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

Carubv10001844m

Common Name

CARUB_v10001844mg

Organism

Capsella rubella

Taxonomic ID

81985

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Capsella

Family

C3H

Protein Properties

Length: 241aa MW: 25324.6 Da PI: 10.3237

Description

C3H family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Carubv10001844m	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	40	63	2	25
-S---SGGGGTS--TTTTT-SS-S CS zf-CCCH 2 ktelCrffartGtCkyGdrCkFaH 25 k ++C f+ C++Gd+C+F H Carubv10001844m 40 KSKPCTKFFSPSGCPFGDNCHFLH 63 678999999999************ PP
2	zf-CCCH	36.7	7.1e-12	209	234	1	27
--S---SGGGGTS--TTTTT-SS-SSS CS zf-CCCH 1 yktelCrffartGtCkyGdrCkFaHgp 27 y+t++C++f++ G C yGdrC+FaHg+ Carubv10001844m 209 YRTKICDRFSK-GNCTYGDRCHFAHGE 234 89*******.***********96 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50103	12.934	38	66	IPR000571	Zinc finger, CCCH-type
SMART	SM00356	0.58	38	65	IPR000571	Zinc finger, CCCH-type
SuperFamily	SSF90229	4.19E-6	39	64	IPR000571	Zinc finger, CCCH-type
Gene3D	G3DSA:4.10.1000.10	1.4E-7	40	63	IPR000571	Zinc finger, CCCH-type
Pfam	PF00642	2.6E-4	40	63	IPR000571	Zinc finger, CCCH-type
SuperFamily	SSF54791	2.63E-14	114	185	IPR004088	K Homology domain, type 1
SMART	SM00322	2.7E-11	115	185	IPR004087	K Homology domain
PROSITE profile	PS50084	14.026	116	180	IPR004088	K Homology domain, type 1
Gene3D	G3DSA:3.30.1370.10	9.2E-16	117	184	IPR004088	K Homology domain, type 1
CDD	cd00105	1.98E-12	118	180	No hit	No description
Pfam	PF00013	1.8E-10	118	181	IPR004088	K Homology domain, type 1
Gene3D	G3DSA:4.10.1000.10	5.1E-16	203	239	IPR000571	Zinc finger, CCCH-type
PROSITE profile	PS50103	16.812	208	235	IPR000571	Zinc finger, CCCH-type
SMART	SM00356	2.5E-8	208	234	IPR000571	Zinc finger, CCCH-type
SuperFamily	SSF90229	1.19E-8	208	238	IPR000571	Zinc finger, CCCH-type
Pfam	PF00642	4.7E-9	209	234	IPR000571	Zinc finger, CCCH-type

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0003723	Molecular Function	RNA binding
GO:0046872	Molecular Function	metal ion binding

Sequence ? help Back to Top
Protein Sequence Length: 241 aa Download sequence Send to blast
MDARKRGRPE AAAPSHNSNG GGFKRSKQEM ESNSTGLGSK SKPCTKFFSP SGCPFGDNCH 60 FLHYVPGGYN AAAQMTNLRP PVAQVSRNMQ ASGGVGGRFS GRGDSGLGPV SMFGASATAK 120 ISVDASLAGA IIGKGGIHSK QICRQTGAKL SIKDHERDPN LKIIELEGTF EQIDVASGMV 180 RELIGRLGSA KKPRGIGGSE GKPHPGSNYR TKICDRFSKG NCTYGDRCHF AHGEAELRKS 240 *

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Carubv10001844m

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	AK117974	0.0	AK117974.1 Arabidopsis thaliana At5g06770 mRNA for unknown protein, complete cds, clone: RAFL19-18-C06.
GenBank	BT005260	0.0	BT005260.1 Arabidopsis thaliana At5g06770 mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_006286555.1	1e-176	zinc finger CCCH domain-containing protein 52 isoform X1
Swissprot	Q9FG30	1e-156	C3H52_ARATH; Zinc finger CCCH domain-containing protein 52
TrEMBL	R0H7D6	1e-175	R0H7D6_9BRAS; Uncharacterized protein
STRING	XP_006286555.1	1e-176	(Capsella rubella)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM2336	28	75

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT5G06770.1	1e-147	C3H family protein

Link Out ? help Back to Top
Phytozome	Carubv10001844m
Entrez Gene	17883676

Publications ? help Back to Top
Yan Z,Jia J,Yan X,Shi H,Han Y Arabidopsis KHZ1 and KHZ2, two novel non-tandem CCCH zinc-finger and K-homolog domain proteins, have redundant roles in the regulation of flowering and senescence. Plant Mol. Biol., 2017. 95(6): p. 549-565 [PMID:29076025]