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

AT1G69180.1

Common Name

CRC, F23O10.23, F4N2.14

Organism

Arabidopsis thaliana

Taxonomic ID

3702

Taxonomic Lineage

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

Family

YABBY

Protein Properties

Length: 181aa MW: 19722.5 Da PI: 10.0212

Description

YABBY family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
AT1G69180.1	genome	TAIR	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	YABBY	137.4	1.7e-42	16	156	5	163
YABBY 5 ssseqvCyvqCnfCntilavsvPstslfkvvtvrCGhCtsllsvnlakasqllaaeshldeslkeelleelkveeenlksnvekeesastsvssekls 102 ++e++ yv+C+ Cntilav +P + ++ +vtv+CGhC +l ++ + + + h + l + +++ + k+ s+s+s ss + AT1G69180.1 16 PQAEHLYYVRCSICNTILAVGIPLKRMLDTVTVKCGHCGNLSFLTT-----TPPLQGH--------V--SLTLQMQSFGGSDYKKGSSSSSSSS---T 95 5789*********************************9755332.....2333333........2..2334456677777777777766666...3 PP YABBY 103 enedeevprvppvirPPekrqrvPsaynrfikeeiqrikasnPdishreafsaaaknWahf 163 ++++ +p +p v++PPek+qr Psaynrf+++eiqrik++nP+i hreafsaaaknWa + AT1G69180.1 96 SSDQPPSPSPPFVVKPPEKKQRLPSAYNRFMRDEIQRIKSANPEIPHREAFSAAAKNWAKY 156 456667777788*********************************************86 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Pfam	PF04690	1.8E-49	18	156	IPR006780	YABBY protein
SuperFamily	SSF47095	2.09E-8	100	155	IPR009071	High mobility group box domain
Gene3D	G3DSA:1.10.30.10	7.1E-5	110	155	IPR009071	High mobility group box domain

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0006355	Biological Process	regulation of transcription, DNA-templated
GO:0009944	Biological Process	polarity specification of adaxial/abaxial axis
GO:0010254	Biological Process	nectary development
GO:0010582	Biological Process	floral meristem determinacy
GO:0030154	Biological Process	cell differentiation
GO:0048479	Biological Process	style development
GO:0005634	Cellular Component	nucleus
GO:0003677	Molecular Function	DNA binding
GO:0003700	Molecular Function	transcription factor activity, sequence-specific DNA binding
GO:0046872	Molecular Function	metal ion binding

Plant Ontology ? help Back to Top
PO Term	PO Category	PO Description
PO:0000037	anatomy	shoot apex
PO:0009009	anatomy	plant embryo
PO:0009010	anatomy	seed
PO:0009031	anatomy	sepal
PO:0009032	anatomy	petal
PO:0009046	anatomy	flower
PO:0009056	anatomy	flower nectary
PO:0009062	anatomy	gynoecium
PO:0020003	anatomy	plant ovule
PO:0025022	anatomy	collective leaf structure
PO:0001078	developmental stage	plant embryo cotyledonary stage
PO:0001081	developmental stage	mature plant embryo stage
PO:0004507	developmental stage	plant embryo bilateral stage
PO:0007611	developmental stage	petal differentiation and expansion stage
PO:0007616	developmental stage	flowering stage

Sequence ? help Back to Top
Protein Sequence Length: 181 aa Download sequence Send to blast
MNLEEKPTMT ASRASPQAEH LYYVRCSICN TILAVGIPLK RMLDTVTVKC GHCGNLSFLT 60 TTPPLQGHVS LTLQMQSFGG SDYKKGSSSS SSSSTSSDQP PSPSPPFVVK PPEKKQRLPS 120 AYNRFMRDEI QRIKSANPEI PHREAFSAAA KNWAKYIPNS PTSITSGGHN MIHGLGFGEK 180 K

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
At.11478	0.0	bud

Expression -- Microarray ? help Back to Top
Source	ID	E-value
Genevisible	260355_at	0.0
Expression Atlas	AT1G69180	-
AtGenExpress	AT1G69180	-
ATTED-II	AT1G69180	-

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
TAIR	Putative transcription factor with zinc finger and helix-loop-helix domains, the later similar to HMG boxes. Involved in specifying abaxial cell fate in the carpel. Four putative LFY binding sites (CCANTG) and two potential binding sites for MADS box proteins known as CArG boxes (CC(A/T)6GG) were found in the region spanning 3.8 Kb upstream of the CRC coding region.
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}.

