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

orange1.1g001158m

Organism

Citrus sinensis

Taxonomic ID

2711

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Sapindales; Rutaceae; Aurantioideae; Citrus

Family

C2H2

Protein Properties

Length: 1136aa MW: 126431 Da PI: 6.1216

Description

C2H2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
orange1.1g001158m	genome	ICGC	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-C2H2	12	0.00066	1044	1067	2	23
EET..TTTEEESSHHHHHHHHHHT CS zf-C2H2 2 kCp..dCgksFsrksnLkrHirtH 23 +Cp Cgk+Fs++ + H+r+H orange1.1g001158m 1044 RCPheGCGKRFSSHKYAIIHQRVH 1067 69999*****************99 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SMART	SM00355	18	1020	1042	IPR015880	Zinc finger, C2H2-like
SuperFamily	SSF57667	1.12E-6	1043	1080	No hit	No description
SMART	SM00355	0.046	1043	1067	IPR015880	Zinc finger, C2H2-like
PROSITE profile	PS50157	12.445	1043	1072	IPR007087	Zinc finger, C2H2
Gene3D	G3DSA:3.30.160.60	1.0E-6	1044	1071	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE pattern	PS00028	0	1045	1067	IPR007087	Zinc finger, C2H2
Gene3D	G3DSA:3.30.160.60	1.5E-10	1072	1097	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profile	PS50157	11.946	1073	1102	IPR007087	Zinc finger, C2H2
SMART	SM00355	0.0016	1073	1097	IPR015880	Zinc finger, C2H2-like
PROSITE pattern	PS00028	0	1075	1097	IPR007087	Zinc finger, C2H2
SuperFamily	SSF57667	1.93E-10	1083	1126	No hit	No description
Gene3D	G3DSA:3.30.160.60	7.9E-12	1098	1126	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profile	PS50157	9.494	1103	1129	IPR007087	Zinc finger, C2H2
SMART	SM00355	0.74	1103	1129	IPR015880	Zinc finger, C2H2-like
PROSITE pattern	PS00028	0	1105	1129	IPR007087	Zinc finger, C2H2

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0009741	Biological Process	response to brassinosteroid
GO:0009826	Biological Process	unidimensional cell growth
GO:0033169	Biological Process	histone H3-K9 demethylation
GO:0048577	Biological Process	negative regulation of short-day photoperiodism, flowering
GO:0048579	Biological Process	negative regulation of long-day photoperiodism, flowering
GO:0005634	Cellular Component	nucleus
GO:0003676	Molecular Function	nucleic acid binding
GO:0046872	Molecular Function	metal ion binding

Sequence ? help Back to Top
Protein Sequence Length: 1136 aa Download sequence Send to blast
MQDSATWLMV AKEAAVRRAA MNYLPMLSHQ QLLYLLTMSF ISRVPRSLLP GARSSRLRDR 60 QKEERELLVK KAFVEDILKE NNILSVLLGR QSTFNAVLWN ADLLPCQSKE SQMPSANETV 120 STTPGETVPN NPYEKHNDHN NLLDEMNVYM EALNDPYMGD DDISRDFHID SGALACVACG 180 ILGFPFMSVV QLSERASIEL LADLVKEGPG VSELKNTHHH TNLDGSVKSS VSDDLCLVPD 240 ISLLQKDLSV PSITKSSRIW NTSNKYLRPR IFCLEHAAQI EEILQSKGGA EILVICHSDY 300 QKIKAHAAAV AEEIGSPFNY IDVPLDAASE EDLHLIDLAI DDGELDECRE DWTSKLGINL 360 RHCVKVRKNS PSMRVQHALS LGDLFSEKSL SSDFSKIKWQ FRRSRSKIKL YGRAHSKPCQ 420 NIEIKKDEVT GRKLDGATVK KEEKLIQYSR RKFKQKPDLS TGACGDQVHP RELLPEVSAA 480 TCDHLDGHNR SDFEINPDGT GNSGSISAGS IHSPIGMSEG LHDIPVREAT SNLSLNYSPS 540 RVADSLATAT LVVDSIVQND TESMKELNIE GDIFHMATCK SAEMQQNSGT DVTSEKTEIS 600 HHTVASNEGS IIMRSDQITE SMTIKNEKCN LASEGHCRKI EDLAPDNSCM ISEACDHMIS 660 DNEVRQNVQS TNGGNDVEPI SCDHKLIDEP PASTGESCED MREISTAESL QDNLQHERNI 720 GNGSNEELVS SSVTMMIQPT SAPMEISEVP SKECAAADLL NVGTKQKLIS SCVSRMEVDQ 780 PSPLKVGGCS EVPIEICTKE DSGADMTLDP RTQLQNHTTA EAIMDELVCN SSAQLEENER 840 IPASVAACSE ESNGIFAEEK MDFDMTIGTQ TKNATSEEPK PTSLIPIDQP IPAVIRKYSR 900 TRRESYSAEK FCNGNEAYSS KDNKERECNE SNLEDPSFSA GKGRKRNREL ERLTENKFNG 960 SGFIRSPCEG LRSRAGKDAA NTSEVDIRKI AEKRATKTMR NRESVPAPCQ DKKKILKGHH 1020 RCDLDGCRMS FETKRELSLH KRNRCPHEGC GKRFSSHKYA IIHQRVHDDE RPLKCPWKGC 1080 SMSFKWAWAR TEHIRVHTGE RPYKCKFEGC GLSFRFVSDI SRHRRKTGHY ENLSA*

