PlantTFDB - Plant Transcription Factor Database @ CBI, PKU

PlantRegMap/PlantTFDB v5.0

Plant Transcription Factor Database

Previous version: v3.0 v4.0

Transcription Factor Information

Basic Information | Signature Domain | Sequence |

Basic Information? help Back to Top

TF ID

GSBRNA2T00005537001

Common Name

GSBRNA2T00005537001, LOC106347039

Organism

Brassica napus

Taxonomic ID

3708

Taxonomic Lineage

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

Family

HB-other

Protein Properties

Length: 342aa MW: 37647.5 Da PI: 8.5854

Description

HB-other family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
GSBRNA2T00005537001	genome	Genoscope	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	Homeobox	16.6	1.3e-05	16	74	9	55
HHHHHHHHHHHHH..SSS--HHHHHHHHHHC..........TS-HHHHHHHHHHHHHHH CS Homeobox 9 keqleeLeelFek..nrypsaeereeLAkkl..........gLterqVkvWFqNrRake 55 +++e+e++ ++ + p +++ e LA+k ++ +q+ +WFqNrR+ GSBRNA2T00005537001 16 LAEVTEMEAVLKQhnTAMPGRDTLEALADKFsdtverkgktVVQFKQIWNWFQNRRYAL 74 556677777777544778999999999999999999999888999***********965 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF46689	1.75E-9	4	77	IPR009057	Homeodomain-like
PROSITE profile	PS50071	8.584	5	77	IPR001356	Homeobox domain
SMART	SM00389	0.0033	7	81	IPR001356	Homeobox domain
CDD	cd00086	6.31E-4	13	75	No hit	No description
Gene3D	G3DSA:1.10.10.60	3.9E-7	13	78	IPR009057	Homeodomain-like
Pfam	PF16719	5.5E-41	138	266	IPR032001	SAWADEE domain

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0003677	Molecular Function	DNA binding
GO:0003682	Molecular Function	chromatin binding

Sequence ? help Back to Top
Protein Sequence Length: 342 aa Download sequence Send to blast
MGRPPSNGSP AFRFNLAEVT EMEAVLKQHN TAMPGRDTLE ALADKFSDTV ERKGKTVVQF 60 KQIWNWFQNR RYALRASRNK VPGKLNVSSM PRSVDPTNPM RNVLPPSTGP KPPHMIGNLS 120 GMTPAPPGVM RSGSDNSYLE FEAKSARDGA WYDVQAFLAH RNLEIGDPEV QVRFAGFEVE 180 EDEWINVKRH VRQRSLPCEA SECVAVLAGD LVLCFQEGKD QALYFDATVL DAQRRRHDVR 240 GCRCRFLVRY SHDQSEQEIV PLRKICRRPE TDYRLQQLHS AANDFANSKP APDAAAKTPL 300 PPSTASVPIV PPDVKDPSLS AASATSAQPS SNAATVPTGS A*

Sequence ? help Back to Top

Protein Sequence Length: 342 aa Download sequence Send to blast

MGRPPSNGSP AFRFNLAEVT EMEAVLKQHN TAMPGRDTLE ALADKFSDTV ERKGKTVVQF  60
KQIWNWFQNR RYALRASRNK VPGKLNVSSM PRSVDPTNPM RNVLPPSTGP KPPHMIGNLS  120
GMTPAPPGVM RSGSDNSYLE FEAKSARDGA WYDVQAFLAH RNLEIGDPEV QVRFAGFEVE  180
EDEWINVKRH VRQRSLPCEA SECVAVLAGD LVLCFQEGKD QALYFDATVL DAQRRRHDVR  240
GCRCRFLVRY SHDQSEQEIV PLRKICRRPE TDYRLQQLHS AANDFANSKP APDAAAKTPL  300
PPSTASVPIV PPDVKDPSLS AASATSAQPS SNAATVPTGS A*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4iuq_A	3e-45	139	270	4	134	SAWADEE HOMEODOMAIN HOMOLOG 1
4iuq_B	3e-45	139	270	4	134	SAWADEE HOMEODOMAIN HOMOLOG 1
4iur_A	3e-45	139	270	4	134	SHH1 SAWADEE
4iur_B	3e-45	139	270	4	134	SHH1 SAWADEE
4iut_A	3e-45	139	270	4	134	SAWADEE HOMEODOMAIN HOMOLOG 1
4iut_B	3e-45	139	270	4	134	SAWADEE HOMEODOMAIN HOMOLOG 1
4iuu_A	3e-45	139	270	4	134	SAWADEE HOMEODOMAIN HOMOLOG 1
4iuu_B	3e-45	139	270	4	134	SAWADEE HOMEODOMAIN HOMOLOG 1
4iuv_A	3e-45	139	270	4	134	SAWADEE HOMEODOMAIN HOMOLOG 1
4iuv_B	3e-45	139	270	4	134	SAWADEE HOMEODOMAIN HOMOLOG 1
Search in ModeBase

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
Bna.10827	0.0	microspore-derived embryo\| root\| seed

Functional Description ? help Back to Top
Source	Description
UniProt	May play a role in the recruitment of Pol IV to genomic regions associated with K9 methylated histone H3 that are targets for RdDM.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	GSBRNA2T00005537001

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	AY093042	1e-175	AY093042.1 Arabidopsis thaliana unknown protein (At3g18380) mRNA, complete cds.
GenBank	BT003428	1e-175	BT003428.1 Arabidopsis thaliana unknown protein (At3g18380) mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_013641996.1	0.0	protein SAWADEE HOMEODOMAIN HOMOLOG 2 isoform X3
Swissprot	Q8RWJ7	0.0	SHH2_ARATH; Protein SAWADEE HOMEODOMAIN HOMOLOG 2
TrEMBL	A0A078G0K4	0.0	A0A078G0K4_BRANA; BnaA01g26780D protein
STRING	Bra037587.1-P	0.0	(Brassica rapa)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM7399	24	37

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT3G18380.3	0.0	sequence-specific DNA binding transcription factors;sequence-specific DNA binding

Link Out ? help Back to Top
Entrez Gene	106347039

Publications ? help Back to Top
Chalhoub B, et al. Plant genetics. Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome. Science, 2014. 345(6199): p. 950-3 [PMID:25146293]