Function -- GeneRIF ? help Back to Top
MADS box proteins may provide general floral factors that must work in conjunction with specific factors in the activation of CRC in the nectaries and carpels. [PMID: 15598802] The data support a hypothesized ancestral role for CRC in carpel development and suggest that novel roles for CRC orthologues in monocots and in core eudicots resulted principally from molecular changes other than those affecting their coding sequences. [PMID: 17650514] Co-expression analysis identifies CRC and AP1 the regulator of Arabidopsis fatty acid biosynthesis. [PMID: 22676405] The feed-forward YUC4 activation by AG and CRC directs a precise change in chromatin state for the shift from floral stem cell maintenance to gynoecium formation. [PMID: 30538233]

Binding Motif ? help Back to Top
Motif ID	Method	Source	Motif file
MP00220	DAP	27203113	Download

Cis-element ? help Back to Top
Source	Link
PlantRegMap	AT1G69180.1

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	Retrieve

Regulation -- ATRM (Manually Curated Upstream Regulators) ? help Back to Top
Source	Upstream Regulator (A: Activate/R: Repress)
ATRM	AT1G54060 (R), AT2G40220 (A), AT3G24650 (A), AT3G26790 (A), AT3G54340 (A), AT4G18960 (A), AT4G36920 (R), AT4G37750 (R), AT5G20240 (A), AT5G61850 (A)

Regulation -- ATRM (Manually Curated Target Genes) ? help Back to Top
Source	Target Gene (A: Activate/R: Repress)
ATRM	AT4G18960(A)

Phenotype -- Mutation ? help Back to Top
Source	ID
T-DNA Express	AT1G69180

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AF132606	0.0	AF132606.1 Arabidopsis thaliana transcription factor CRC mRNA, complete cds.
GenBank	AK229609	0.0	AK229609.1 Arabidopsis thaliana mRNA for transcription factor CRC, complete cds, clone: RAFL19-52-F14.
GenBank	BT008618	0.0	BT008618.1 Arabidopsis thaliana clone RAFL19-52-F14 (R50809) putative transcription factor CRC (At1g69180) mRNA, complete cds.
GenBank	DQ446412	0.0	DQ446412.1 Arabidopsis thaliana clone pENTR221-At1g69180 transcription factor CRC (At1g69180) mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	NP_177078.1	1e-133	Plant-specific transcription factor YABBY family protein
Swissprot	Q8L925	1e-135	CRC_ARATH; Protein CRABS CLAW
TrEMBL	Q1PFF1	1e-132	Q1PFF1_ARATH; Transcription factor CRC
STRING	AT1G69180.1	1e-133	(Arabidopsis thaliana)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM9725	28	35
Representative plant	OGRP9069	11	14

Link Out ? help Back to Top
Phytozome	AT1G69180.1
Entrez Gene	843249
iHOP	AT1G69180
wikigenes	AT1G69180

