Zic3 (Zic family member 3) - Rat Genome Database

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Gene: Zic3 (Zic family member 3) Rattus norvegicus
Analyze
Symbol: Zic3
Name: Zic family member 3 (Ensembl:zinc finger protein of the cerebellum 3)
RGD ID: 1561261
Description: Predicted to enable DNA-binding transcription activator activity, RNA polymerase II-specific; RNA polymerase II cis-regulatory region sequence-specific DNA binding activity; and transcription coactivator activity. Predicted to be involved in several processes, including nervous system development; regionalization; and regulation of DNA-templated transcription. Predicted to act upstream of or within anterior/posterior pattern specification; heart looping; and positive regulation of transcription by RNA polymerase II. Predicted to be located in cytoplasm and nucleoplasm. Predicted to be active in nucleus. Human ortholog(s) of this gene implicated in X-linked VACTERL association; situs inversus; and visceral heterotaxy. Orthologous to human ZIC3 (Zic family member 3); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 3,7-dihydropurine-6-thione; bisphenol A.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC367944; RGD1561261; similar to Zinc finger protein ZIC 3 (Zinc finger protein of the cerebellum 3); Zic family member 3 (odd-paired homolog, Drosophila); zinc finger protein of the cerebellum 3; zinc finger protein ZIC 3
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2X136,123,662 - 136,134,295 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX136,124,026 - 136,134,746 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_UtxX138,319,794 - 138,329,814 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0X141,857,250 - 141,867,266 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0X139,427,350 - 139,437,366 (+)NCBIRnor_WKY
Rnor_6.0X140,875,191 - 140,888,344 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX140,878,216 - 140,888,795 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X140,918,894 - 140,931,861 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X143,128,118 - 143,139,155 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
CeleraX132,262,545 - 132,272,607 (+)NCBICelera
Cytogenetic MapXq36NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
anterior/posterior pattern specification  (ISO)
atrial cardiac muscle tissue development  (ISO)
axial mesoderm development  (ISO)
biological_process  (ND)
central nervous system development  (IBA)
central nervous system segmentation  (ISO)
cranial skeletal system development  (ISO)
determination of digestive tract left/right asymmetry  (ISO)
determination of left/right asymmetry in nervous system  (ISO)
determination of left/right symmetry  (ISO)
determination of liver left/right asymmetry  (ISO)
determination of pancreatic left/right asymmetry  (ISO)
embryonic pattern specification  (ISO)
face development  (ISO)
forebrain development  (ISO)
gastrulation  (ISO)
gene expression  (ISO)
germ-line stem cell population maintenance  (ISO)
heart development  (ISO)
heart looping  (ISO)
hippocampus development  (ISO)
left/right axis specification  (ISO)
left/right pattern formation  (ISO)
limb morphogenesis  (ISO)
lung development  (ISO)
maintenance of cell number  (ISO)
mesoderm development  (ISO)
mRNA transcription by RNA polymerase II  (ISO)
neural plate development  (ISO)
neuron differentiation  (ISO)
olfactory bulb development  (ISO)
outer ear morphogenesis  (ISO)
paraxial mesoderm development  (ISO)
pattern specification process  (ISO)
positive regulation of DNA-templated transcription  (ISO)
positive regulation of transcription by RNA polymerase II  (IBA,ISO)
primitive streak formation  (ISO)
regulation of DNA-binding transcription factor activity  (ISO)
regulation of transcription by RNA polymerase II  (IBA)
skeletal system development  (ISO)
smoothened signaling pathway  (ISO)
stem cell differentiation  (ISO)
stem cell population maintenance  (ISO)

Cellular Component
cellular_component  (ND)
cytoplasm  (ISO)
nucleoplasm  (ISO)
nucleus  (IBA,ISO)

References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. X-linked situs abnormalities result from mutations in ZIC3. Gebbia M, etal., Nat Genet. 1997 Nov;17(3):305-8.
3. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
4. Preaxial polydactyly caused by Gli3 haploinsufficiency is rescued by Zic3 loss of function in mice. Quinn ME, etal., Hum Mol Genet. 2012 Apr 15;21(8):1888-96. doi: 10.1093/hmg/dds002. Epub 2012 Jan 10.
5. GOA pipeline RGD automated data pipeline
6. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
7. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
8. Comprehensive gene review and curation RGD comprehensive gene curation
Additional References at PubMed
PMID:11053430   PMID:11238441   PMID:11959836   PMID:15207726   PMID:15384171   PMID:16496285   PMID:17764085   PMID:18298960  


