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

Rsa1.0_54972.1_g00001.1

Organism

Raphanus sativus

Taxonomic ID

3726

Taxonomic Lineage

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

Family

HB-other

Protein Properties

Length: 59aa MW: 7062.14 Da PI: 9.7131

Description

HB-other family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Rsa1.0_54972.1_g00001.1	genome	RGD	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	Homeobox	57.5	2.2e-18	6	59	3	52
--SS--HHHHHHHHHHHHHSSS--HHHHHHHHHHC....TS-HHHHHHHHHHHH CS Homeobox 3 kRttftkeqleeLeelFeknrypsaeereeLAkkl....gLterqVkvWFqNrR 52 k ++t+eq+e+Le+++ ++++p+ +r++L +++ +++ +q+kvWFqNrR Rsa1.0_54972.1_g00001.1 6 KYVRYTPEQVEALERVYTECPKPTSLRRQQLIRECpilsNIEPKQIKVWFQNRR 59 5679*************************************************9 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50071	14.447	1	59	IPR001356	Homeobox domain
SMART	SM00389	7.4E-5	3	59	IPR001356	Homeobox domain
SuperFamily	SSF46689	1.33E-15	6	59	IPR009057	Homeodomain-like
Pfam	PF00046	6.0E-16	6	59	IPR001356	Homeobox domain
CDD	cd00086	3.60E-12	6	59	No hit	No description
Gene3D	G3DSA:1.10.10.60	6.8E-18	9	59	IPR009057	Homeodomain-like

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

Sequence ? help Back to Top
Protein Sequence Length: 59 aa Download sequence Send to blast
GLDSGKYVRY TPEQVEALER VYTECPKPTS LRRQQLIREC PILSNIEPKQ IKVWFQNRR

Functional Description ? help Back to Top
Source	Description
UniProt	Probable transcription factor involved in the determination of adaxial-abaxial polarity in ovule primordium. Specifies adaxial leaf fates. {ECO:0000269\|PubMed:11395776, ECO:0000269\|PubMed:15328016, ECO:0000269\|PubMed:15598805}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Rsa1.0_54972.1_g00001.1

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: Repressed by miR165 and miR166. {ECO:0000269\|PubMed:14999284, ECO:0000269\|PubMed:16033795, ECO:0000269\|PubMed:17237362}.

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	AC003096	4e-57	AC003096.3 Arabidopsis thaliana chromosome 2 clone T29F13 map ve016, complete sequence.
GenBank	CP002685	4e-57	CP002685.1 Arabidopsis thaliana chromosome 2, complete sequence.
GenBank	Y11122	4e-57	Y11122.1 A.thaliana ATHB-14 gene.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_009143747.1	7e-35	PREDICTED: homeobox-leucine zipper protein ATHB-14
Swissprot	O04291	1e-35	ATB14_ARATH; Homeobox-leucine zipper protein ATHB-14
TrEMBL	A0A087H2M0	9e-34	A0A087H2M0_ARAAL; Uncharacterized protein
STRING	A0A087H2M0	2e-34	(Arabis alpina)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM18074	5	9

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT2G34710.1	4e-38	HD-ZIP family protein

Publications ? help Back to Top
Ding Y, et al. Four distinct types of dehydration stress memory genes in Arabidopsis thaliana. BMC Plant Biol., 2013. 13: p. 229 [PMID:24377444] 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] Müller CJ, et al. PHABULOSA Mediates an Auxin Signaling Loop to Regulate Vascular Patterning in Arabidopsis. Plant Physiol., 2016. 170(2): p. 956-70 [PMID:26637548] Yamada T,Sasaki Y,Hashimoto K,Nakajima K,Gasser CS CORONA, PHABULOSA and PHAVOLUTA collaborate with BELL1 to confine WUSCHEL expression to the nucellus in Arabidopsis ovules. Development, 2016. 143(3): p. 422-6 [PMID:26700684] Kim ES, et al. HAWAIIAN SKIRT regulates the quiescent center-independent meristem activity in Arabidopsis roots. Physiol Plant, 2016. 157(2): p. 221-33 [PMID:26968317] Husbands AY,Aggarwal V,Ha T,Timmermans MC In Planta Single-Molecule Pull-Down Reveals Tetrameric Stoichiometry of HD-ZIPIII:LITTLE ZIPPER Complexes. Plant Cell, 2016. 28(8): p. 1783-94 [PMID:27385814] Di Ruocco G, et al. Differential spatial distribution of miR165/6 determines variability in plant root anatomy. Development, 2018. [PMID:29158439] Wójcik AM,Nodine MD,Gaj MD miR160 and miR166/165 Contribute to the LEC2-Mediated Auxin Response Involved in the Somatic Embryogenesis Induction in Arabidopsis. Front Plant Sci, 2017. 8: p. 2024 [PMID:29321785] Hashimoto K,Miyashima S,Sato-Nara K,Yamada T,Nakajima K Functionally Diversified Members of the MIR165/6 Gene Family Regulate Ovule Morphogenesis in Arabidopsis thaliana. Plant Cell Physiol., 2018. 59(5): p. 1017-1026 [PMID:29462472]