Publications ? help Back to Top
Alvarez J,Smyth DR CRABS CLAW and SPATULA, two Arabidopsis genes that control carpel development in parallel with AGAMOUS. Development, 1999. 126(11): p. 2377-86 [PMID:10225997] Bowman JL,Smyth DR CRABS CLAW, a gene that regulates carpel and nectary development in Arabidopsis, encodes a novel protein with zinc finger and helix-loop-helix domains. Development, 1999. 126(11): p. 2387-96 [PMID:10225998] Bowman JL,Baum SF,Eshed Y,Putterill J,Alvarez J Molecular genetics of gynoecium development in Arabidopsis. Curr. Top. Dev. Biol., 1999. 45: p. 155-205 [PMID:10332605] Siegfried KR, et al. Members of the YABBY gene family specify abaxial cell fate in Arabidopsis. Development, 1999. 126(18): p. 4117-28 [PMID:10457020] Eshed Y,Baum SF,Bowman JL Distinct mechanisms promote polarity establishment in carpels of Arabidopsis. Cell, 1999. 99(2): p. 199-209 [PMID:10535738] Golz JF,Hudson A Plant development: YABBYs claw to the fore. Curr. Biol., 1999. 9(22): p. R861-3 [PMID:10574752] Bowman JL The YABBY gene family and abaxial cell fate. Curr. Opin. Plant Biol., 2000. 3(1): p. 17-22 [PMID:10679447] Desfeux C,Clough SJ,Bent AF Female reproductive tissues are the primary target of Agrobacterium-mediated transformation by the Arabidopsis floral-dip method. Plant Physiol., 2000. 123(3): p. 895-904 [PMID:10889238] S Regulation and function of the Arabidopsis ABA-insensitive4 gene in seed and abscisic acid response signaling networks. Plant Physiol., 2000. 124(4): p. 1752-65 [PMID:11115891] Riechmann JL, et al. Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes. Science, 2000. 290(5499): p. 2105-10 [PMID:11118137] Heisler MG,Atkinson A,Bylstra YH,Walsh R,Smyth DR SPATULA, a gene that controls development of carpel margin tissues in Arabidopsis, encodes a bHLH protein. Development, 2001. 128(7): p. 1089-98 [PMID:11245574] Kerstetter RA,Bollman K,Taylor RA,Bomblies K,Poethig RS KANADI regulates organ polarity in Arabidopsis. Nature, 2001. 411(6838): p. 706-9 [PMID:11395775] Baum SF,Eshed Y,Bowman JL The Arabidopsis nectary is an ABC-independent floral structure. Development, 2001. 128(22): p. 4657-67 [PMID:11714690] Suzuki M,Kao CY,Cocciolone S,McCarty DR Maize VP1 complements Arabidopsis abi3 and confers a novel ABA/auxin interaction in roots. Plant J., 2001. 28(4): p. 409-18 [PMID:11737778] Meister RJ,Kotow LM,Gasser CS SUPERMAN attenuates positive INNER NO OUTER autoregulation to maintain polar development of Arabidopsis ovule outer integuments. Development, 2002. 129(18): p. 4281-9 [PMID:12183380] Kuusk S,Sohlberg JJ,Long JA,Fridborg I,Sundberg E STY1 and STY2 promote the formation of apical tissues during Arabidopsis gynoecium development. Development, 2002. 129(20): p. 4707-17 [PMID:12361963] Yamada K, et al. Empirical analysis of transcriptional activity in the Arabidopsis genome. Science, 2003. 302(5646): p. 842-6 [PMID:14593172] Yamaguchi T, et al. The YABBY gene DROOPING LEAF regulates carpel specification and midrib development in Oryza sativa. Plant Cell, 2004. 16(2): p. 500-9 [PMID:14729915] Lee JY, et al. Activation of CRABS CLAW in the Nectaries and Carpels of Arabidopsis. Plant Cell, 2005. 17(1): p. 25-36 [PMID:15598802] Meister RJ,Oldenhof H,Bowman JL,Gasser CS Multiple protein regions contribute to differential activities of YABBY proteins in reproductive development. Plant Physiol., 2005. 137(2): p. 651-62 [PMID:15665244] Kagaya Y, et al. Indirect ABA-dependent regulation of seed storage protein genes by FUSCA3 transcription factor in Arabidopsis. Plant Cell Physiol., 2005. 46(2): p. 300-11 [PMID:15695463] Fourquin C,Vinauger-Douard M,Fogliani B,Dumas C,Scutt CP Evidence that CRABS CLAW and TOUSLED have conserved their roles in carpel development since the ancestor of the extant angiosperms. Proc. Natl. Acad. Sci. U.S.A., 2005. 102(12): p. 4649-54 [PMID:15767586] Lee JY, et al. Recruitment of CRABS CLAW to promote nectary development within the eudicot clade. Development, 2005. 132(22): p. 5021-32 [PMID:16236772] Li Q,Wang BC,Xu Y,Zhu YX Systematic studies of 12S seed storage protein accumulation and degradation patterns during Arabidopsis seed maturation and early seedling germination stages. J. Biochem. Mol. Biol., 2007. 