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

Pavir.1KG481300.2.p

Organism

Panicum virgatum

Taxonomic ID

38727

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; PACMAD clade; Panicoideae; Panicodae; Paniceae; Panicinae; Panicum

Family

C3H

Protein Properties

Length: 360aa MW: 40170 Da PI: 7.2009

Description

C3H family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Pavir.1KG481300.2.p	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-CCCH	18.2	4.4e-06	148	163	11	26
GTS--TTTTT-SS-SS CS zf-CCCH 11 rtGtCkyGdrCkFaHg 26 + GtC+yG C+ +Hg Pavir.1KG481300.2.p 148 AAGTCPYGKDCSQMHG 163 57*************9 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SMART	SM00356	0.083	1	27	IPR000571	Zinc finger, CCCH-type
PROSITE profile	PS50103	14.023	1	28	IPR000571	Zinc finger, CCCH-type
SuperFamily	SSF90229	1.16E-5	4	26	IPR000571	Zinc finger, CCCH-type
SMART	SM00356	16	28	49	IPR000571	Zinc finger, CCCH-type
PROSITE profile	PS50103	7.225	33	50	IPR000571	Zinc finger, CCCH-type
PROSITE profile	PS50103	11.066	138	165	IPR000571	Zinc finger, CCCH-type
SMART	SM00356	0.68	138	164	IPR000571	Zinc finger, CCCH-type
SuperFamily	SSF57850	2.99E-13	192	271	No hit	No description
Gene3D	G3DSA:3.30.40.10	3.4E-10	201	266	IPR013083	Zinc finger, RING/FYVE/PHD-type
CDD	cd00162	0.00108	206	266	No hit	No description
Pfam	PF13639	5.4E-8	206	265	IPR001841	Zinc finger, RING-type
PROSITE profile	PS50089	12.297	207	265	IPR001841	Zinc finger, RING-type
SMART	SM00184	1.2E-6	207	264	IPR001841	Zinc finger, RING-type
PROSITE pattern	PS00518	0	231	240	IPR017907	Zinc finger, RING-type, conserved site
SMART	SM00356	0.067	294	322	IPR000571	Zinc finger, CCCH-type
PROSITE profile	PS50103	13.516	294	323	IPR000571	Zinc finger, CCCH-type

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0005515	Molecular Function	protein binding
GO:0008270	Molecular Function	zinc ion binding

Sequence ? help Back to Top
Protein Sequence Length: 360 aa Download sequence Send to blast
MSKRVPCKFF LHGACYKGDY CEFSHDCNDR PDNKGACSFG SRCRNEHVEI HWNRPQPATT 60 AAHVSSNSSQ LVASSGGPHC SECQTDQCDQ TQQICKSTTT HSAQQPAWAD DYHEHDTPGD 120 ANSWPSDQAV ENQTSQHPAH MPLCSSAAAG TCPYGKDCSQ MHGDLCTFCE KQCLHPHRPD 180 ESGLHVELCK KNNRLLEALR KSEDIECGVC LDRVLSKPMA AERRFGLLSD CDHSFCISCI 240 RNWRSTSPTS GMDVNSTLRA CPICRKLSYY VVPSTTWYSS KEEKQEIIEG YKAKLRSIDC 300 KHFDFGKGTC PFGGSCFYKH AYRDGRLEEA LLNHNDADGA RATIARLMRL SYLLTRLHV*

Sequence ? help Back to Top

Protein Sequence Length: 360 aa Download sequence Send to blast

MSKRVPCKFF LHGACYKGDY CEFSHDCNDR PDNKGACSFG SRCRNEHVEI HWNRPQPATT  60
AAHVSSNSSQ LVASSGGPHC SECQTDQCDQ TQQICKSTTT HSAQQPAWAD DYHEHDTPGD  120
ANSWPSDQAV ENQTSQHPAH MPLCSSAAAG TCPYGKDCSQ MHGDLCTFCE KQCLHPHRPD  180
ESGLHVELCK KNNRLLEALR KSEDIECGVC LDRVLSKPMA AERRFGLLSD CDHSFCISCI  240
RNWRSTSPTS GMDVNSTLRA CPICRKLSYY VVPSTTWYSS KEEKQEIIEG YKAKLRSIDC  300
KHFDFGKGTC PFGGSCFYKH AYRDGRLEEA LLNHNDADGA RATIARLMRL SYLLTRLHV*

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
Pvr.18643	0.0	callus\| leaf\| stem

Expression -- Description ? help Back to Top
Source	Description
Uniprot	DEVELOPMENTAL STAGE: Expressed in dry seeds. Increased expression throughout imbibition and germination and when radicle and shoots are emerging. Up-regulated during cell differentiation. {ECO:0000269\|PubMed:17870591}.
Uniprot	TISSUE SPECIFICITY: Expressed in primary roots and leaves. Detected in vascular bundle tissues. {ECO:0000269\|PubMed:17870591}.

Functional Description ? help Back to Top
Source	Description
UniProt	E3 ubiquitin ligase catalyzing the covalent attachment of ubiquitin moieties onto substrate proteins. {ECO:0000250}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Pavir.1KG481300.2.p

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	BT054550	0.0	BT054550.1 Zea mays full-length cDNA clone ZM_BFc0152O03 mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_025798941.1	0.0	E3 ubiquitin-protein ligase makorin-like isoform X2
Swissprot	Q5ZA07	1e-158	C3H41_ORYSJ; E3 ubiquitin-protein ligase makorin
TrEMBL	A0A2T7FBC6	0.0	A0A2T7FBC6_9POAL; Uncharacterized protein
STRING	Pavir.Ab03056.1.p	0.0	(Panicum virgatum)

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT3G08505.2	1e-120	C3H family protein

Link Out ? help Back to Top
Phytozome	Pavir.1KG481300.2.p

Publications ? help Back to Top
Kikuchi S, et al. Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice. Science, 2003. 301(5631): p. 376-9 [PMID:12869764] Sahi VP, et al. A molecular insight into Darwin's "plant brain hypothesis" through expression pattern study of the MKRN gene in plant embryo compared with mouse embryo. Plant Signal Behav, 2012. 7(3): p. 375-81 [PMID:22499205] Wadekar HB,Sahi VP,Morita EH,Abe S MKRN expression pattern during embryonic and post-embryonic organogenesis in rice (Oryza sativa L. var. Nipponbare). Planta, 2013. 237(4): p. 1083-95 [PMID:23262670]