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

676741644

Organism

Sisymbrium irio

Taxonomic ID

3730

Taxonomic Lineage

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

Family

HD-ZIP

Protein Properties

Length: 813aa MW: 89488.6 Da PI: 5.7326

Description

HD-ZIP family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
676741644	genome	VEGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	Homeobox	56.5	4.8e-18	25	83	3	57
--SS--HHHHHHHHHHHHHSSS--HHHHHHHHHHC....TS-HHHHHHHHHHHHHHHHC CS Homeobox 3 kRttftkeqleeLeelFeknrypsaeereeLAkkl....gLterqVkvWFqNrRakekk 57 k ++t+eq+e+Le++++++++ps +r++L +++ +++ +q+kvWFqNrR ++k+ 676741644 25 KYVRYTAEQVEALERVYAECPKPSSLRRQQLIRECsilaNIEPKQIKVWFQNRRCRDKQ 83 56789***************************************************996 PP
2	START	108.9	8e-35	183	334	56	202
CHHHHHHHHHCCCGGCT-TT-SEEEEEEEECTT..EEEEEEEEXXTTXX-SSX.EEEEEEEEEEE.TTS-EEEEEEEEE-TTS--....-TTSEE-EESS CS START 56 mvlallveellddkeqWdetlakaetlevissg..galqlmvaelqalsplvp.RdfvfvRyirqlgagdwvivdvSvdseqkppe...sssvvRaellp 149 m+ + +e+l+d++ W +++++ e+ g g+++l +++++a+++l+p Rdf+++Ry+ +l g++v++++S++ p+ s++vRae+l 676741644 183 MPGM-KIAEILKDRPSWFRDCRSLEVFTMFPAGngGTIELVYMQTYAPTTLAPaRDFWTLRYTTSLDNGSFVVCERSLSGSGAGPNaasASQFVRAEMLS 281 5556.5677888888*********999999999****************************************999999989999***** PP EEEEEEEECTCEEEEEEEE-EE--SSXXHHHHHHHHHHHHHHHHHHHHHHTXX CS START 150 Sgiliepksnghskvtwvehvdlkgrlphwllrslvksglaegaktwvatlqr 202 Sg+li+p+++g+s +++v+h +l++++++ +lr+l++s+ + ++k++ ++l++ 676741644 282 SGYLIRPCDGGGSIIHIVDHLNLEAWSVPDVLRPLYESSKVVAQKMTISALRY 334 *********************************************999987 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50071	15.305	20	84	IPR001356	Homeobox domain
SuperFamily	SSF46689	1.07E-16	21	87	IPR009057	Homeodomain-like
SMART	SM00389	2.0E-16	22	88	IPR001356	Homeobox domain
CDD	cd00086	5.88E-16	25	85	No hit	No description
Pfam	PF00046	1.2E-15	26	83	IPR001356	Homeobox domain
Gene3D	G3DSA:1.10.10.60	2.9E-18	27	80	IPR009057	Homeodomain-like
CDD	cd14686	3.11E-6	77	116	No hit	No description
Gene3D	G3DSA:1.20.5.170	7.3E-4	81	130	No hit	No description
SMART	SM00234	1.9E-19	127	338	IPR002913	START domain
PROSITE profile	PS50848	21.884	158	347	IPR002913	START domain
SuperFamily	SSF55961	2.75E-27	160	340	No hit	No description
Gene3D	G3DSA:3.30.530.20	3.8E-16	186	333	IPR023393	START-like domain
Pfam	PF01852	9.7E-32	188	335	IPR002913	START domain
Pfam	PF08670	1.4E-47	662	812	IPR013978	MEKHLA

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0009855	Biological Process	determination of bilateral symmetry
GO:0009944	Biological Process	polarity specification of adaxial/abaxial axis
GO:0009956	Biological Process	radial pattern formation
GO:0010014	Biological Process	meristem initiation
GO:0010051	Biological Process	xylem and phloem pattern formation
GO:0010089	Biological Process	xylem development
GO:0030154	Biological Process	cell differentiation
GO:0005634	Cellular Component	nucleus
GO:0008289	Molecular Function	lipid binding
GO:0044212	Molecular Function	transcription regulatory region DNA binding

