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Protein

Squamosa promoter-binding-like protein 4

Gene

SPL4

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Trans-acting factor that binds specifically to the consensus nucleotide sequence 5'-TNCGTACAA-3' of AP1 promoter. Promotes both vegetative phase change and flowering.2 Publications

Cofactori

Zn2+Note: Binds 2 Zn2+ ions per subunit.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi54 – 541Zinc 1
Metal bindingi59 – 591Zinc 1
Metal bindingi76 – 761Zinc 1
Metal bindingi79 – 791Zinc 1
Metal bindingi95 – 951Zinc 2
Metal bindingi98 – 981Zinc 2
Metal bindingi102 – 1021Zinc 2
Metal bindingi114 – 1141Zinc 2

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri51 – 12878SBP-typePROSITE-ProRule annotationAdd
BLAST

GO - Molecular functioni

  • DNA binding Source: UniProtKB-KW
  • metal ion binding Source: UniProtKB-KW
  • transcription factor activity, sequence-specific DNA binding Source: TAIR

GO - Biological processi

  • flower development Source: InterPro
  • regulation of transcription, DNA-templated Source: TAIR
  • regulation of vegetative phase change Source: TAIR
  • transcription, DNA-templated Source: UniProtKB-KW
Complete GO annotation...

Keywords - Biological processi

Transcription, Transcription regulation

Keywords - Ligandi

DNA-binding, Metal-binding, Zinc

Names & Taxonomyi

Protein namesi
Recommended name:
Squamosa promoter-binding-like protein 4
Gene namesi
Name:SPL4
Ordered Locus Names:At1g53160
ORF Names:F12M16.2
OrganismiArabidopsis thaliana (Mouse-ear cress)
Taxonomic identifieri3702 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
Proteomesi
  • UP000006548 Componenti: Chromosome 1

Organism-specific databases

TAIRiAT1G53160.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 174174Squamosa promoter-binding-like protein 4PRO_0000132725Add
BLAST

Proteomic databases

PaxDbiQ9S7A9.

PTM databases

iPTMnetiQ9S7A9.

Expressioni

Tissue specificityi

Expressed in the rib meristem and inter-primordial tissue of the inflorescence apex.1 Publication

Developmental stagei

Increases during floral transition and stay high thereafter.2 Publications

Inductioni

Negatively regulated by microRNAs miR156 and miR157.2 Publications

Gene expression databases

GenevisibleiQ9S7A9. AT.

Interactioni

Protein-protein interaction databases

BioGridi26974. 1 interaction.
STRINGi3702.AT1G53160.1.

Structurei

Secondary structure

1
174
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi68 – 725Combined sources
Helixi77 – 804Combined sources
Beta strandi85 – 873Combined sources
Beta strandi90 – 945Combined sources
Turni96 – 983Combined sources
Beta strandi99 – 1035Combined sources
Turni104 – 1063Combined sources
Turni116 – 1194Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1UL4NMR-A51-131[»]
ProteinModelPortaliQ9S7A9.
SMRiQ9S7A9. Positions 51-131.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9S7A9.

Family & Domainsi

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi111 – 12717Bipartite nuclear localization signalSequence analysisAdd
BLAST

Domaini

The SBP-type zinc finger is required for the binding to DNA.By similarity

Sequence similaritiesi

Contains 1 SBP-type zinc finger.PROSITE-ProRule annotation

Zinc finger

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri51 – 12878SBP-typePROSITE-ProRule annotationAdd
BLAST

Keywords - Domaini

Zinc-finger

Phylogenomic databases

eggNOGiENOG410J055. Eukaryota.
ENOG410YKCI. LUCA.
HOGENOMiHOG000005763.
InParanoidiQ9S7A9.
OMAiERSRVEM.
PhylomeDBiQ9S7A9.

