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_009126588.1

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: 846aa MW: 92971.7 Da PI: 5.8114

Description

HD-ZIP family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
XP_009126588.1	genome	NCBI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	Homeobox	56.2	6e-18	27	85	3	57
--SS--HHHHHHHHHHHHHSSS--HHHHHHHHHHC....TS-HHHHHHHHHHHHHHHHC CS Homeobox 3 kRttftkeqleeLeelFeknrypsaeereeLAkkl....gLterqVkvWFqNrRakekk 57 k ++t+eq+e+Le+++ ++++ps +r++L +++ +++ +q+kvWFqNrR ++k+ XP_009126588.1 27 KYVRYTSEQVEALERVYSECPKPSSLRRQQLIRECsilaNIEPKQIKVWFQNRRCRDKQ 85 5679****************************************************996 PP
2	START	154.2	1.1e-48	163	368	2	202
HHHHHHHHHHHHHHHC-TT-EEEEEXCCTTEEEEEEESSS.SCEEEEEEEECCSCHHHHHHHHHCCCGGCT-TT-SEEEEEEEECTT..EEEEEE CS START 2 laeeaaqelvkkalaeepgWvkssesengdevlqkfeeskvdsgealrasgvvdmvlallveellddkeqWdetlakaetlevissg..galqlm 94 +aee+++e+++ka+ ++ Wv+++ +++g++++ +f+ s+ +sg a+ra+g+v ++ +e+l+d++ W + +++ e++ g g+++l XP_009126588.1 163 IAEETLAEFLSKATGTAVDWVQMPGMKPGPDSVGIFAISQRCSGVAARACGLVSLEPL-KIAEILKDRPSWYRECRSLEVYTMFPAGngGTIELV 256 7899****************************************************.7777777777**********999999** PP EEXXTTXX-SSX.EEEEEEEEEEE.TTS-EEEEEEEEE-TTS--....-TTSEE-EESSEEEEEEEECTCEEEEEEEE-EE--SSXXHHHHHHHH CS START 95 vaelqalsplvp.RdfvfvRyirqlgagdwvivdvSvdseqkppe...sssvvRaellpSgiliepksnghskvtwvehvdlkgrlphwllrslv 185 +++++a+++l+p Rdf+++Ry+ +l g++v++++S++ p+ s++vRae+l Sg+li+p+++g+s +++v+h +l++++++ +lr+l+ XP_009126588.1 257 YMQTYAPTTLAPaRDFWTLRYTTSLDNGSYVVCERSLSGSGAGPSpasASQFVRAEMLSSGYLIRPCDGGGSIIHIVDHLNLEAWSVPDVLRPLY 351 **********************************988888889999***************************************** PP HHHHHHHHHHHHHHTXX CS START 186 ksglaegaktwvatlqr 202 +s+ + ++k++ ++l++ XP_009126588.1 352 ESSKVVAQKMTISALRY 368 *********999987 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Gene3D	G3DSA:1.10.10.60	1.1E-18	9	82	IPR009057	Homeodomain-like
PROSITE profile	PS50071	15.467	22	86	IPR001356	Homeobox domain
SuperFamily	SSF46689	9.84E-17	23	89	IPR009057	Homeodomain-like
SMART	SM00389	1.2E-15	24	90	IPR001356	Homeobox domain
CDD	cd00086	1.07E-15	27	87	No hit	No description
Pfam	PF00046	1.5E-15	28	85	IPR001356	Homeobox domain
CDD	cd14686	3.27E-6	79	118	No hit	No description
Gene3D	G3DSA:1.20.5.170	7.7E-4	83	132	No hit	No description
PROSITE profile	PS50848	27.176	153	381	IPR002913	START domain
CDD	cd08875	9.98E-67	158	373	No hit	No description
Gene3D	G3DSA:3.30.530.20	9.7E-20	160	367	IPR023393	START-like domain
SuperFamily	SSF55961	4.4E-34	162	374	No hit	No description
SMART	SM00234	1.1E-38	162	372	IPR002913	START domain
Pfam	PF01852	2.1E-46	163	369	IPR002913	START domain
Pfam	PF08670	2.0E-47	697	845	IPR013978	MEKHLA

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0003677	Molecular Function	DNA binding
GO:0008289	Molecular Function	lipid binding

