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

Csa20g026940.1

Organism

Camelina sativa

Taxonomic ID

90675

Taxonomic Lineage

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

Family

C3H

Protein Properties

Length: 729aa MW: 78181.9 Da PI: 6.7433

Description

C3H family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Csa20g026940.1	genome	CSGP	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-CCCH	33.8	5.7e-11	53	78	2	27
-S---SGGGGTS--TTTTT-SS-SSS CS zf-CCCH 2 ktelCrffartGtCkyGdrCkFaHgp 27 +++ C +f rtG C yG+rC+F+H+p Csa20g026940.1 53 DEPDCIYFTRTGGCGYGSRCRFNHPP 78 6899********************96 PP
2	zf-CCCH	38	2.7e-12	101	126	2	27
-S---SGGGGTS--TTTTT-SS-SSS CS zf-CCCH 2 ktelCrffartGtCkyGdrCkFaHgp 27 +++ C++f+rtGtCk+G++Ck++H++ Csa20g026940.1 101 GQPVCQHFMRTGTCKFGASCKYHHPR 126 5789********************96 PP
3	zf-CCCH	39.1	1.2e-12	150	174	2	26
-S---SGGGGTS--TTTTT-SS-SS CS zf-CCCH 2 ktelCrffartGtCkyGdrCkFaHg 26 ++++C++f+rtG+Ck+G++C+F+H+ Csa20g026940.1 150 GEKECSYFMRTGQCKFGSTCRFHHP 174 7899********************9 PP
4	zf-CCCH	40.5	4.4e-13	298	323	2	27
-S---SGGGGTS--TTTTT-SS-SSS CS zf-CCCH 2 ktelCrffartGtCkyGdrCkFaHgp 27 +++C++f+rtG Ck+G++C+F+H++ Csa20g026940.1 298 EQPECQYFMRTGDCKFGSSCRFHHPM 323 5799********************95 PP
5	zf-CCCH	27	7.9e-09	345	367	4	26
---SGGGGTS--TTTTT-SS-SS CS zf-CCCH 4 elCrffartGtCkyGdrCkFaHg 26 + C++f + G Ck+G+ CkF H+ Csa20g026940.1 345 AQCSHFVEHGVCKFGPACKFDHS 367 67********************8 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50103	13.986	51	79	IPR000571	Zinc finger, CCCH-type
SMART	SM00356	1.3E-4	51	78	IPR000571	Zinc finger, CCCH-type
Pfam	PF00642	1.4E-8	53	78	IPR000571	Zinc finger, CCCH-type
SuperFamily	SSF90229	2.09E-5	56	79	IPR000571	Zinc finger, CCCH-type
Gene3D	G3DSA:4.10.1000.10	3.0E-5	57	77	IPR000571	Zinc finger, CCCH-type
SMART	SM00356	2.5E-6	99	126	IPR000571	Zinc finger, CCCH-type
PROSITE profile	PS50103	16.277	99	127	IPR000571	Zinc finger, CCCH-type
SuperFamily	SSF90229	3.66E-6	100	126	IPR000571	Zinc finger, CCCH-type
Pfam	PF00642	6.8E-10	101	126	IPR000571	Zinc finger, CCCH-type
Gene3D	G3DSA:4.10.1000.10	4.5E-5	104	126	IPR000571	Zinc finger, CCCH-type
SMART	SM00356	1.5E-6	148	175	IPR000571	Zinc finger, CCCH-type
PROSITE profile	PS50103	15.45	148	176	IPR000571	Zinc finger, CCCH-type
Pfam	PF00642	3.6E-10	150	174	IPR000571	Zinc finger, CCCH-type
SuperFamily	SSF90229	4.45E-6	151	175	IPR000571	Zinc finger, CCCH-type
Gene3D	G3DSA:4.10.1000.10	1.9E-4	154	173	IPR000571	Zinc finger, CCCH-type
SMART	SM00356	2.2E-6	296	323	IPR000571	Zinc finger, CCCH-type
PROSITE profile	PS50103	15.798	296	324	IPR000571	Zinc finger, CCCH-type
SuperFamily	SSF90229	4.06E-6	297	324	IPR000571	Zinc finger, CCCH-type
Pfam	PF00642	2.5E-10	299	323	IPR000571	Zinc finger, CCCH-type
Gene3D	G3DSA:4.10.1000.10	8.3E-5	302	322	IPR000571	Zinc finger, CCCH-type
SMART	SM00356	0.0025	341	368	IPR000571	Zinc finger, CCCH-type
PROSITE profile	PS50103	12.99	341	369	IPR000571	Zinc finger, CCCH-type
Pfam	PF00642	1.8E-6	345	367	IPR000571	Zinc finger, CCCH-type
SuperFamily	SSF90229	3.79E-5	345	369	IPR000571	Zinc finger, CCCH-type
SuperFamily	SSF54211	2.43E-45	491	662	IPR020568	Ribosomal protein S5 domain 2-type fold
Gene3D	G3DSA:3.30.230.70	2.3E-30	494	715	IPR027408	PNPase/RNase PH domain
CDD	cd11370	4.32E-135	495	720	No hit	No description
Pfam	PF01138	7.0E-36	505	635	IPR001247	Exoribonuclease, phosphorolytic domain 1
SuperFamily	SSF55666	2.38E-24	635	721	IPR015847	Exoribonuclease, phosphorolytic domain 2
Pfam	PF03725	1.1E-7	639	703	IPR015847	Exoribonuclease, phosphorolytic domain 2

