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Protein

Zinc finger protein ZIC 3

Gene

zic3

Organism
Xenopus laevis (African clawed frog)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at transcript leveli

Functioni

Probably acts as a transcriptional activator. May bind to the minimal GLI-consensus sequence 5'-GGGTGGTC-3'. Can determine the ectodermal cell fate and promote the earliest step of neural and neural crest development. Involved in establishing left-right asymmetry in the embryo.3 Publications

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri222 – 25736C2H2-type 1; atypicalPROSITE-ProRule annotationAdd
BLAST
Zinc fingeri266 – 29328C2H2-type 2; atypicalPROSITE-ProRule annotationAdd
BLAST
Zinc fingeri299 – 32325C2H2-type 3PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri329 – 35325C2H2-type 4PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri359 – 38123C2H2-type 5PROSITE-ProRule annotationAdd
BLAST

GO - Molecular functioni

GO - Biological processi

  • determination of left/right symmetry Source: UniProtKB
  • embryonic axis specification Source: UniProtKB
  • nervous system development Source: UniProtKB-KW
  • neural crest cell fate commitment Source: UniProtKB
  • positive regulation of transcription, DNA-templated Source: UniProtKB
  • positive regulation of transcription from RNA polymerase II promoter Source: UniProtKB
  • transcription, DNA-templated Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Activator, Developmental protein

Keywords - Biological processi

Differentiation, Neurogenesis, Transcription, Transcription regulation

Keywords - Ligandi

DNA-binding, Metal-binding, Zinc

Names & Taxonomyi

Protein namesi
Recommended name:
Zinc finger protein ZIC 3
Short name:
XZic3
Short name:
XlZic3
Alternative name(s):
Zinc finger protein Zic3-A
Zinc finger protein of the cerebellum 3
Gene namesi
Name:zic3
Synonyms:zic3-a
OrganismiXenopus laevis (African clawed frog)
Taxonomic identifieri8355 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiAmphibiaBatrachiaAnuraPipoideaPipidaeXenopodinaeXenopusXenopus

Organism-specific databases

XenbaseiXB-GENE-865376. zic3.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 441441Zinc finger protein ZIC 3PRO_0000047252Add
BLAST

Expressioni

Tissue specificityi

First detected at early gastrula (stage 10.25) in the dorsal lip and prospective neural plate. Also expressed in the mesoderm at early gastrulation, with expression strongest on the dorsal side. Mesodermal expression continues at stage 12 but is hardly detectable after stage 14. As gastrulation proceeds, expression decreases in the dorsal lip and increases in the prospective neural plate. At the neural plate stage (stage 14), expressed strongly in the prospective mesencephalon and anterior rhombencephalon, after which expression becomes stronger in the anterior neural folds. At early tailbud stage (stage 20), expression becomes restricted to the dorsal region of forebrain, midbrain and hindbrain, and weakly to the dorsal trunk. After mid-tailbud stage, expression decreases in the diencephalon, appears in the lateral mesoderm of the tailbud region and becomes restricted in the dorsal part of the neural tube.3 Publications

Developmental stagei

Expressed zygotically. First expressed from the late blastula.3 Publications

Inductioni

By dvr1/vg1, activin and t/bra in the mesoderm. By heteromeric AP-1 (fos/jun) during activin signaling. By increases in Ca2+ in the dorsal ectoderm, triggered by planar signals from the mesoderm. Suppressed by bmp-signaling. By pbx1 and meis1. By zic1, zic2 and zic3 but not zic5.7 Publications

Structurei

3D structure databases

ProteinModelPortaliO57311.
SMRiO57311. Positions 216-382.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domaini

The C2H2-type 3, 4 and 5 zinc finger domains are necessary for transcription activation (By similarity). The zinc fingers and the N-terminus are independently important for establishing the L/R axis.By similarity1 Publication

Sequence similaritiesi

Contains 5 C2H2-type zinc fingers.PROSITE-ProRule annotation

Zinc finger

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri222 – 25736C2H2-type 1; atypicalPROSITE-ProRule annotationAdd
BLAST
Zinc fingeri266 – 29328C2H2-type 2; atypicalPROSITE-ProRule annotationAdd
BLAST
Zinc fingeri299 – 32325C2H2-type 3PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri329 – 35325C2H2-type 4PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri359 – 38123C2H2-type 5PROSITE-ProRule annotationAdd
BLAST

Keywords - Domaini

Repeat, Zinc-finger

Phylogenomic databases

HOVERGENiHBG007135.
KOiK18487.

