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

Carubv10022415m

Common Name

CARUB_v10022415mg

Organism

Capsella rubella

Taxonomic ID

81985

Taxonomic Lineage

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

Family

ARF

Protein Properties

Length: 666aa MW: 73854.9 Da PI: 5.9786

Description

ARF family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Carubv10022415m	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	B3	68.8	7.6e-22	124	225	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+++++W +++i+r++++r++lt+GW+ Fv++++L +gD ++F + Carubv10022415m 124 FCKTLTASDTSTHGGFSVLRRHADDClppldmsQQP--PWQELVATDLHNNEWHFRHIFRGQPRRHLLTTGWSVFVSSKKLVAGDAFIFL--RG 213 99**************************964333..4459********************************************..34 PP SEE..EEEEE-S CS B3 88 sefelvvkvfrk 99 +++el+v+v+r+ Carubv10022415m 214 ENEELRVGVRRH 225 88889**996 PP
2	Auxin_resp	112.3	4.7e-37	250	332	1	83
Auxin_resp 1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsLk 83 aaha++t+++F+v+Y+Pr+s+seF+v+v+++++a ++k+svGmRfkm+fe+e+++e+r+sGt+vgv++ +++ W++S+WrsLk Carubv10022415m 250 AAHAITTGTIFSVFYKPRTSRSEFIVSVNRYLEAKTQKLSVGMRFKMRFEGEEAPEKRFSGTIVGVQENKSSVWHDSEWRSLK 332 79*******************************************************************************96 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF101936	3.53E-44	113	253	IPR015300	DNA-binding pseudobarrel domain
Gene3D	G3DSA:2.40.330.10	4.1E-40	121	239	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	1.88E-19	122	224	No hit	No description
Pfam	PF02362	1.1E-19	124	225	IPR003340	B3 DNA binding domain
SMART	SM01019	4.9E-21	124	226	IPR003340	B3 DNA binding domain
PROSITE profile	PS50863	10.588	124	226	IPR003340	B3 DNA binding domain
Pfam	PF06507	3.5E-34	250	332	IPR010525	Auxin response factor
Pfam	PF02309	2.7E-11	537	632	IPR033389	AUX/IAA domain
PROSITE profile	PS51745	30.558	542	635	IPR000270	PB1 domain
SuperFamily	SSF54277	1.44E-11	544	619	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: 666 aa Download sequence Send to blast
MAATNPSSEK PGGVLSDALC RELWHACAGP LVTLPREGER VYYFPEGHME QLEASMHQGL 60 EQQMPSFNLP SKILCKVINI QRRAEPETDE VYAQITLLPE LDQSEPISPD APVQEPEKCT 120 VHSFCKTLTA SDTSTHGGFS VLRRHADDCL PPLDMSQQPP WQELVATDLH NNEWHFRHIF 180 RGQPRRHLLT TGWSVFVSSK KLVAGDAFIF LRGENEELRV GVRRHMRQQT NVPSSVISSH 240 SMHIGVLATA AHAITTGTIF SVFYKPRTSR SEFIVSVNRY LEAKTQKLSV GMRFKMRFEG 300 EEAPEKRFSG TIVGVQENKS SVWHDSEWRS LKVQWDEPSS VFRPERVSPW ELEPLVANST 360 PSSQPQPPQR NKRPRPPGLP APTTGPSAAV TPDSVWKSPA DTPSSVPLFS PPAKAAMFGP 420 GGNKSFGVSI GSAFWPTHAD SAAESFASAF NNESTEKKQT NGNVCRLFGF ELVENVNVDE 480 CFSAASVSGA VAVDQPVPSN EFDSGQQSEP LNINQSDIPS GSGDPEKSSL RSPQESQSRQ 540 IRSCTKVHMQ GSAVGRAVDL TRSECYEDLF KKLEEMFDIK GELIESTKKW QVVYTDDEDD 600 MMMVGDDPWN EFCGMVRKIF IYTPEEVKKL SPKNKLTVNA RMQPKNDVEE NGNTEGRSSS 660 MAGSR*

Sequence ? help Back to Top

Protein Sequence Length: 666 aa Download sequence Send to blast

MAATNPSSEK PGGVLSDALC RELWHACAGP LVTLPREGER VYYFPEGHME QLEASMHQGL  60
EQQMPSFNLP SKILCKVINI QRRAEPETDE VYAQITLLPE LDQSEPISPD APVQEPEKCT  120
VHSFCKTLTA SDTSTHGGFS VLRRHADDCL PPLDMSQQPP WQELVATDLH NNEWHFRHIF  180
RGQPRRHLLT TGWSVFVSSK KLVAGDAFIF LRGENEELRV GVRRHMRQQT NVPSSVISSH  240
SMHIGVLATA AHAITTGTIF SVFYKPRTSR SEFIVSVNRY LEAKTQKLSV GMRFKMRFEG  300
EEAPEKRFSG TIVGVQENKS SVWHDSEWRS LKVQWDEPSS VFRPERVSPW ELEPLVANST  360
PSSQPQPPQR NKRPRPPGLP APTTGPSAAV TPDSVWKSPA DTPSSVPLFS PPAKAAMFGP  420
GGNKSFGVSI GSAFWPTHAD SAAESFASAF NNESTEKKQT NGNVCRLFGF ELVENVNVDE  480
CFSAASVSGA VAVDQPVPSN EFDSGQQSEP LNINQSDIPS GSGDPEKSSL RSPQESQSRQ  540
IRSCTKVHMQ GSAVGRAVDL TRSECYEDLF KKLEEMFDIK GELIESTKKW QVVYTDDEDD  600
MMMVGDDPWN EFCGMVRKIF IYTPEEVKKL SPKNKLTVNA RMQPKNDVEE NGNTEGRSSS  660
MAGSR*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4ldv_A	0.0	1	359	1	359	Auxin response factor 1
4ldw_A	0.0	1	359	1	359	Auxin response factor 1
4ldw_B	0.0	1	359	1	359	Auxin response factor 1
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Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	371	375	KRPRP

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

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Carubv10022415m

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

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AK317214	0.0	AK317214.1 Arabidopsis thaliana AT1G59750 mRNA, complete cds, clone: RAFL22-03-B07.
GenBank	ATU83245	0.0	U83245.1 Arabidopsis thaliana auxin response factor 1 (ARF1) mRNA, complete cds.
GenBank	BT002748	0.0	BT002748.1 Arabidopsis thaliana clone C105458 auxin response factor 1 (At1g59750) mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_006300434.1	0.0	auxin response factor 1 isoform X1
Refseq	XP_023644040.1	0.0	auxin response factor 1 isoform X1
Refseq	XP_023644041.1	0.0	auxin response factor 1 isoform X1
Swissprot	Q8L7G0	0.0	ARFA_ARATH; Auxin response factor 1
TrEMBL	R0GC66	0.0	R0GC66_9BRAS; Auxin response factor
STRING	XP_006300434.1	0.0	(Capsella rubella)

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
AT1G59750.3	0.0	auxin response factor 1

Link Out ? help Back to Top
Phytozome	Carubv10022415m
Entrez Gene	17895753

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]