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Q700D2

- JKD_ARATH

UniProt

Q700D2 - JKD_ARATH

Protein

Zinc finger protein JACKDAW

Gene

JKD

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 95 (01 Oct 2014)
      Sequence version 1 (05 Jul 2004)
      Previous versions | rss
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    Functioni

    Probable transcription factor that regulates tissue boundaries and asymmetric cell division by a rapid up-regulation of 'SCARECROW' (SCR), thus controlling the nuclear localization of 'SHORT-ROOT' (SHR) and restricting its action. Required for radial patterning and stem cell maintenance. Counteracted by 'MAGPIE' (MGP).1 Publication

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Zinc fingeri82 – 10423C2H2-type 1PROSITE-ProRule annotationAdd
    BLAST
    Zinc fingeri159 – 18224C2H2-type 2; degeneratePROSITE-ProRule annotationAdd
    BLAST

    GO - Molecular functioni

    1. DNA binding Source: UniProtKB-KW
    2. metal ion binding Source: UniProtKB-KW
    3. protein binding Source: IntAct
    4. protein homodimerization activity Source: TAIR
    5. sequence-specific DNA binding transcription factor activity Source: TAIR

    GO - Biological processi

    1. regulation of cell division Source: TAIR
    2. regulation of epidermal cell differentiation Source: TAIR
    3. regulation of meristem growth Source: TAIR
    4. regulation of transcription, DNA-templated Source: TAIR
    5. root development Source: TAIR
    6. transcription, DNA-templated Source: UniProtKB-KW

    Keywords - Biological processi

    Transcription, Transcription regulation

    Keywords - Ligandi

    DNA-binding, Metal-binding, Zinc

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Zinc finger protein JACKDAW
    Alternative name(s):
    ID1-like zinc finger protein 3
    Gene namesi
    Name:JKD
    Synonyms:IDZ3
    Ordered Locus Names:At5g03150
    ORF Names:F15A17.180
    OrganismiArabidopsis thaliana (Mouse-ear cress)
    Taxonomic identifieri3702 [NCBI]
    Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
    ProteomesiUP000006548: Chromosome 5

    Organism-specific databases

    TAIRiAT5G03150.

    Subcellular locationi

    Nucleus 1 Publication

    GO - Cellular componenti

    1. nucleus Source: UniProtKB-SubCell

    Keywords - Cellular componenti

    Nucleus

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 503503Zinc finger protein JACKDAWPRO_0000337840Add
    BLAST

    Proteomic databases

    PaxDbiQ700D2.
    PRIDEiQ700D2.

    Expressioni

    Tissue specificityi

    Expressed in the quiescent center, the ground tissue stem cells and to a lesser extent in mature cortex and endodermis cells.1 Publication

    Developmental stagei

    Start to accumulate during the 16- to 32-cell stage of embryogenesis.1 Publication

    Gene expression databases

    GenevestigatoriQ700D2.

    Interactioni

    Subunit structurei

    Interacts with SHR, SCR, MGP and itself.1 Publication

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    MGPQ9ZWA63EBI-1568562,EBI-1568600

    Protein-protein interaction databases

    IntActiQ700D2. 3 interactions.

    Structurei

    3D structure databases

    ProteinModelPortaliQ700D2.
    SMRiQ700D2. Positions 72-213.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Compositional bias

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Compositional biasi222 – 24524Asn-richAdd
    BLAST
    Compositional biasi300 – 415116Ser-richAdd
    BLAST

    Sequence similaritiesi

    Contains 2 C2H2-type zinc fingers.PROSITE-ProRule annotation

    Zinc finger

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Zinc fingeri82 – 10423C2H2-type 1PROSITE-ProRule annotationAdd
    BLAST
    Zinc fingeri159 – 18224C2H2-type 2; degeneratePROSITE-ProRule annotationAdd
    BLAST

    Keywords - Domaini

    Repeat, Zinc-finger

    Phylogenomic databases

    eggNOGiNOG331143.
    HOGENOMiHOG000237608.
    InParanoidiQ700D2.
    OMAiMASTGNH.
    PhylomeDBiQ700D2.