Family and domain databases

Gene3Di3.30.160.60. 4 hits.
InterProiIPR007087. Znf_C2H2.
IPR015880. Znf_C2H2-like.
IPR013087. Znf_C2H2/integrase_DNA-bd.
[Graphical view]
PfamiPF00096. zf-C2H2. 2 hits.
[Graphical view]
SMARTiSM00355. ZnF_C2H2. 5 hits.
[Graphical view]
PROSITEiPS00028. ZINC_FINGER_C2H2_1. 3 hits.
PS50157. ZINC_FINGER_C2H2_2. 4 hits.
[Graphical view]

Sequencei

Sequence statusi: Complete.

O57311-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTMLLDGGPQ FPTLGVGGFG TARHHEMSNR DAGMGLNPFT EPSHAAAFKL
60 70 80 90 100
SPASHDLSSS QSSAFTPQAS GYASSLGHHA GQVPSYGGAA FNSTRDFLFR
110 120 130 140 150
NRNSGIADSS SAGSQHGLFA NHGPPGIGEP PGHLIFPGLH EQSSSHTSSN
160 170 180 190 200
GHVVNGQMHL GLRGDIFGRP DPYRAVPSPR TDHYAAAQFH NYNHMNMSMN
210 220 230 240 250
VAAHHGQGAF FRYMRQPIKQ ELSCKWLEES TMNHPQKTCD RTFSSMHELV
260 270 280 290 300
THMTMEHVGG PEQNNHICYW EECPRGGKSF KAKYKLVNHI RVHTGEKPFP
310 320 330 340 350
CPFPGCGKIF ARSENLKIHK RTHTGEKPFK CEFEGCDRRF ANSSDRKKHM
360 370 380 390 400
HVHTSDKPYI CKVCDKSYTH PSSLRKHMKV HESQGSDSSP AASSGYESAT
410 420 430 440
PPAMVSANSE EPSKNSSATH QTNNNSHNTG LLPPNFNEWY V
Length:441
Mass (Da):48,485
Last modified:February 10, 2009 - v3
Checksum:i5D7959E98217E886
GO

Sequence cautioni

The sequence AAH57699.2 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti17 – 171G → R in AAG09377 (PubMed:15557819).Curated
Sequence conflicti74 – 741S → N in BAA23874 (PubMed:9342348).Curated
Sequence conflicti207 – 2071Q → P in BAA23874 (PubMed:9342348).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB005292 mRNA. Translation: BAA23874.2.
BC057699 mRNA. Translation: AAH57699.2. Different initiation.
BC082617 mRNA. Translation: AAH82617.1.
AF179297 Genomic DNA. Translation: AAG09377.1.
AF506277 Genomic DNA. Translation: AAP20808.1.
AF506278 Genomic DNA. Translation: AAP20809.1.
RefSeqiNP_001081088.1. NM_001087619.1.
UniGeneiXl.7969.

Genome annotation databases

GeneIDi394375.
KEGGixla:394375.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB005292 mRNA. Translation: BAA23874.2.
BC057699 mRNA. Translation: AAH57699.2. Different initiation.
BC082617 mRNA. Translation: AAH82617.1.
AF179297 Genomic DNA. Translation: AAG09377.1.
AF506277 Genomic DNA. Translation: AAP20808.1.
AF506278 Genomic DNA. Translation: AAP20809.1.
RefSeqiNP_001081088.1. NM_001087619.1.
UniGeneiXl.7969.

3D structure databases

ProteinModelPortaliO57311.
SMRiO57311. Positions 216-382.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi394375.
KEGGixla:394375.

Organism-specific databases

CTDi7547.
XenbaseiXB-GENE-865376. zic3.

Phylogenomic databases

HOVERGENiHBG007135.
KOiK18487.

