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_009103179.1

Organism

Brassica rapa

Taxonomic ID

3711

Taxonomic Lineage

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

Family

YABBY

Protein Properties

Length: 230aa MW: 26069.7 Da PI: 5.6119

Description

YABBY family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
XP_009103179.1	genome	NCBI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	YABBY	240	5e-74	12	194	2	169
YABBY 2 dvfssseqvCyvqCnfCntilavsvPstslfkvvtvrCGhCtsllsvnlakas....qllaaeshldeslkee.........lleelkveeenlk 83 ++f+ ++q+C+vqC+fC+til+vsvP+tsl++vvtvrCGhCtsllsvnl+kas +ll++ shlde + +++ve+e++k XP_009103179.1 12 QLFDLPGQICHVQCGFCTTILLVSVPFTSLSMVVTVRCGHCTSLLSVNLMKASfiplHLLTSLSHLDEVPVTYilctekeevAATTDGVEKEAWK 106 78999********************************************9999999****9976555666667776677899*** PP YABBY 84 snvekeesastsvsse.klsenedeevprvpp.virPPekrqrvPsaynrfikeeiqrikasnPdishreafsaaaknWahfPkihfg 169 +++eke+s++t v+s+ + +e+ed++v+rv++ v++PPekrqr+Psayn+fikeei+r+ka+nP+++h+eafs+aaknWahfP++ ++ XP_009103179.1 107 VTQEKENSPTTLVTSSdNEDEDEDKDVSRVYQvVNKPPEKRQRAPSAYNCFIKEEIRRLKAQNPSMAHKEAFSLAAKNWAHFPPVQNK 194 ****999876551559999*****899***********************************************9887 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Pfam	PF04690	7.0E-60	17	193	IPR006780	YABBY protein
SuperFamily	SSF47095	4.71E-9	135	190	IPR009071	High mobility group box domain
Gene3D	G3DSA:1.10.30.10	6.6E-6	141	191	IPR009071	High mobility group box domain
CDD	cd00084	0.00214	149	185	No hit	No description

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0007275	Biological Process	multicellular organism development

Sequence ? help Back to Top
Protein Sequence Length: 230 aa Download sequence Send to blast
MTKMANMTTL NQLFDLPGQI CHVQCGFCTT ILLVSVPFTS LSMVVTVRCG HCTSLLSVNL 60 MKASFIPLHL LTSLSHLDEV PVTYILCTEK EEVAATTDGV EKEAWKVTQE KENSPTTLVT 120 SSDNEDEDED KDVSRVYQVV NKPPEKRQRA PSAYNCFIKE EIRRLKAQNP SMAHKEAFSL 180 AAKNWAHFPP VQNKRTASDQ CFCEEDNNVL LSCNALEDHE GLWYLREKRW

Expression -- Description ? help Back to Top
Source	Description
Uniprot	DEVELOPMENTAL STAGE: First detected in a group of around 15 epidermal cells on the abaxial half of each ovule primordium (chalaza, outer integument initiation sites). Later present in the outer cell layer of the outer integument on the abaxial side of the ovule primordium. Confined to the chalazal end of the integument and disappears after anthesis. Also present in embryos at the globular stage. {ECO:0000269\|PubMed:10601041, ECO:0000269\|PubMed:12183380, ECO:0000269\|PubMed:12183381}.

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	XP_009103179.1

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	AB493475	1e-126	AB493475.1 Arabidopsis thaliana At1g23420 mRNA for hypothetical protein, partial cds, clone: RAAt1g23420.
GenBank	AF195047	1e-126	AF195047.1 Arabidopsis thaliana INNER NO OUTER (INO) mRNA, complete cds.
GenBank	BT026410	1e-126	BT026410.1 Arabidopsis thaliana At1g23420 mRNA, complete cds.
GenBank	DQ446281	1e-126	DQ446281.1 Arabidopsis thaliana clone pENTR221-At1g23420 inner no outer protein (At1g23420) mRNA, complete cds.
GenBank	DQ652855	1e-126	DQ652855.1 Arabidopsis thaliana clone 0000017089_0000011971 unknown mRNA.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_022544519.1	1e-163	axial regulator YABBY 4 isoform X1
Swissprot	Q9LDT3	1e-125	YAB4_ARATH; Axial regulator YABBY 4
TrEMBL	A0A3P5YGQ6	1e-135	A0A3P5YGQ6_BRACM; Uncharacterized protein
STRING	Bra012373.1-P	1e-134	(Brassica rapa)

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT1G23420.1	1e-122	YABBY family protein

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]