    Family and domain databases

    Gene3Di3.30.160.60. 2 hits.
    InterProiIPR007087. Znf_C2H2.
    IPR015880. Znf_C2H2-like.
    IPR013087. Znf_C2H2/integrase_DNA-bd.
    [Graphical view]
    PfamiPF00096. zf-C2H2. 1 hit.
    [Graphical view]
    SMARTiSM00355. ZnF_C2H2. 3 hits.
    [Graphical view]
    PROSITEiPS00028. ZINC_FINGER_C2H2_1. 1 hit.
    PS50157. ZINC_FINGER_C2H2_2. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    Q700D2-1 [UniParc]FASTAAdd to Basket

    « Hide

    MQMIPGDPFS ISSSMGGFVH QETHLHHLQQ QIPDLNPNSN PNPNAKPNSS    50
    SAKKKRNQPG TPDPDADVIA LSPTTLMATN RFVCEICNKG FQRDQNLQLH 100
    RRGHNLPWKL KQRSKQEVIK KKVYICPIKT CVHHDASRAL GDLTGIKKHY 150
    SRKHGEKKWK CEKCSKKYAV QSDWKAHAKT CGTREYKCDC GTLFSRKDSF 200
    ITHRAFCDAL TEEGARMSSL SNNNPVISTT NLNFGNESNV MNNPNLPHGF 250
    VHRGVHHPDI NAAISQFGLG FGHDLSAMHA QGLSEMVQMA STGNHHLFPS 300
    SSSSLPDFSG HHQFQIPMTS TNPSLTLSSS STSQQTSASL QHQTLKDSSF 350
    SPLFSSSSEN KQNKPLSPMS ATALLQKAAQ MGSTRSNSST APSFFAGPTM 400
    TSSSATASPP PRSSSPMMIQ QQLNNFNTNV LRENHNRAPP PLSGVSTSSV 450
    DNNPFQSNRS GLNPAQQMGL TRDFLGVSNE HHPHQTGRRP FLPQELARFA 500
    PLG 503
    Length:503
    Mass (Da):55,201
    Last modified:July 5, 2004 - v1
    Checksum:i49F387E021AB0A97
    GO

    Sequence cautioni

    The sequence BAB08375.1 differs from that shown. Reason: Erroneous gene model prediction.
    The sequence CAB86082.1 differs from that shown. Reason: Erroneous gene model prediction.

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti435 – 4351H → R in BAF00785. 1 PublicationCurated

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AY568665 mRNA. Translation: AAS79555.1.
    AJ630493 mRNA. Translation: CAG25866.1.
    AJ621494 mRNA. Translation: CAF18563.1.
    AB005240 Genomic DNA. Translation: BAB08375.1. Sequence problems.
    AL163002 Genomic DNA. Translation: CAB86082.1. Sequence problems.
    CP002688 Genomic DNA. Translation: AED90561.1.
    AK228895 mRNA. Translation: BAF00785.1.
    PIRiT48336.
    RefSeqiNP_195935.2. NM_120393.5.
    UniGeneiAt.1592.

    Genome annotation databases

    EnsemblPlantsiAT5G03150.1; AT5G03150.1; AT5G03150.
    GeneIDi831919.
    KEGGiath:AT5G03150.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AY568665 mRNA. Translation: AAS79555.1 .
    AJ630493 mRNA. Translation: CAG25866.1 .
    AJ621494 mRNA. Translation: CAF18563.1 .
    AB005240 Genomic DNA. Translation: BAB08375.1 . Sequence problems.
    AL163002 Genomic DNA. Translation: CAB86082.1 . Sequence problems.
    CP002688 Genomic DNA. Translation: AED90561.1 .
    AK228895 mRNA. Translation: BAF00785.1 .
    PIRi T48336.
    RefSeqi NP_195935.2. NM_120393.5.
    UniGenei At.1592.

    3D structure databases

    ProteinModelPortali Q700D2.
    SMRi Q700D2. Positions 72-213.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    IntActi Q700D2. 3 interactions.

    Proteomic databases

    PaxDbi Q700D2.
    PRIDEi Q700D2.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblPlantsi AT5G03150.1 ; AT5G03150.1 ; AT5G03150 .
    GeneIDi 831919.
    KEGGi ath:AT5G03150.

    Organism-specific databases

    TAIRi AT5G03150.

    Phylogenomic databases

    eggNOGi NOG331143.
    HOGENOMi HOG000237608.
    InParanoidi Q700D2.
    OMAi MASTGNH.
    PhylomeDBi Q700D2.

    Gene expression databases

    Genevestigatori Q700D2.

