PlantTFDB - Plant Transcription Factor Database @ CBI, PKU

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

Family

RAV

Protein Properties

Length: 372aa MW: 41069.5 Da PI: 9.9591

Description

RAV family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
XP_009115339.1	genome	NCBI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	AP2	39.8	1.1e-12	68	116	1	55
AP2 1 sgykGVrwdkkrgrWvAeIrdpsengkrkrfslgkfgtaeeAakaaiaarkkleg 55 s++kGV + +grW A+I++ ++r++lg+f +eeAa+ ++ a+++++g XP_009115339.1 68 SKFKGVVPQP-NGRWGAQIYEK-----HQRVWLGTFNEEEEAAASYDIAARRFRG 116 79**9888.8*****3.....5***********************98 PP
2	B3	101.3	5.4e-32	196	305	1	95
EEEE-..-HHHHTT-EE--HHH.HTT...............---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EE CS B3 1 ffkvltpsdvlksgrlvlpkkfaeeh...............ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfv 80 f+k+ tpsdv+k++rlv+pk++ae+h ++++++ + led++g++W+++++y+++s++yvltkGW++Fvk+++L++gD+v XP_009115339.1 196 FEKAVTPSDVGKLNRLVIPKQHAEKHfplpamttatvvtamTPSPTKGVLINLEDRTGKVWRFRYSYWNSSQSYVLTKGWSRFVKEKNLRAGDVV 290 89**************************999999999985567799******************************************* PP EEEE-SSSEE..EEE CS B3 81 vFkldgrsefelvvk 95 F+++ +++l++ XP_009115339.1 291 CFERSTGPDRQLYID 305 *876677767665 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
CDD	cd00018	1.50E-24	68	123	No hit	No description
SuperFamily	SSF54171	3.33E-16	68	124	IPR016177	DNA-binding domain
Pfam	PF00847	8.4E-7	68	116	IPR001471	AP2/ERF domain
PROSITE profile	PS51032	19.454	69	124	IPR001471	AP2/ERF domain
SMART	SM00380	6.5E-28	69	130	IPR001471	AP2/ERF domain
Gene3D	G3DSA:3.30.730.10	1.5E-19	69	124	IPR001471	AP2/ERF domain
Gene3D	G3DSA:2.40.330.10	3.3E-40	190	312	IPR015300	DNA-binding pseudobarrel domain
SuperFamily	SSF101936	4.58E-31	194	300	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	1.34E-28	195	295	No hit	No description
SMART	SM01019	1.1E-24	196	310	IPR003340	B3 DNA binding domain
PROSITE profile	PS50863	13.803	196	310	IPR003340	B3 DNA binding domain
Pfam	PF02362	1.1E-28	196	305	IPR003340	B3 DNA binding domain

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0006355	Biological Process	regulation of transcription, DNA-templated
GO:0048573	Biological Process	photoperiodism, flowering
GO:0003677	Molecular Function	DNA binding
GO:0003700	Molecular Function	transcription factor activity, sequence-specific DNA binding

Sequence ? help Back to Top
Protein Sequence Length: 372 aa Download sequence Send to blast
MDNSCIDDST SNTSGSLSTS TLSAKKKLSP PPPPPATMRL YRMGSGGSSV VLDSENGVET 60 ESRKLPSSKF KGVVPQPNGR WGAQIYEKHQ RVWLGTFNEE EEAAASYDIA ARRFRGRDAV 120 TNFKSPALDG TDAESAFLEA HSKAEIVDML RKHTYADELQ QSKRKFLDGN GKRCGSGTAA 180 MSKGNDGVSR AREVLFEKAV TPSDVGKLNR LVIPKQHAEK HFPLPAMTTA TVVTAMTPSP 240 TKGVLINLED RTGKVWRFRY SYWNSSQSYV LTKGWSRFVK EKNLRAGDVV CFERSTGPDR 300 QLYIDWKVQS GKEEITPVQS VVRLFGVNIF NETTNAKPND VAVECGGKKR SREVDLFALG 360 CSKKQTMMIN AL

