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Q9SZF7

- SHR_ARATH

UniProt

Q9SZF7 - SHR_ARATH

Protein

Protein SHORT-ROOT

Gene

SHR

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 84 (01 Oct 2014)
      Sequence version 1 (01 May 2000)
      Previous versions | rss
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    Functioni

    Transcription factor required for quiescent center cells specification and maintenance of surrounding stem cells, and for the asymmetric cell division involved in radial pattern formation in roots. Essential for both cell division and cell specification. Regulates the radial organization of the shoot axial organs and is required for normal shoot gravitropism. Directly controls the transcription of SCR, and when associated with SCR, of MGP, RLK, TRI, NUC and SCL3.6 Publications

    GO - Molecular functioni

    1. protein binding Source: IntAct
    2. sequence-specific DNA binding Source: TAIR
    3. sequence-specific DNA binding transcription factor activity Source: TAIR

    GO - Biological processi

    1. asymmetric cell division Source: TAIR
    2. iron ion homeostasis Source: TAIR
    3. leaf development Source: TAIR
    4. negative regulation of mitotic cell cycle Source: TAIR
    5. radial pattern formation Source: TAIR
    6. regulation of hormone metabolic process Source: TAIR
    7. transcription, DNA-templated Source: UniProtKB-KW

    Keywords - Molecular functioni

    Developmental protein

    Keywords - Biological processi

    Transcription, Transcription regulation

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Protein SHORT-ROOT
    Short name:
    AtSHR
    Alternative name(s):
    GRAS family protein 26
    Short name:
    AtGRAS-26
    Protein SHOOT GRAVITROPISM 7
    Gene namesi
    Name:SHR
    Synonyms:SGR7
    Ordered Locus Names:At4g37650
    ORF Names:F19F18.140
    OrganismiArabidopsis thaliana (Mouse-ear cress)
    Taxonomic identifieri3702 [NCBI]
    Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
    ProteomesiUP000006548: Chromosome 4

    Organism-specific databases

    TAIRiAT4G37650.

    Subcellular locationi

    Cytoplasm. Nucleus
    Note: Cytoplasm and nucleus in the stele. Restricted to the nucleus in adjacent cells.

    GO - Cellular componenti

    1. cytoplasm Source: UniProtKB-SubCell
    2. nucleus Source: TAIR

    Keywords - Cellular componenti

    Cytoplasm, Nucleus

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi289 – 2891T → I or E: Loss of both export from the stele and activity. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 531531Protein SHORT-ROOTPRO_0000329423Add
    BLAST

    Proteomic databases

    PaxDbiQ9SZF7.
    PRIDEiQ9SZF7.

    Expressioni

    Tissue specificityi

    Expressed in the stele and the quiescent center. Not detected in the ground tissue cell lineage. The SHR protein moves from the stele to a single layer of adjacent cells, where it enters the nucleus.4 Publications

    Developmental stagei

    Expressed in the procambium during embryogenesis.1 Publication

    Gene expression databases

    GenevestigatoriQ9SZF7.

    Interactioni

    Subunit structurei

    Interacts with SCR, SCL23, JKD and MGP.4 Publications

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    SCRQ9M38411EBI-1250472,EBI-1250484

    Protein-protein interaction databases

    BioGridi15200. 1 interaction.
    IntActiQ9SZF7. 6 interactions.

    Family & Domainsi

    Motif

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Motifi256 – 2605VHIID

    Compositional bias

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Compositional biasi11 – 155Poly-Gln
    Compositional biasi29 – 346Poly-Thr
    Compositional biasi65 – 695Poly-Ser
    Compositional biasi70 – 767His-rich
    Compositional biasi104 – 1107Poly-Ala

    Sequence similaritiesi

    Belongs to the GRAS family.Curated

    Phylogenomic databases

    eggNOGiNOG301144.
    HOGENOMiHOG000078767.
    InParanoidiQ9SZF7.
    OMAiRTDETPH.
    PhylomeDBiQ9SZF7.