40(3): p. 373-81 [PMID:17562289] Fourquin C,Vinauger-Douard M,Chambrier P,Berne-Dedieu A,Scutt CP Functional conservation between CRABS CLAW orthologues from widely diverged angiosperms. Ann. Bot., 2007. 100(3): p. 651-7 [PMID:17650514] Azhakanandam S,Nole-Wilson S,Bao F,Franks RG SEUSS and AINTEGUMENTA mediate patterning and ovule initiation during gynoecium medial domain development. Plant Physiol., 2008. 146(3): p. 1165-81 [PMID:18184731] Gallagher TL,Gasser CS Independence and interaction of regions of the INNER NO OUTER protein in growth control during ovule development. Plant Physiol., 2008. 147(1): p. 306-15 [PMID:18326791] Prunet N, et al. REBELOTE, SQUINT, and ULTRAPETALA1 function redundantly in the temporal regulation of floral meristem termination in Arabidopsis thaliana. Plant Cell, 2008. 20(4): p. 901-19 [PMID:18441215] Tang X, et al. The Arabidopsis BRAHMA chromatin-remodeling ATPase is involved in repression of seed maturation genes in leaves. Plant Physiol., 2008. 147(3): p. 1143-57 [PMID:18508955] Gao MJ, et al. Repression of seed maturation genes by a trihelix transcriptional repressor in Arabidopsis seedlings. Plant Cell, 2009. 21(1): p. 54-71 [PMID:19155348] Wang A, et al. Isolation and functional analysis of LiYAB1, a YABBY family gene, from lily (Lilium longiflorum). J. Plant Physiol., 2009. 166(9): p. 988-95 [PMID:19157639] Orashakova S,Lange M,Lange S,Wege S,Becker A The CRABS CLAW ortholog from California poppy (Eschscholzia californica, Papaveraceae), EcCRC, is involved in floral meristem termination, gynoecium differentiation and ovule initiation. Plant J., 2009. 58(4): p. 682-93 [PMID:19175766] Skinner DJ,Gasser CS Expression-based discovery of candidate ovule development regulators through transcriptional profiling of ovule mutants. BMC Plant Biol., 2009. 9: p. 29 [PMID:19291320] Ishikawa M, et al. The spatial expression patterns of DROOPING LEAF orthologs suggest a conserved function in grasses. Genes Genet. Syst., 2009. 84(2): p. 137-46 [PMID:19556707] Fernandez AI, et al. Flexible tools for gene expression and silencing in tomato. Plant Physiol., 2009. 151(4): p. 1729-40 [PMID:19812183] Larue CT,Wen J,Walker JC Genetic interactions between the miRNA164-CUC2 regulatory module and BREVIPEDICELLUS in Arabidopsis developmental patterning. Plant Signal Behav, 2009. 4(7): p. 666-8 [PMID:19820320] Colombo M, et al. A new role for the SHATTERPROOF genes during Arabidopsis gynoecium development. Dev. Biol., 2010. 337(2): p. 294-302 [PMID:19900437] Hanada K, et al. Functional compensation of primary and secondary metabolites by duplicate genes in Arabidopsis thaliana. Mol. Biol. Evol., 2011. 28(1): p. 377-82 [PMID:20736450] Nakayama H,Yamaguchi T,Tsukaya H Expression patterns of AaDL, a CRABS CLAW ortholog in Asparagus asparagoides (Asparagaceae), demonstrate a stepwise evolution of CRC/DL subfamily of YABBY genes. Am. J. Bot., 2010. 97(4): p. 591-600 [PMID:21622421] Bartholmes C,Hidalgo O,Gleissberg S Evolution of the YABBY gene family with emphasis on the basal eudicot Eschscholzia californica (Papaveraceae). Plant Biol (Stuttg), 2012. 14(1): p. 11-23 [PMID:21974722] Han X,Yin L,Xue H Co-expression analysis identifies CRC and AP1 the regulator of Arabidopsis fatty acid biosynthesis. J Integr Plant Biol, 2012. 54(7): p. 486-99 [PMID:22676405] Z The class II HD-ZIP JAIBA gene is involved in meristematic activity and important for gynoecium and fruit development in Arabidopsis. Plant Signal Behav, 2012. 7(11): p. 1501-3 [PMID:22951401] Sun W, et al. Characterization of a Crabs Claw Gene in basal eudicot species Epimedium sagittatum (Berberidaceae). Int J Mol Sci, 2013. 14(1): p. 1119-31 [PMID:23299438] Yumul RE, et al. POWERDRESS and diversified expression of the MIR172 gene family bolster the floral stem cell network. PLoS Genet., 2013. 9(1): p. e1003218 [PMID:23349639] 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] Jin J, et al. An Arabidopsis Transcriptional Regulatory Map Reveals Distinct Functional and Evolutionary Features of Novel Transcription Factors. Mol. Biol. Evol., 2015. 32(7): p. 1767-73 [PMID:25750178] 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]