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

Ciclev10000491m

Common Name

CICLE_v10000491mg

Organism

Citrus clementina

Taxonomic ID

85681

Taxonomic Lineage

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

Family

ARF

Protein Properties

Length: 683aa MW: 75901.4 Da PI: 6.2389

Description

ARF family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Ciclev10000491m	genome	ICGC	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	B3	71.2	1.3e-22	131	232	1	99
EEEE-..-HHHHTT-EE--HHH.HTT.......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SS CS B3 1 ffkvltpsdvlksgrlvlpkkfaeeh.......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgr 87 f+k+lt sd++++g +++ +++a+++ +++ ++l+ +d++g++W +++i+r++++r++lt+GW+ Fv++++L +gD ++F + Ciclev10000491m 131 FCKTLTASDTSTHGGFSVLRRHADDClppldmsQQP--PWQELVATDLHGNEWHFRHIFRGQPRRHLLTTGWSVFVSSKKLVAGDAFIFL--RG 220 99**************************964333..4459********************************************..34 PP SEE..EEEEE-S CS B3 88 sefelvvkvfrk 99 +++el+v+v+r+ Ciclev10000491m 221 ENEELRVGVRRH 232 88889**996 PP
2	Auxin_resp	111.8	6.8e-37	257	339	1	83
Auxin_resp 1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsLk 83 a+ha++t++ F+++Y+Pr+s+seF+v+v+k+++a ++k+svGmRfkm fe+e+++err+sGt+vgv d+ ++ W++S+WrsLk Ciclev10000491m 257 ASHAIATGTLFSIFYKPRTSRSEFIVSVNKYLEAKRHKLSVGMRFKMTFEGEEVPERRFSGTIVGVGDCRSSVWQDSEWRSLK 339 789******************************************************************************96 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF101936	3.79E-44	121	260	IPR015300	DNA-binding pseudobarrel domain
Gene3D	G3DSA:2.40.330.10	3.6E-41	128	246	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	2.42E-20	129	231	No hit	No description
SMART	SM01019	3.1E-22	131	233	IPR003340	B3 DNA binding domain
Pfam	PF02362	1.9E-20	131	232	IPR003340	B3 DNA binding domain
PROSITE profile	PS50863	11.124	131	233	IPR003340	B3 DNA binding domain
Pfam	PF06507	1.1E-34	257	339	IPR010525	Auxin response factor
Pfam	PF02309	2.4E-12	555	648	IPR033389	AUX/IAA domain
PROSITE profile	PS51745	28.221	558	651	IPR000270	PB1 domain
SuperFamily	SSF54277	6.15E-12	560	635	No hit	No description

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0009734	Biological Process	auxin-activated signaling pathway
GO:0010150	Biological Process	leaf senescence
GO:0045892	Biological Process	negative regulation of transcription, DNA-templated
GO:0005634	Cellular Component	nucleus
GO:0003677	Molecular Function	DNA binding
GO:0042802	Molecular Function	identical protein binding

Sequence ? help Back to Top
Protein Sequence Length: 683 aa Download sequence Send to blast
MAFAAAAAPL NHASGGPRTG GSNDALYREL WHACAGPLVT LPREGERVYY FPQGHMEQLE 60 ASMHQGLEQQ MPSFNLPSKI LCKVVNVQRR AEPETDEVYA QITLLPEPDQ SEVTSPDPPI 120 PEPEKCTVHS FCKTLTASDT STHGGFSVLR RHADDCLPPL DMSQQPPWQE LVATDLHGNE 180 WHFRHIFRGQ PRRHLLTTGW SVFVSSKKLV AGDAFIFLRG ENEELRVGVR RHMRQQTNMP 240 SSVISSHSMH LGVLATASHA IATGTLFSIF YKPRTSRSEF IVSVNKYLEA KRHKLSVGMR 300 FKMTFEGEEV PERRFSGTIV GVGDCRSSVW QDSEWRSLKV QWDEPSSILR PERVSSWELE 360 PLVATTTTTN AQPAQRNKRS RPPVLPSPAA DISVLGMWKS HVESSAFSYC DSPQGRDLYP 420 SPKFSTATKG NHFGLSGNKS LAAVSSNSMY WPNRAENVTE SFAPVVNKEC SEKRQGNGNT 480 CRLFGIQLVD NSNVEEASPA FTMSGAMGDD RAIPCLDADS DQHSEPSNIN RSDVPSVSCD 540 AEKSCLRSPQ ESQSRQIRSC TKVHMQGIAV GRAVDLTRFD CYEDLLKKLE EMFDIEGDLC 600 GSTKKWQVVY TDDEDDMMMV GDDPWHEFCS MVRKIFIYTA EEVKKLSPKV KLPGNEELNA 660 GKPDVEVVVN TDDRSSIVGP GC*