    Family and domain databases

    InterProiIPR005202. TF_GRAS.
    [Graphical view]
    PfamiPF03514. GRAS. 1 hit.
    [Graphical view]
    PROSITEiPS50985. GRAS. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    Q9SZF7-1 [UniParc]FASTAAdd to Basket

    « Hide

    MDTLFRLVSL QQQQQSDSII TNQSSLSRTS TTTTGSPQTA YHYNFPQNDV    50
    VEECFNFFMD EEDLSSSSSH HNHHNHNNPN TYYSPFTTPT QYHPATSSTP 100
    SSTAAAAALA SPYSSSGHHN DPSAFSIPQT PPSFDFSANA KWADSVLLEA 150
    ARAFSDKDTA RAQQILWTLN ELSSPYGDTE QKLASYFLQA LFNRMTGSGE 200
    RCYRTMVTAA ATEKTCSFES TRKTVLKFQE VSPWATFGHV AANGAILEAV 250
    DGEAKIHIVD ISSTFCTQWP TLLEALATRS DDTPHLRLTT VVVANKFVND 300
    QTASHRMMKE IGNRMEKFAR LMGVPFKFNI IHHVGDLSEF DLNELDVKPD 350
    EVLAINCVGA MHGIASRGSP RDAVISSFRR LRPRIVTVVE EEADLVGEEE 400
    GGFDDEFLRG FGECLRWFRV CFESWEESFP RTSNERLMLE RAAGRAIVDL 450
    VACEPSDSTE RRETARKWSR RMRNSGFGAV GYSDEVADDV RALLRRYKEG 500
    VWSMVQCPDA AGIFLCWRDQ PVVWASAWRP T 531
    Length:531
    Mass (Da):59,462
    Last modified:May 1, 2000 - v1
    Checksum:iF43EEC5F7AA0CA1C
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti233 – 2331P → S in AAL69513. 1 PublicationCurated

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AF233752 Genomic DNA. Translation: AAF75234.1.
    AL035605 Genomic DNA. Translation: CAB38304.1.
    AL161591 Genomic DNA. Translation: CAB80430.1.
    CP002687 Genomic DNA. Translation: AEE86820.1.
    BT033026 mRNA. Translation: ACE62894.1.
    AY074547 mRNA. Translation: AAL69513.1.
    PIRiT04722.
    RefSeqiNP_195480.1. NM_119928.2.
    UniGeneiAt.2816.
    At.71893.

    Genome annotation databases

    EnsemblPlantsiAT4G37650.1; AT4G37650.1; AT4G37650.
    GeneIDi829919.
    KEGGiath:AT4G37650.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AF233752 Genomic DNA. Translation: AAF75234.1 .
    AL035605 Genomic DNA. Translation: CAB38304.1 .
    AL161591 Genomic DNA. Translation: CAB80430.1 .
    CP002687 Genomic DNA. Translation: AEE86820.1 .
    BT033026 mRNA. Translation: ACE62894.1 .
    AY074547 mRNA. Translation: AAL69513.1 .
    PIRi T04722.
    RefSeqi NP_195480.1. NM_119928.2.
    UniGenei At.2816.
    At.71893.

    3D structure databases

    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 15200. 1 interaction.
    IntActi Q9SZF7. 6 interactions.

    Proteomic databases

    PaxDbi Q9SZF7.
    PRIDEi Q9SZF7.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblPlantsi AT4G37650.1 ; AT4G37650.1 ; AT4G37650 .
    GeneIDi 829919.
    KEGGi ath:AT4G37650.

    Organism-specific databases

    GeneFarmi 4260. 427.
    TAIRi AT4G37650.

    Phylogenomic databases

    eggNOGi NOG301144.
    HOGENOMi HOG000078767.
    InParanoidi Q9SZF7.
    OMAi RTDETPH.
    PhylomeDBi Q9SZF7.

    Gene expression databases

    Genevestigatori Q9SZF7.

