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

GSBRNA2T00157869001

Common Name

GSBRNA2T00157869001

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

HD-ZIP

Protein Properties

Length: 733aa MW: 80464 Da PI: 5.7574

Description

HD-ZIP family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
GSBRNA2T00157869001	genome	Genoscope	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	Homeobox	59.9	4e-19	63	118	1	56
TT--SS--HHHHHHHHHHHHHSSS--HHHHHHHHHHCTS-HHHHHHHHHHHHHHHH CS Homeobox 1 rrkRttftkeqleeLeelFeknrypsaeereeLAkklgLterqVkvWFqNrRakek 56 +++ +++t+ q++eLe++F+++++p+ ++r+eL++ l L+ qVk+WFqN+R+++k GSBRNA2T00157869001 63 KKRYHRHTQRQIQELESFFKECPHPDDKQRKELSRDLCLEPLQVKFWFQNKRTQMK 118 688999***********************************************998 PP
2	START	208.3	2.9e-65	254	473	1	206
HHHHHHHHHHHHHHHHC-TT-EEEE...EXCCTTEEEEEEESSS......SCEEEEEEEECCSCHHHHHHHHHCCCGGCT-TT-S....E CS START 1 elaeeaaqelvkkalaeepgWvkss...esengdevlqkfeeskv.....dsgealrasgvvdmvlallveellddkeqWdetla....k 78 ela +a++elv++a+a++p+Wv+ + +n++e ++f+++ + ++ea+r+s+vv+m++ +lve+l+d++ qW+ + + GSBRNA2T00157869001 254 ELAVAAMEELVRMAQAGDPLWVSTGnsmDLPNEEEDFRTFPRGIGpkplgLRTEASRESAVVIMNHINLVEILMDVN-QWSCVFSgivsR 342 57899****************9998999********999****************************.******** PP EEEEEEECTT......EEEEEEEEXXTTXX-SSX.EEEEEEEEEEE.TTS-EEEEEEEEE-TTS--.-TTSEE-EESSEEEEEEEECTCE CS START 79 aetlevissg......galqlmvaelqalsplvp.RdfvfvRyirqlgagdwvivdvSvdseqkppesssvvRaellpSgiliepksngh 161 a tlev+s+g galq+m+ae+q++splvp R+ +fvRy++q+++g+w++vdvS+ds +++ + R +++pSg+li++++ng+ GSBRNA2T00157869001 343 ALTLEVLSTGvagnynGALQVMTAEFQVPSPLVPtRENYFVRYCKQHSDGSWAVVDVSLDSLRPNL----ISRTRRRPSGCLIQELPNGY 428 ************************************************************96....7999************ PP EEEEEEE-EE--SSXXHHHHHHHHHHHHHHHHHHHHHHTXXXXXX CS START 162 skvtwvehvdlkgrlphwllrslvksglaegaktwvatlqrqcek 206 skvtw+eh+++++r++h ++++lv+sgla+gak+wv+tl+rqce+ GSBRNA2T00157869001 429 SKVTWIEHMEVDDRSVHTMYKPLVHSGLAFGAKRWVSTLERQCER 473 *****************************************97 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Gene3D	G3DSA:1.10.10.60	6.4E-23	44	118	IPR009057	Homeodomain-like
SuperFamily	SSF46689	3.04E-18	50	120	IPR009057	Homeodomain-like
PROSITE profile	PS50071	16.422	60	120	IPR001356	Homeobox domain
SMART	SM00389	1.5E-15	61	124	IPR001356	Homeobox domain
Pfam	PF00046	1.0E-16	63	118	IPR001356	Homeobox domain
CDD	cd00086	4.59E-17	63	121	No hit	No description
PROSITE pattern	PS00027	0	95	118	IPR017970	Homeobox, conserved site
PROSITE profile	PS50848	44.868	245	476	IPR002913	START domain
SuperFamily	SSF55961	5.08E-35	246	475	No hit	No description
CDD	cd08875	5.12E-122	249	472	No hit	No description
SMART	SM00234	2.0E-70	254	473	IPR002913	START domain
Pfam	PF01852	1.8E-54	255	473	IPR002913	START domain
Gene3D	G3DSA:3.30.530.20	4.3E-5	352	472	IPR023393	START-like domain
SuperFamily	SSF55961	8.93E-25	493	720	No hit	No description

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0006355	Biological Process	regulation of transcription, DNA-templated
GO:0005634	Cellular Component	nucleus
GO:0008289	Molecular Function	lipid binding
GO:0043565	Molecular Function	sequence-specific DNA binding