Sequence ? help Back to Top
Protein Sequence Length: 846 aa Download sequence Send to blast
MEMMEVANHG ERSTSDSMNR HLDSNGKYVR YTSEQVEALE RVYSECPKPS SLRRQQLIRE 60 CSILANIEPK QIKVWFQNRR CRDKQRKEAS RLQSVNRKLS AMNKLLMEEN DRLQKQVSQL 120 VCENGYMKQQ LTTVVNDVSC DSVVTTPQHS LRDANSHAGL ISIAEETLAE FLSKATGTAV 180 DWVQMPGMKP GPDSVGIFAI SQRCSGVAAR ACGLVSLEPL KIAEILKDRP SWYRECRSLE 240 VYTMFPAGNG GTIELVYMQT YAPTTLAPAR DFWTLRYTTS LDNGSYVVCE RSLSGSGAGP 300 SPASASQFVR AEMLSSGYLI RPCDGGGSII HIVDHLNLEA WSVPDVLRPL YESSKVVAQK 360 MTISALRYIR QLAQESNGEL VYGLGKQPAV LRTFSQRLSR GFNDAVNGFG DDGWSTMHCD 420 GAEDIILAIN STKHLSNISS SLSFLGGVLC AKATMLLQNV PPAVLIQFLR EHRSEWADFH 480 VDAYSAATLK AGAFAYPGVR PTRFTGSQII MPLGHTIEHE EMLEVVRLEG HSLAQEDAFM 540 SRDVHLLQIC TGIDENAVGA CSELIFAPIN EIFPDDAPLV PSGFRVIPID AKTGDAQDLI 600 TSNHRTLDLT SSLEVGPSPE TASGNSSSSC SSSRCILTIA FQFPFEPNLQ ENVAGMACQY 660 VRSVISSVQR VAMAISPSGI SPGLGSKLSP GSPEAVTLSQ WISQSYTHHF GSELVTIDSL 720 ESNDSVLKLI WNHQDAILCC TLKPQPVFMF ANQAGLDMLE TTLVALQDIT LEKIFDESGR 780 KALCSDFAKL MQQGFACLPS GICLSTMGRH VTYEQAVAWK VFAFENDNNN NNLHCLAFSF 840 VNWSFV

Sequence ? help Back to Top

Protein Sequence Length: 846 aa Download sequence Send to blast

MEMMEVANHG ERSTSDSMNR HLDSNGKYVR YTSEQVEALE RVYSECPKPS SLRRQQLIRE  60
CSILANIEPK QIKVWFQNRR CRDKQRKEAS RLQSVNRKLS AMNKLLMEEN DRLQKQVSQL  120
VCENGYMKQQ LTTVVNDVSC DSVVTTPQHS LRDANSHAGL ISIAEETLAE FLSKATGTAV  180
DWVQMPGMKP GPDSVGIFAI SQRCSGVAAR ACGLVSLEPL KIAEILKDRP SWYRECRSLE  240
VYTMFPAGNG GTIELVYMQT YAPTTLAPAR DFWTLRYTTS LDNGSYVVCE RSLSGSGAGP  300
SPASASQFVR AEMLSSGYLI RPCDGGGSII HIVDHLNLEA WSVPDVLRPL YESSKVVAQK  360
MTISALRYIR QLAQESNGEL VYGLGKQPAV LRTFSQRLSR GFNDAVNGFG DDGWSTMHCD  420
GAEDIILAIN STKHLSNISS SLSFLGGVLC AKATMLLQNV PPAVLIQFLR EHRSEWADFH  480
VDAYSAATLK AGAFAYPGVR PTRFTGSQII MPLGHTIEHE EMLEVVRLEG HSLAQEDAFM  540
SRDVHLLQIC TGIDENAVGA CSELIFAPIN EIFPDDAPLV PSGFRVIPID AKTGDAQDLI  600
TSNHRTLDLT SSLEVGPSPE TASGNSSSSC SSSRCILTIA FQFPFEPNLQ ENVAGMACQY  660
VRSVISSVQR VAMAISPSGI SPGLGSKLSP GSPEAVTLSQ WISQSYTHHF GSELVTIDSL  720
ESNDSVLKLI WNHQDAILCC TLKPQPVFMF ANQAGLDMLE TTLVALQDIT LEKIFDESGR  780
KALCSDFAKL MQQGFACLPS GICLSTMGRH VTYEQAVAWK VFAFENDNNN NNLHCLAFSF  840
VNWSFV

