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

Carubv10012024m

Common Name

CARUB_v10012024mg

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: 236aa MW: 26224.6 Da PI: 6.3395

Description

YABBY family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Carubv10012024m	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	YABBY	242.9	6.6e-75	13	184	2	169
YABBY 2 dvfssseqvCyvqCnfCntilavsvPstslfkvvtvrCGhCtsllsvnlakas....qllaaeshldeslkeelleelkveeen.lksnveke. 89 ++f+ ++q+C+vqC+fC+til+vsvP+tsl++vvtvrCGhC+sllsvnl+kas +lla+ shlde++kee++++++veee+ lk+n +++ Carubv10012024m 13 HLFDLPGQICHVQCGFCTTILLVSVPFTSLSMVVTVRCGHCSSLLSVNLMKASfiplHLLASLSHLDEAGKEEVAATTGVEEEEaLKVNSQEKe 106 78999********************************************9999999***************99987651565554440 PP YABBY 90 esastsvsseklsenedeevprvpp.virPPekrqrvPsaynrfikeeiqrikasnPdishreafsaaaknWahfPkihfg 169 +s++t vss s+nede+v+rv++ v++PPekrqr+Psayn+fikeei+r+k++nP+++h+eafs+aaknWahfP++ ++ Carubv10012024m 107 NSPTTLVSS---SDNEDEDVTRVYQvVNKPPEKRQRAPSAYNCFIKEEIRRLKSQNPSMAHKEAFSLAAKNWAHFPPVLNK 184 344444444...99*******899**********************************************99766 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Pfam	PF04690	3.0E-59	18	181	IPR006780	YABBY protein
SuperFamily	SSF47095	1.57E-8	126	180	IPR009071	High mobility group box domain
Gene3D	G3DSA:1.10.30.10	1.1E-5	131	179	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:0048481	Biological Process	plant ovule development
GO:0005634	Cellular Component	nucleus

Sequence ? help Back to Top
Protein Sequence Length: 236 aa Download sequence Send to blast
MTKIPNMTTT LNHLFDLPGQ ICHVQCGFCT TILLVSVPFT SLSMVVTVRC GHCSSLLSVN 60 LMKASFIPLH LLASLSHLDE AGKEEVAATT GVEEEEALKV NSQEKENSPT TLVSSSDNED 120 EDVTRVYQVV NKPPEKRQRA PSAYNCFIKE EIRRLKSQNP SMAHKEAFSL AAKNWAHFPP 180 VLNKRAASSD HCYCEDQDNN AIPPCNALED HEESNNGFRE RKAQRHSIWG KSPFE*

Functional Description ? help Back to Top
Source	Description
UniProt	Essential for the formation and the abaxial-adaxial asymmetric growth of the ovule outer integument. {ECO:0000269\|PubMed:10601041, ECO:0000269\|PubMed:12183380, ECO:0000269\|PubMed:9093862, ECO:0000269\|PubMed:9118807}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Carubv10012024m

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: Autoinduction down-regulated by SUP in adaxial region of the ovule outer integument. Negatively and spatially regulated by HLL, ANT, BELL1, NZZ/SPL and SUP. {ECO:0000269\|PubMed:10601041, ECO:0000269\|PubMed:12183380, ECO:0000269\|PubMed:12183381}.

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	AF195047	0.0	AF195047.1 Arabidopsis thaliana INNER NO OUTER (INO) mRNA, complete cds.
GenBank	BT026410	0.0	BT026410.1 Arabidopsis thaliana At1g23420 mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_006304946.1	1e-177	axial regulator YABBY 4
Swissprot	Q9LDT3	1e-147	YAB4_ARATH; Axial regulator YABBY 4
TrEMBL	R0I693	1e-175	R0I693_9BRAS; Uncharacterized protein
STRING	Cagra.0605s0067.1.p	1e-176	(Capsella grandiflora)
STRING	XP_006304946.1	1e-176	(Capsella rubella)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM8044	27	40

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT1G23420.1	1e-140	YABBY family protein

Link Out ? help Back to Top
Phytozome	Carubv10012024m
Entrez Gene	17899688

Publications ? help Back to Top
Lora J,Hormaza JI,Herrero M Transition from two to one integument in Prunus species: expression pattern of INNER NO OUTER (INO), ABERRANT TESTA SHAPE (ATS) and ETTIN (ETT). New Phytol., 2015. 208(2): p. 584-95 [PMID:25991552] Skinner DJ,Brown RH,Kuzoff RK,Gasser CS Conservation of the role of INNER NO OUTER in development of unitegmic ovules of the Solanaceae despite a divergence in protein function. BMC Plant Biol., 2016. 16(1): p. 143 [PMID:27350128] Simon MK,Skinner DJ,Gallagher TL,Gasser CS Integument Development in Arabidopsis Depends on Interaction of YABBY Protein INNER NO OUTER with Coactivators and Corepressors. Genetics, 2017. 207(4): p. 1489-1500 [PMID:28971961]