Genomics

Comparative Map Data
Zic3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2X136,123,662 - 136,134,295 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX136,124,026 - 136,134,746 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_UtxX138,319,794 - 138,329,814 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0X141,857,250 - 141,867,266 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0X139,427,350 - 139,437,366 (+)NCBIRnor_WKY
Rnor_6.0X140,875,191 - 140,888,344 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX140,878,216 - 140,888,795 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X140,918,894 - 140,931,861 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X143,128,118 - 143,139,155 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
CeleraX132,262,545 - 132,272,607 (+)NCBICelera
Cytogenetic MapXq36NCBI
ZIC3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38X137,566,127 - 137,577,691 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 EnsemblX137,566,127 - 137,577,691 (+)EnsemblGRCh38hg38GRCh38
GRCh37X136,648,286 - 136,659,850 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36X136,476,012 - 136,481,925 (+)NCBINCBI36Build 36hg18NCBI36
Build 34X136,373,865 - 136,379,777NCBI
CeleraX137,014,356 - 137,020,269 (+)NCBICelera
Cytogenetic MapXq26.3NCBI
HuRefX125,916,990 - 125,922,902 (+)NCBIHuRef
CHM1_1X136,559,744 - 136,565,657 (+)NCBICHM1_1
T2T-CHM13v2.0X135,876,075 - 135,887,645 (+)NCBIT2T-CHM13v2.0
Zic3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X57,075,988 - 57,081,990 (+)NCBIGRCm39GRCm39mm39
GRCm39 EnsemblX57,068,060 - 57,087,096 (+)EnsemblGRCm39 Ensembl
GRCm38X58,030,628 - 58,036,630 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX58,022,700 - 58,041,736 (+)EnsemblGRCm38mm10GRCm38
MGSCv37X55,283,805 - 55,289,807 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36X54,377,427 - 54,382,686 (+)NCBIMGSCv36mm8
CeleraX44,504,773 - 44,510,775 (+)NCBICelera
Cytogenetic MapXA6NCBI
cM MapX32.56NCBI
Zic3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554897,560,684 - 7,571,892 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554897,560,684 - 7,571,739 (-)NCBIChiLan1.0ChiLan1.0
ZIC3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1X136,954,024 - 136,968,240 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 EnsemblX136,954,024 - 136,967,819 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0X126,691,534 - 126,705,788 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
ZIC3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X107,822,002 - 107,833,582 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 EnsemblX107,821,948 - 107,833,597 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_TashaX93,648,940 - 93,660,520 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0X109,807,663 - 109,819,246 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 EnsemblX109,807,645 - 109,818,795 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1X106,941,593 - 106,953,174 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0X109,131,179 - 109,142,752 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0X108,775,722 - 108,787,305 (+)NCBIUU_Cfam_GSD_1.0
Zic3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X105,821,756 - 105,833,208 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365139,786,709 - 9,793,077 (-)EnsemblSpeTri2.0
SpeTri2.0NW_0049365139,780,895 - 9,792,865 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
ZIC3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX112,593,301 - 112,604,814 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1X112,592,951 - 112,605,087 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X128,551,482 - 128,563,009 (+)NCBISscrofa10.2Sscrofa10.2susScr3
ZIC3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X112,597,329 - 112,609,411 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 EnsemblX112,598,466 - 112,601,803 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366606550,341,148 - 50,352,637 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Zic3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248089,200,952 - 9,212,093 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248089,201,025 - 9,212,192 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Zic3
27 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:101
Count of miRNA genes:82
Interacting mature miRNAs:98
Transcripts:ENSRNOT00000019431
Prediction methods:Miranda, Pita, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1598837Memor13Memory QTL 133.2exploratory behavior trait (VT:0010471)difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)X41052407146860749Rat
1598872Memor14Memory QTL 144.5exploratory behavior trait (VT:0010471)difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)X93956491138956491Rat
738025Stresp3Stress response QTL 34.610.0066stress-related behavior trait (VT:0010451)defensive burying - approachX100567703150256146Rat
1598809Memor15Memory QTL 154.4exploratory behavior trait (VT:0010471)difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)X103312877148312877Rat
1598856Memor1Memory QTL 11.9exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)X103312877148312877Rat
738029Stresp2Stress response QTL 23.40.0004stress-related behavior trait (VT:0010451)defensive burying - approachX112934952138400867Rat
10059603Bw174Body weight QTL 1743.40.025body mass (VT:0001259)body weight (CMO:0000012)X113937816152453651Rat
634346Insul4Insulin level QTL 40blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)X126975089152453651Rat

