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

29780.m001361

Common Name

RCOM_0775730

Organism

Ricinus communis

Taxonomic ID

3988

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Malpighiales; Euphorbiaceae; Acalyphoideae; Acalypheae; Ricinus

Family

C2H2

Protein Properties

Length: 571aa MW: 61219.9 Da PI: 9.5667

Description

C2H2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
29780.m001361	genome	JCVI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-C2H2	16.2	2.9e-05	80	102	1	23
EEETTTTEEESSHHHHHHHHHHT CS zf-C2H2 1 ykCpdCgksFsrksnLkrHirtH 23 + C+ C+k F r nL+ H r H 29780.m001361 80 FICEVCNKGFQREQNLQLHRRGH 102 89*******************88 PP
2	zf-C2H2	13.2	0.00027	156	178	1	23
EEETTTTEEESSHHHHHHHHHHT CS zf-C2H2 1 ykCpdCgksFsrksnLkrHirtH 23 +kC++C+k++ +s+ k H +t+ 29780.m001361 156 WKCEKCSKRYAVQSDWKAHSKTC 178 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	6.3E-6	79	102	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamily	SSF57667	2.58E-7	79	102	No hit	No description
Pfam	PF12171	2.8E-5	80	102	IPR022755	Zinc finger, double-stranded RNA binding
SMART	SM00355	0.0052	80	102	IPR015880	Zinc finger, C2H2-like
PROSITE profile	PS50157	10.99	80	102	IPR007087	Zinc finger, C2H2
PROSITE pattern	PS00028	0	82	102	IPR007087	Zinc finger, C2H2
SMART	SM00355	150	121	151	IPR015880	Zinc finger, C2H2-like
Gene3D	G3DSA:3.30.160.60	2.1E-5	144	177	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamily	SSF57667	2.58E-7	151	176	No hit	No description
SMART	SM00355	130	156	176	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: 571 aa Download sequence Send to blast
MAAASSSSPF FRAREENHNQ MMQQNSSTTT TSSTAPATAP QKKKRNQPGT PCNFWHFPFA 60 DPDAEVIALS PKTLMATNRF ICEVCNKGFQ REQNLQLHRR GHNLPWKLKQ KTTKEVKRKV 120 YLCPEPTCVH HDASRALGDL TGIKKHYSRK HGEKKWKCEK CSKRYAVQSD WKAHSKTCGT 180 REYRCDCGTL FSRRDSFITH RAFCDALAQE SARHPTGLNT IGSHLYGNNH MSLGLSQVGS 240 PISSLQDQNH SSSNLLRLGS AGAAKFEHII PPSNSTSLPT MPASAFFMSD ANQGSFSNKP 300 LHGLMQLPDL QSATNNSSVA TNLFNLSFFS NNSPGNRISN SDNGNSSTAA TNLVNSGFLS 360 PNPFNGGNGG QGSTIFANNM GDPVGSGIPS LYSNSMQQEN ITPHMSATAL LQKAAQMGST 420 TSSNNNSTLL RGLGSSSSTG NKSDRSPLVS ANFGSSFGNA KIGDHHHQGL GTQIESENQL 480 QGLMNSLANG GSSIFGGGHG QDNGFGGFTS SGISLEQPHN STSFSNVDEA NKLTLDFLGV 540 GGMVRNIGGQ HGINLSALDT EIKSAQANKP F

Sequence ? help Back to Top

Protein Sequence Length: 571 aa Download sequence Send to blast

MAAASSSSPF FRAREENHNQ MMQQNSSTTT TSSTAPATAP QKKKRNQPGT PCNFWHFPFA  60
DPDAEVIALS PKTLMATNRF ICEVCNKGFQ REQNLQLHRR GHNLPWKLKQ KTTKEVKRKV  120
YLCPEPTCVH HDASRALGDL TGIKKHYSRK HGEKKWKCEK CSKRYAVQSD WKAHSKTCGT  180
REYRCDCGTL FSRRDSFITH RAFCDALAQE SARHPTGLNT IGSHLYGNNH MSLGLSQVGS  240
PISSLQDQNH SSSNLLRLGS AGAAKFEHII PPSNSTSLPT MPASAFFMSD ANQGSFSNKP  300
LHGLMQLPDL QSATNNSSVA TNLFNLSFFS NNSPGNRISN SDNGNSSTAA TNLVNSGFLS  360
PNPFNGGNGG QGSTIFANNM GDPVGSGIPS LYSNSMQQEN ITPHMSATAL LQKAAQMGST  420
TSSNNNSTLL RGLGSSSSTG NKSDRSPLVS ANFGSSFGNA KIGDHHHQGL GTQIESENQL  480
QGLMNSLANG GSSIFGGGHG QDNGFGGFTS SGISLEQPHN STSFSNVDEA NKLTLDFLGV  540
GGMVRNIGGQ HGINLSALDT EIKSAQANKP F

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5b3h_C	2e-35	152	213	3	64	Zinc finger protein JACKDAW
5b3h_F	2e-35	152	213	3	64	Zinc finger protein JACKDAW
Search in ModeBase

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}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	29780.m001361

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

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AC208494	1e-145	AC208494.1 Populus trichocarpa clone JGIACSB265-L05, complete sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_015576494.1	0.0	protein indeterminate-domain 5, chloroplastic
Swissprot	Q9ZUL3	1e-139	IDD5_ARATH; Protein indeterminate-domain 5, chloroplastic
TrEMBL	B9S7A8	0.0	B9S7A8_RICCO; Zinc finger protein, putative
STRING	XP_002521877.1	0.0	(Ricinus communis)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Fabids	OGEF1536	33	97

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT2G02070.1	1e-117	indeterminate(ID)-domain 5

Link Out ? help Back to Top
Phytozome	29780.m001361

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]