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

Ciclev10033770m

Common Name

CICLE_v10033770mg

Organism

Citrus clementina

Taxonomic ID

85681

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Sapindales; Rutaceae; Aurantioideae; Citrus

Family

YABBY

Protein Properties

Length: 175aa MW: 19289.9 Da PI: 9.3991

Description

YABBY family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Ciclev10033770m	genome	ICGC	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	YABBY	146.3	3e-45	14	155	5	163
YABBY 5 ssseqvCyvqCnfCntilavsvPstslfkvvtvrCGhCtsllsvnlakasqllaaeshldeslkeelleelkveeenlksnvekeesastsvss 98 +se++Cyv+CnfCnt+lav +P + l+ +vtv+CGhC++l ++ + q+ +++ l+++e++ n+ k +as+s ss Ciclev10033770m 14 PQSEHLCYVRCNFCNTVLAVGIPCKRLLDTVTVKCGHCSNLSFLSTRP-PQQGPSQM------------SLRFQEKQSFCNDFKLGNASSSSSS 94 679**********************************985533332.23334433............4555555555566666665555554 PP YABBY 99 eklsenedeevprvppvirPPekrqrvPsaynrfikeeiqrikasnPdishreafsaaaknWahf 163 ++++ +p++p v++PPek+ r Psaynrf+keeiqrika+ P+i hreafs+aaknWa + Ciclev10033770m 95 ----TSSEPLSPKAPFVVKPPEKKHRLPSAYNRFMKEEIQRIKAATPEIPHREAFSTAAKNWARY 155 ....455667899999*********************************************76 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Pfam	PF04690	1.5E-54	15	155	IPR006780	YABBY protein
SuperFamily	SSF47095	6.81E-8	99	153	IPR009071	High mobility group box domain
Gene3D	G3DSA:1.10.30.10	1.0E-4	109	154	IPR009071	High mobility group box domain

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0010254	Biological Process	nectary development
GO:0010582	Biological Process	floral meristem determinacy
GO:0048479	Biological Process	style development

Sequence ? help Back to Top
Protein Sequence Length: 175 aa Download sequence Send to blast
MNLEDSISTD LQVPQSEHLC YVRCNFCNTV LAVGIPCKRL LDTVTVKCGH CSNLSFLSTR 60 PPQQGPSQMS LRFQEKQSFC NDFKLGNASS SSSSTSSEPL SPKAPFVVKP PEKKHRLPSA 120 YNRFMKEEIQ RIKAATPEIP HREAFSTAAK NWARYIPNSL AGSTSGSSSH VRDR*

Expression -- Description ? help Back to Top
Source	Description
Uniprot	DEVELOPMENTAL STAGE: In carpels, expression starts when the gynoecial primordia becomes distinct. First expressed in the lateral region of each carpel. Later resolves into two distinct domains, epidermal and internal. In epidermal tissues, mostly localized on the outer surface, successively from the base to the tip of the gynoecium and finally confined to the valve region before disappearing during last flowering stages. In internal tissues, first confined to four discrete zones adjacent to the future placental tissue occupying the full length of the elongating cylinder, declining from the apical regions and disappearing after the ovule primordia arise. Before nectaries initiation, expression occupies a ring of receptacle cells between the stamen and sepal primordia, from where nectaries will develop. Strongly expressed in nectaries until latest flowering stages. {ECO:0000269\|PubMed:10225998}.
Uniprot	TISSUE SPECIFICITY: Restricted to flowers, mostly in carpels and nectaries. Expressed at low levels in sepal primordia (buds), sepal receptacle and developing petal. Not detected in placental tissues, septum, stigma and ovules. {ECO:0000269\|PubMed:10225998}.

Functional Description ? help Back to Top
Source	Description
UniProt	Transcription factor required for the initiation of nectary development. Also involved in suppressing early radial growth of the gynoecium, in promoting its later elongation and in fusion of its carpels by regulating both cell division and expansion. Establishes the polar differentiation in the carpels by specifying abaxial cell fate in the ovary wall. Regulates both cell division and expansion. {ECO:0000269\|PubMed:10225997, ECO:0000269\|PubMed:10225998, ECO:0000269\|PubMed:10535738, ECO:0000269\|PubMed:11714690, ECO:0000269\|PubMed:15598802, ECO:0000269\|Ref.10}.

Binding Motif ? help Back to Top
Motif ID	Method	Source	Motif file
MP00220	DAP	Transfer from AT1G69180	Download

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: Down-regulated by SPT and by A class genes AP2 and LUG in the outer whorl. In the third whorl, B class genes AP3 and PI, and the C class gene AG act redundantly with each other and in combination with SEP1, SEP2, SEP3, SHP1 and SHP2 to activate CRC in nectaries and carpels. LFY enhances its expression. {ECO:0000269\|PubMed:10225998, ECO:0000269\|PubMed:15598802}.

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	AY854804	2e-45	AY854804.1 Gossypium hirsutum isolate 1 CRABS CLAW mRNA, partial cds.
GenBank	AY854805	2e-45	AY854805.1 Gossypium hirsutum isolate 2 CRABS CLAW mRNA, partial cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_006437883.2	1e-124	protein CRABS CLAW
Swissprot	Q8L925	5e-65	CRC_ARATH; Protein CRABS CLAW
TrEMBL	V4STH0	1e-126	V4STH0_9ROSI; Uncharacterized protein
STRING	XP_006437883.1	1e-127	(Citrus clementina)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM9725	28	35

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT1G69180.1	2e-64	YABBY family protein

Link Out ? help Back to Top
Phytozome	Ciclev10033770m
Entrez Gene	18044265

Publications ? help Back to Top
Fourquin C,Primo A,Martínez-Fernández I,Huet-Trujillo E,Ferrándiz C The CRC orthologue from Pisum sativum shows conserved functions in carpel morphogenesis and vascular development. Ann. Bot., 2014. 114(7): p. 1535-44 [PMID:24989787] Pfannebecker KC,Lange M,Rupp O,Becker A Seed Plant-Specific Gene Lineages Involved in Carpel Development. Mol. Biol. Evol., 2017. 34(4): p. 925-942 [PMID:28087776] Yamaguchi N,Huang J,Xu Y,Tanoi K,Ito T Fine-tuning of auxin homeostasis governs the transition from floral stem cell maintenance to gynoecium formation. Nat Commun, 2017. 8(1): p. 1125 [PMID:29066759] Yamaguchi N, et al. Chromatin-mediated feed-forward auxin biosynthesis in floral meristem determinacy. Nat Commun, 2018. 9(1): p. 5290 [PMID:30538233]