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

Neem_11528_f_1

Organism

Azadirachta indica

Taxonomic ID

124943

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Sapindales; Meliaceae; Azadirachta

Family

SBP

Protein Properties

Length: 772aa MW: 86294.2 Da PI: 8.104

Description

SBP family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Neem_11528_f_1	genome	NGD	View Nucleic Acid

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	SBP	116.1	1.9e-36	73	150	1	78
--SSTT-----TT--HHHHHTT--HHHHT-S-EEETTEEEEE-TTTSSEEETTT--SS--S-STTTT-------S--- CS SBP 1 lCqvegCeadlseakeyhrrhkvCevhskapvvlvsgleqrfCqqCsrfhelsefDeekrsCrrrLakhnerrrkkqa 78 +Cqv gCead+se+k yh+rh+vC +++a++vl++g+++r+CqqC++fh ls+fDe+krsCrr+L++hn+rrr+k+ Neem_11528_f_1 73 RCQVSGCEADISELKGYHKRHRVCLRCANASAVLLDGESKRYCQQCGKFHILSDFDEGKRSCRRKLERHNNRRRRKSV 150 6*************************************************************************9875 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Gene3D	G3DSA:4.10.1100.10	1.1E-27	70	135	IPR004333	Transcription factor, SBP-box
PROSITE profile	PS51141	29.624	71	148	IPR004333	Transcription factor, SBP-box
SuperFamily	SSF103612	1.1E-33	72	151	IPR004333	Transcription factor, SBP-box
Pfam	PF03110	2.5E-27	74	148	IPR004333	Transcription factor, SBP-box

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0006355	Biological Process	regulation of transcription, DNA-templated
GO:0055070	Biological Process	copper ion homeostasis
GO:0005634	Cellular Component	nucleus
GO:0003677	Molecular Function	DNA binding

Sequence ? help Back to Top
Protein Sequence Length: 772 aa Download sequence Send to blast
MNPNKHRKAT NRCHDFPTLA KISIIIGLTC SNFLAGRIPC ACPEIDEKLE EEEAGLPGKK 60 RARTVRAGVG QARCQVSGCE ADISELKGYH KRHRVCLRCA NASAVLLDGE SKRYCQQCGK 120 FHILSDFDEG KRSCRRKLER HNNRRRRKSV DSKGAVDNEP PGASHSEDIV CDDDAGKDSL 180 CLSSQITDQE TFLEAEDGHV TGLNSAPNAQ NVNSDSGISF AASGEIRIDG GKDNSKTSPS 240 PSYCDNKSSY SSMCPTGRIS FKLYDWNPAE FPRRLRHQIF QWLASMPVEL EGYIRPGCTI 300 LTIFVAMPKI MWMKLYADPI RYVHDFVIAP GRMLSGRGPM FVHLNNMIFH VKDGTSVMKV 360 NVEVQAPRLH YVHPTCFEAG KPMEFVACGS NLLQSKFRFL ISFAGKYLPY VYRIASPHGE 420 TDGDPLTFDH QLYKIRVPHT EPNLFGPAFI EVENESGLSN FIPVLIGDKE TCSEMKIIQQ 480 RFEASLITKR SQLMAGDSLS NLCGISALRQ KTFTELLVDI AWLLKVPASE SFLYFMSSSR 540 VQRFNCLFSF LINNESTVIL EKLLQNLKIL MDSMEFNSAI NGINDADLGL LFKYMDNARE 600 ILQRKLQKDG GLMQHAVNIV QERICGSQSS FQSNLLVPST SQVRASILSY RGSNKMILDH 660 DLDTRSNTKL GVMVYSAAVD RCETTPLLNK EVIMNVNLIK EWPRKSCGHI LSGTVLSSRP 720 AIFVIVMAAV CFGVCVVVLH PQKIKYEAEV TWCTCKVVVH LDPDGRATWD IA