Family and domain databases

Gene3Di3.30.160.60. 4 hits.
InterProiIPR007087. Znf_C2H2.
IPR015880. Znf_C2H2-like.
IPR013087. Znf_C2H2/integrase_DNA-bd.
[Graphical view]
PfamiPF00096. zf-C2H2. 2 hits.
[Graphical view]
SMARTiSM00355. ZnF_C2H2. 5 hits.
[Graphical view]
PROSITEiPS00028. ZINC_FINGER_C2H2_1. 3 hits.
PS50157. ZINC_FINGER_C2H2_2. 4 hits.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Xenopus Zic3, a primary regulator both in neural and neural crest development."
    Nakata K., Nagai T., Aruga J., Mikoshiba K.
    Proc. Natl. Acad. Sci. U.S.A. 94:11980-11985(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, TISSUE SPECIFICITY, DEVELOPMENTAL STAGE, INDUCTION.
    Tissue: Neurula.
  2. Nakata K., Nagai T., Aruga J., Mikoshiba K.
    Submitted (NOV-1999) to the EMBL/GenBank/DDBJ databases
    Cited for: SEQUENCE REVISION TO 17.
  3. NIH - Xenopus Gene Collection (XGC) project
    Submitted (SEP-2004) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Tissue: Gastrula.
  4. "Transcriptional regulation of Zic3 by heterodimeric AP-1(c-Jun/c-Fos) during Xenopus development."
    Lee S.Y., Lee H.-S., Moon J.-S., Kim J.-I., Park J.-B., Lee J.-Y., Park M.J., Kim J.
    Exp. Mol. Med. 36:468-475(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-33, INDUCTION.
  5. "Identification of a phylogenetically conserved activin-responsive enhancer in the Zic3 gene."
    Weber J.R., Sokol S.Y.
    Mech. Dev. 120:955-964(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 319-331 AND 374-386.
  6. "Xenopus Zic family and its role in neural and neural crest development."
    Nakata K., Nagai T., Aruga J., Mikoshiba K.
    Mech. Dev. 75:43-51(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: DEVELOPMENTAL STAGE.
  7. "Zic3 is involved in the left-right specification of the Xenopus embryo."
    Kitaguchi T., Nagai T., Nakata K., Aruga J., Mikoshiba K.
    Development 127:4787-4795(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, TISSUE SPECIFICITY, DOMAIN, INDUCTION.
  8. "A novel member of the Xenopus Zic family, Zic5, mediates neural crest development."
    Nakata K., Koyabu Y., Aruga J., Mikoshiba K.
    Mech. Dev. 99:83-91(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: INDUCTION.
  9. "Xenopus Brachyury regulates mesodermal expression of Zic3, a gene controlling left-right asymmetry."
    Kitaguchi T., Mizugishi K., Hatayama M., Aruga J., Mikoshiba K.
    Dev. Growth Differ. 44:55-61(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, INDUCTION.
  10. "Calcium transients triggered by planar signals induce the expression of ZIC3 gene during neural induction in Xenopus."
    Leclerc C., Lee M., Webb S.E., Moreau M., Miller A.L.
    Dev. Biol. 261:381-390(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: INDUCTION.
  11. "Pbx1 and Meis1 regulate activity of the Xenopus laevis Zic3 promoter through a highly conserved region."
    Kelly L.E., Carrel T.L., Herman G.E., El-Hodiri H.M.
    Biochem. Biophys. Res. Commun. 344:1031-1037(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: INDUCTION.
  12. "Xenopus Zic4: conservation and diversification of expression profiles and protein function among the Xenopus Zic family."
    Fujimi T.J., Mikoshiba K., Aruga J.
    Dev. Dyn. 235:3379-3386(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: TISSUE SPECIFICITY, DEVELOPMENTAL STAGE.

Entry informationi

Entry nameiZIC3_XENLA
AccessioniPrimary (citable) accession number: O57311
Secondary accession number(s): Q640K7
, Q6PF77, Q7ZZN6, Q7ZZN7, Q9DG65
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 2, 2004
Last sequence update: February 10, 2009
Last modified: October 14, 2015
This is version 88 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Documents

  1. 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.