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Plant Transcription
Factor Database
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Transcription Factor Information
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Basic
Information? help
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| TF ID |
AT5G03150.1 |
| Common Name | F15A17.180, IDD10, IDZ3, JKD |
| Organism |
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| Taxonomic ID |
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| Taxonomic Lineage |
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis
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| Family |
C2H2 |
| Protein Properties |
Length: 503aa MW: 55200.9 Da PI: 10.2046 |
| Description |
C2H2-like zinc finger protein |
| Gene Model |
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| Signature Domain? help Back to Top |
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| No. |
Domain |
Score |
E-value |
Start |
End |
HMM Start |
HMM End |
| 1 | zf-C2H2 | 17.2 | 1.4e-05 | 82 | 104 | 1 | 23 |
EEETTTTEEESSHHHHHHHHHHT CS
zf-C2H2 1 ykCpdCgksFsrksnLkrHirtH 23
++C++C+k F r nL+ H r H
AT5G03150.1 82 FVCEICNKGFQRDQNLQLHRRGH 104
89*******************88 PP
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| 2 | zf-C2H2 | 14.1 | 0.00014 | 159 | 181 | 1 | 23 |
EEETTTTEEESSHHHHHHHHHHT CS
zf-C2H2 1 ykCpdCgksFsrksnLkrHirtH 23
+kC++C+k + +s+ k H +t+
AT5G03150.1 159 WKCEKCSKKYAVQSDWKAHAKTC 181
58******************998 PP
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| Gene Ontology ? help Back to Top |
| GO Term |
GO Category |
GO Description |
| GO:0006355 | Biological Process | regulation of transcription, DNA-templated |
| GO:0010075 | Biological Process | regulation of meristem growth |
| GO:0045604 | Biological Process | regulation of epidermal cell differentiation |
| GO:0048364 | Biological Process | root development |
| GO:0051302 | Biological Process | regulation of cell division |
| GO:0005634 | Cellular Component | nucleus |
| GO:0003677 | Molecular Function | DNA binding |
| GO:0003700 | Molecular Function | transcription factor activity, sequence-specific DNA binding |
| GO:0008270 | Molecular Function | zinc ion binding |
| GO:0042803 | Molecular Function | protein homodimerization activity |
| Sequence ? help Back to Top |
| Protein Sequence Length: 503 aa
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MQMIPGDPFS ISSSMGGFVH QETHLHHLQQ QIPDLNPNSN PNPNAKPNSS SAKKKRNQPG 60
TPDPDADVIA LSPTTLMATN RFVCEICNKG FQRDQNLQLH RRGHNLPWKL KQRSKQEVIK 120
KKVYICPIKT CVHHDASRAL GDLTGIKKHY SRKHGEKKWK CEKCSKKYAV QSDWKAHAKT 180
CGTREYKCDC GTLFSRKDSF ITHRAFCDAL TEEGARMSSL SNNNPVISTT NLNFGNESNV 240
MNNPNLPHGF VHRGVHHPDI NAAISQFGLG FGHDLSAMHA QGLSEMVQMA STGNHHLFPS 300
SSSSLPDFSG HHQFQIPMTS TNPSLTLSSS STSQQTSASL QHQTLKDSSF SPLFSSSSEN 360
KQNKPLSPMS ATALLQKAAQ MGSTRSNSST APSFFAGPTM TSSSATASPP PRSSSPMMIQ 420
QQLNNFNTNV LRENHNRAPP PLSGVSTSSV DNNPFQSNRS GLNPAQQMGL TRDFLGVSNE 480
HHPHQTGRRP FLPQELARFA PLG
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| Expression --
Description ? help
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| Source |
Description |
| Uniprot | DEVELOPMENTAL STAGE: Start to accumulate during the 16- to 32-cell stage of embryogenesis. {ECO:0000269|PubMed:17785527}. |
| Uniprot | TISSUE SPECIFICITY: Expressed in the quiescent center, the ground tissue stem cells and to a lesser extent in mature cortex and endodermis cells. {ECO:0000269|PubMed:17785527}. |
| Functional Description ? help
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| Source |
Description |
| TAIR | JKD is a nuclear-localized putative transcription factor with three zinc finger domains. jkd mutants show a number of root patterning defects including ectopic periclinal divisions in the cortex, increased cell numbers in the cortical and epidermal layers, a disrupted QC marker expression pattern, and disorganized QC and columella cells. jkd mutants also have a reduced number of meristematic cells in their roots. JKD can interact with the SCR and SHR proteins implicated in root patterning, as well as another zinc finger transcription factor, MAGPIE. All of these interactions require the first zinc finger in JKD according to a Y2H assay. There are also transcriptional interactions among these proteins. The initiation of JKD transcription does not appear to depend on SCR and SHR, but later expression in the post-embryonic QC cells and ground tissue initials is reduced in scr and shr mutants. JKD also appears to be required for SCR transcription beginning in the embryo. There is also some evidence that JKD plays a role in promoting the movement of SHR into the nucleus, particularly in QC cells, but this may be indirect. |
| UniProt | Transcription factor that, together with BIB, regulates tissue boundaries and asymmetric cell division by a rapid up-regulation of 'SCARECROW' (SCR), thus controlling the nuclear localization of 'SHORT-ROOT' (SHR) and restricting its action (PubMed:17785527, PubMed:25829440). Binds DNA via its zinc fingers (PubMed:28211915, PubMed:24821766). Recognizes and binds to SCL3 promoter sequence 5'-AGACAA-3' to promotes its expression when in complex with RGA (PubMed:24821766). Confines CYCD6 expression to the cortex-endodermis initial/daughter (CEI/CEID) tissues (PubMed:25829440). Required for radial patterning and stem cell maintenance (PubMed:17785527). Counteracted by 'MAGPIE' (MGP) (PubMed:17785527). Binds to the SCR and MGP promoter sequences (PubMed:21935722). Controls position-dependent signals that regulate epidermal-cell-type patterning (PubMed:20356954). {ECO:0000269|PubMed:17785527, ECO:0000269|PubMed:20356954, ECO:0000269|PubMed:21935722, ECO:0000269|PubMed:24821766, ECO:0000269|PubMed:25829440, ECO:0000269|PubMed:28211915}. |
| Function -- GeneRIF ? help
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- Findings are consistent with a model where JKD induces a signal in every cortex cell that is more abundant in the hair cell position owing to the larger surface contact of cells located over a cleft.
