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

orange1.1g014041m

Common Name

CISIN_1g011146mg

Organism

Citrus sinensis

Taxonomic ID

2711

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Sapindales; Rutaceae; Aurantioideae; Citrus

Family

C2H2

Protein Properties

Length: 433aa MW: 47947.6 Da PI: 9.9529

Description

C2H2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
orange1.1g014041m	genome	ICGC	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-C2H2	14.3	0.00012	66	86	3	23
ETTTTEEESSHHHHHHHHHHT CS zf-C2H2 3 CpdCgksFsrksnLkrHirtH 23 C++C+k F r nL+ H r H orange1.1g014041m 66 CEICNKGFQRDQNLQLHRRGH 86 *******************88 PP
2	zf-C2H2	12.1	0.00059	140	162	1	23
EEETTTTEEESSHHHHHHHHHHT CS zf-C2H2 1 ykCpdCgksFsrksnLkrHirtH 23 +kC++C+k + +s+ k H + + orange1.1g014041m 140 WKCEKCSKKYAVQSDWKAHSKIC 162 58*****************9876 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Gene3D	G3DSA:3.30.160.60	1.9E-5	63	86	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamily	SSF57667	4.57E-7	63	86	No hit	No description
SMART	SM00355	0.11	64	86	IPR015880	Zinc finger, C2H2-like
PROSITE profile	PS50157	10.824	64	86	IPR007087	Zinc finger, C2H2
PROSITE pattern	PS00028	0	66	86	IPR007087	Zinc finger, C2H2
SMART	SM00355	110	105	135	IPR015880	Zinc finger, C2H2-like
Gene3D	G3DSA:3.30.160.60	1.3E-4	128	161	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamily	SSF57667	4.57E-7	135	160	No hit	No description
SMART	SM00355	140	140	160	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: 433 aa Download sequence Send to blast
MMSQDHGLSV PSTLKGFVQE PNSNPNPNPS SNQLKRKRNL PGTPDPDAEV IALSPKSLMA 60 TNRFLCEICN KGFQRDQNLQ LHRRGHNLPW KLKQRTNKEV RKKVYICPEK SCVHHDPSRA 120 LGDLTGIKKH FSRKHGEKKW KCEKCSKKYA VQSDWKAHSK ICGTREYRCD CGTLFSRKDS 180 FITHRAFCDA LAEESARFTT ISSTNPQAAA AIPQFSSVFR QQQQSAPGSE LAGGANLSMS 240 SSSSLPRGIP KEEEENKAYN LSESMTSLYP SNQSGQQQQQ QQQQQQQGLA HMSATALLQK 300 AAQMGSTRSN ANNSTGFGLM STSFNSFNQT DKNELHKFFK QPNQQVADND QNLNELIMNS 360 FSCPTNMGAV AGSSNASLLM ANAKNASNEA ERRLTRDFLG VGVESSRPLS QQELAKFMNL 420 SSQYGGNPHH RS*

Sequence ? help Back to Top

Protein Sequence Length: 433 aa Download sequence Send to blast

MMSQDHGLSV PSTLKGFVQE PNSNPNPNPS SNQLKRKRNL PGTPDPDAEV IALSPKSLMA  60
TNRFLCEICN KGFQRDQNLQ LHRRGHNLPW KLKQRTNKEV RKKVYICPEK SCVHHDPSRA  120
LGDLTGIKKH FSRKHGEKKW KCEKCSKKYA VQSDWKAHSK ICGTREYRCD CGTLFSRKDS  180
FITHRAFCDA LAEESARFTT ISSTNPQAAA AIPQFSSVFR QQQQSAPGSE LAGGANLSMS  240
SSSSLPRGIP KEEEENKAYN LSESMTSLYP SNQSGQQQQQ QQQQQQQGLA HMSATALLQK  300
AAQMGSTRSN ANNSTGFGLM STSFNSFNQT DKNELHKFFK QPNQQVADND QNLNELIMNS  360
FSCPTNMGAV AGSSNASLLM ANAKNASNEA ERRLTRDFLG VGVESSRPLS QQELAKFMNL  420
SSQYGGNPHH RS*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5b3h_C	3e-38	136	205	3	72	Zinc finger protein JACKDAW
5b3h_F	3e-38	136	205	3	72	Zinc finger protein JACKDAW
Search in ModeBase

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	90	102	KLKQRTNKEVRKK

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
Csi.919	0.0	callus\| flower\| fruit\| stem

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}.

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_006424606.1	0.0	protein indeterminate-domain 9
Refseq	XP_006488129.1	0.0	protein indeterminate-domain 9 isoform X2
Swissprot	Q700D2	1e-120	IDD10_ARATH; Zinc finger protein JACKDAW
TrEMBL	A0A067GCM0	0.0	A0A067GCM0_CITSI; Uncharacterized protein
STRING	XP_006488129.1	0.0	(Citrus sinensis)
STRING	XP_006424606.1	0.0	(Citrus clementina)

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT3G45260.1	1e-105	C2H2-like zinc finger protein

Link Out ? help Back to Top
Phytozome	orange1.1g014041m

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]