PlantRegMap/PlantTFDB v5.0
Plant Transcription
Factor Database
|
Home TFext BLAST Prediction Download Help About Links PlantRegMap |
Transcription Factor Information
Basic Information? help Back to Top | |||||||||
---|---|---|---|---|---|---|---|---|---|
TF ID | AT5G03150.1 | ||||||||
Common Name | F15A17.180, IDD10, IDZ3, JKD | ||||||||
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 | C2H2 | ||||||||
Protein Properties | Length: 503aa MW: 55200.9 Da PI: 10.2046 | ||||||||
Description | C2H2-like zinc finger protein | ||||||||
Gene Model |
|
Signature Domain? help Back to Top | |||||||
---|---|---|---|---|---|---|---|
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 | |||||||
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 |
Protein Features ? help Back to Top | ||||||
---|---|---|---|---|---|---|
Database | Entry ID | E-value | Start | End | InterPro ID | Description |
Gene3D | G3DSA:3.30.160.60 | 1.7E-5 | 81 | 104 | IPR013087 | Zinc finger C2H2-type/integrase DNA-binding domain |
SuperFamily | SSF57667 | 2.85E-7 | 81 | 104 | No hit | No description |
Pfam | PF12171 | 8.0E-5 | 82 | 104 | IPR022755 | Zinc finger, double-stranded RNA binding |
PROSITE profile | PS50157 | 10.949 | 82 | 104 | IPR007087 | Zinc finger, C2H2 |
SMART | SM00355 | 0.017 | 82 | 104 | IPR015880 | Zinc finger, C2H2-like |
PROSITE pattern | PS00028 | 0 | 84 | 104 | IPR007087 | Zinc finger, C2H2 |
SMART | SM00355 | 78 | 124 | 154 | IPR015880 | Zinc finger, C2H2-like |
Gene3D | G3DSA:3.30.160.60 | 2.7E-5 | 147 | 180 | IPR013087 | Zinc finger C2H2-type/integrase DNA-binding domain |
SuperFamily | SSF57667 | 2.85E-7 | 154 | 179 | No hit | No description |
SMART | SM00355 | 140 | 159 | 179 | IPR015880 | Zinc finger, C2H2-like |
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 |
Plant Ontology ? help Back to Top | ||||||
---|---|---|---|---|---|---|
PO Term | PO Category | PO Description | ||||
PO:0000037 | anatomy | shoot apex | ||||
PO:0000293 | anatomy | guard cell | ||||
PO:0009005 | anatomy | root | ||||
PO:0009009 | anatomy | plant embryo | ||||
PO:0009010 | anatomy | seed | ||||
PO:0009046 | anatomy | flower | ||||
PO:0025022 | anatomy | collective leaf structure | ||||
PO:0001078 | developmental stage | plant embryo cotyledonary stage | ||||
PO:0001081 | developmental stage | mature plant embryo stage | ||||
PO:0001180 | developmental stage | plant proembryo stage | ||||
PO:0001185 | developmental stage | plant embryo globular stage | ||||
PO:0004507 | developmental stage | plant embryo bilateral stage | ||||
PO:0007611 | developmental stage | petal differentiation and expansion stage |
Sequence ? help Back to Top |
---|
Protein Sequence Length: 503 aa Download sequence Send to blast |
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 |
3D Structure ? help Back to Top | ||||||
---|---|---|---|---|---|---|
PDB ID | Evalue | Query Start | Query End | Hit Start | Hit End | Description |
5b3h_C | 3e-44 | 155 | 224 | 3 | 72 | Zinc finger protein JACKDAW |
5b3h_F | 3e-44 | 155 | 224 | 3 | 72 | Zinc finger protein JACKDAW |
Search in ModeBase |
Expression -- UniGene ? help Back to Top | ||||||
---|---|---|---|---|---|---|
UniGene ID | E-value | Expressed in | ||||
At.1592 | 0.0 | root |
Expression -- Microarray ? help Back to Top | ||||||
---|---|---|---|---|---|---|
Source | ID | E-value | ||||
GEO | 186519671 | 0.0 | ||||
Genevisible | 250982_at | 0.0 | ||||
Expression Atlas | AT5G03150 | - | ||||
AtGenExpress | AT5G03150 | - | ||||
ATTED-II | AT5G03150 | - |
Expression -- Description ? help Back to Top | ||||||
---|---|---|---|---|---|---|
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 Back to Top | ||||||
---|---|---|---|---|---|---|
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 Back to Top | ||||||
---|---|---|---|---|---|---|
|
Binding Motif ? help Back to Top | |||
---|---|---|---|
Motif ID | Method | Source | Motif file |
MP00485 | DAP | 27203113 | Download |
Cis-element ? help Back to Top | |
---|---|
Source | Link |
PlantRegMap | AT5G03150.1 |
Regulation -- Description ? help Back to Top | ||||||
---|---|---|---|---|---|---|
Source | Description | |||||
UniProt | INDUCTION: Not regulated by SCR and SHR. {ECO:0000269|PubMed:21935722}. |
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 | AT3G54220 (A), AT4G37650 (A) |
Regulation -- ATRM (Manually Curated Target Genes) ? help Back to Top | ||||||
---|---|---|---|---|---|---|
Source | Target Gene (A: Activate/R: Repress) | |||||
ATRM | AT3G54220(A) |
Interaction ? help Back to Top | ||||||
---|---|---|---|---|---|---|
Source | Intact With | |||||
BioGRID | AT1G50420 | |||||
IntAct | Search Q700D2 |
Phenotype -- Mutation ? help Back to Top | ||||||
---|---|---|---|---|---|---|
Source | ID | |||||
T-DNA Express | AT5G03150 |
Annotation -- Nucleotide ? help Back to Top | ||||||
---|---|---|---|---|---|---|
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. |
Annotation -- Protein ? help Back to Top | |||||||
---|---|---|---|---|---|---|---|
Source | Hit ID | E-value | Description | ||||
Refseq | NP_195935.2 | 0.0 | C2H2-like zinc finger protein | ||||
Swissprot | Q700D2 | 0.0 | IDD10_ARATH; Zinc finger protein JACKDAW | ||||
TrEMBL | A0A178UG83 | 0.0 | A0A178UG83_ARATH; JKD | ||||
STRING | AT5G03150.1 | 0.0 | (Arabidopsis thaliana) |
Orthologous Group ? help Back to Top | |||
---|---|---|---|
Lineage | Orthologous Group ID | Taxa Number | Gene Number |
Malvids | OGEM155 | 28 | 306 | Representative plant | OGRP95 | 16 | 242 |
Link Out ? help Back to Top | |
---|---|
Phytozome | AT5G03150.1 |
Entrez Gene | 831919 |
iHOP | AT5G03150 |
wikigenes | AT5G03150 |