Family and domain databases

Gene3Di4.10.1100.10. 1 hit.
InterProiIPR017238. SBP_fam.
IPR004333. Transcpt_factor_SBP-box.
[Graphical view]
PfamiPF03110. SBP. 1 hit.
[Graphical view]
PIRSFiPIRSF037575. SBP. 1 hit.
SUPFAMiSSF103612. SSF103612. 1 hit.
PROSITEiPS51141. ZF_SBP. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q9S7A9-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MEGKRSQGQG YMKKKSYLVE EDMETDTDEE EEVGRDRVRG SRGSINRGGS
60 70 80 90 100
LRLCQVDRCT ADMKEAKLYH RRHKVCEVHA KASSVFLSGL NQRFCQQCSR
110 120 130 140 150
FHDLQEFDEA KRSCRRRLAG HNERRRKSSG ESTYGEGSGR RGINGQVVMQ
160 170
NQERSRVEMT LPMPNSSFKR PQIR
Length:174
Mass (Da):20,120
Last modified:May 1, 2000 - v1
Checksum:iB569272D389655AB
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AJ011630 Genomic DNA. Translation: CAB56582.1.
AJ011631 mRNA. Translation: CAB56583.1.
AJ011632 mRNA. Translation: CAB56584.1.
AC008007 Genomic DNA. Translation: AAF69527.1.
CP002684 Genomic DNA. Translation: AEE32896.1.
CP002684 Genomic DNA. Translation: AEE32897.1.
BT002856 mRNA. Translation: AAO22673.1.
BT004391 mRNA. Translation: AAO42385.1.
AY084902 mRNA. Translation: AAM61465.1.
PIRiT52599.
T52600.
RefSeqiNP_175723.1. NM_104194.3.
NP_974014.1. NM_202285.1.
UniGeneiAt.496.

Genome annotation databases

EnsemblPlantsiAT1G53160.1; AT1G53160.1; AT1G53160.
AT1G53160.2; AT1G53160.2; AT1G53160.
GeneIDi841749.
GrameneiAT1G53160.1; AT1G53160.1; AT1G53160.
AT1G53160.2; AT1G53160.2; AT1G53160.
KEGGiath:AT1G53160.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AJ011630 Genomic DNA. Translation: CAB56582.1.
AJ011631 mRNA. Translation: CAB56583.1.
AJ011632 mRNA. Translation: CAB56584.1.
AC008007 Genomic DNA. Translation: AAF69527.1.
CP002684 Genomic DNA. Translation: AEE32896.1.
CP002684 Genomic DNA. Translation: AEE32897.1.
BT002856 mRNA. Translation: AAO22673.1.
BT004391 mRNA. Translation: AAO42385.1.
AY084902 mRNA. Translation: AAM61465.1.
PIRiT52599.
T52600.
RefSeqiNP_175723.1. NM_104194.3.
NP_974014.1. NM_202285.1.
UniGeneiAt.496.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1UL4NMR-A51-131[»]
ProteinModelPortaliQ9S7A9.
SMRiQ9S7A9. Positions 51-131.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi26974. 1 interaction.
STRINGi3702.AT1G53160.1.

PTM databases

iPTMnetiQ9S7A9.

Proteomic databases

PaxDbiQ9S7A9.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsiAT1G53160.1; AT1G53160.1; AT1G53160.
AT1G53160.2; AT1G53160.2; AT1G53160.
GeneIDi841749.
GrameneiAT1G53160.1; AT1G53160.1; AT1G53160.
AT1G53160.2; AT1G53160.2; AT1G53160.
KEGGiath:AT1G53160.

Organism-specific databases

TAIRiAT1G53160.

Phylogenomic databases

eggNOGiENOG410J055. Eukaryota.
ENOG410YKCI. LUCA.
HOGENOMiHOG000005763.
InParanoidiQ9S7A9.
OMAiERSRVEM.
PhylomeDBiQ9S7A9.

Miscellaneous databases

EvolutionaryTraceiQ9S7A9.
PROiQ9S7A9.

Gene expression databases

GenevisibleiQ9S7A9. AT.