Sequence ? help Back to Top

Protein Sequence Length: 372 aa Download sequence Send to blast

MDNSCIDDST SNTSGSLSTS TLSAKKKLSP PPPPPATMRL YRMGSGGSSV VLDSENGVET  60
ESRKLPSSKF KGVVPQPNGR WGAQIYEKHQ RVWLGTFNEE EEAAASYDIA ARRFRGRDAV  120
TNFKSPALDG TDAESAFLEA HSKAEIVDML RKHTYADELQ QSKRKFLDGN GKRCGSGTAA  180
MSKGNDGVSR AREVLFEKAV TPSDVGKLNR LVIPKQHAEK HFPLPAMTTA TVVTAMTPSP  240
TKGVLINLED RTGKVWRFRY SYWNSSQSYV LTKGWSRFVK EKNLRAGDVV CFERSTGPDR  300
QLYIDWKVQS GKEEITPVQS VVRLFGVNIF NETTNAKPND VAVECGGKKR SREVDLFALG  360
CSKKQTMMIN AL

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
1wid_A	2e-57	193	313	11	121	DNA-binding protein RAV1
Search in ModeBase

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
Bra.5517	0.0	leaf\| root

Expression -- Description ? help Back to Top
Source	Description
Uniprot	TISSUE SPECIFICITY: Expressed in leaves. {ECO:0000269\|PubMed:18718758}.

Functional Description ? help Back to Top
Source	Description
UniProt	Transcriptional repressor of flowering time on long day plants. Acts directly on FT expression by binding 5'-CAACA-3' and 5'-CACCTG-3 sequences. Functionally redundant with TEM2. {ECO:0000269\|PubMed:18718758}.

Binding Motif ? help Back to Top
Motif ID	Method	Source	Motif file
MP00024	PBM	Transfer from AT1G25560	Download

Cis-element ? help Back to Top
Source	Link
PlantRegMap	XP_009115339.1

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: Expressed with a circadian rhythm showing a peak at dawn. {ECO:0000269\|PubMed:18718758}.

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_009115339.1	0.0	PREDICTED: AP2/ERF and B3 domain-containing transcription repressor TEM1-like
Swissprot	Q9C6M5	0.0	RAVL1_ARATH; AP2/ERF and B3 domain-containing transcription repressor TEM1
TrEMBL	M4E7I0	0.0	M4E7I0_BRARP; Uncharacterized protein
STRING	Bra024735.1-P	0.0	(Brassica rapa)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM848	27	121

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT1G25560.1	0.0	RAV family protein

Publications ? help Back to Top
Ding Y, et al. Four distinct types of dehydration stress memory genes in Arabidopsis thaliana. BMC Plant Biol., 2013. 13: p. 229 [PMID:24377444] Choi D, et al. iNID: an analytical framework for identifying network models for interplays among developmental signaling in Arabidopsis. Mol Plant, 2014. 7(5): p. 792-813 [PMID:24380880] Sgamma T,Jackson A,Muleo R,Thomas B,Massiah A TEMPRANILLO is a regulator of juvenility in plants. Sci Rep, 2014. 4: p. 3704 [PMID:24424565] Matías-Hernández L,Aguilar-Jaramillo AE,Marín-González E,Suárez-López P,Pelaz S RAV genes: regulation of floral induction and beyond. Ann. Bot., 2014. 114(7): p. 1459-70 [PMID:24812253] Marín-González E, et al. SHORT VEGETATIVE PHASE Up-Regulates TEMPRANILLO2 Floral Repressor at Low Ambient Temperatures. Plant Physiol., 2015. 169(2): p. 1214-24 [PMID:26243615] Matías-Hernández L, et al. TEMPRANILLO Reveals the Mesophyll as Crucial for Epidermal Trichome Formation. Plant Physiol., 2016. 170(3): p. 1624-39 [PMID:26802039]