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

XP_009134323.1

Organism

Brassica rapa

Taxonomic ID

3711

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: 737aa MW: 80732.7 Da PI: 5.6612

Description

HD-ZIP family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
XP_009134323.1	genome	NCBI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	Homeobox	61.3	1.5e-19	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 XP_009134323.1 63 KKRYHRHTQRQIQELESFFKECPHPDDKQRKELSRDLGLEPLQIKFWFQNKRTQMK 118 688999***********************************************998 PP
2	START	214	5.4e-67	253	472	1	206
HHHHHHHHHHHHHHHHC-TT-EEEE...EXCCTTEEEEEEESSS......SCEEEEEEEECCSCHHHHHHHHHCCCGGCT-TT-S....EEEEEE CS START 1 elaeeaaqelvkkalaeepgWvkss...esengdevlqkfeeskv.....dsgealrasgvvdmvlallveellddkeqWdetla....kaetle 83 ela +a++elv++a +++p+Wv+ e++n++e+ ++f+++ + ++ea+r+s+vv+m++ +lve+l+d++ qW+ + +a tle XP_009134323.1 253 ELAVAAMEELVRMARVGDPLWVSTDnsnEILNEEEYFRTFPRGIGpkplgLRSEASRESAVVIMNHINLVEILMDVN-QWSCVFSgivsRALTLE 346 57899****************99999**********999****************************.************* PP EECTT......EEEEEEEEXXTTXX-SSX.EEEEEEEEEEE.TTS-EEEEEEEEE-TTS--.-TTSEE-EESSEEEEEEEECTCEEEEEEEE-EE CS START 84 vissg......galqlmvaelqalsplvp.RdfvfvRyirqlgagdwvivdvSvdseqkppesssvvRaellpSgiliepksnghskvtwvehvd 171 v+s+g galq+m+ae+q++splvp R+ +fvRy++q+++g+w++vdvS+ds +++p + R +++pSg+li++++ng+skvtwveh+ XP_009134323.1 347 VLSTGvagnynGALQVMTAEFQVPSPLVPtRENYFVRYCKQHSDGSWAVVDVSLDSLRPNP----ISRTRRRPSGCLIQELPNGYSKVTWVEHMG 437 ********************************************************9....69999********************* PP --SSXXHHHHHHHHHHHHHHHHHHHHHHTXXXXXX CS START 172 lkgrlphwllrslvksglaegaktwvatlqrqcek 206 +++r++h ++++lv+sgla+ga++wv+tl+rqce+ XP_009134323.1 438 VDDRSVHTMYKPLVHSGLAFGARRWVSTLERQCER 472 *******************************97 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Gene3D	G3DSA:1.10.10.60	1.3E-23	44	118	IPR009057	Homeodomain-like
SuperFamily	SSF46689	1.46E-18	50	120	IPR009057	Homeodomain-like
PROSITE profile	PS50071	16.957	60	120	IPR001356	Homeobox domain
SMART	SM00389	3.7E-18	61	124	IPR001356	Homeobox domain
CDD	cd00086	2.34E-18	63	121	No hit	No description
Pfam	PF00046	3.7E-17	63	118	IPR001356	Homeobox domain
PROSITE pattern	PS00027	0	95	118	IPR017970	Homeobox, conserved site
PROSITE profile	PS50848	44.745	244	475	IPR002913	START domain
SuperFamily	SSF55961	9.75E-36	246	474	No hit	No description
CDD	cd08875	2.15E-124	248	471	No hit	No description
SMART	SM00234	3.5E-74	253	472	IPR002913	START domain
Pfam	PF01852	4.8E-56	254	472	IPR002913	START domain
Gene3D	G3DSA:3.30.530.20	3.3E-5	350	463	IPR023393	START-like domain
SuperFamily	SSF55961	9.62E-22	492	725	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:0008289	Molecular Function	lipid binding
GO:0043565	Molecular Function	sequence-specific DNA binding

