PlantTFDB - Plant Transcription Factor Database @ CBI, PKU

PlantRegMap/PlantTFDB v5.0

Plant Transcription Factor Database

Previous version: v3.0 v4.0

Transcription Factor Information

Basic Information | Signature Domain | Sequence |

Basic Information? help Back to Top

TF ID

GSBRNA2T00021575001

Common Name

GSBRNA2T00021575001

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

HB-other

Protein Properties

Length: 133aa MW: 15989.9 Da PI: 6.8798

Description

HB-other family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
GSBRNA2T00021575001	genome	Genoscope	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	Homeobox	65.4	7.6e-21	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 GSBRNA2T00021575001 63 KKRYHRHTQRQIQELESFFKECPHPDDKQRKELSRELNLEPLQVKFWFQNKRTQMK 118 678899***********************************************998 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Gene3D	G3DSA:1.10.10.60	5.2E-24	44	118	IPR009057	Homeodomain-like
SuperFamily	SSF46689	5.56E-20	51	118	IPR009057	Homeodomain-like
PROSITE profile	PS50071	16.876	60	120	IPR001356	Homeobox domain
SMART	SM00389	1.2E-17	61	124	IPR001356	Homeobox domain
CDD	cd00086	1.35E-16	63	118	No hit	No description
Pfam	PF00046	1.6E-18	63	118	IPR001356	Homeobox domain
PROSITE pattern	PS00027	0	95	118	IPR017970	Homeobox, conserved site

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:0043565	Molecular Function	sequence-specific DNA binding

Sequence ? help Back to Top
Protein Sequence Length: 133 aa Download sequence Send to blast
MYQPNMFESH HHMFDMTPKN SDNDLGLTGS REDDFETKSG AEVTMENPLE EELQDPNQRP 60 NKKKRYHRHT QRQIQELESF FKECPHPDDK QRKELSRELN LEPLQVKFWF QNKRTQMKVH 120 TRANCYSFCI FI*

Expression -- Description ? help Back to Top
Source	Description
Uniprot	DEVELOPMENTAL STAGE: First expressed in the apical cell after the first asymmetric division of the zygote. Expressed in all proembryo cells until the eight-cell stage, and then restricted to the protoderm in the 16-cell proembryo. Not detected in the torpedo stage, but reappeared later in the L1 layer of the shoot apical meristem in the mature embryo. After germination, the L1 layer-specific expression pattern is maintained in the vegetative shoot apical meristem, inflorescence, floral meristems, and the young floral organ primordia. Finally, expressed in the protoderm of the ovule primordia and integuments and gradually restricted to the endothelium surrounding the embryo sac. {ECO:0000269\|PubMed:10571886, ECO:0000269\|PubMed:8989876}.

Functional Description ? help Back to Top
Source	Description
UniProt	Probable transcription factor involved in cell specification and pattern formation during embryogenesis. 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 PDF2. {ECO:0000269\|PubMed:11439135, ECO:0000269\|PubMed:12505995}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	GSBRNA2T00021575001

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	AK229970	1e-128	AK229970.1 Arabidopsis thaliana mRNA for L1 specific homeobox gene ATML1/ovule-specific homeobox protein A20, complete cds, clone: RAFL22-43-B20.
GenBank	AY091104	1e-128	AY091104.1 Arabidopsis thaliana putative L1-specific homeobox gene ATML1/ovule-specific homeobox protein A20 (At4g21750) mRNA, complete cds.
GenBank	AY150491	1e-128	AY150491.1 Arabidopsis thaliana putative L1-specific homeobox gene ATML1/ovule-specific homeobox protein A20 (At4g21750) mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_013598423.1	3e-81	PREDICTED: homeobox-leucine zipper protein MERISTEM L1
Refseq	XP_013598424.1	3e-81	PREDICTED: homeobox-leucine zipper protein MERISTEM L1
Refseq	XP_013598425.1	3e-81	PREDICTED: homeobox-leucine zipper protein MERISTEM L1
Refseq	XP_013696499.1	4e-81	homeobox-leucine zipper protein MERISTEM L1
Refseq	XP_013696501.1	4e-81	homeobox-leucine zipper protein MERISTEM L1
Refseq	XP_013696503.1	4e-81	homeobox-leucine zipper protein MERISTEM L1 isoform X2
Refseq	XP_018477464.1	4e-81	PREDICTED: homeobox-leucine zipper protein MERISTEM L1
Refseq	XP_022546647.1	4e-81	homeobox-leucine zipper protein MERISTEM L1 isoform X1
Refseq	XP_022546648.1	4e-81	homeobox-leucine zipper protein MERISTEM L1
Swissprot	Q8RWU4	4e-78	ATML1_ARATH; Homeobox-leucine zipper protein MERISTEM L1
TrEMBL	A0A078GCK0	8e-95	A0A078GCK0_BRANA; BnaC07g30910D protein
STRING	Bo7g107550.1	1e-80	(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
AT4G21750.2	2e-80	HD-ZIP family protein

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] Takada S,Takada N,Yoshida A Induction of epidermal cell fate in Arabidopsis shoots. Plant Signal Behav, 2013. 8(11): p. e26236 [PMID:23989220] 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] Liang Z,Brown RC,Fletcher JC,Opsahl-Sorteberg HG Calpain-Mediated Positional Information Directs Cell Wall Orientation to Sustain Plant Stem Cell Activity, Growth and Development. Plant Cell Physiol., 2015. 56(9): p. 1855-66 [PMID:26220906] Katagiri Y, et al. The coordination of ploidy and cell size differs between cell layers in leaves. Development, 2016. 143(7): p. 1120-5 [PMID:26903507] Seeliger I, et al. The AP2-type transcription factors DORNRÖSCHEN and DORNRÖSCHEN-LIKE promote G1/S transition. Mol. Genet. Genomics, 2016. 291(5): p. 1835-49 [PMID:27277595] Schwarz EM,Roeder AH Transcriptomic Effects of the Cell Cycle Regulator LGO in Arabidopsis Sepals. Front Plant Sci, 2016. 7: p. 1744 [PMID:27920789] Meyer HM, et al. Fluctuations of the transcription factor ATML1 generate the pattern of giant cells in the Arabidopsis sepal. Elife, 2018. [PMID:28145865]