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: 729 aa Download sequence Send to blast
MERYGGAGEE EPRSDPSLEW SAPGDETGIE ASMWRLGLQG GGGDDDSLPE RPDEPDCIYF 60 TRTGGCGYGS RCRFNHPPDR APVFGGGLRT EAAGQFPERM GQPVCQHFMR TGTCKFGASC 120 KYHHPRQGGG RGDSVIPISL NYMGFPLRPG EKECSYFMRT GQCKFGSTCR FHHPVPPGVQ 180 APSAGPTMYP SLQSRSVVPS SQQYGVVLAR PQLLPGSYVP SPYGYGQMVL HPGMVPYSGW 240 NPYQASVSAI PSPGTQPSMG TSSVYGIRPL SPSAPAYQSG PSSTGISNKE QTFPQRPEQP 300 ECQYFMRTGD CKFGSSCRFH HPMEAASPKD ITLSHIGLPL RPGAAQCSHF VEHGVCKFGP 360 ACKFDHSIGS SSLSYNPSAS SLTDMPVAPH PLGSSSLGTL APTSSSSSSS SEQCTELLSS 420 SSIKPITTTA GGTETVSSST TSGVNHPEPA AETNKDNSAS IEAKTSGLSY HVHSIPSYGH 480 LLCGFTTMEY VNPEGLRLDG RRFNEMRQIV AEVGVVSKAD GSAVFEMGNT KVIAAVYGPR 540 EIQNKSLQKK NDHALVLCEY SMAQFSTGDR RRQKFDRRST ELSLVIRQTM EACILTELLP 600 HSQIDIFLQV LQADGGTRSA CINAATLALA DAGIPMRDLA VSCSAGYLNS TPLLDLNYVE 660 DSAGGADVTV GILPKLDKVT LLQMDAKLPM ETFETVFALA SEGCKAIAER IREVLQENTK 720 QLEYRRAA*

Sequence ? help Back to Top

Protein Sequence Length: 729 aa Download sequence Send to blast

MERYGGAGEE EPRSDPSLEW SAPGDETGIE ASMWRLGLQG GGGDDDSLPE RPDEPDCIYF  60
TRTGGCGYGS RCRFNHPPDR APVFGGGLRT EAAGQFPERM GQPVCQHFMR TGTCKFGASC  120
KYHHPRQGGG RGDSVIPISL NYMGFPLRPG EKECSYFMRT GQCKFGSTCR FHHPVPPGVQ  180
APSAGPTMYP SLQSRSVVPS SQQYGVVLAR PQLLPGSYVP SPYGYGQMVL HPGMVPYSGW  240
NPYQASVSAI PSPGTQPSMG TSSVYGIRPL SPSAPAYQSG PSSTGISNKE QTFPQRPEQP  300
ECQYFMRTGD CKFGSSCRFH HPMEAASPKD ITLSHIGLPL RPGAAQCSHF VEHGVCKFGP  360
ACKFDHSIGS SSLSYNPSAS SLTDMPVAPH PLGSSSLGTL APTSSSSSSS SEQCTELLSS  420
SSIKPITTTA GGTETVSSST TSGVNHPEPA AETNKDNSAS IEAKTSGLSY HVHSIPSYGH  480
LLCGFTTMEY VNPEGLRLDG RRFNEMRQIV AEVGVVSKAD GSAVFEMGNT KVIAAVYGPR  540
EIQNKSLQKK NDHALVLCEY SMAQFSTGDR RRQKFDRRST ELSLVIRQTM EACILTELLP  600
HSQIDIFLQV LQADGGTRSA CINAATLALA DAGIPMRDLA VSCSAGYLNS TPLLDLNYVE  660
DSAGGADVTV GILPKLDKVT LLQMDAKLPM ETFETVFALA SEGCKAIAER IREVLQENTK  720
QLEYRRAA*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
2nn6_B	2e-70	488	721	8	242	Exosome complex exonuclease RRP41
6d6q_B	2e-70	488	721	8	242	Exosome complex component RRP41
6d6r_B	2e-70	488	721	8	242	Exosome complex component RRP41
6h25_B	1e-70	488	721	8	242	Exosome complex component RRP41
Search in ModeBase

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Csa20g026940.1

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	AK118846	0.0	AK118846.1 Arabidopsis thaliana At3g61620 mRNA for putative exonuclease RRP41, complete cds, clone: RAFL21-17-J09.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_010492866.1	0.0	PREDICTED: zinc finger CCCH domain-containing protein 58-like isoform X1
Swissprot	Q6NPN3	0.0	C3H58_ARATH; Zinc finger CCCH domain-containing protein 58
TrEMBL	R0HAE2	0.0	R0HAE2_9BRAS; Uncharacterized protein
STRING	XP_010492866.1	0.0	(Camelina sativa)

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
AT5G18550.1	0.0	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]