    Family and domain databases

    InterProi IPR005202. TF_GRAS.
    [Graphical view ]
    Pfami PF03514. GRAS. 1 hit.
    [Graphical view ]
    PROSITEi PS50985. GRAS. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "The SHORT-ROOT gene controls radial patterning of the Arabidopsis root through radial signaling."
      Helariutta Y., Fukaki H., Wysocka-Diller J.W., Nakajima K., Jung J., Sena G., Hauser M.-T., Benfey P.N.
      Cell 101:555-567(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION, TISSUE SPECIFICITY, DEVELOPMENTAL STAGE.
    2. "Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana."
      Mayer K.F.X., Schueller C., Wambutt R., Murphy G., Volckaert G., Pohl T., Duesterhoeft A., Stiekema W., Entian K.-D., Terryn N., Harris B., Ansorge W., Brandt P., Grivell L.A., Rieger M., Weichselgartner M., de Simone V., Obermaier B.
      , Mache R., Mueller M., Kreis M., Delseny M., Puigdomenech P., Watson M., Schmidtheini T., Reichert B., Portetelle D., Perez-Alonso M., Boutry M., Bancroft I., Vos P., Hoheisel J., Zimmermann W., Wedler H., Ridley P., Langham S.-A., McCullagh B., Bilham L., Robben J., van der Schueren J., Grymonprez B., Chuang Y.-J., Vandenbussche F., Braeken M., Weltjens I., Voet M., Bastiaens I., Aert R., Defoor E., Weitzenegger T., Bothe G., Ramsperger U., Hilbert H., Braun M., Holzer E., Brandt A., Peters S., van Staveren M., Dirkse W., Mooijman P., Klein Lankhorst R., Rose M., Hauf J., Koetter P., Berneiser S., Hempel S., Feldpausch M., Lamberth S., Van den Daele H., De Keyser A., Buysshaert C., Gielen J., Villarroel R., De Clercq R., van Montagu M., Rogers J., Cronin A., Quail M.A., Bray-Allen S., Clark L., Doggett J., Hall S., Kay M., Lennard N., McLay K., Mayes R., Pettett A., Rajandream M.A., Lyne M., Benes V., Rechmann S., Borkova D., Bloecker H., Scharfe M., Grimm M., Loehnert T.-H., Dose S., de Haan M., Maarse A.C., Schaefer M., Mueller-Auer S., Gabel C., Fuchs M., Fartmann B., Granderath K., Dauner D., Herzl A., Neumann S., Argiriou A., Vitale D., Liguori R., Piravandi E., Massenet O., Quigley F., Clabauld G., Muendlein A., Felber R., Schnabl S., Hiller R., Schmidt W., Lecharny A., Aubourg S., Chefdor F., Cooke R., Berger C., Monfort A., Casacuberta E., Gibbons T., Weber N., Vandenbol M., Bargues M., Terol J., Torres A., Perez-Perez A., Purnelle B., Bent E., Johnson S., Tacon D., Jesse T., Heijnen L., Schwarz S., Scholler P., Heber S., Francs P., Bielke C., Frishman D., Haase D., Lemcke K., Mewes H.-W., Stocker S., Zaccaria P., Bevan M., Wilson R.K., de la Bastide M., Habermann K., Parnell L., Dedhia N., Gnoj L., Schutz K., Huang E., Spiegel L., Sekhon M., Murray J., Sheet P., Cordes M., Abu-Threideh J., Stoneking T., Kalicki J., Graves T., Harmon G., Edwards J., Latreille P., Courtney L., Cloud J., Abbott A., Scott K., Johnson D., Minx P., Bentley D., Fulton B., Miller N., Greco T., Kemp K., Kramer J., Fulton L., Mardis E., Dante M., Pepin K., Hillier L.W., Nelson J., Spieth J., Ryan E., Andrews S., Geisel C., Layman D., Du H., Ali J., Berghoff A., Jones K., Drone K., Cotton M., Joshu C., Antonoiu B., Zidanic M., Strong C., Sun H., Lamar B., Yordan C., Ma P., Zhong J., Preston R., Vil D., Shekher M., Matero A., Shah R., Swaby I.K., O'Shaughnessy A., Rodriguez M., Hoffman J., Till S., Granat S., Shohdy N., Hasegawa A., Hameed A., Lodhi M., Johnson A., Chen E., Marra M.A., Martienssen R., McCombie W.R.
      Nature 402:769-777(1999) [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. "Arabidopsis ORF clones."
