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

RrC2305_p2

Organism

Raphanus raphanistrum

Taxonomic ID

109996

Taxonomic Lineage

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

Family

C3H

Protein Properties

Length: 410aa MW: 42169.7 Da PI: 7.1824

Description

C3H family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
RrC2305_p2	genome	MSU	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-CCCH	37.2	5e-12	48	72	3	27
S---SGGGGTS--TTTTT-SS-SSS CS zf-CCCH 3 telCrffartGtCkyGdrCkFaHgp 27 ++ C +++rtG C yG+rC+F+H++ RrC2305_p2 48 EPDCIYYLRTGVCGYGSRCRFNHPR 72 689********************96 PP
2	zf-CCCH	32	2e-10	98	117	8	27
GGGGTS--TTTTT-SS-SSS CS zf-CCCH 8 ffartGtCkyGdrCkFaHgp 27 +f+rtGtCkyG++Ck++H++ RrC2305_p2 98 HFMRTGTCKYGASCKYHHPR 117 8*****************96 PP
3	zf-CCCH	40.1	6.2e-13	258	283	2	27
-S---SGGGGTS--TTTTT-SS-SSS CS zf-CCCH 2 ktelCrffartGtCkyGdrCkFaHgp 27 ++++C++f+rtG Ck+G++C+++H+p RrC2305_p2 258 DQPECQYFMRTGDCKFGASCRYHHPP 283 689*********************97 PP
4	zf-CCCH	32.8	1.2e-10	305	330	2	27
-S---SGGGGTS--TTTTT-SS-SSS CS zf-CCCH 2 ktelCrffartGtCkyGdrCkFaHgp 27 + + C +fa+ G+Ck+G+ CkF H++ RrC2305_p2 305 GVAQCTHFAQHGICKFGPACKFDHSM 330 6788********************85 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SMART	SM00356	2.7E-5	45	72	IPR000571	Zinc finger, CCCH-type
PROSITE profile	PS50103	14.023	45	73	IPR000571	Zinc finger, CCCH-type
Pfam	PF00642	1.9E-9	48	72	IPR000571	Zinc finger, CCCH-type
SuperFamily	SSF90229	2.35E-6	49	73	IPR000571	Zinc finger, CCCH-type
Gene3D	G3DSA:4.10.1000.10	1.7E-5	51	72	IPR000571	Zinc finger, CCCH-type
SMART	SM00356	0.16	94	117	IPR000571	Zinc finger, CCCH-type
PROSITE profile	PS50103	11.047	97	118	IPR000571	Zinc finger, CCCH-type
Gene3D	G3DSA:4.10.1000.10	2.7E-4	98	117	IPR000571	Zinc finger, CCCH-type
Pfam	PF00642	5.4E-8	98	117	IPR000571	Zinc finger, CCCH-type
SMART	SM00356	5.4E-6	256	283	IPR000571	Zinc finger, CCCH-type
PROSITE profile	PS50103	15.798	256	284	IPR000571	Zinc finger, CCCH-type
Pfam	PF00642	3.4E-10	258	283	IPR000571	Zinc finger, CCCH-type
SuperFamily	SSF90229	1.31E-5	259	283	IPR000571	Zinc finger, CCCH-type
Gene3D	G3DSA:4.10.1000.10	5.7E-5	262	282	IPR000571	Zinc finger, CCCH-type
SMART	SM00356	1.4E-4	303	330	IPR000571	Zinc finger, CCCH-type
PROSITE profile	PS50103	13.554	303	331	IPR000571	Zinc finger, CCCH-type
Pfam	PF00642	2.9E-8	305	329	IPR000571	Zinc finger, CCCH-type
SuperFamily	SSF90229	1.57E-5	306	330	IPR000571	Zinc finger, CCCH-type

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

Sequence ? help Back to Top
Protein Sequence Length: 410 aa Download sequence Send to blast
MERYGRAGEE GPRSDPSIEW TSRGVEGLSG GGAGGGGGGE AYPERSNEPD CIYYLRTGVC 60 GYGSRCRFNH PRDRGAVVGA VRGGGGDGAL PERMGQPHFM RTGTCKYGAS CKYHHPRQGG 120 GGSVAPVSLS YLGYPLRPIQ PSSASATAAA AATDTDYLSN NSISTNTFVS AIRPYGPPPM 180 VLPPGMVTYP NWNPYPASLT AMPSPGTGTQ PSIGSSSVYG GVTQLSPSGT AYTTGTYLSG 240 GPSLTTTSKE QSFPQRPDQP ECQYFMRTGD CKFGASCRYH HPPLDAVQPQ TGVLLSSIGL 300 PLRPGVAQCT HFAQHGICKF GPACKFDHSM ASSLSYSPSA SSLTDMPVAP YPIGSSSLSG 360 ASAPVSSSIE TTTAEAVTAV VSGVNSQELA ETGGDSASVS GSIEAKTSSS

Sequence ? help Back to Top

Protein Sequence Length: 410 aa Download sequence Send to blast

MERYGRAGEE GPRSDPSIEW TSRGVEGLSG GGAGGGGGGE AYPERSNEPD CIYYLRTGVC  60
GYGSRCRFNH PRDRGAVVGA VRGGGGDGAL PERMGQPHFM RTGTCKYGAS CKYHHPRQGG  120
GGSVAPVSLS YLGYPLRPIQ PSSASATAAA AATDTDYLSN NSISTNTFVS AIRPYGPPPM  180
VLPPGMVTYP NWNPYPASLT AMPSPGTGTQ PSIGSSSVYG GVTQLSPSGT AYTTGTYLSG  240
GPSLTTTSKE QSFPQRPDQP ECQYFMRTGD CKFGASCRYH HPPLDAVQPQ TGVLLSSIGL  300
PLRPGVAQCT HFAQHGICKF GPACKFDHSM ASSLSYSPSA SSLTDMPVAP YPIGSSSLSG  360
ASAPVSSSIE TTTAEAVTAV VSGVNSQELA ETGGDSASVS GSIEAKTSSS

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	AC189233	1e-98	AC189233.2 Brassica rapa subsp. pekinensis cultivar Inbred line 'Chiifu' clone KBrB013O20, complete sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_018492151.1	0.0	PREDICTED: zinc finger CCCH domain-containing protein 34-like isoform X1
Swissprot	Q9SQU4	1e-164	C3H34_ARATH; Zinc finger CCCH domain-containing protein 34
TrEMBL	M4CAG7	0.0	M4CAG7_BRARP; Uncharacterized protein
STRING	Bra001196.1-P	0.0	(Brassica rapa)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM1779	27	86

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT3G06410.1	1e-105	C3H family protein

Publications ? help Back to Top
Duarte JM, et al. Expression pattern shifts following duplication indicative of subfunctionalization and neofunctionalization in regulatory genes of Arabidopsis. Mol. Biol. Evol., 2006. 23(2): p. 469-78 [PMID:16280546]