Family and domain databases

Gene3Di4.10.1100.10. 1 hit.
InterProiIPR017238. SBP_fam.
IPR004333. Transcpt_factor_SBP-box.
[Graphical view]
PfamiPF03110. SBP. 1 hit.
[Graphical view]
PIRSFiPIRSF037575. SBP. 1 hit.
SUPFAMiSSF103612. SSF103612. 1 hit.
PROSITEiPS51141. ZF_SBP. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Molecular characterization of the Arabidopsis SBP-box genes."
    Cardon G.H., Hoehmann S., Klein J., Nettesheim K., Saedler H., Huijser P.
    Gene 237:91-104(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA / MRNA], FUNCTION, TISSUE SPECIFICITY, DEVELOPMENTAL STAGE.
    Strain: cv. Columbia and cv. Landsberg erecta.
    Tissue: Flower.
  2. "Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana."
    Theologis A., Ecker J.R., Palm C.J., Federspiel N.A., Kaul S., White O., Alonso J., Altafi H., Araujo R., Bowman C.L., Brooks S.Y., Buehler E., Chan A., Chao Q., Chen H., Cheuk R.F., Chin C.W., Chung M.K.
    , Conn L., Conway A.B., Conway A.R., Creasy T.H., Dewar K., Dunn P., Etgu P., Feldblyum T.V., Feng J.-D., Fong B., Fujii C.Y., Gill J.E., Goldsmith A.D., Haas B., Hansen N.F., Hughes B., Huizar L., Hunter J.L., Jenkins J., Johnson-Hopson C., Khan S., Khaykin E., Kim C.J., Koo H.L., Kremenetskaia I., Kurtz D.B., Kwan A., Lam B., Langin-Hooper S., Lee A., Lee J.M., Lenz C.A., Li J.H., Li Y.-P., Lin X., Liu S.X., Liu Z.A., Luros J.S., Maiti R., Marziali A., Militscher J., Miranda M., Nguyen M., Nierman W.C., Osborne B.I., Pai G., Peterson J., Pham P.K., Rizzo M., Rooney T., Rowley D., Sakano H., Salzberg S.L., Schwartz J.R., Shinn P., Southwick A.M., Sun H., Tallon L.J., Tambunga G., Toriumi M.J., Town C.D., Utterback T., Van Aken S., Vaysberg M., Vysotskaia V.S., Walker M., Wu D., Yu G., Fraser C.M., Venter J.C., Davis R.W.
    Nature 408:816-820(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: cv. Columbia.
  3. The Arabidopsis Information Resource (TAIR)
    Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases
    Cited for: GENOME REANNOTATION.
    Strain: cv. Columbia.
  4. "Empirical analysis of transcriptional activity in the Arabidopsis genome."
    Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M., Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G., Liu S.X., Lam B., Sakano H., Wu T., Yu G.
    , Miranda M., Quach H.L., Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C., Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J., Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A., Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C., Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X., Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M., Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K., Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A., Ecker J.R.
    Science 302:842-846(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Strain: cv. Columbia.
  5. "Full-length cDNA from Arabidopsis thaliana."
    Brover V.V., Troukhan M.E., Alexandrov N.A., Lu Y.-P., Flavell R.B., Feldmann K.A.
    Submitted (MAR-2002) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
  6. Cited for: INDUCTION.
  7. "Dissection of floral induction pathways using global expression analysis."
    Schmid M., Uhlenhaut N.H., Godard F., Demar M., Bressan R., Weigel D., Lohmann J.U.
    Development 130:6001-6012(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: DEVELOPMENTAL STAGE.
  8. "A novel zinc-binding motif revealed by solution structures of DNA-binding domains of Arabidopsis SBP-family transcription factors."
    Yamasaki K., Kigawa T., Inoue M., Tateno M., Yamasaki T., Yabuki T., Aoki M., Seki E., Matsuda T., Nunokawa E., Ishizuka Y., Terada T., Shirouzu M., Osanai T., Tanaka A., Seki M., Shinozaki K., Yokoyama S.
    J. Mol. Biol. 337:49-63(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: STRUCTURE BY NMR OF 51-132, ZINC-BINDING SITES CYS-54; CYS-59; CYS-76; HIS-79; CYS-95; CYS-98; HIS-102 AND CYS-114.
  9. "Functional dissection of the plant-specific SBP-domain: overlap of the DNA-binding and nuclear localization domains."
    Birkenbihl R.P., Jach G., Saedler H., Huijser P.
    J. Mol. Biol. 352:585-596(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUBCELLULAR LOCATION.
  10. "Temporal regulation of shoot development in Arabidopsis thaliana by miR156 and its target SPL3."
    Wu G., Poethig R.S.
    Development 133:3539-3547(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, INDUCTION.

Entry informationi

Entry nameiSPL4_ARATH
AccessioniPrimary (citable) accession number: Q9S7A9
Secondary accession number(s): Q9SMX8
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 7, 2005
Last sequence update: May 1, 2000
Last modified: June 8, 2016
This is version 104 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Arabidopsis thaliana
    Arabidopsis thaliana: entries and gene names
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.