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Protein

Zinc finger protein JACKDAW

Gene

JKD

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

Functioni

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(PubMed:17785527). Required for radial patterning and stem cell maintenance(PubMed:17785527). Counteracted by 'MAGPIE' (MGP)(PubMed:17785527). Binds to the SCR and MGP promoter sequences (PubMed:21935722). Controls position-dependent signals that regulate epidermal-cell-type patterning (PubMed:20356954).3 Publications

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri82 – 10423C2H2-type 1PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri124 – 15431C2H2-type 2CuratedAdd
BLAST
Zinc fingeri159 – 18325CCHC-type 1; atypicalCuratedAdd
BLAST
Zinc fingeri186 – 20924CCHC-type 2; atypicalCuratedAdd
BLAST

GO - Molecular functioni

  1. DNA binding Source: UniProtKB-KW
  2. metal ion binding Source: UniProtKB-KW
  3. protein homodimerization activity Source: TAIR
  4. 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
Complete GO annotation...

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 31 Publication
Protein indeterminate-domain 101 Publication
Gene namesi
Name:JKD
Synonyms:IDD101 Publication, IDZ31 Publication
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
Complete GO annotation...

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

Inductioni

Not regulated by SCR and SHR.1 Publication

Gene expression databases

GenevestigatoriQ700D2.

Interactioni

Subunit structurei

Interacts with SHR, SCR, MGP and itself (PubMed:17785527). Interacts with SIEL (PubMed:21924907).2 Publications

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.CuratedPROSITE-ProRule annotation
Contains 2 CCHC-type zinc fingers.Curated

Zinc finger

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri82 – 10423C2H2-type 1PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri124 – 15431C2H2-type 2CuratedAdd
BLAST
Zinc fingeri159 – 18325CCHC-type 1; atypicalCuratedAdd
BLAST
Zinc fingeri186 – 20924CCHC-type 2; atypicalCuratedAdd
BLAST

Keywords - Domaini

Repeat, Zinc-finger

Phylogenomic databases

eggNOGiNOG331143.
HOGENOMiHOG000237608.
InParanoidiQ700D2.
OMAiMNSSAMG.
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

        10         20         30         40         50
MQMIPGDPFS ISSSMGGFVH QETHLHHLQQ QIPDLNPNSN PNPNAKPNSS
60 70 80 90 100
SAKKKRNQPG TPDPDADVIA LSPTTLMATN RFVCEICNKG FQRDQNLQLH
110 120 130 140 150
RRGHNLPWKL KQRSKQEVIK KKVYICPIKT CVHHDASRAL GDLTGIKKHY
160 170 180 190 200
SRKHGEKKWK CEKCSKKYAV QSDWKAHAKT CGTREYKCDC GTLFSRKDSF
210 220 230 240 250
ITHRAFCDAL TEEGARMSSL SNNNPVISTT NLNFGNESNV MNNPNLPHGF
260 270 280 290 300
VHRGVHHPDI NAAISQFGLG FGHDLSAMHA QGLSEMVQMA STGNHHLFPS
310 320 330 340 350
SSSSLPDFSG HHQFQIPMTS TNPSLTLSSS STSQQTSASL QHQTLKDSSF
360 370 380 390 400
SPLFSSSSEN KQNKPLSPMS ATALLQKAAQ MGSTRSNSST APSFFAGPTM
410 420 430 440 450
TSSSATASPP PRSSSPMMIQ QQLNNFNTNV LRENHNRAPP PLSGVSTSSV
460 470 480 490 500
DNNPFQSNRS GLNPAQQMGL TRDFLGVSNE HHPHQTGRRP FLPQELARFA

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

Experimental Info

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

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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:
EMBLi
GenBanki
DDBJi
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.

3D structure databases

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

Protein-protein interaction databases

IntActiQ700D2. 3 interactions.

Proteomic databases

PaxDbiQ700D2.
PRIDEiQ700D2.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

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

Organism-specific databases

TAIRiAT5G03150.

Phylogenomic databases

eggNOGiNOG331143.
HOGENOMiHOG000237608.
InParanoidiQ700D2.
OMAiMNSSAMG.
PhylomeDBiQ700D2.

Gene expression databases

GenevestigatoriQ700D2.

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]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  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. "The maize INDETERMINATE1 flowering time regulator defines a highly conserved zinc finger protein family in higher plants."
    Colasanti J., Tremblay R., Wong A.Y., Coneva V., Kozaki A., Mable B.K.
    BMC Genomics 7:158-158(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: GENE FAMILY, NOMENCLATURE.
  8. "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.
  9. "JACKDAW controls epidermal patterning in the Arabidopsis root meristem through a non-cell-autonomous mechanism."
    Hassan H., Scheres B., Blilou I.
    Development 137:1523-1529(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  10. "An essential protein that interacts with endosomes and promotes movement of the SHORT-ROOT transcription factor."
    Koizumi K., Wu S., MacRae-Crerar A., Gallagher K.L.
    Curr. Biol. 21:1559-1564(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH SIEL.
  11. "Activity of transcription factor JACKDAW is essential for SHR/SCR-dependent activation of SCARECROW and MAGPIE and is modulated by reciprocal interactions with MAGPIE, SCARECROW and SHORT ROOT."
    Ogasawara H., Kaimi R., Colasanti J., Kozaki A.
    Plant Mol. Biol. 77:489-499(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, INDUCTION.

Entry informationi

Entry nameiIDD10_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: January 7, 2015
This is version 97 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

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 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.