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

RrC283_p9

Organism

Raphanus raphanistrum

Taxonomic ID

109996

Taxonomic Lineage

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

Family

MYB_related

Protein Properties

Length: 693aa MW: 76302.1 Da PI: 5.8572

Description

MYB_related family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
RrC283_p9	genome	MSU	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	Myb_DNA-binding	28.2	4.5e-09	40	81	1	47
TSSS-HHHHHHHHHHHHHTTTT-HHHHHHHHTTTS-HHHHHHHHHHH CS Myb_DNA-binding 1 rgrWTteEdellvdavkqlGggtWktIartmgkgRtlkqcksrwqky 47 r +WT+ E++++++a +++ + Wk+I +g k ++s+ qky RrC283_p9 40 RESWTEGEHDKFLEALQLFDRD-WKKIEDFVG-S---KTIRSHAQKY 81 789***************77.*****.5...566***99 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF46689	1.05E-11	34	87	IPR009057	Homeodomain-like
PROSITE profile	PS51294	11.219	35	86	IPR017930	Myb domain
TIGRFAMs	TIGR01557	1.2E-14	38	84	IPR006447	Myb domain, plants
SMART	SM00717	1.3E-4	39	84	IPR001005	SANT/Myb domain
Pfam	PF00249	8.2E-7	40	81	IPR001005	SANT/Myb domain
CDD	cd00167	1.22E-4	42	82	No hit	No description
Pfam	PF10018	4.3E-11	413	559	IPR019258	Mediator complex, subunit Med4

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0006357	Biological Process	regulation of transcription from RNA polymerase II promoter
GO:0016592	Cellular Component	mediator complex
GO:0001104	Molecular Function	RNA polymerase II transcription cofactor activity
GO:0003677	Molecular Function	DNA binding

Sequence ? help Back to Top
Protein Sequence Length: 693 aa Download sequence Send to blast
MTSSSSLSSN PVVAEERPST DLTETTTTTV RKAYTITKSR ESWTEGEHDK FLEALQLFDR 60 DWKKIEDFVG SKTIRSHAQK YFLKVQKNGT LAHVPPPRPK RKAAHPYPQK ASKNAQMSLH 120 VSMAFPTQIN NVPGYTSWDD DTSALLNIAV VLPKDELATL CLPDFAEVYN FIGSVFDPDI 180 KGRMKKLKEM DPINFETVLL LMRNLTVNLA NPDFEPARGS AGTLVKNQTS DISSWELLAH 240 NNCSISYQEV LRCTLPRLFS NFSPAAKMLQ HQIGQSPARL GLTGPGSPSV QNLTPSRHGH 300 PTSSSSSQSH HHQQQIQQPP PNLPPSSSAV AASASSSTAI SSSALLSLLP PLPRAQALLQ 360 QMAVLSSKLF DVSPNRAHWL SAFRGSLPSF LSSHSLPPPP PLENPNPSST KEILSQFNSL 420 QTQLFEAVTE LQEILDLQDA KQKLAREIKS KDSSLLAFAN KLKEAERVLD MLVDDYSDYR 480 KPKRTKTVAE DDDDDEDSSS STTTVSSQIK LKDILAYAHK ISYTTFAPPE FGAGQAPLRG 540 ALPPAPQDEQ MRASQLYAFA DLDIGLPKTV ENIEKKVEAL IEPPPPPPDL SAIQGMLPQN 600 IAVPSGWKPG MPVELPKDWR LPPPPPGWKP GDPVVLPPEL VPPPRAQEQQ QQVRPPQGLH 660 RPPDVIHVRE VQLDILEDDS SEYSSEDSSD DEE

Sequence ? help Back to Top

Protein Sequence Length: 693 aa Download sequence Send to blast

MTSSSSLSSN PVVAEERPST DLTETTTTTV RKAYTITKSR ESWTEGEHDK FLEALQLFDR  60
DWKKIEDFVG SKTIRSHAQK YFLKVQKNGT LAHVPPPRPK RKAAHPYPQK ASKNAQMSLH  120
VSMAFPTQIN NVPGYTSWDD DTSALLNIAV VLPKDELATL CLPDFAEVYN FIGSVFDPDI  180
KGRMKKLKEM DPINFETVLL LMRNLTVNLA NPDFEPARGS AGTLVKNQTS DISSWELLAH  240
NNCSISYQEV LRCTLPRLFS NFSPAAKMLQ HQIGQSPARL GLTGPGSPSV QNLTPSRHGH  300
PTSSSSSQSH HHQQQIQQPP PNLPPSSSAV AASASSSTAI SSSALLSLLP PLPRAQALLQ  360
QMAVLSSKLF DVSPNRAHWL SAFRGSLPSF LSSHSLPPPP PLENPNPSST KEILSQFNSL  420
QTQLFEAVTE LQEILDLQDA KQKLAREIKS KDSSLLAFAN KLKEAERVLD MLVDDYSDYR  480
KPKRTKTVAE DDDDDEDSSS STTTVSSQIK LKDILAYAHK ISYTTFAPPE FGAGQAPLRG  540
ALPPAPQDEQ MRASQLYAFA DLDIGLPKTV ENIEKKVEAL IEPPPPPPDL SAIQGMLPQN  600
IAVPSGWKPG MPVELPKDWR LPPPPPGWKP GDPVVLPPEL VPPPRAQEQQ QQVRPPQGLH  660
RPPDVIHVRE VQLDILEDDS SEYSSEDSSD DEE

Functional Description ? help Back to Top
Source	Description
UniProt	Component of the Mediator complex, a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors (By similarity). {ECO:0000250}.

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_013611601.1	0.0	PREDICTED: mediator of RNA polymerase II transcription subunit 4
Refseq	XP_013747655.1	0.0	mediator of RNA polymerase II transcription subunit 4-like
Swissprot	Q9LZ00	1e-173	MED4_ARATH; Mediator of RNA polymerase II transcription subunit 4
TrEMBL	A0A0D3EI91	0.0	A0A0D3EI91_BRAOL; Uncharacterized protein
TrEMBL	A0A3P6EQD7	0.0	A0A3P6EQD7_BRAOL; Uncharacterized protein
STRING	Bo9g183320.1	0.0	(Brassica oleracea)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM9487	4	4

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT5G02840.3	3e-97	LHY/CCA1-like 1

Publications ? help Back to Top
Mathur S,Vyas S,Kapoor S,Tyagi AK The Mediator complex in plants: structure, phylogeny, and expression profiling of representative genes in a dicot (Arabidopsis) and a monocot (rice) during reproduction and abiotic stress. Plant Physiol., 2011. 157(4): p. 1609-27 [PMID:22021418] Li W, et al. SAD1, an RNA polymerase I subunit A34.5 of rice, interacts with Mediator and controls various aspects of plant development. Plant J., 2015. 81(2): p. 282-91 [PMID:25404280]