PlantTFDB
Plant Transcription Factor Database
v4.0
Previous version: v3.0
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID AT1G69180.1
Common NameCRC, F23O10.23, F4N2.14
Organism
Taxonomic ID
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
AT1G69180.1genomeTAIRView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1YABBY137.41.7e-42161565163
        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
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PfamPF046901.8E-4918156IPR006780YABBY protein
SuperFamilySSF470952.09E-8100155IPR009071High mobility group box domain
Gene3DG3DSA:1.10.30.107.1E-5110155IPR009071High mobility group box domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0009944Biological Processpolarity specification of adaxial/abaxial axis
GO:0010254Biological Processnectary development
GO:0010582Biological Processfloral meristem determinacy
GO:0030154Biological Processcell differentiation
GO:0048479Biological Processstyle development
GO:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
GO:0046872Molecular Functionmetal ion binding
Plant Ontology ? help Back to Top
PO Term PO Category PO Description
PO:0000037anatomyshoot apex
PO:0009009anatomyplant embryo
PO:0009010anatomyseed
PO:0009031anatomysepal
PO:0009032anatomypetal
PO:0009046anatomyflower
PO:0009056anatomyflower nectary
PO:0009062anatomygynoecium
PO:0020003anatomyplant ovule
PO:0025022anatomycollective leaf structure
PO:0001078developmental stageplant embryo cotyledonary stage
PO:0001081developmental stagemature plant embryo stage
PO:0004507developmental stageplant embryo bilateral stage
PO:0007611developmental stagepetal differentiation and expansion stage
PO:0007616developmental stageflowering 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.114780.0bud
Expression -- Microarray ? help Back to Top
Source ID E-value
Genevisible260355_at0.0
Expression AtlasAT1G69180-
AtGenExpressAT1G69180-
ATTED-IIAT1G69180-
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL 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}.
UniprotTISSUE 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
TAIRPutative 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.
UniProtTranscription 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
  1. 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]
  2. 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]
  3. Co-expression analysis identifies CRC and AP1 the regulator of Arabidopsis fatty acid biosynthesis.
    [PMID: 22676405]
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00220DAP27203113Download
Motif logo
Cis-element ? help Back to Top
SourceLink
PlantRegMapAT1G69180.1
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: 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
PlantRegMapRetrieveRetrieve
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 ExpressAT1G69180
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAF1326060.0AF132606.1 Arabidopsis thaliana transcription factor CRC mRNA, complete cds.
GenBankAK2296090.0AK229609.1 Arabidopsis thaliana mRNA for transcription factor CRC, complete cds, clone: RAFL19-52-F14.
GenBankBT0086180.0BT008618.1 Arabidopsis thaliana clone RAFL19-52-F14 (R50809) putative transcription factor CRC (At1g69180) mRNA, complete cds.
GenBankDQ4464120.0DQ446412.1 Arabidopsis thaliana clone pENTR221-At1g69180 transcription factor CRC (At1g69180) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_177078.11e-134putative transcription factor CRABS CLAW
SwissprotQ8L9251e-136CRC_ARATH; Protein CRABS CLAW
TrEMBLQ1PFF11e-134Q1PFF1_ARATH; Transcription factor CRC
STRINGAT1G69180.11e-133(Arabidopsis thaliana)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM97252835
Representative plantOGRP90691114
Publications ? help Back to Top
  1. 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]
  2. 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]
  3. 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]
  4. 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]
  5. Eshed Y,Baum SF,Bowman JL
    Distinct mechanisms promote polarity establishment in carpels of Arabidopsis.
    Cell, 1999. 99(2): p. 199-209
    [PMID:10535738]
  6. Golz JF,Hudson A
    Plant development: YABBYs claw to the fore.
    Curr. Biol., 1999. 9(22): p. R861-3
    [PMID:10574752]
  7. Bowman JL
    The YABBY gene family and abaxial cell fate.
    Curr. Opin. Plant Biol., 2000. 3(1): p. 17-22
    [PMID:10679447]
  8. 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]
  9. 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]
  10. Riechmann JL, et al.
    Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes.
    Science, 2000. 290(5499): p. 2105-10
    [PMID:11118137]
  11. 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]
  12. 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]
  13. Baum SF,Eshed Y,Bowman JL
    The Arabidopsis nectary is an ABC-independent floral structure.
    Development, 2001. 128(22): p. 4657-67
    [PMID:11714690]
  14. 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]
  15. 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]
  16. 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]
  17. Yamada K, et al.
    Empirical analysis of transcriptional activity in the Arabidopsis genome.
    Science, 2003. 302(5646): p. 842-6
    [PMID:14593172]
  18. 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]
  19. 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]
  20. 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]
  21. 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]
  22. 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]
  23. 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]
  24. 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]
  25. 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]
  26. 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]
  27. 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]
  28. 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]
  29. 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]
  30. 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]
  31. 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]
  32. 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]
  33. 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]
  34. 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]
  35. Fernandez AI, et al.
    Flexible tools for gene expression and silencing in tomato.
    Plant Physiol., 2009. 151(4): p. 1729-40
    [PMID:19812183]
  36. 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]
  37. 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]
  38. 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]
  39. 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]
  40. 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]
  41. 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]
  42. 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]
  43. 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]
  44. 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]
  45. 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]