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

Ciclev10000982m

Common Name

CICLE_v10000982mg

Organism

Citrus clementina

Taxonomic ID

85681

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: 484aa MW: 52768.8 Da PI: 9.009

Description

C2H2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Ciclev10000982m	genome	ICGC	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-C2H2	17.3	1.4e-05	100	122	1	23
EEETTTTEEESSHHHHHHHHHHT CS zf-C2H2 1 ykCpdCgksFsrksnLkrHirtH 23 ++C++C+k F r nL+ H r H Ciclev10000982m 100 FVCEICNKGFQRDQNLQLHRRGH 122 89*******************88 PP
2	zf-C2H2	12.2	0.00056	176	198	1	23
EEETTTTEEESSHHHHHHHHHHT CS zf-C2H2 1 ykCpdCgksFsrksnLkrHirtH 23 +kC +C+k + +s+ k H +t+ Ciclev10000982m 176 WKCDKCSKKYAVQSDWKAHSKTC 198 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	1.6E-5	99	122	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamily	SSF57667	2.44E-7	99	122	No hit	No description
PROSITE profile	PS50157	10.949	100	122	IPR007087	Zinc finger, C2H2
SMART	SM00355	0.017	100	122	IPR015880	Zinc finger, C2H2-like
Pfam	PF12171	7.6E-5	100	122	IPR022755	Zinc finger, double-stranded RNA binding
PROSITE pattern	PS00028	0	102	122	IPR007087	Zinc finger, C2H2
SMART	SM00355	96	141	171	IPR015880	Zinc finger, C2H2-like
Gene3D	G3DSA:3.30.160.60	1.7E-4	164	197	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamily	SSF57667	2.44E-7	171	196	No hit	No description
SMART	SM00355	150	176	196	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: 484 aa Download sequence Send to blast
MSNITGDAVS FSSSGNNINN HHHHGEEVHQ QQGLVSQFLV TNSLASSTTT ATNNSSSNGS 60 SSTTQPPPPA KRKRNLPGNP DPTAEVIALS PNSLMATNRF VCEICNKGFQ RDQNLQLHRR 120 GHNLPWKLRQ RSTTEIRKRV YVCPEPSCVH HNPARALGDL TGIKKHFSRK HGEKKWKCDK 180 CSKKYAVQSD WKAHSKTCGT KEYKCDCGTI FSRRDSFITH RAFCDALAEE SQKANQGVNP 240 QLGHVSEHIS SMPINNHTEN NNNPLAHHEL MPMPPKPFNT MAAASIFESS NNNLQQSAAA 300 SASLSATALL QKAAQMGATA SNGSMISSPM MHKSLVTSMA PPSFVAIPKD HQSLSAAAAS 360 MEEISLSSSA QFFSANIGHA EGSSAMNDVG MFYRFLDQNN AALMKSLEHD ESNKSGNNQS 420 VLNNGDVMTV DFMGIGGSRT RNHFQQQQSQ ELKFGSGISN IGQPRMQSLS HFQQQQQDVP 480 FLN*

Sequence ? help Back to Top

Protein Sequence Length: 484 aa Download sequence Send to blast

MSNITGDAVS FSSSGNNINN HHHHGEEVHQ QQGLVSQFLV TNSLASSTTT ATNNSSSNGS  60
SSTTQPPPPA KRKRNLPGNP DPTAEVIALS PNSLMATNRF VCEICNKGFQ RDQNLQLHRR  120
GHNLPWKLRQ RSTTEIRKRV YVCPEPSCVH HNPARALGDL TGIKKHFSRK HGEKKWKCDK  180
CSKKYAVQSD WKAHSKTCGT KEYKCDCGTI FSRRDSFITH RAFCDALAEE SQKANQGVNP  240
QLGHVSEHIS SMPINNHTEN NNNPLAHHEL MPMPPKPFNT MAAASIFESS NNNLQQSAAA  300
SASLSATALL QKAAQMGATA SNGSMISSPM MHKSLVTSMA PPSFVAIPKD HQSLSAAAAS  360
MEEISLSSSA QFFSANIGHA EGSSAMNDVG MFYRFLDQNN AALMKSLEHD ESNKSGNNQS  420
VLNNGDVMTV DFMGIGGSRT RNHFQQQQSQ ELKFGSGISN IGQPRMQSLS HFQQQQQDVP  480
FLN*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5b3h_C	3e-33	172	233	3	64	Zinc finger protein JACKDAW
5b3h_F	3e-33	172	233	3	64	Zinc finger protein JACKDAW
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Expression -- Description ? help Back to Top
Source	Description
Uniprot	TISSUE SPECIFICITY: Observed in vegetative tissues. Mainly expressed in hypocotyls, petioles, shoot apices, root tips, and trichomes, and, at low levels, in leaves, stems and flowers. {ECO:0000269\|PubMed:25035403}.

Functional Description ? help Back to Top
Source	Description
UniProt	Transcription factor that acts as a positive regulator of gibberellin (GA) action, homeostasis and signaling. GA converts the GAF1 complex from transcriptional activator to repressor via the degradation of DELLA proteins. {ECO:0000269\|PubMed:25035403}.

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_006433386.1	0.0	protein indeterminate-domain 2
Refseq	XP_006472060.1	0.0	protein indeterminate-domain 2-like
Swissprot	Q9SCQ6	1e-114	IDD2_ARATH; Zinc finger protein GAI-ASSOCIATED FACTOR 1
TrEMBL	V4TAN5	0.0	V4TAN5_9ROSI; Uncharacterized protein
STRING	XP_006472060.1	0.0	(Citrus sinensis)
STRING	XP_006433386.1	0.0	(Citrus clementina)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM15443	8	18

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT1G03840.1	1e-101	C2H2 family protein

Link Out ? help Back to Top
Phytozome	Ciclev10000982m
Entrez Gene	18041512

Publications ? help Back to Top
Fukazawa J, et al. DELLAs function as coactivators of GAI-ASSOCIATED FACTOR1 in regulation of gibberellin homeostasis and signaling in Arabidopsis. Plant Cell, 2014. 26(7): p. 2920-38 [PMID:25035403] Moreno-Risueno MA, et al. Transcriptional control of tissue formation throughout root development. Science, 2015. 350(6259): p. 426-30 [PMID:26494755] Khare D, et al. Root avoidance of toxic metals requires the GeBP-LIKE 4 transcription factor in Arabidopsis thaliana. New Phytol., 2017. 213(3): p. 1257-1273 [PMID:27768815]