Sequence ? help Back to Top

Protein Sequence Length: 772 aa Download sequence Send to blast

MNPNKHRKAT NRCHDFPTLA KISIIIGLTC SNFLAGRIPC ACPEIDEKLE EEEAGLPGKK  60
RARTVRAGVG QARCQVSGCE ADISELKGYH KRHRVCLRCA NASAVLLDGE SKRYCQQCGK  120
FHILSDFDEG KRSCRRKLER HNNRRRRKSV DSKGAVDNEP PGASHSEDIV CDDDAGKDSL  180
CLSSQITDQE TFLEAEDGHV TGLNSAPNAQ NVNSDSGISF AASGEIRIDG GKDNSKTSPS  240
PSYCDNKSSY SSMCPTGRIS FKLYDWNPAE FPRRLRHQIF QWLASMPVEL EGYIRPGCTI  300
LTIFVAMPKI MWMKLYADPI RYVHDFVIAP GRMLSGRGPM FVHLNNMIFH VKDGTSVMKV  360
NVEVQAPRLH YVHPTCFEAG KPMEFVACGS NLLQSKFRFL ISFAGKYLPY VYRIASPHGE  420
TDGDPLTFDH QLYKIRVPHT EPNLFGPAFI EVENESGLSN FIPVLIGDKE TCSEMKIIQQ  480
RFEASLITKR SQLMAGDSLS NLCGISALRQ KTFTELLVDI AWLLKVPASE SFLYFMSSSR  540
VQRFNCLFSF LINNESTVIL EKLLQNLKIL MDSMEFNSAI NGINDADLGL LFKYMDNARE  600
ILQRKLQKDG GLMQHAVNIV QERICGSQSS FQSNLLVPST SQVRASILSY RGSNKMILDH  660
DLDTRSNTKL GVMVYSAAVD RCETTPLLNK EVIMNVNLIK EWPRKSCGHI LSGTVLSSRP  720
AIFVIVMAAV CFGVCVVVLH PQKIKYEAEV TWCTCKVVVH LDPDGRATWD IA

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
1ul5_A	3e-42	72	154	4	86	squamosa promoter binding protein-like 7
Search in ModeBase

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	134	146	RRKLERHNNRRRR

Functional Description ? help Back to Top
Source	Description
UniProt	Transcription factor that participates in reprogramming global gene expression during copper deficiency in order to improve the metal uptake and prioritize its distribution to copper proteins of major importance (Probable). Binds directly to 5'-GTAC-3' motifs in the microRNA (miRNA) promoter of the stress-responsive miRNAs miR398b and miR398c to activate their transcription. During copper deficiency, activates the copper transporters COPT1 and COPT2, and the copper chaperone CCH, directly or indirectly via miRNAs. Required for the expression of the miRNAs miR397, miR408 and miR857 (PubMed:19122104). Acts coordinately with HY5 to regulate miR408 and its target genes in response to changes in light and copper conditions (PubMed:25516599). Activates miR857 and its target genes in response to low copper conditions (PubMed:26511915). Involved in cadmium stress response by regulating miR397a, miR398b, miR398c and miR857 (PubMed:27352843). Required for iron homeostasis during copper deficiency (PubMed:22374396). {ECO:0000269\|PubMed:19122104, ECO:0000269\|PubMed:22374396, ECO:0000269\|PubMed:25516599, ECO:0000269\|PubMed:26511915, ECO:0000269\|PubMed:27352843}.

Binding Motif ? help Back to Top
Motif ID	Method	Source	Motif file
MP00604	PBM	Transfer from AT5G18830	Download

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_006419724.1	0.0	squamosa promoter-binding-like protein 7 isoform X1
Swissprot	Q8S9G8	0.0	SPL7_ARATH; Squamosa promoter-binding-like protein 7
TrEMBL	V4U134	0.0	V4U134_9ROSI; Uncharacterized protein
STRING	XP_006419724.1	0.0	(Citrus clementina)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM6358	26	44

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT5G18830.1	0.0	squamosa promoter binding protein-like 7

Publications ? help Back to Top
Zhang H, et al. MicroRNA408 is critical for the HY5-SPL7 gene network that mediates the coordinated response to light and copper. Plant Cell, 2014. 26(12): p. 4933-53 [PMID:25516599] Zhao Y, et al. MicroRNA857 Is Involved in the Regulation of Secondary Growth of Vascular Tissues in Arabidopsis. Plant Physiol., 2015. 169(4): p. 2539-52 [PMID:26511915] Perea-García A, et al. Modulation of copper deficiency responses by diurnal and circadian rhythms in Arabidopsis thaliana. J. Exp. Bot., 2016. 67(1): p. 391-403 [PMID:26516126] Gielen H,Remans T,Vangronsveld J,Cuypers A Toxicity responses of Cu and Cd: the involvement of miRNAs and the transcription factor SPL7. BMC Plant Biol., 2016. 16(1): p. 145 [PMID:27352843] Yan J, et al. Arabidopsis Pollen Fertility Requires the Transcription Factors CITF1 and SPL7 That Regulate Copper Delivery to Anthers and Jasmonic Acid Synthesis. Plant Cell, 2017. 29(12): p. 3012-3029 [PMID:29114014] Araki R, et al. SPL7 locally regulates copper-homeostasis-related genes in Arabidopsis. J. Plant Physiol., 2018. [PMID:29635212]