Sequence ? help Back to Top
Protein Sequence Length: 733 aa Download sequence Send to blast
MYHPSMFESH HMFDMTTKST SDNDLGITGS REDEFETKSG TEVTTENPSG EELQDPNQRP 60 NKKKRYHRHT QRQIQELESF FKECPHPDDK QRKELSRDLC LEPLQVKFWF QNKRTQMKAQ 120 HERHENQILK SDNDKLRAEN NRYKEALSNA TCPNCGGPAA IGEMSFDEQH LRIENVRLRE 180 EIDRISAIAA KYVGKPVGSS FAPLEIHAPS RSLELEVGNF GNQTTGFVGD MYGTGDILRS 240 VSIPSDTDKP MIVELAVAAM EELVRMAQAG DPLWVSTGNS MDLPNEEEDF RTFPRGIGPK 300 PLGLRTEASR ESAVVIMNHI NLVEILMDVN QWSCVFSGIV SRALTLEVLS TGVAGNYNGA 360 LQVMTAEFQV PSPLVPTREN YFVRYCKQHS DGSWAVVDVS LDSLRPNLIS RTRRRPSGCL 420 IQELPNGYSK VTWIEHMEVD DRSVHTMYKP LVHSGLAFGA KRWVSTLERQ CERLASSMAS 480 NIPASDLSVI TSPEGRKSML KLAERMVMSF CTGVGASTAH AWTTMSSTGS DDVRVMTRKS 540 MDDPGRPPGI VLSAATSFWI PVAPKRVFDF LRDENSRSEW DILSNGGMVQ EMAHIANGRE 600 PGNCVSLLRV NSGNSSQSNM LILQESCTDA SGSYVIYAPV DIVAMNVVLS GGDPDYVALL 660 PSGFAILPDV VSSSSASGSC GSLLTVAFQI LVDSVPTAKL SLGSVATVNS LIKCTVERIK 720 AALACDVGGG AP*

Sequence ? help Back to Top

Protein Sequence Length: 733 aa Download sequence Send to blast

MYHPSMFESH HMFDMTTKST SDNDLGITGS REDEFETKSG TEVTTENPSG EELQDPNQRP  60
NKKKRYHRHT QRQIQELESF FKECPHPDDK QRKELSRDLC LEPLQVKFWF QNKRTQMKAQ  120
HERHENQILK SDNDKLRAEN NRYKEALSNA TCPNCGGPAA IGEMSFDEQH LRIENVRLRE  180
EIDRISAIAA KYVGKPVGSS FAPLEIHAPS RSLELEVGNF GNQTTGFVGD MYGTGDILRS  240
VSIPSDTDKP MIVELAVAAM EELVRMAQAG DPLWVSTGNS MDLPNEEEDF RTFPRGIGPK  300
PLGLRTEASR ESAVVIMNHI NLVEILMDVN QWSCVFSGIV SRALTLEVLS TGVAGNYNGA  360
LQVMTAEFQV PSPLVPTREN YFVRYCKQHS DGSWAVVDVS LDSLRPNLIS RTRRRPSGCL  420
IQELPNGYSK VTWIEHMEVD DRSVHTMYKP LVHSGLAFGA KRWVSTLERQ CERLASSMAS  480
NIPASDLSVI TSPEGRKSML KLAERMVMSF CTGVGASTAH AWTTMSSTGS DDVRVMTRKS  540
MDDPGRPPGI VLSAATSFWI PVAPKRVFDF LRDENSRSEW DILSNGGMVQ EMAHIANGRE  600
PGNCVSLLRV NSGNSSQSNM LILQESCTDA SGSYVIYAPV DIVAMNVVLS GGDPDYVALL  660
PSGFAILPDV VSSSSASGSC GSLLTVAFQI LVDSVPTAKL SLGSVATVNS LIKCTVERIK  720
AALACDVGGG AP*

Expression -- Description ? help Back to Top
Source	Description
Uniprot	TISSUE SPECIFICITY: Specifically expressed in the layer 1 (L1) of shoot meristems. {ECO:0000269\|PubMed:12505995}.

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}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	GSBRNA2T00157869001

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	0.0	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_013662000.1	0.0	homeobox-leucine zipper protein PROTODERMAL FACTOR 2 isoform X2
Refseq	XP_013662001.1	0.0	homeobox-leucine zipper protein PROTODERMAL FACTOR 2 isoform X2
Swissprot	Q93V99	0.0	PDF2_ARATH; Homeobox-leucine zipper protein PROTODERMAL FACTOR 2
TrEMBL	A0A078FUG0	0.0	A0A078FUG0_BRANA; BnaA09g20170D protein
STRING	Bra029527.1-P	0.0	(Brassica rapa)

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	0.0	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] 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]