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

Thecc1EG008374t2

Common Name

TCM_008374

Organism

Theobroma cacao

Taxonomic ID

3641

Taxonomic Lineage

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

Family

ARF

Protein Properties

Length: 818aa MW: 91270.1 Da PI: 6.7467

Description

ARF family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Thecc1EG008374t2	genome	CGD	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	B3	74.8	1e-23	140	241	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+e+ + k++ +++l+ +d++g++W++++i+r++++r++l++GW+ Fv++++L +gD ++F + Thecc1EG008374t2 140 FCKTLTASDTSTHGGFSVLRRHADEClppldmS-KQPPTQELVAKDLHGNEWRFRHIFRGQPRRHLLQSGWSLFVSSKKLVAGDAFIFL--RG 229 99***************************63.4445569********************************************..44 PP SEE..EEEEE-S CS B3 88 sefelvvkvfrk 99 +++el+v+v+r+ Thecc1EG008374t2 230 ETGELRVGVRRA 241 9999***996 PP
2	Auxin_resp	116.1	3.1e-38	266	348	1	83
Auxin_resp 1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsLk 83 a+ha+st+++F+v+Y+Pr+s++eF+v+++k+++++k+++s+G Rfkm+fe+e+++e+r+sG v+g +d+dp+rWp+SkWr+Lk Thecc1EG008374t2 266 AWHAVSTGTMFTVYYKPRTSPAEFIVPFHKYMESIKNNYSIGLRFKMRFEGEEAPEQRFSGSVIGYEDADPIRWPGSKWRCLK 348 89*******************************************************************************96 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Gene3D	G3DSA:2.40.330.10	9.5E-41	134	255	IPR015300	DNA-binding pseudobarrel domain
SuperFamily	SSF101936	7.72E-39	136	269	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	5.24E-21	138	240	No hit	No description
SMART	SM01019	5.6E-23	140	242	IPR003340	B3 DNA binding domain
PROSITE profile	PS50863	11.843	140	242	IPR003340	B3 DNA binding domain
Pfam	PF02362	9.7E-22	140	241	IPR003340	B3 DNA binding domain
Pfam	PF06507	7.9E-36	266	348	IPR010525	Auxin response factor
PROSITE profile	PS51745	22.345	698	792	IPR000270	PB1 domain
SuperFamily	SSF54277	9.81E-9	700	776	No hit	No description
Pfam	PF02309	1.9E-5	746	784	IPR033389	AUX/IAA domain

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0006355	Biological Process	regulation of transcription, DNA-templated
GO:0009734	Biological Process	auxin-activated signaling pathway
GO:0005634	Cellular Component	nucleus
GO:0003677	Molecular Function	DNA binding
GO:0005515	Molecular Function	protein binding

Sequence ? help Back to Top
Protein Sequence Length: 818 aa Download sequence Send to blast
MDYNDAAMAT HGSAPSVTCK KSIGYGAVDS GDELYRELWH ACAGPLATVP RQGDLVFYFL 60 QGHIEQVEAS RNQVSDQQTP AYDLPPKILC RVVNVQFKAE SDTDEVFAQV SLLPLPKQDE 120 NSVEKEGELP PAQRARVHSF CKTLTASDTS THGGFSVLRR HADECLPPLD MSKQPPTQEL 180 VAKDLHGNEW RFRHIFRGQP RRHLLQSGWS LFVSSKKLVA GDAFIFLRGE TGELRVGVRR 240 AMRQASNVSS SVISSQSMHI GVLATAWHAV STGTMFTVYY KPRTSPAEFI VPFHKYMESI 300 KNNYSIGLRF KMRFEGEEAP EQRFSGSVIG YEDADPIRWP GSKWRCLKVH WDETSPFHRP 360 DRVSPWKVEP ALPPAVDVLP NSRLKRSHAN VASSPSDSLV LTREGSSKTT MDSSLDNGFR 420 RTLQGQKSLS QRDTLAESKY PSEGQDQTEM GFGKQRLAPQ DTLPQVIHGE KSTSPTPVSW 480 TLQKLYKFGQ PSVEQNSSNI DQLKTDIFDK GHLFELPGCP QTMMHSSASV NLLGAEEKKL 540 NYQDYFPVRP GAVEGYNRPH GSDFQQQPGK WLLPLLPITH SGKLPPVDIL NSQPLSSQLK 600 DNVKSEGDGI CKLFGISLVS NTMPTELSVP HTKSIPKPLR QIASDHPQDS GCDLMLEQSK 660 CSKFDEIALG DDEEGKPVHT SEELPGDILR KFQGGSARTC IKVVHKQGIA VGRSVDLTKF 720 NGYDELIAEL DRTFEFDGEL ISPNKKWLVV FTDDEDDMML VGDDPWKEFC TMVRRIFIYT 780 GEEIKRMDAR PFNPKVEENS PGKDQKTNLM HRASVSG*