Expression -- Description ? help Back to Top
Source	Description
Uniprot	DEVELOPMENTAL STAGE: Expressed at the earliest stages and throughout LSM initiation and development. In embryo development, expressed at the heart stage until the 'walking stick' stage in the adaxial portion of the cotyledon primordia, the shoot apical meristem (SAM) and the vascular precursor cells of the hypocotyl and root. In developing flowers, expressed first at stage 1 in the center of L3 layer and then expands to the center of L2 and L1 layers. Expressed in the center of flower meristem through stages 4 and 5. At stage 6, expressed in the adaxial side of the carpel primordia and then on the adaxial carpel face. {ECO:0000269\|PubMed:11169198}.
Uniprot	TISSUE SPECIFICITY: Expressed in the interfascicular regions of stem and vascular bundles of young roots and leaves. {ECO:0000269\|PubMed:10559440}.

Functional Description ? help Back to Top
Source	Description
UniProt	Probable transcription factor involved in the regulation of interfascicular fiber (cortical cells) and secondary xylem differentiation in the inflorescence stems. Required for lateral shoot meristems (LSMs) and flower meristems (FMs) initiation. May be involved in the determination of vascular patterning and organ polarity (PubMed:10559440, PubMed:11169198, PubMed:11402186, PubMed:15111711, PubMed:15598805, PubMed:7555701). Directly regulates the expression of AGO10, ZPR1, ZPR2, ZPR3 and ZPR4 (PubMed:22781836). Required to regulate adaxial-abaxial polarity and leaf axial patterning (PubMed:20807212). {ECO:0000269\|PubMed:10559440, ECO:0000269\|PubMed:11169198, ECO:0000269\|PubMed:11402186, ECO:0000269\|PubMed:15111711, ECO:0000269\|PubMed:15598805, ECO:0000269\|PubMed:20807212, ECO:0000269\|PubMed:22781836, ECO:0000269\|PubMed:7555701}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	XP_009126588.1

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: By auxin. Repressed by ZPR and miR165. Induced by DOF5.1 (PubMed:20807212). {ECO:0000269\|PubMed:15111711, ECO:0000269\|PubMed:17237362, ECO:0000269\|PubMed:20807212}.

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	AF188994	0.0	AF188994.1 Arabidopsis thaliana homeodomain-leucine zipper protein interfascicular fiberless 1 (IFL1) mRNA, complete cds.
GenBank	AF233592	0.0	AF233592.1 Arabidopsis thaliana REVOLUTA mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_009126588.1	0.0	PREDICTED: homeobox-leucine zipper protein REVOLUTA-like
Swissprot	Q9SE43	0.0	REV_ARATH; Homeobox-leucine zipper protein REVOLUTA
TrEMBL	M4DUP3	0.0	M4DUP3_BRARP; Uncharacterized protein
STRING	Bra020236.1-P	0.0	(Brassica rapa)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM4779	27	54

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT5G60690.1	0.0	HD-ZIP family protein

Publications ? help Back to Top
Lian H,Li X,Liu Z,He Y HYL1 is required for establishment of stamen architecture with four microsporangia in Arabidopsis. J. Exp. Bot., 2013. 64(11): p. 3397-410 [PMID:23918970] Ding Y, et al. Four distinct types of dehydration stress memory genes in Arabidopsis thaliana. BMC Plant Biol., 2013. 13: p. 229 [PMID:24377444] Baima S, et al. Negative feedback regulation of auxin signaling by ATHB8/ACL5-BUD2 transcription module. Mol Plant, 2014. 7(6): p. 1006-1025 [PMID:24777988] Jia X, et al. Functional plasticity of miR165/166 in plant development revealed by small tandem target mimic. Plant Sci., 2015. 233: p. 11-21 [PMID:25711809] Roodbarkelari F,Du F,Truernit E,Laux T ZLL/AGO10 maintains shoot meristem stem cells during Arabidopsis embryogenesis by down-regulating ARF2-mediated auxin response. BMC Biol., 2015. 13: p. 74 [PMID:26358077] Shi B, et al. Two-Step Regulation of a Meristematic Cell Population Acting in Shoot Branching in Arabidopsis. PLoS Genet., 2016. 12(7): p. e1006168 [PMID:27398935]