PlantTFDB - Plant Transcription Factor Database @ CBI, PKU

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Malvales; Malvaceae; Malvoideae; Gossypium

Family

C2H2

Protein Properties

Length: 496aa MW: 51628.9 Da PI: 8.9192

Description

C2H2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Gorai.009G203800.1	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-C2H2	17.2	1.4e-05	69	91	1	23
EEETTTTEEESSHHHHHHHHHHT CS zf-C2H2 1 ykCpdCgksFsrksnLkrHirtH 23 ++C++C+k F r nL+ H r H Gorai.009G203800.1 69 FVCEICNKGFQRDQNLQLHRRGH 91 89*******************88 PP
2	zf-C2H2	15.8	4.1e-05	145	167	1	23
EEETTTTEEESSHHHHHHHHHHT CS zf-C2H2 1 ykCpdCgksFsrksnLkrHirtH 23 +kC+ C+k + +s+ k H++t+ Gorai.009G203800.1 145 WKCERCSKKYAVQSDWKAHMKTC 167 58*******************98 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF57667	4.17E-7	68	91	No hit	No description
Gene3D	G3DSA:3.30.160.60	1.6E-5	68	91	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SMART	SM00355	0.017	69	91	IPR015880	Zinc finger, C2H2-like
PROSITE profile	PS50157	10.949	69	91	IPR007087	Zinc finger, C2H2
Pfam	PF12171	7.9E-5	69	91	IPR022755	Zinc finger, double-stranded RNA binding
PROSITE pattern	PS00028	0	71	91	IPR007087	Zinc finger, C2H2
SMART	SM00355	220	110	140	IPR015880	Zinc finger, C2H2-like
Gene3D	G3DSA:3.30.160.60	9.9E-5	133	166	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamily	SSF57667	4.17E-7	140	166	No hit	No description
SMART	SM00355	77	145	165	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: 496 aa Download sequence Send to blast
MVELENSSAM TVSTASGEAT ASSLGNQIQD NQLTGGGPPK KKRNLPGMPD PDAEVIALSP 60 KTLLATNRFV CEICNKGFQR DQNLQLHRRG HNLPWKLRQR TSKEIRKRVY VCPEPSCVHH 120 NPARALGDLT GIKKHFCRKH GERKWKCERC SKKYAVQSDW KAHMKTCGTR EYKCDCGTIF 180 SRRDSFITHR AFCDALAEES ARTQTLGVAN PEGNINVNGN GSGNTTMVGG GAAATSPPPQ 240 PLTPSTTSVV SPGLSIQSSE VPENPMGLSP AAATTATANV FASIFAPNSQ PSKISAPSSF 300 LQATTPLERT SLSLSSPLYL SNNGSSIFTR PENDHCHYAP SPQPAMSATA LLQKAAQMGA 360 AASNPSLLRG LGLAVSSASP AGQDPNVKSE SNTATASLGL GFPSNGSSEL TNPMIGSSSL 420 FGNKPTTLDL LGLGMADGGA SSSGLSALLT SFGGGFNAGA ATATSYGAGG SNNSPIETWE 480 GGAERKHNGP ANAML*

Sequence ? help Back to Top

Protein Sequence Length: 496 aa Download sequence Send to blast

MVELENSSAM TVSTASGEAT ASSLGNQIQD NQLTGGGPPK KKRNLPGMPD PDAEVIALSP  60
KTLLATNRFV CEICNKGFQR DQNLQLHRRG HNLPWKLRQR TSKEIRKRVY VCPEPSCVHH  120
NPARALGDLT GIKKHFCRKH GERKWKCERC SKKYAVQSDW KAHMKTCGTR EYKCDCGTIF  180
SRRDSFITHR AFCDALAEES ARTQTLGVAN PEGNINVNGN GSGNTTMVGG GAAATSPPPQ  240
PLTPSTTSVV SPGLSIQSSE VPENPMGLSP AAATTATANV FASIFAPNSQ PSKISAPSSF  300
LQATTPLERT SLSLSSPLYL SNNGSSIFTR PENDHCHYAP SPQPAMSATA LLQKAAQMGA  360
AASNPSLLRG LGLAVSSASP AGQDPNVKSE SNTATASLGL GFPSNGSSEL TNPMIGSSSL  420
FGNKPTTLDL LGLGMADGGA SSSGLSALLT SFGGGFNAGA ATATSYGAGG SNNSPIETWE  480
GGAERKHNGP ANAML*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5b3h_C	2e-36	141	206	3	68	Zinc finger protein JACKDAW
5b3h_F	2e-36	141	206	3	68	Zinc finger protein JACKDAW
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Expression -- Description ? help Back to Top
Source	Description
Uniprot	DEVELOPMENTAL STAGE: Strongly up-regulated during seed development. {ECO:0000269\|PubMed:21571950}.
Uniprot	TISSUE SPECIFICITY: At 3 days post anthesis (DPA), expressed in the chalazal endosperm region. By 6 DPA, expressed in the endosperm and embryo. In fully germinated seed, strongest expression in the root tip and not detected in the cotyledons. In 4-days old seedlings, restricted to the vasculature of the cotyledons, the shoot apical meristem region, and the root tip. By 8 days, restricted to newly emerged leaves. {ECO:0000269\|PubMed:21571950}.

Functional Description ? help Back to Top
Source	Description
UniProt	Transcription factor promoting the transition to germination by regulating light and hormonal signaling during seed maturation (PubMed:21571950). Acts as a positive regulator of phytochrome and/or gibberellin action (PubMed:21571950, PubMed:25035403). {ECO:0000269\|PubMed:21571950, ECO:0000269\|PubMed:25035403}.

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	HQ526115	7e-42	HQ526115.1 Gossypium herbaceum clone NBRI_D2_1707 simple sequence repeat marker, mRNA sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_012444978.1	0.0	PREDICTED: protein indeterminate-domain 2-like
Swissprot	Q9LVQ7	1e-144	IDD1_ARATH; Zinc finger protein ENHYDROUS
TrEMBL	A0A0D2TSX8	0.0	A0A0D2TSX8_GOSRA; Uncharacterized protein
STRING	Gorai.009G203800.1	0.0	(Gossypium raimondii)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM155	28	306

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT3G50700.1	1e-126	indeterminate(ID)-domain 2

Link Out ? help Back to Top
Phytozome	Gorai.009G203800.1
Entrez Gene	105769102

Publications ? help Back to Top
Paterson AH, et al. Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres. Nature, 2012. 492(7429): p. 423-7 [PMID:23257886] Fukazawa J, et al. DELLAs function as coactivators of GAI-ASSOCIATED FACTOR1 in regulation of gibberellin homeostasis and signaling in Arabidopsis. Plant Cell, 2014. 26(7): p. 2920-38 [PMID:25035403] Moreno-Risueno MA, et al. Transcriptional control of tissue formation throughout root development. Science, 2015. 350(6259): p. 426-30 [PMID:26494755]