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

RrC11563_p1

Organism

Raphanus raphanistrum

Taxonomic ID

109996

Taxonomic Lineage

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

Family

YABBY

Protein Properties

Length: 233aa MW: 26038.7 Da PI: 7.2025

Description

YABBY family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
RrC11563_p1	genome	MSU	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	YABBY	272.9	4e-84	25	194	5	170
YABBY 5 ssseqvCyvqCnfCntilavsvPstslfkvvtvrCGhCtsllsvnlakasqllaaeshldeslkee.......lleelkveeenlksnvekeesasts 95 s seq+CyvqCn+C+tilavsvP+ts+fk+vtvrCG+Ct+l+s ++++s +l+a+++l+ +l ++ +l elk++ +n+++++++++ ++++ RrC11563_p1 25 SPSEQLCYVQCNYCETILAVSVPYTSMFKTVTVRCGCCTNLIS--VNMRSLVLPASNQLQLQLGPHsyftpqnILGELKDAPSNMNMMMMNQHPNMND 120 789**************************************..5678999**********9*************************** PP YABBY 96 vsseklsenedeevprvppvirPPekrqrvPsaynrfikeeiqrikasnPdishreafsaaaknWahfPkihfgl 170 ++s+ ++ ++++e+p++ppv+rPPekrqrvPsaynrfikeeiqrika+nPdishreafsaaaknWahfP+ihfgl RrC11563_p1 121 IPSF-MDLHQQHEIPKAPPVNRPPEKRQRVPSAYNRFIKEEIQRIKAGNPDISHREAFSAAAKNWAHFPHIHFGL 194 6.5******************************************************************97 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Pfam	PF04690	1.7E-70	26	194	IPR006780	YABBY protein
SuperFamily	SSF47095	7.59E-8	140	187	IPR009071	High mobility group box domain
Gene3D	G3DSA:1.10.30.10	8.6E-5	142	188	IPR009071	High mobility group box domain

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: 233 aa Download sequence Send to blast
MSMSSMSSPS SAVFSPENLS PDPLSPSEQL CYVQCNYCET ILAVSVPYTS MFKTVTVRCG 60 CCTNLISVNM RSLVLPASNQ LQLQLGPHSY FTPQNILGEL KDAPSNMNMM MMNQHPNMND 120 IPSFMDLHQQ HEIPKAPPVN RPPEKRQRVP SAYNRFIKEE IQRIKAGNPD ISHREAFSAA 180 AKNWAHFPHI HFGLSPDNQP VKKTNMPQQE GEDNMGMREG FYAPAANVGA IPY

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:10323860, PubMed:10331982, PubMed:10457020, PubMed:11812777, PubMed:12417699, PubMed:9878633, Ref.3, Ref.6, PubMed:19837869). Required during flower formation and development, particularly for the patterning of floral organs. Positive regulator of class B (AP3 and PI) activity in whorls 2 and 3. Negative regulator of class B activity in whorl 1 and of SUP activity in whorl 3. Interacts with class A proteins (AP1, AP2 and LUG) to repress class C (AG) activity in whorls 1 and 2. Contributes to the repression of KNOX genes (STM, KNAT1/BP and KNAT2) to avoid ectopic meristems. Binds DNA without sequence specificity. In vitro, can compete and displace the AP1 protein binding to DNA containing CArG box (PubMed:10323860, PubMed:10331982, PubMed:10457020, PubMed:11812777, PubMed:12417699, PubMed:9878633, Ref.3, Ref.6). {ECO:0000269\|PubMed:10323860, ECO:0000269\|PubMed:10331982, ECO:0000269\|PubMed:10457020, ECO:0000269\|PubMed:11812777, ECO:0000269\|PubMed:12417699, ECO:0000269\|PubMed:19837869, ECO:0000269\|PubMed:9878633, ECO:0000269\|Ref.3, ECO:0000269\|Ref.6}.

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	JQ828987	0.0	JQ828987.1 Brassica rapa var. parachinensis YABBY1 (YABBY1) mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_018480712.1	1e-175	PREDICTED: axial regulator YABBY 1-like isoform X1
Swissprot	O22152	1e-139	YAB1_ARATH; Axial regulator YABBY 1
TrEMBL	A0A397ZR05	1e-171	A0A397ZR05_BRACM; Uncharacterized protein
TrEMBL	I1VHY7	1e-171	I1VHY7_BRARP; Putative male sterile protein
TrEMBL	I3QKS1	1e-171	I3QKS1_BRARC; YABBY1
STRING	Bra040322.1-P	1e-171	(Brassica rapa)

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
AT2G45190.1	1e-135	YABBY family protein

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] Lian H,Li X,Liu Z,He Y HYL1 is required for establishment of stamen architecture with four microsporangia in Arabidopsis. J. Exp. Bot., 2013. 64(11): p. 3397-410 [PMID:23918970] Tameshige T, et al. Pattern dynamics in adaxial-abaxial specific gene expression are modulated by a plastid retrograde signal during Arabidopsis thaliana leaf development. PLoS Genet., 2013. 9(7): p. e1003655 [PMID:23935517] Boter M, et al. FILAMENTOUS FLOWER Is a Direct Target of JAZ3 and Modulates Responses to Jasmonate. Plant Cell, 2015. 27(11): p. 3160-74 [PMID:26530088] Douglas SJ,Li B,Kliebenstein DJ,Nambara E,Riggs CD A novel Filamentous Flower mutant suppresses brevipedicellus developmental defects and modulates glucosinolate and auxin levels. PLoS ONE, 2017. 12(5): p. e0177045 [PMID:28493925] Tanaka W,Toriba T,Hirano HY Three TOB1-related YABBY genes are required to maintain proper function of the spikelet and branch meristems in rice. New Phytol., 2017. 215(2): p. 825-839 [PMID:28556940] Silverblatt-Buser EW,Frick MA,Rabeler C,Kaplinsky NJ Genetic Interactions Between BOB1 and Multiple 26S Proteasome Subunits Suggest a Role for Proteostasis in Regulating Arabidopsis Development. G3 (Bethesda), 2018. 8(4): p. 1379-1390 [PMID:29487187]