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

XP_013606416.1

Organism

Brassica oleracea

Taxonomic ID

3712

Taxonomic Lineage

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

Family

C2H2

Protein Properties

Length: 514aa MW: 56662.3 Da PI: 10.0117

Description

C2H2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
XP_013606416.1	genome	NCBI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-C2H2	17.2	1.5e-05	82	104	1	23
EEETTTTEEESSHHHHHHHHHHT CS zf-C2H2 1 ykCpdCgksFsrksnLkrHirtH 23 ++C++C+k F r nL+ H r H XP_013606416.1 82 FVCEICNKGFQRDQNLQLHRRGH 104 89*******************88 PP
2	zf-C2H2	15	7.1e-05	159	181	1	23
EEETTTTEEESSHHHHHHHHHHT CS zf-C2H2 1 ykCpdCgksFsrksnLkrHirtH 23 +kC++C+k + +s+ k H +t+ XP_013606416.1 159 FKCEKCSKKYAVQSDWKAHAKTC 181 89******************998 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF57667	8.03E-8	81	104	No hit	No description
Gene3D	G3DSA:3.30.160.60	1.7E-5	81	104	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profile	PS50157	10.949	82	104	IPR007087	Zinc finger, C2H2
Pfam	PF12171	8.2E-5	82	104	IPR022755	Zinc finger, double-stranded RNA binding
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	1.3E-5	147	180	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamily	SSF57667	8.03E-8	154	179	No hit	No description
SMART	SM00355	92	159	179	IPR015880	Zinc finger, C2H2-like

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0003676	Molecular Function	nucleic acid binding
GO:0046872	Molecular Function	metal ion binding

Sequence ? help Back to Top
Protein Sequence Length: 514 aa Download sequence Send to blast
MQMIPGDPFS ISSSMGGFVH QEQHLHHLQQ HIQDINPNSN PNPNAKPNSS SAKKKRNQPG 60 TPDPDADVIA LSPTTLMATN RFVCEICNKG FQRDQNLQLH RRGHNLPWKL KQRSNKEVIK 120 KKVYICPIKT CVHHDSARAL GDLTGIKKHY SRKHGEKKFK CEKCSKKYAV QSDWKAHAKT 180 CGTREYKCDC GTLFSRKDSF ITHRAFCDAL TEEGARMSSL SNNSAISTTT MTTNLNFGND 240 SHVMNNPNLP HGFVHRGVHH PDINAAISQF GLGFGNDLTG MHPQGLSEMV QMTSSGNHHL 300 FPLSSSSVLP DFSGHHHNQQ FQIPTSSTNP NFTFSSSSIS QQTSASLPSL QQQHQTPKDS 360 SFSPLFSSSC ETKQNKPLSP MSATALLQKA AQMGSTRSNS TTAPSIFAGP TMTSSSSAAS 420 HPPPRSSSPM MIQQQLNNNF NTIVPRDTHN LAPPTTSSVE NNYRFQSNRS STNPVQQMGL 480 TRDFLGVSNE HHPHQTAHRP FLPQELARFA PSSG

Sequence ? help Back to Top

Protein Sequence Length: 514 aa Download sequence Send to blast

MQMIPGDPFS ISSSMGGFVH QEQHLHHLQQ HIQDINPNSN PNPNAKPNSS SAKKKRNQPG  60
TPDPDADVIA LSPTTLMATN RFVCEICNKG FQRDQNLQLH RRGHNLPWKL KQRSNKEVIK  120
KKVYICPIKT CVHHDSARAL GDLTGIKKHY SRKHGEKKFK CEKCSKKYAV QSDWKAHAKT  180
CGTREYKCDC GTLFSRKDSF ITHRAFCDAL TEEGARMSSL SNNSAISTTT MTTNLNFGND  240
SHVMNNPNLP HGFVHRGVHH PDINAAISQF GLGFGNDLTG MHPQGLSEMV QMTSSGNHHL  300
FPLSSSSVLP DFSGHHHNQQ FQIPTSSTNP NFTFSSSSIS QQTSASLPSL QQQHQTPKDS  360
SFSPLFSSSC ETKQNKPLSP MSATALLQKA AQMGSTRSNS TTAPSIFAGP TMTSSSSAAS  420
HPPPRSSSPM MIQQQLNNNF NTIVPRDTHN LAPPTTSSVE NNYRFQSNRS STNPVQQMGL  480
TRDFLGVSNE HHPHQTAHRP FLPQELARFA PSSG

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5b3h_C	7e-42	155	224	3	72	Zinc finger protein JACKDAW
5b3h_F	7e-42	155	224	3	72	Zinc finger protein JACKDAW
Search in ModeBase

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
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}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	XP_013606416.1

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	-

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_013606415.1	0.0	PREDICTED: zinc finger protein JACKDAW-like
Refseq	XP_013606416.1	0.0	PREDICTED: zinc finger protein JACKDAW-like
Swissprot	Q700D2	0.0	IDD10_ARATH; Zinc finger protein JACKDAW
TrEMBL	A0A0D3EI76	0.0	A0A0D3EI76_BRAOL; Uncharacterized protein
TrEMBL	A0A3P6EQB2	0.0	A0A3P6EQB2_BRAOL; Uncharacterized protein
STRING	Bo9g183170.1	0.0	(Brassica oleracea)

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT5G03150.1	0.0	C2H2-like zinc finger protein

Publications ? help Back to Top
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]