Sequence ? help Back to Top
Protein Sequence Length: 813 aa Download sequence Send to blast
MEMAVANHRE RSSDSMNRHL DSSGKYVRYT AEQVEALERV YAECPKPSSL RRQQLIRECS 60 ILANIEPKQI KVWFQNRRCR DKQRKEASRL QSVNRKLSAM NKLLMEENDR LQKQVSQLVC 120 ENGYMKQQLT TVVNDASCDS VVTTPQHSLR DATSPAGLLS IAEETLAEFL SKATGTAVDW 180 VQMPGMKIAE ILKDRPSWFR DCRSLEVFTM FPAGNGGTIE LVYMQTYAPT TLAPARDFWT 240 LRYTTSLDNG SFVVCERSLS GSGAGPNAAS ASQFVRAEML SSGYLIRPCD GGGSIIHIVD 300 HLNLEAWSVP DVLRPLYESS KVVAQKMTIS ALRYIRQLAQ ESNGELVYGL GRQPAVLRTF 360 SQRLSRGFND AVNGFGDDGW STMHCDGAED IIVAINSTKH LNNISNSLSF LGGVLCAKAS 420 MLLQNVPPAV LIRFLREHRS EWADFNVDAY SAATLKAGTF AYPGMRPTRF TGSQIIMPLG 480 HTIEHEEMLE VVRLEGHSLA QEDAFMSRDV HLLQICTGID ENAVGACSEL IFAPINEMFP 540 DDAPLVPSGF RVIPVDSKTG DAQDQLTANH RTLDLTSSLE VGPSLENASG NSSSSSSSRC 600 ILTIAFQFPF ENNLQDNVAG MACQYVRSVI SSVQRVAMAI SPSGISPSLG SKLSPGSPEA 660 VTLAQWISQS YTHHLGSELL TIDSLGSNDS VLKLLWDHQD AILCCSLKPQ PVFMFANQAG 720 LDMLETTLVA LQDITLEKIF DESGRKALCS DFAKLMQQGF ACLPSGICLS TMGRHVTYEQ 780 AVAWKVFAAS ENNDDNNNTL HCLAFSFVNW SFV

Sequence ? help Back to Top

Protein Sequence Length: 813 aa Download sequence Send to blast

MEMAVANHRE RSSDSMNRHL DSSGKYVRYT AEQVEALERV YAECPKPSSL RRQQLIRECS  60
ILANIEPKQI KVWFQNRRCR DKQRKEASRL QSVNRKLSAM NKLLMEENDR LQKQVSQLVC  120
ENGYMKQQLT TVVNDASCDS VVTTPQHSLR DATSPAGLLS IAEETLAEFL SKATGTAVDW  180
VQMPGMKIAE ILKDRPSWFR DCRSLEVFTM FPAGNGGTIE LVYMQTYAPT TLAPARDFWT  240
LRYTTSLDNG SFVVCERSLS GSGAGPNAAS ASQFVRAEML SSGYLIRPCD GGGSIIHIVD  300
HLNLEAWSVP DVLRPLYESS KVVAQKMTIS ALRYIRQLAQ ESNGELVYGL GRQPAVLRTF  360
SQRLSRGFND AVNGFGDDGW STMHCDGAED IIVAINSTKH LNNISNSLSF LGGVLCAKAS  420
MLLQNVPPAV LIRFLREHRS EWADFNVDAY SAATLKAGTF AYPGMRPTRF TGSQIIMPLG  480
HTIEHEEMLE VVRLEGHSLA QEDAFMSRDV HLLQICTGID ENAVGACSEL IFAPINEMFP  540
DDAPLVPSGF RVIPVDSKTG DAQDQLTANH RTLDLTSSLE VGPSLENASG NSSSSSSSRC  600
ILTIAFQFPF ENNLQDNVAG MACQYVRSVI SSVQRVAMAI SPSGISPSLG SKLSPGSPEA  660
VTLAQWISQS YTHHLGSELL TIDSLGSNDS VLKLLWDHQD AILCCSLKPQ PVFMFANQAG  720
LDMLETTLVA LQDITLEKIF DESGRKALCS DFAKLMQQGF ACLPSGICLS TMGRHVTYEQ  780
AVAWKVFAAS ENNDDNNNTL HCLAFSFVNW SFV

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	676741644

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	AK353169	0.0	AK353169.1 Thellungiella halophila mRNA, complete cds, clone: RTFL01-22-E05.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_009120605.1	0.0	PREDICTED: homeobox-leucine zipper protein REVOLUTA
Refseq	XP_009120606.1	0.0	PREDICTED: homeobox-leucine zipper protein REVOLUTA
Swissprot	Q9SE43	0.0	REV_ARATH; Homeobox-leucine zipper protein REVOLUTA
TrEMBL	A0A1J3F1X7	0.0	A0A1J3F1X7_NOCCA; Homeobox-leucine zipper protein REVOLUTA (Fragment)
TrEMBL	A0A1J3F5L8	0.0	A0A1J3F5L8_NOCCA; Homeobox-leucine zipper protein REVOLUTA (Fragment)
STRING	Bra002458.1-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]