Sequence ? help Back to Top

Protein Sequence Length: 1136 aa Download sequence Send to blast

MQDSATWLMV AKEAAVRRAA MNYLPMLSHQ QLLYLLTMSF ISRVPRSLLP GARSSRLRDR  60
QKEERELLVK KAFVEDILKE NNILSVLLGR QSTFNAVLWN ADLLPCQSKE SQMPSANETV  120
STTPGETVPN NPYEKHNDHN NLLDEMNVYM EALNDPYMGD DDISRDFHID SGALACVACG  180
ILGFPFMSVV QLSERASIEL LADLVKEGPG VSELKNTHHH TNLDGSVKSS VSDDLCLVPD  240
ISLLQKDLSV PSITKSSRIW NTSNKYLRPR IFCLEHAAQI EEILQSKGGA EILVICHSDY  300
QKIKAHAAAV AEEIGSPFNY IDVPLDAASE EDLHLIDLAI DDGELDECRE DWTSKLGINL  360
RHCVKVRKNS PSMRVQHALS LGDLFSEKSL SSDFSKIKWQ FRRSRSKIKL YGRAHSKPCQ  420
NIEIKKDEVT GRKLDGATVK KEEKLIQYSR RKFKQKPDLS TGACGDQVHP RELLPEVSAA  480
TCDHLDGHNR SDFEINPDGT GNSGSISAGS IHSPIGMSEG LHDIPVREAT SNLSLNYSPS  540
RVADSLATAT LVVDSIVQND TESMKELNIE GDIFHMATCK SAEMQQNSGT DVTSEKTEIS  600
HHTVASNEGS IIMRSDQITE SMTIKNEKCN LASEGHCRKI EDLAPDNSCM ISEACDHMIS  660
DNEVRQNVQS TNGGNDVEPI SCDHKLIDEP PASTGESCED MREISTAESL QDNLQHERNI  720
GNGSNEELVS SSVTMMIQPT SAPMEISEVP SKECAAADLL NVGTKQKLIS SCVSRMEVDQ  780
PSPLKVGGCS EVPIEICTKE DSGADMTLDP RTQLQNHTTA EAIMDELVCN SSAQLEENER  840
IPASVAACSE ESNGIFAEEK MDFDMTIGTQ TKNATSEEPK PTSLIPIDQP IPAVIRKYSR  900
TRRESYSAEK FCNGNEAYSS KDNKERECNE SNLEDPSFSA GKGRKRNREL ERLTENKFNG  960
SGFIRSPCEG LRSRAGKDAA NTSEVDIRKI AEKRATKTMR NRESVPAPCQ DKKKILKGHH  1020
RCDLDGCRMS FETKRELSLH KRNRCPHEGC GKRFSSHKYA IIHQRVHDDE RPLKCPWKGC  1080
SMSFKWAWAR TEHIRVHTGE RPYKCKFEGC GLSFRFVSDI SRHRRKTGHY ENLSA*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
6a57_A	2e-52	1020	1129	23	132	Lysine-specific demethylase REF6
6a58_A	2e-52	1020	1129	23	132	Lysine-specific demethylase REF6
6a59_A	2e-52	1020	1129	23	132	Lysine-specific demethylase REF6
Search in ModeBase

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
Csi.460	0.0	fruit

Expression -- Description ? help Back to Top
Source	Description
Uniprot	TISSUE SPECIFICITY: Expressed at low levels in cotyledons and leaves. Detected in inflorescences, stems, roots and siliques but not in shoot apical meristems or root tips. {ECO:0000269\|PubMed:15377760, ECO:0000269\|PubMed:18713399}.

Functional Description ? help Back to Top
Source	Description
UniProt	Acts probably as a histone 'Lys-4' (H3K4me) demethylase. Involved in transcriptional gene regulation. Acts as a repressor of the photoperiodic flowering pathway and of FT. Binds around the transcription start site of the FT locus. {ECO:0000269\|PubMed:15377760, ECO:0000269\|PubMed:18467490, ECO:0000269\|PubMed:19946624}.

Regulation -- PlantRegMap ? help Back to Top
Source	Upstream Regulator	Target Gene
PlantRegMap	Retrieve	-

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_006436450.1	0.0	probable lysine-specific demethylase ELF6
Refseq	XP_006485645.1	0.0	probable lysine-specific demethylase ELF6
Swissprot	Q6BDA0	1e-133	ELF6_ARATH; Probable lysine-specific demethylase ELF6
TrEMBL	A0A2H5PYG0	0.0	A0A2H5PYG0_CITUN; Uncharacterized protein
STRING	XP_006485645.1	0.0	(Citrus sinensis)
STRING	XP_006436450.1	0.0	(Citrus clementina)

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT5G04240.1	1e-135	C2H2 family protein

Link Out ? help Back to Top
Phytozome	orange1.1g001158m

Publications ? help Back to Top
Heidari B,Nemie-Feyissa D,Kangasjärvi S,Lillo C Antagonistic regulation of flowering time through distinct regulatory subunits of protein phosphatase 2A. PLoS ONE, 2013. 8(7): p. e67987 [PMID:23976921] Ding Y, et al. Four distinct types of dehydration stress memory genes in Arabidopsis thaliana. BMC Plant Biol., 2013. 13: p. 229 [PMID:24377444] Crevillén P, et al. Epigenetic reprogramming that prevents transgenerational inheritance of the vernalized state. Nature, 2014. 515(7528): p. 587-90 [PMID:25219852] Yang H,Howard M,Dean C Physical coupling of activation and derepression activities to maintain an active transcriptional state at FLC. Proc. Natl. Acad. Sci. U.S.A., 2016. 113(33): p. 9369-74 [PMID:27482092]