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

Pavir.4KG237900.2.p

Organism

Panicum virgatum

Taxonomic ID

38727

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; PACMAD clade; Panicoideae; Panicodae; Paniceae; Panicinae; Panicum

Family

SBP

Protein Properties

Length: 642aa MW: 70927.7 Da PI: 5.118

Description

SBP family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Pavir.4KG237900.2.p	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	SBP	112.4	2.7e-35	180	254	2	76
-SSTT-----TT--HHHHHTT--HHHHT-S-EEETTEEEEE-TTTSSEEETTT--SS--S-STTTT-------S- CS SBP 2 CqvegCeadlseakeyhrrhkvCevhskapvvlvsgleqrfCqqCsrfhelsefDeekrsCrrrLakhnerrrkk 76 Cqv+gCead+ e+k yhrrh+vC +++a++vl++g+++r+CqqC++fh l +fDe+krsCrr+L++hn+rrr+k Pavir.4KG237900.2.p 180 CQVPGCEADIRELKGYHRRHRVCLRCAHASAVLLDGVQKRYCQQCGKFHVLLDFDEDKRSCRRKLERHNKRRRRK 254 ************************************************************************997 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Gene3D	G3DSA:4.10.1100.10	6.8E-27	177	241	IPR004333	Transcription factor, SBP-box
PROSITE profile	PS51141	29.581	177	254	IPR004333	Transcription factor, SBP-box
SuperFamily	SSF103612	1.7E-33	178	258	IPR004333	Transcription factor, SBP-box
Pfam	PF03110	6.0E-27	180	254	IPR004333	Transcription factor, SBP-box

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0005634	Cellular Component	nucleus
GO:0003677	Molecular Function	DNA binding

Sequence ? help Back to Top
Protein Sequence Length: 642 aa Download sequence Send to blast
MDAADSGGGA AADAGEPLWD WGNLLDFVQD DDSLVLPWDN AAGIGASDPT EAVAPMLPAP 60 LSQPSEPEPE LQPELEPEPE AEPGPVLPPP PLRVQGIGRR VRKRDPRLVC PNYLAGRVPC 120 ACPEVDEMVA AAEVEDVATE FLAGARKKTK TAARRGKAGA AGGGGTAGGT VRAAGMEMKC 180 QVPGCEADIR ELKGYHRRHR VCLRCAHASA VLLDGVQKRY CQQCGKFHVL LDFDEDKRSC 240 RRKLERHNKR RRRKPDSKGM LDKEIDEQLD LSADVSGDGE LREENMEGTT SEMLETVLSN 300 KVLDRGTPAG SEDVLSSPTC TQPSLQNEQS KSVVTFAASV EACIGAKQEN AKLTTNSPMH 360 DTKSAYSSSC PTGRISFKLY DWNPAEFPRR LRHQIFEWLA SMPVELEGYI RPGCTILTVF 420 VAMPQHMWDK LSDDAANLLR NLVNSPNSLL LGKGAFFIHV NNMIFQVLKD GATLMSTRLD 480 VQSPRIDYVH PTWFEAGKPV ELMLCGNFLD QPKFRSLLSF DGDYLKHDCY RLTSRDAIDC 540 AENVDLILDS QHEFFRINIT QTRPEIHGPA FVEVSIIFFD NLDQIPSLNF CYGHLPLEFM 600 VNLIVLKAWC GESIIKYTGE CLSAFREGFF FLSFFCNLPS S*

Sequence ? help Back to Top

Protein Sequence Length: 642 aa Download sequence Send to blast

MDAADSGGGA AADAGEPLWD WGNLLDFVQD DDSLVLPWDN AAGIGASDPT EAVAPMLPAP  60
LSQPSEPEPE LQPELEPEPE AEPGPVLPPP PLRVQGIGRR VRKRDPRLVC PNYLAGRVPC  120
ACPEVDEMVA AAEVEDVATE FLAGARKKTK TAARRGKAGA AGGGGTAGGT VRAAGMEMKC  180
QVPGCEADIR ELKGYHRRHR VCLRCAHASA VLLDGVQKRY CQQCGKFHVL LDFDEDKRSC  240
RRKLERHNKR RRRKPDSKGM LDKEIDEQLD LSADVSGDGE LREENMEGTT SEMLETVLSN  300
KVLDRGTPAG SEDVLSSPTC TQPSLQNEQS KSVVTFAASV EACIGAKQEN AKLTTNSPMH  360
DTKSAYSSSC PTGRISFKLY DWNPAEFPRR LRHQIFEWLA SMPVELEGYI RPGCTILTVF  420
VAMPQHMWDK LSDDAANLLR NLVNSPNSLL LGKGAFFIHV NNMIFQVLKD GATLMSTRLD  480
VQSPRIDYVH PTWFEAGKPV ELMLCGNFLD QPKFRSLLSF DGDYLKHDCY RLTSRDAIDC  540
AENVDLILDS QHEFFRINIT QTRPEIHGPA FVEVSIIFFD NLDQIPSLNF CYGHLPLEFM  600
VNLIVLKAWC GESIIKYTGE CLSAFREGFF FLSFFCNLPS S*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
1ul5_A	9e-38	175	259	1	85	squamosa promoter binding protein-like 7
Search in ModeBase

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	236	254	KRSCRRKLERHNKRRRRKP
2	240	252	RRKLERHNKRRRR
3	247	254	NKRRRRKP
4	248	253	KRRRRK

Expression -- Description ? help Back to Top
Source	Description
Uniprot	TISSUE SPECIFICITY: Ubiquitous. {ECO:0000269\|PubMed:16861571}.

Functional Description ? help Back to Top
Source	Description
UniProt	Trans-acting factor that binds specifically to the consensus nucleotide sequence 5'-TNCGTACAA-3'. {ECO:0000250}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Pavir.4KG237900.2.p

Regulation -- PlantRegMap ? help Back to Top
Source	Upstream Regulator	Target Gene
PlantRegMap	Retrieve	-

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_025805456.1	0.0	squamosa promoter-binding-like protein 9
Swissprot	Q6I576	0.0	SPL9_ORYSJ; Squamosa promoter-binding-like protein 9
TrEMBL	A0A3L6T078	0.0	A0A3L6T078_PANMI; Squamosa promoter-binding-like protein 9
STRING	Pavir.J00965.1.p	0.0	(Panicum virgatum)

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT5G18830.2	1e-113	squamosa promoter binding protein-like 7

Link Out ? help Back to Top
Phytozome	Pavir.4KG237900.2.p

Publications ? help Back to Top
Kikuchi S, et al. Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice. Science, 2003. 301(5631): p. 376-9 [PMID:12869764] Cheng CH, et al. A fine physical map of the rice chromosome 5. Mol. Genet. Genomics, 2005. 274(4): p. 337-45 [PMID:16261349]