[PMID: 20356954] - JKD directly regulates SCR and MGP expression in cooperation with SHR, SCR and MGP.
[PMID: 21935722] - In the crystal structures of the SHR-SCR binary and JACKDAW (JKD)/IDD10-SHR-SCR ternary complexes, each GRAS domain comprises one alpha/beta core subdomain with an alpha-helical cap that mediates heterodimerization by forming an intermolecular helix bundle.
[PMID: 28211915]
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| Regulation -- Description ? help
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| Source |
Description |
| UniProt | INDUCTION: Not regulated by SCR and SHR. {ECO:0000269|PubMed:21935722}. |
| Annotation --
Nucleotide ? help
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| Source |
Hit ID |
E-value |
Description |
| GenBank | AJ621494 | 0.0 | AJ621494.1 Arabidopsis thaliana mRNA for ID1-like zinc finger protein 3 (idz3 gene). |
| GenBank | AJ630493 | 0.0 | AJ630493.1 Arabidopsis thaliana mRNA for hypothetical protein, clone At5g03150. |
| Publications
? help Back to Top |
- Riechmann JL, et al.
Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes.
Science, 2000. 290(5499): p. 2105-10
[PMID:11118137] - Gong W, et al.
Genome-wide ORFeome cloning and analysis of Arabidopsis transcription factor genes.
Plant Physiol., 2004. 135(2): p. 773-82
[PMID:15208423] - Englbrecht CC,Schoof H,B
Conservation, diversification and expansion of C2H2 zinc finger proteins in the Arabidopsis thaliana genome.
BMC Genomics, 2004. 5(1): p. 39
[PMID:15236668] - Nawy T, et al.
Transcriptional profile of the Arabidopsis root quiescent center.
Plant Cell, 2005. 17(7): p. 1908-25
[PMID:15937229] - Colasanti J, et al.
The maize INDETERMINATE1 flowering time regulator defines a highly conserved zinc finger protein family in higher plants.
BMC Genomics, 2006. 7: p. 158
[PMID:16784536] - Morita MT, et al.
A C2H2-type zinc finger protein, SGR5, is involved in early events of gravitropism in Arabidopsis inflorescence stems.
Plant J., 2006. 47(4): p. 619-28
[PMID:16813575] - Welch D, et al.
Arabidopsis JACKDAW and MAGPIE zinc finger proteins delimit asymmetric cell division and stabilize tissue boundaries by restricting SHORT-ROOT action.
Genes Dev., 2007. 21(17): p. 2196-204
[PMID:17785527] - Hassan H,Scheres B,Blilou I
JACKDAW controls epidermal patterning in the Arabidopsis root meristem through a non-cell-autonomous mechanism.
Development, 2010. 137(9): p. 1523-9
[PMID:20356954] - Koizumi K,Wu S,MacRae-Crerar A,Gallagher KL
An essential protein that interacts with endosomes and promotes movement of the SHORT-ROOT transcription factor.
Curr. Biol., 2011. 21(18): p. 1559-64
[PMID:21924907] - Ogasawara H,Kaimi R,Colasanti J,Kozaki A
Activity of transcription factor JACKDAW is essential for SHR/SCR-dependent activation of SCARECROW and MAGPIE and is modulated by reciprocal interactions with MAGPIE, SCARECROW and SHORT ROOT.
Plant Mol. Biol., 2011. 77(4-5): p. 489-99
[PMID:21935722] - Yoshida H, et al.
DELLA protein functions as a transcriptional activator through the DNA binding of the indeterminate domain family proteins.
Proc. Natl. Acad. Sci. U.S.A., 2014. 111(21): p. 7861-6
[PMID:24821766] - 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] - Moreno-Risueno MA, et al.
Transcriptional control of tissue formation throughout root development.
Science, 2015. 350(6259): p. 426-30
[PMID:26494755] - Hirano Y, et al.
Structure of the SHR-SCR heterodimer bound to the BIRD/IDD transcriptional factor JKD.
Nat Plants, 2017. 3: p. 17010
[PMID:28211915] - Kobayashi A,Miura S,Kozaki A
INDETERMINATE DOMAIN PROTEIN binding sequences in the 5'-untranslated region and promoter of the SCARECROW gene play crucial and distinct roles in regulating SCARECROW expression in roots and leaves.
Plant Mol. Biol., 2017. 94(1-2): p. 1-13
[PMID:28324206] - Long Y, et al.
In vivo FRET-FLIM reveals cell-type-specific protein interactions in Arabidopsis roots.
Nature, 2017. 548(7665): p. 97-102
[PMID:28746306] - Bustillo-Avendaño E, et al.
Regulation of Hormonal Control, Cell Reprogramming, and Patterning during De Novo Root Organogenesis.
Plant Physiol., 2018. 176(2): p. 1709-1727
[PMID:29233938]
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