      De Los Reyes C., Quan R., Chen H., Bautista V.R., Kim C.J., Ecker J.R.
      Submitted (JUN-2008) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
      Strain: cv. Columbia.
    5. "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] OF 54-531.
      Strain: cv. Columbia.
    6. "Genetic evidence that the endodermis is essential for shoot gravitropism in Arabidopsis thaliana."
      Fukaki H., Wysocka-Diller J.W., Kato T., Fujisawa H., Benfey P.N., Tasaka M.
      Plant J. 14:425-430(1998) [PubMed] [Europe PMC] [Abstract]
      Cited for: IDENTIFICATION, FUNCTION.
    7. "Intercellular movement of the putative transcription factor SHR in root patterning."
      Nakajima K., Sena G., Nawy T., Benfey P.N.
      Nature 413:307-311(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: TISSUE SPECIFICITY, SUBCELLULAR LOCATION, TRANSLOCATION.
    8. "SCARECROW is involved in positioning the stem cell niche in the Arabidopsis root meristem."
      Sabatini S., Heidstra R., Wildwater M., Scheres B.
      Genes Dev. 17:354-358(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION.
    9. "Mosaic analyses using marked activation and deletion clones dissect Arabidopsis SCARECROW action in asymmetric cell division."
      Heidstra R., Welch D., Scheres B.
      Genes Dev. 18:1964-1969(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, TISSUE SPECIFICITY.
    10. "A broad competence to respond to SHORT ROOT revealed by tissue-specific ectopic expression."
      Sena G., Jung J.W., Benfey P.N.
      Development 131:2817-2826(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: TISSUE SPECIFICITY, TRANSLOCATION.
    11. "Mechanisms regulating SHORT-ROOT intercellular movement."
      Gallagher K.L., Paquette A.J., Nakajima K., Benfey P.N.
      Curr. Biol. 14:1847-1851(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: SUBCELLULAR LOCATION, MUTAGENESIS OF THR-289.
    12. Cited for: FUNCTION, INTERACTION WITH SCR.
    13. "An evolutionarily conserved mechanism delimiting SHR movement defines a single layer of endodermis in plants."
      Cui H., Levesque M.P., Vernoux T., Jung J.W., Paquette A.J., Gallagher K.L., Wang J.Y., Blilou I., Scheres B., Benfey P.N.
      Science 316:421-425(2007) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, INTERACTION WITH SCR.
    14. "Arabidopsis JACKDAW and MAGPIE zinc finger proteins delimit asymmetric cell division and stabilize tissue boundaries by restricting SHORT-ROOT action."
      Welch D., Hassan H., Blilou I., Immink R., Heidstra R., Scheres B.
      Genes Dev. 21:2196-2204(2007) [PubMed] [Europe PMC] [Abstract]
      Cited for: INTERACTION WITH JKD AND MGP.
    15. Cited for: INTERACTION WITH SCR AND SCL23.

    Entry informationi

    Entry nameiSHR_ARATH
    AccessioniPrimary (citable) accession number: Q9SZF7
    Secondary accession number(s): B3DNN8, Q8RU28
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: April 8, 2008
    Last sequence update: May 1, 2000
    Last modified: October 1, 2014
    This is version 84 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programPlant Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    Moves from the stele into the adjacent cell layer where it locates in the nucleus to controls SCR transcription and endodermis specification.

    Keywords - Technical termi

    Complete proteome, Reference proteome

    Documents

    1. Arabidopsis thaliana
      Arabidopsis thaliana: entries and gene names
    2. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3