entrez Gene	17887996

Publications ? help Back to Top
Duarte JM, et al. Expression pattern shifts following duplication indicative of subfunctionalization and neofunctionalization in regulatory genes of Arabidopsis. Mol. Biol. Evol., 2006. 23(2): p. 469-78 [PMID:16280546] Stief A, et al. Arabidopsis miR156 Regulates Tolerance to Recurring Environmental Stress through SPL Transcription Factors. Plant Cell, 2014. 26(4): p. 1792-1807 [PMID:24769482] Yu ZX, et al. Progressive Regulation of Sesquiterpene Biosynthesis in Arabidopsis and Patchouli (Pogostemon cablin) by the miR156-Targeted SPL Transcription Factors. Mol Plant, 2015. [PMID:25355059] Yu N,Niu QW,Ng KH,Chua NH The role of miR156/SPLs modules in Arabidopsis lateral root development. Plant J., 2015. 83(4): p. 673-85 [PMID:26096676] Morea EG, et al. Functional and evolutionary analyses of the miR156 and miR529 families in land plants. BMC Plant Biol., 2016. 16: p. 40 [PMID:26841873] Hyun Y, et al. Multi-layered Regulation of SPL15 and Cooperation with SOC1 Integrate Endogenous Flowering Pathways at the Arabidopsis Shoot Meristem. Dev. Cell, 2016. 37(3): p. 254-66 [PMID:27134142] Xu M, et al. Developmental Functions of miR156-Regulated SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) Genes in Arabidopsis thaliana. PLoS Genet., 2016. 12(8): p. e1006263 [PMID:27541584] Mahmood K,Xu Z,El-Kereamy A,Casaretto JA,Rothstein SJ The Arabidopsis Transcription Factor ANAC032 Represses Anthocyanin Biosynthesis in Response to High Sucrose and Oxidative and Abiotic Stresses. Front Plant Sci, 2016. 7: p. 1548 [PMID:27790239] Mao YB, et al. Jasmonate response decay and defense metabolite accumulation contributes to age-regulated dynamics of plant insect resistance. Nat Commun, 2017. 8: p. 13925 [PMID:28067238] Nguyen ST,Greaves T,McCurdy DW Heteroblastic Development of Transfer Cells Is Controlled by the microRNA miR156/SPL Module. Plant Physiol., 2017. 173(3): p. 1676-1691 [PMID:28082719] Duan HC, et al. ALKBH10B Is an RNA N6-Methyladenosine Demethylase Affecting Arabidopsis Floral Transition. Plant Cell, 2017. 29(12): p. 2995-3011 [PMID:29180595] Dotto M,Gómez MS,Soto MS,Casati P UV-B radiation delays flowering time through changes in the PRC2 complex activity and miR156 levels in Arabidopsis thaliana. Plant Cell Environ., 2018. 41(6): p. 1394-1406 [PMID:29447428] He J, et al. Threshold-dependent repression of SPL gene expression by miR156/miR157 controls vegetative phase change in Arabidopsis thaliana. PLoS Genet., 2018. 14(4): p. e1007337 [PMID:29672610]