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

orange1.1g008103m

Common Name

CISIN_1g006491mg

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: 578aa MW: 62320 Da PI: 9.0224

Description

C2H2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
orange1.1g008103m	genome	ICGC	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-C2H2	16.2	3e-05	6	28	1	23
EEETTTTEEESSHHHHHHHHHHT CS zf-C2H2 1 ykCpdCgksFsrksnLkrHirtH 23 + C+ C+k F r nL+ H r H orange1.1g008103m 6 FICEVCNKGFQREQNLQLHRRGH 28 89*******************88 PP
2	zf-C2H2	13.2	0.00028	82	104	1	23
EEETTTTEEESSHHHHHHHHHHT CS zf-C2H2 1 ykCpdCgksFsrksnLkrHirtH 23 +kC++C+k++ +s+ k H +t+ orange1.1g008103m 82 WKCEKCSKRYAVQSDWKAHSKTC 104 58*****************9998 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Gene3D	G3DSA:3.30.160.60	6.4E-6	5	28	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamily	SSF57667	2.09E-7	5	28	No hit	No description
PROSITE profile	PS50157	10.99	6	28	IPR007087	Zinc finger, C2H2
Pfam	PF12171	2.8E-5	6	28	IPR022755	Zinc finger, double-stranded RNA binding
SMART	SM00355	0.0052	6	28	IPR015880	Zinc finger, C2H2-like
PROSITE pattern	PS00028	0	8	28	IPR007087	Zinc finger, C2H2
SMART	SM00355	130	47	77	IPR015880	Zinc finger, C2H2-like
Gene3D	G3DSA:3.30.160.60	2.1E-5	70	103	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamily	SSF57667	2.09E-7	77	102	No hit	No description
SMART	SM00355	130	82	102	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: 578 aa Download sequence Send to blast
MATNRFICEV CNKGFQREQN LQLHRRGHNL PWKLKQKTTK EVKRKVYLCP EPTCVHHDPS 60 RALGDLTGIK KHYSRKHGEK KWKCEKCSKR YAVQSDWKAH SKTCGTREYR CDCGTLFSRR 120 DSFITHRAFC DALAQESARH QPSLSAIGSH LYASTNNMAL GLSQVGPQLS SIKDHHQTNQ 180 SGDILCLGGS GSRSTPFDHL LSPSMGSSSS SFRPPQSLAS TPFFMQESNQ NYHEEQQQHQ 240 QGLLPNKPPP FHGLMQFADL QNNPNNSNPV TNSAAAANNL FNLSFLSNSS STNSLSNSNS 300 NNNNNNASNL MLSAAGGHHH HFNNNEQNGT ASTGTGGVDH HQGTNNNLFT NNLISDHQIS 360 SGAVPSLFST SSVHQNETMV PHMSATALLQ KAAQMGSTSS NNNTASLLRS FGGSSSSSGS 420 KPNNNNNNFG GAGNVFGGPG SSENDNSSSI HDLMNPFAAT NSSIFGTGSN DQVNAFSGQD 480 QNHHRRHHHH HPNYEAKLHH NMNAGMGGSD RMTRDFLGVG QIVRSVSGGF QQREKQQQQH 540 GGVIDVSSLD SERNITAPTS QSFGGGGGGG GGGGSFH*

Sequence ? help Back to Top

Protein Sequence Length: 578 aa Download sequence Send to blast

MATNRFICEV CNKGFQREQN LQLHRRGHNL PWKLKQKTTK EVKRKVYLCP EPTCVHHDPS  60
RALGDLTGIK KHYSRKHGEK KWKCEKCSKR YAVQSDWKAH SKTCGTREYR CDCGTLFSRR  120
DSFITHRAFC DALAQESARH QPSLSAIGSH LYASTNNMAL GLSQVGPQLS SIKDHHQTNQ  180
SGDILCLGGS GSRSTPFDHL LSPSMGSSSS SFRPPQSLAS TPFFMQESNQ NYHEEQQQHQ  240
QGLLPNKPPP FHGLMQFADL QNNPNNSNPV TNSAAAANNL FNLSFLSNSS STNSLSNSNS  300
NNNNNNASNL MLSAAGGHHH HFNNNEQNGT ASTGTGGVDH HQGTNNNLFT NNLISDHQIS  360
SGAVPSLFST SSVHQNETMV PHMSATALLQ KAAQMGSTSS NNNTASLLRS FGGSSSSSGS  420
KPNNNNNNFG GAGNVFGGPG SSENDNSSSI HDLMNPFAAT NSSIFGTGSN DQVNAFSGQD  480
QNHHRRHHHH HPNYEAKLHH NMNAGMGGSD RMTRDFLGVG QIVRSVSGGF QQREKQQQQH  540
GGVIDVSSLD SERNITAPTS QSFGGGGGGG GGGGSFH*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5b3h_C	1e-33	78	139	3	64	Zinc finger protein JACKDAW
5b3h_F	1e-33	78	139	3	64	Zinc finger protein JACKDAW
Search in ModeBase

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
Csi.4892	0.0	flower

Expression -- Description ? help Back to Top
Source	Description
Uniprot	TISSUE SPECIFICITY: Highly expressed in leaf tissues. {ECO:0000305\|PubMed:22898356}.

Functional Description ? help Back to Top
Source	Description
UniProt	Transcription factor acting as a positive regulator of the starch synthase SS4. Controls chloroplast development and starch granule formation (PubMed:22898356). Binds DNA via its zinc fingers (PubMed:24821766). Recognizes and binds to SCL3 promoter sequence 5'-AGACAA-3' to promotes its expression when in complex with RGA (PubMed:24821766). {ECO:0000269\|PubMed:22898356, ECO:0000269\|PubMed:24821766}.

Binding Motif ? help Back to Top
Motif ID	Method	Source	Motif file
MP00255	DAP	Transfer from AT2G02070	Download

Regulation -- PlantRegMap ? help Back to Top
Source	Upstream Regulator	Target Gene
PlantRegMap	Retrieve	Retrieve

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AC208494	1e-122	AC208494.1 Populus trichocarpa clone JGIACSB265-L05, complete sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_006470878.1	0.0	protein indeterminate-domain 5, chloroplastic-like isoform X1
Swissprot	Q9ZUL3	1e-126	IDD5_ARATH; Protein indeterminate-domain 5, chloroplastic
TrEMBL	A0A067EEN7	0.0	A0A067EEN7_CITSI; Uncharacterized protein
STRING	XP_006470878.1	0.0	(Citrus sinensis)

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT2G02070.1	1e-102	indeterminate(ID)-domain 5

Link Out ? help Back to Top
Phytozome	orange1.1g008103m

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]