Sequence ? help Back to Top

Protein Sequence Length: 683 aa Download sequence Send to blast

MAFAAAAAPL NHASGGPRTG GSNDALYREL WHACAGPLVT LPREGERVYY FPQGHMEQLE  60
ASMHQGLEQQ MPSFNLPSKI LCKVVNVQRR AEPETDEVYA QITLLPEPDQ SEVTSPDPPI  120
PEPEKCTVHS FCKTLTASDT STHGGFSVLR RHADDCLPPL DMSQQPPWQE LVATDLHGNE  180
WHFRHIFRGQ PRRHLLTTGW SVFVSSKKLV AGDAFIFLRG ENEELRVGVR RHMRQQTNMP  240
SSVISSHSMH LGVLATASHA IATGTLFSIF YKPRTSRSEF IVSVNKYLEA KRHKLSVGMR  300
FKMTFEGEEV PERRFSGTIV GVGDCRSSVW QDSEWRSLKV QWDEPSSILR PERVSSWELE  360
PLVATTTTTN AQPAQRNKRS RPPVLPSPAA DISVLGMWKS HVESSAFSYC DSPQGRDLYP  420
SPKFSTATKG NHFGLSGNKS LAAVSSNSMY WPNRAENVTE SFAPVVNKEC SEKRQGNGNT  480
CRLFGIQLVD NSNVEEASPA FTMSGAMGDD RAIPCLDADS DQHSEPSNIN RSDVPSVSCD  540
AEKSCLRSPQ ESQSRQIRSC TKVHMQGIAV GRAVDLTRFD CYEDLLKKLE EMFDIEGDLC  600
GSTKKWQVVY TDDEDDMMMV GDDPWHEFCS MVRKIFIYTA EEVKKLSPKV KLPGNEELNA  660
GKPDVEVVVN TDDRSSIVGP GC*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4ldv_A	0.0	8	362	2	355	Auxin response factor 1
4ldw_A	0.0	8	362	2	355	Auxin response factor 1
4ldw_B	0.0	8	362	2	355	Auxin response factor 1
4ldx_A	0.0	8	362	2	355	Auxin response factor 1
4ldx_B	0.0	8	362	2	355	Auxin response factor 1
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Expression -- Description ? help Back to Top
Source	Description
Uniprot	DEVELOPMENTAL STAGE: Expressed in the sepals and carpels of young flower buds. At stage 10 of flower development, expression in the carpels becomes restricted to the style. Also expressed in anthers and filaments. At stage 13, expressed in the region at the top of the pedicel, including the abscission zone. {ECO:0000269\|PubMed:16176952}.
Uniprot	TISSUE SPECIFICITY: Expressed in the whole plant. {ECO:0000269\|PubMed:10476078}.

Functional Description ? help Back to Top
Source	Description
UniProt	Auxin response factors (ARFs) are transcriptional factors that bind specifically to the DNA sequence 5'-TGTCTC-3' found in the auxin-responsive promoter elements (AuxREs). Seems to act as transcriptional repressor. Formation of heterodimers with Aux/IAA proteins may alter their ability to modulate early auxin response genes expression. Promotes flowering, stamen development, floral organ abscission and fruit dehiscence. Acts as repressor of IAA2, IAA3 and IAA7. {ECO:0000269\|PubMed:12036261, ECO:0000269\|PubMed:16176952}.

Binding Motif ? help Back to Top
Motif ID	Method	Source	Motif file
MP00097	PBM	Transfer from AT1G59750	Download

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

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_006431443.1	0.0	auxin response factor 1 isoform X1
Refseq	XP_024039738.1	0.0	auxin response factor 1 isoform X1
Refseq	XP_024039739.1	0.0	auxin response factor 1 isoform X1
Swissprot	Q8L7G0	0.0	ARFA_ARATH; Auxin response factor 1
TrEMBL	V4SAY2	0.0	V4SAY2_9ROSI; Auxin response factor
STRING	XP_006431443.1	0.0	(Citrus clementina)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM8825	22	27

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT1G59750.4	0.0	auxin response factor 1

Link Out ? help Back to Top
Phytozome	Ciclev10000491m
Entrez Gene	18040560

Publications ? help Back to Top
Montesinos JC,Pastor-Cantizano N,Robinson DG,Marcote MJ,Aniento F Arabidopsis p24δ5 and p24δ9 facilitate Coat Protein I-dependent transport of the K/HDEL receptor ERD2 from the Golgi to the endoplasmic reticulum. Plant J., 2014. 80(6): p. 1014-30 [PMID:25312353] Marais C, et al. The Qb-SNARE Memb11 interacts specifically with Arf1 in the Golgi apparatus of Arabidopsis thaliana. J. Exp. Bot., 2015. 66(21): p. 6665-78 [PMID:26208648] Wójcikowska B,Gaj MD Expression profiling of AUXIN RESPONSE FACTOR genes during somatic embryogenesis induction in Arabidopsis. Plant Cell Rep., 2017. 36(6): p. 843-858 [PMID:28255787] Zhang M,Hu X,Zhu M,Xu M,Wang L Transcription factors NF-YA2 and NF-YA10 regulate leaf growth via auxin signaling in Arabidopsis. Sci Rep, 2017. 7(1): p. 1395 [PMID:28469131]