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

RrC12713_p1

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

HB-other

Protein Properties

Length: 118aa MW: 14145.6 Da PI: 6.8005

Description

HB-other family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
RrC12713_p1	genome	MSU	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	Homeobox	64.9	1.1e-20	63	118	1	56
TT--SS--HHHHHHHHHHHHHSSS--HHHHHHHHHHCTS-HHHHHHHHHHHHHHHH CS Homeobox 1 rrkRttftkeqleeLeelFeknrypsaeereeLAkklgLterqVkvWFqNrRakek 56 +++ +++t+ q++eLe++F+++++p+ ++r+eL++ lgL+ q+k+WFqN+R+++k RrC12713_p1 63 KKRYHRHTQRQIQELESFFKECPHPDDKQRKELSRDLGLEPLQIKFWFQNKRTQMK 118 688999***********************************************998 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Gene3D	G3DSA:1.10.10.60	8.4E-25	42	118	IPR009057	Homeodomain-like
SuperFamily	SSF46689	1.45E-19	49	118	IPR009057	Homeodomain-like
PROSITE profile	PS50071	17.038	60	118	IPR001356	Homeobox domain
SMART	SM00389	7.5E-12	61	118	IPR001356	Homeobox domain
CDD	cd00086	3.67E-16	63	118	No hit	No description
Pfam	PF00046	2.6E-18	63	118	IPR001356	Homeobox domain
PRINTS	PR00031	4.3E-5	91	100	IPR000047	Helix-turn-helix motif
PROSITE pattern	PS00027	0	95	118	IPR017970	Homeobox, conserved site
PRINTS	PR00031	4.3E-5	100	116	IPR000047	Helix-turn-helix motif

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0006355	Biological Process	regulation of transcription, DNA-templated
GO:0043565	Molecular Function	sequence-specific DNA binding

Sequence ? help Back to Top
Protein Sequence Length: 118 aa Download sequence Send to blast
MYHPNMFEGH HMFDMTTKST SDNDFGITGS REDDFETKSG TEVTNENPSG EELQDPNQRP 60 NKKKRYHRHT QRQIQELESF FKECPHPDDK QRKELSRDLG LEPLQIKFWF QNKRTQMK

Functional Description ? help Back to Top
Source	Description
UniProt	Probable transcription factor that binds to the L1 box DNA sequence 5'-TAAATG[CT]A-3'. Plays a role in maintaining the identity of L1 cells, possibly by interacting with their L1 box or other target-gene promoters. Functionally redundant to ATML1. {ECO:0000269\|PubMed:12505995}.

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

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AK352868	1e-149	AK352868.1 Thellungiella halophila mRNA, complete cds, clone: RTFL01-14-J22.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_018472664.1	2e-81	PREDICTED: homeobox-leucine zipper protein PROTODERMAL FACTOR 2
Refseq	XP_018472665.1	2e-81	PREDICTED: homeobox-leucine zipper protein PROTODERMAL FACTOR 2
Swissprot	Q93V99	4e-77	PDF2_ARATH; Homeobox-leucine zipper protein PROTODERMAL FACTOR 2
TrEMBL	A0A0D3B8G4	2e-78	A0A0D3B8G4_BRAOL; Uncharacterized protein
STRING	Bo3g048340.1	3e-79	(Brassica oleracea)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM491	28	149

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT4G04890.1	2e-79	protodermal factor 2

Publications ? help Back to Top
Duarte JM, et al. Expression pattern shifts following duplication indicative of subfunctionalization and neofunctionalization in regulatory genes of Arabidopsis. Mol. Biol. Evol., 2006. 23(2): p. 469-78 [PMID:16280546] Ding Y, et al. Four distinct types of dehydration stress memory genes in Arabidopsis thaliana. BMC Plant Biol., 2013. 13: p. 229 [PMID:24377444]