Sequence ? help Back to Top

Protein Sequence Length: 818 aa Download sequence Send to blast

MDYNDAAMAT HGSAPSVTCK KSIGYGAVDS GDELYRELWH ACAGPLATVP RQGDLVFYFL  60
QGHIEQVEAS RNQVSDQQTP AYDLPPKILC RVVNVQFKAE SDTDEVFAQV SLLPLPKQDE  120
NSVEKEGELP PAQRARVHSF CKTLTASDTS THGGFSVLRR HADECLPPLD MSKQPPTQEL  180
VAKDLHGNEW RFRHIFRGQP RRHLLQSGWS LFVSSKKLVA GDAFIFLRGE TGELRVGVRR  240
AMRQASNVSS SVISSQSMHI GVLATAWHAV STGTMFTVYY KPRTSPAEFI VPFHKYMESI  300
KNNYSIGLRF KMRFEGEEAP EQRFSGSVIG YEDADPIRWP GSKWRCLKVH WDETSPFHRP  360
DRVSPWKVEP ALPPAVDVLP NSRLKRSHAN VASSPSDSLV LTREGSSKTT MDSSLDNGFR  420
RTLQGQKSLS QRDTLAESKY PSEGQDQTEM GFGKQRLAPQ DTLPQVIHGE KSTSPTPVSW  480
TLQKLYKFGQ PSVEQNSSNI DQLKTDIFDK GHLFELPGCP QTMMHSSASV NLLGAEEKKL  540
NYQDYFPVRP GAVEGYNRPH GSDFQQQPGK WLLPLLPITH SGKLPPVDIL NSQPLSSQLK  600
DNVKSEGDGI CKLFGISLVS NTMPTELSVP HTKSIPKPLR QIASDHPQDS GCDLMLEQSK  660
CSKFDEIALG DDEEGKPVHT SEELPGDILR KFQGGSARTC IKVVHKQGIA VGRSVDLTKF  720
NGYDELIAEL DRTFEFDGEL ISPNKKWLVV FTDDEDDMML VGDDPWKEFC TMVRRIFIYT  780
GEEIKRMDAR PFNPKVEENS PGKDQKTNLM HRASVSG*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4ldv_A	1e-163	32	370	17	354	Auxin response factor 1
4ldw_A	1e-163	32	370	17	354	Auxin response factor 1
4ldw_B	1e-163	32	370	17	354	Auxin response factor 1
4ldx_A	1e-163	32	370	17	354	Auxin response factor 1
4ldx_B	1e-163	32	370	17	354	Auxin response factor 1
Search in ModeBase

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) (By similarity). Could act as transcriptional activator or repressor (PubMed:26959229, PubMed:26716451, PubMed:27645097, PubMed:28167023). Involved in the control of fruit ripening process (PubMed:26959229, PubMed:26716451, PubMed:28167023). Regulates expression of a number of ripening regulators, transcription factors, and ethylene biosynthesis and signaling components (PubMed:26959229, PubMed:26716451). May act as a transcriptional repressor of auxin-responsive genes (PubMed:26716451). Regulates vegetative growth, lateral root formation and flower organ senescence, possibly partially by regulating gene expression of auxin and ethylene response factor (ERF) genes (PubMed:28167023). Plays a negative role in axillary shoot meristem formation (PubMed:27645097). {ECO:0000255\|RuleBase:RU004561, ECO:0000269\|PubMed:26716451, ECO:0000269\|PubMed:26959229, ECO:0000269\|PubMed:27645097, ECO:0000269\|PubMed:28167023}.

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: By tomato fruit ripening. Expression in tomato fruits is up-regulated by exogenous application of ethylene and down-regulated by inhibition of ethylene receptors with 1-methylcyclopropene (1-MCP) (PubMed:26959229, PubMed:26716451). Up-regulated by plant hormone abscisic acid (ABA) in tomato fruits (PubMed:26959229). Expression is not up-regulated by plant hormone auxin in tomato fruits (PubMed:26716451). Up-regulated by auxin and gibberellic acid (GA), and down-regulated by ethylene in seedlings (PubMed:28167023). Down-regulated during decapitation-induced axillary shoot development and by excision of immature leaves. Down-regulation is inhibited by the application of auxin on the cut surface (PubMed:27645097). {ECO:0000269\|PubMed:26716451, ECO:0000269\|PubMed:26959229, ECO:0000269\|PubMed:27645097, ECO:0000269\|PubMed:28167023}.

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_017971698.1	0.0	PREDICTED: auxin response factor 2
Swissprot	Q2LAJ3	0.0	ARF2A_SOLLC; Auxin response factor 2A
TrEMBL	A0A061E5N3	0.0	A0A061E5N3_THECC; Auxin response factor
STRING	EOX99641	0.0	(Theobroma cacao)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM5348	26	47

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT5G62000.4	0.0	auxin response factor 2

Link Out ? help Back to Top
Phytozome	Thecc1EG008374t2
Entrez Gene	18608851

Publications ? help Back to Top
Tomato Genome Consortium The tomato genome sequence provides insights into fleshy fruit evolution. Nature, 2012. 485(7400): p. 635-41 [PMID:22660326] Motamayor JC, et al. The genome sequence of the most widely cultivated cacao type and its use to identify candidate genes regulating pod color. Genome Biol., 2013. 14(6): p. r53 [PMID:23731509] Breitel DA, et al. AUXIN RESPONSE FACTOR 2 Intersects Hormonal Signals in the Regulation of Tomato Fruit Ripening. PLoS Genet., 2016. 12(3): p. e1005903 [PMID:26959229] Xu T, et al. SlARF2a plays a negative role in mediating axillary shoot formation. Sci Rep, 2016. 6: p. 33728 [PMID:27645097] Ren Z,Liu R,Gu W,Dong X The Solanum lycopersicum auxin response factor SlARF2 participates in regulating lateral root formation and flower organ senescence. Plant Sci., 2017. 256: p. 103-111 [PMID:28167023]