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

Carubv10001833m

Common Name

CARUB_v10001833mg

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

YABBY

Protein Properties

Length: 243aa MW: 26506 Da PI: 8.5222

Description

YABBY family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Carubv10001833m	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	YABBY	272.9	3.9e-84	17	201	2	170
YABBY 2 dvfssseqvCyvqCnfCntilavsvPstslfkvvtvrCGhCtsllsvnlakasqllaaeshldeslkee.......lleelkveeenlksnvek 88 d+ sss+q+Cyv+CnfC+t+lavsvP +slfk+vtvrCGhC++llsv +++++ ll+++s++++s+ + llee+++ ++n+++n+++ Carubv10001833m 17 DHISSSDQLCYVHCNFCDTVLAVSVPPSSLFKTVTVRCGHCSNLLSVAVNMRALLLPSVSNIGHSFISPtpppppnLLEEMRSGGQNINMNMIM 110 7899***********************************************************99888999999***********998 PP YABBY 89 eesa.stsvssekl........senedeevprvppvirPPekrqrvPsaynrfikeeiqrikasnPdishreafsaaaknWahfPkihfgl 170 ++++ +++++e+l +++ +e+pr+pp++rPPekrqrvPsaynrfikeeiqrika+nPdishreafsaaaknWahfP+ihfgl Carubv10001833m 111 SHHHgGAHHPNESLamgtrngrVDHHLQEMPRPPPANRPPEKRQRVPSAYNRFIKEEIQRIKAGNPDISHREAFSAAAKNWAHFPHIHFGL 201 87652678889888999999988999*************************************************************97 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Pfam	PF04690	1.3E-68	21	201	IPR006780	YABBY protein
SuperFamily	SSF47095	7.33E-8	146	194	IPR009071	High mobility group box domain
Gene3D	G3DSA:1.10.30.10	9.1E-5	149	195	IPR009071	High mobility group box domain

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0009944	Biological Process	polarity specification of adaxial/abaxial axis
GO:0010154	Biological Process	fruit development
GO:0010158	Biological Process	abaxial cell fate specification
GO:1902183	Biological Process	regulation of shoot apical meristem development
GO:2000024	Biological Process	regulation of leaf development

Sequence ? help Back to Top
Protein Sequence Length: 243 aa Download sequence Send to blast
MSSMSMSSSS APAYPPDHIS SSDQLCYVHC NFCDTVLAVS VPPSSLFKTV TVRCGHCSNL 60 LSVAVNMRAL LLPSVSNIGH SFISPTPPPP PNLLEEMRSG GQNINMNMIM SHHHGGAHHP 120 NESLAMGTRN GRVDHHLQEM PRPPPANRPP EKRQRVPSAY NRFIKEEIQR IKAGNPDISH 180 REAFSAAAKN WAHFPHIHFG LMADHPPTKK ANVRQQEGED VMMGSSREGF YGSAANVGVT 240 HN*

Functional Description ? help Back to Top
Source	Description
UniProt	Involved in the abaxial cell fate determination during embryogenesis and organogenesis. Regulates the initiation of embryonic shoot apical meristem (SAM) development (PubMed:10457020, PubMed:12417699, PubMed:19837869). Contributes to the repression of KNOX genes (STM, KNAT1/BP and KNAT2) to avoid ectopic meristems. Binds DNA without sequence specificity (PubMed:10457020, PubMed:12417699). {ECO:0000269\|PubMed:10457020, ECO:0000269\|PubMed:12417699, ECO:0000269\|PubMed:19837869}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Carubv10001833m

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	AF136540	0.0	AF136540.1 Arabidopsis thaliana YABBY3 (YABBY3) mRNA, complete cds.
GenBank	AY037186	0.0	AY037186.1 Arabidopsis thaliana AT4g00180/F6N15_22 mRNA, complete cds.
GenBank	BT002662	0.0	BT002662.1 Arabidopsis thaliana At4g00180/F6N15_22 gene, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_006288552.1	1e-180	axial regulator YABBY 3 isoform X2
Swissprot	Q9XFB1	1e-136	YAB3_ARATH; Axial regulator YABBY 3
TrEMBL	R0H942	1e-179	R0H942_9BRAS; Uncharacterized protein
STRING	XP_006288552.1	1e-180	(Capsella rubella)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM2217	28	77

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT4G00180.1	1e-139	YABBY family protein

Link Out ? help Back to Top
Phytozome	Carubv10001833m
Entrez Gene	17883345

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] Yadav RK, et al. Plant stem cell maintenance involves direct transcriptional repression of differentiation program. Mol. Syst. Biol., 2013. 9: p. 654 [PMID:23549482]