Sequence ? help Back to Top
Protein Sequence Length: 737 aa Download sequence Send to blast
MYHPNMFESH HMFDMTTKST SDNDFGITGS REDDFETKSG TEVTTENPSG EELQDPNQRP 60 NKKKRYHRHT QRQIQELESF FKECPHPDDK QRKELSRDLG LEPLQIKFWF QNKRTQMKAQ 120 HERHDNQILK SDNDKLRAEN NRYKEALSNA TCPSCGGPAA TGEMSFDEQH LRIENARLRE 180 EIDRISAIAA KYVGKPIGSS FAPLAIQGPS RSLDLEVGNF GNQAGFVGEM YGTGDILRPV 240 SIPSESDKPM IIELAVAAME ELVRMARVGD PLWVSTDNSN EILNEEEYFR TFPRGIGPKP 300 LGLRSEASRE SAVVIMNHIN LVEILMDVNQ WSCVFSGIVS RALTLEVLST GVAGNYNGAL 360 QVMTAEFQVP SPLVPTRENY FVRYCKQHSD GSWAVVDVSL DSLRPNPISR TRRRPSGCLI 420 QELPNGYSKV TWVEHMGVDD RSVHTMYKPL VHSGLAFGAR RWVSTLERQC ERLASSMASN 480 IPASDLSVIT SPEGRKSMLK LAESMXIGAS TAHAWTTMSS TGSDDVRVMT RKSMDDPGRP 540 PGIVLSAATS FWIPVAPKRV FDFLRDENSR SEWDILSNGG MVQEMAHIAN GREPGNCVSL 600 LRVNSGNSSQ SNMLILQESC TDASGSYVIY APVDIVAMNV VLSGGDPDYV ALLPSGFAIL 660 PDGSVGGGGD GNQEVVSSST ASESCGSLLT VAFQILVDSV PTAKLSLGSV ATVNSLIKCT 720 VERIKAAVAG DRGGGGP

Sequence ? help Back to Top

Protein Sequence Length: 737 aa Download sequence Send to blast

MYHPNMFESH HMFDMTTKST SDNDFGITGS REDDFETKSG TEVTTENPSG EELQDPNQRP  60
NKKKRYHRHT QRQIQELESF FKECPHPDDK QRKELSRDLG LEPLQIKFWF QNKRTQMKAQ  120
HERHDNQILK SDNDKLRAEN NRYKEALSNA TCPSCGGPAA TGEMSFDEQH LRIENARLRE  180
EIDRISAIAA KYVGKPIGSS FAPLAIQGPS RSLDLEVGNF GNQAGFVGEM YGTGDILRPV  240
SIPSESDKPM IIELAVAAME ELVRMARVGD PLWVSTDNSN EILNEEEYFR TFPRGIGPKP  300
LGLRSEASRE SAVVIMNHIN LVEILMDVNQ WSCVFSGIVS RALTLEVLST GVAGNYNGAL  360
QVMTAEFQVP SPLVPTRENY FVRYCKQHSD GSWAVVDVSL DSLRPNPISR TRRRPSGCLI  420
QELPNGYSKV TWVEHMGVDD RSVHTMYKPL VHSGLAFGAR RWVSTLERQC ERLASSMASN  480
IPASDLSVIT SPEGRKSMLK LAESMXIGAS TAHAWTTMSS TGSDDVRVMT RKSMDDPGRP  540
PGIVLSAATS FWIPVAPKRV FDFLRDENSR SEWDILSNGG MVQEMAHIAN GREPGNCVSL  600
LRVNSGNSSQ SNMLILQESC TDASGSYVIY APVDIVAMNV VLSGGDPDYV ALLPSGFAIL  660
PDGSVGGGGD GNQEVVSSST ASESCGSLLT VAFQILVDSV PTAKLSLGSV ATVNSLIKCT  720
VERIKAAVAG DRGGGGP

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	XP_009134323.1

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_009134323.1	0.0	PREDICTED: LOW QUALITY PROTEIN: homeobox-leucine zipper protein PROTODERMAL FACTOR 2-like
Swissprot	Q93V99	0.0	PDF2_ARATH; Homeobox-leucine zipper protein PROTODERMAL FACTOR 2
TrEMBL	A0A3P6A9L9	0.0	A0A3P6A9L9_BRACM; Uncharacterized protein
STRING	Bo3g048340.1	0.0	(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	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]