Markers in Region
RH130454  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X136,129,289 - 136,129,480 (+)MAPPERmRatBN7.2
Rnor_6.0X140,883,479 - 140,883,669NCBIRnor6.0
Rnor_5.0X140,926,996 - 140,927,186UniSTSRnor5.0
RGSC_v3.4X143,133,707 - 143,133,897UniSTSRGSC3.4
CeleraX132,267,559 - 132,267,749UniSTS
RH 3.4 MapX971.3UniSTS
Cytogenetic MapXq36UniSTS
ZIC3  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X136,128,488 - 136,128,633 (+)MAPPERmRatBN7.2
Rnor_6.0X140,882,678 - 140,882,822NCBIRnor6.0
Rnor_5.0X140,926,195 - 140,926,339UniSTSRnor5.0
RGSC_v3.4X143,132,906 - 143,133,050UniSTSRGSC3.4
CeleraX132,266,758 - 132,266,902UniSTS
Cytogenetic MapXq36UniSTS


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system musculoskeletal system nervous system renal system reproductive system respiratory system
High
Medium 53
Low 1 2 3 1 1 1 21 1 16 1
Below cutoff 4 16 8 6 8 2 1 18 5

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000075840   ⟹   ENSRNOP00000067915
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX136,124,198 - 136,127,761 (+)Ensembl
Rnor_6.0 EnsemblX140,878,216 - 140,883,816 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000077026   ⟹   ENSRNOP00000068130
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX136,124,026 - 136,134,746 (+)Ensembl
Rnor_6.0 EnsemblX140,878,216 - 140,888,795 (+)Ensembl
RefSeq Acc Id: NM_001109019   ⟹   NP_001102489
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X136,124,276 - 136,134,295 (+)NCBI
Rnor_6.0X140,878,465 - 140,888,344 (+)NCBI
Rnor_5.0X140,918,894 - 140,931,861 (+)NCBI
RGSC_v3.4X143,128,118 - 143,139,155 (+)RGD
CeleraX132,262,545 - 132,272,607 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039099956   ⟹   XP_038955884
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X136,123,662 - 136,129,627 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001102489 (Get FASTA)   NCBI Sequence Viewer  
  NP_001398746 (Get FASTA)   NCBI Sequence Viewer  
  XP_038955884 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL86160 (Get FASTA)   NCBI Sequence Viewer  
  EDL86161 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001102489   ⟸   NM_001109019
- Sequence:
RefSeq Acc Id: ENSRNOP00000068130   ⟸   ENSRNOT00000077026
RefSeq Acc Id: ENSRNOP00000067915   ⟸   ENSRNOT00000075840
RefSeq Acc Id: XP_038955884   ⟸   XM_039099956
- Peptide Label: isoform X1
Protein Domains
C2H2-type

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-A0A096MIX7-F1-model_v2 AlphaFold A0A096MIX7 1-466 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1561261 AgrOrtholog
BioCyc Gene G2FUF-895 BioCyc
Ensembl Genes ENSRNOG00000000861 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000067915 ENTREZGENE
  ENSRNOP00000067915.2 UniProtKB/TrEMBL
  ENSRNOP00000068130.2 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000075840 ENTREZGENE
  ENSRNOT00000075840.3 UniProtKB/TrEMBL
  ENSRNOT00000077026.2 UniProtKB/TrEMBL
InterPro Znf_C2H2/integrase_DNA-bd UniProtKB/TrEMBL
  Znf_C2H2_sf UniProtKB/TrEMBL
  Znf_ZIC UniProtKB/TrEMBL
NCBI Gene 367944 ENTREZGENE
Pfam zf-C2H2 UniProtKB/TrEMBL
  zf_ZIC UniProtKB/TrEMBL
PhenoGen Zic3 PhenoGen
PROSITE ZINC_FINGER_C2H2_1 UniProtKB/TrEMBL
  ZINC_FINGER_C2H2_2 UniProtKB/TrEMBL
SMART ZnF_C2H2 UniProtKB/TrEMBL
Superfamily-SCOP SSF57667 UniProtKB/TrEMBL
UniProt A0A096MIX7 ENTREZGENE, UniProtKB/TrEMBL
  A0A096MJH5_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2011-08-01 Zic3  Zic family member 3  Zic3  Zic family member 3 (odd-paired homolog, Drosophila)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-09-25 Zic3  Zic family member 3 (odd-paired homolog, Drosophila)  Zic3  zinc finger protein of the cerebellum 3  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-02-29 Zic3  zinc finger protein of the cerebellum 3  RGD1561261_predicted  similar to Zinc finger protein ZIC 3 (Zinc finger protein of the cerebellum 3) (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-07 RGD1561261_predicted  similar to Zinc finger protein ZIC 3 (Zinc finger protein of the cerebellum 3) (predicted)  LOC367944  similar to Zinc finger protein ZIC 3 (Zinc finger protein of the cerebellum 3)  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC367944  similar to Zinc finger protein ZIC 3 (Zinc finger protein of the cerebellum 3)      Symbol and Name status set to provisional 70820 PROVISIONAL