    Family and domain databases

    Gene3Di 3.30.160.60. 2 hits.
    InterProi IPR007087. Znf_C2H2.
    IPR015880. Znf_C2H2-like.
    IPR013087. Znf_C2H2/integrase_DNA-bd.
    [Graphical view ]
    Pfami PF00096. zf-C2H2. 1 hit.
    [Graphical view ]
    SMARTi SM00355. ZnF_C2H2. 3 hits.
    [Graphical view ]
    PROSITEi PS00028. ZINC_FINGER_C2H2_1. 1 hit.
    PS50157. ZINC_FINGER_C2H2_2. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. Cited for: NUCLEOTIDE SEQUENCE [MRNA].
    2. "INDETERMINATE1-like genes in Arabidopsis."
      Dewald M., Fritz J., Merkle T.
      Submitted (JAN-2004) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [MRNA].
    3. "Structural analysis of Arabidopsis thaliana chromosome 5. I. Sequence features of the 1.6 Mb regions covered by twenty physically assigned P1 clones."
      Sato S., Kotani H., Nakamura Y., Kaneko T., Asamizu E., Fukami M., Miyajima N., Tabata S.
      DNA Res. 4:215-230(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: cv. Columbia.
    4. "Sequence and analysis of chromosome 5 of the plant Arabidopsis thaliana."
      Tabata S., Kaneko T., Nakamura Y., Kotani H., Kato T., Asamizu E., Miyajima N., Sasamoto S., Kimura T., Hosouchi T., Kawashima K., Kohara M., Matsumoto M., Matsuno A., Muraki A., Nakayama S., Nakazaki N., Naruo K.
      , Okumura S., Shinpo S., Takeuchi C., Wada T., Watanabe A., Yamada M., Yasuda M., Sato S., de la Bastide M., Huang E., Spiegel L., Gnoj L., O'Shaughnessy A., Preston R., Habermann K., Murray J., Johnson D., Rohlfing T., Nelson J., Stoneking T., Pepin K., Spieth J., Sekhon M., Armstrong J., Becker M., Belter E., Cordum H., Cordes M., Courtney L., Courtney W., Dante M., Du H., Edwards J., Fryman J., Haakensen B., Lamar E., Latreille P., Leonard S., Meyer R., Mulvaney E., Ozersky P., Riley A., Strowmatt C., Wagner-McPherson C., Wollam A., Yoakum M., Bell M., Dedhia N., Parnell L., Shah R., Rodriguez M., Hoon See L., Vil D., Baker J., Kirchoff K., Toth K., King L., Bahret A., Miller B., Marra M.A., Martienssen R., McCombie W.R., Wilson R.K., Murphy G., Bancroft I., Volckaert G., Wambutt R., Duesterhoeft A., Stiekema W., Pohl T., Entian K.-D., Terryn N., Hartley N., Bent E., Johnson S., Langham S.-A., McCullagh B., Robben J., Grymonprez B., Zimmermann W., Ramsperger U., Wedler H., Balke K., Wedler E., Peters S., van Staveren M., Dirkse W., Mooijman P., Klein Lankhorst R., Weitzenegger T., Bothe G., Rose M., Hauf J., Berneiser S., Hempel S., Feldpausch M., Lamberth S., Villarroel R., Gielen J., Ardiles W., Bents O., Lemcke K., Kolesov G., Mayer K.F.X., Rudd S., Schoof H., Schueller C., Zaccaria P., Mewes H.-W., Bevan M., Fransz P.F.
      Nature 408:823-826(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: cv. Columbia.
    5. The Arabidopsis Information Resource (TAIR)
      Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases
      Cited for: GENOME REANNOTATION.
      Strain: cv. Columbia.
    6. "Large-scale analysis of RIKEN Arabidopsis full-length (RAFL) cDNAs."
      Totoki Y., Seki M., Ishida J., Nakajima M., Enju A., Kamiya A., Narusaka M., Shin-i T., Nakagawa M., Sakamoto N., Oishi K., Kohara Y., Kobayashi M., Toyoda A., Sakaki Y., Sakurai T., Iida K., Akiyama K.
      , Satou M., Toyoda T., Konagaya A., Carninci P., Kawai J., Hayashizaki Y., Shinozaki K.
      Submitted (JUL-2006) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 7-503.
      Strain: cv. Columbia.
    7. "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: FUNCTION, TISSUE SPECIFICITY, DEVELOPMENTAL STAGE, SUBCELLULAR LOCATION, INTERACTION WITH SHR; SCR; MGP AND ITSELF.

    Entry informationi

    Entry nameiJKD_ARATH
    AccessioniPrimary (citable) accession number: Q700D2
    Secondary accession number(s): Q0WQ14, Q9FYN0, Q9LYX0
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: June 10, 2008
    Last sequence update: July 5, 2004
    Last modified: October 1, 2014
    This is version 95 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programPlant Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    Early initiation of expression in ground tissue is SHR- and SCR-independent but later maintenance becomes dependent on both.

    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