Zic2 (Zic family member 2) - Rat Genome Database

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Gene: Zic2 (Zic family member 2) Rattus norvegicus
Analyze
Symbol: Zic2
Name: Zic family member 2
RGD ID: 1311174
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 chromatin DNA binding activity. Predicted to be involved in several processes, including nervous system development; regulation of DNA-templated transcription; and visual perception. Predicted to act upstream of or within several processes, including neural crest cell differentiation; neural tube closure; and nodal signaling pathway. Predicted to be located in cytoplasm and nuclear body. Predicted to be active in nucleus. Human ortholog(s) of this gene implicated in holoprosencephaly and holoprosencephaly 5. Orthologous to human ZIC2 (Zic family member 2); PARTICIPATES IN Hedgehog signaling pathway; INTERACTS WITH 17beta-estradiol; 2,3,7,8-Tetrachlorodibenzofuran; 6-propyl-2-thiouracil.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC361096; Zic family member 2 (odd-paired homolog, Drosophila); zinc finger protein of the cerebellum 2; zinc finger protein ZIC 2
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr815105,982,711 - 105,988,167 (+)NCBIGRCr8
mRatBN7.21599,576,697 - 99,581,522 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1599,576,697 - 99,581,522 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx15103,509,279 - 103,514,110 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.015104,604,163 - 104,609,002 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.015101,531,399 - 101,536,238 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.015108,908,366 - 108,913,812 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl15108,908,607 - 108,912,737 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.015112,296,472 - 112,301,371 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.415107,609,060 - 107,613,169 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.115107,624,839 - 107,629,424 (+)NCBI
Celera1598,350,700 - 98,355,483 (+)NCBICelera
Cytogenetic Map15q25NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
cytoplasm  (ISO)
nuclear body  (IEA,ISO)
nucleoplasm  (ISO)
nucleus  (ISO)

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. The genetic association database. Becker KG, etal., Nat Genet. 2004 May;36(5):431-2.
2. Immunolocalization of Zic2 expression in the developing mouse forebrain. Brown LY, etal., Gene Expr Patterns 2003 Jun;3(3):361-7.
3. Holoprosencephaly due to mutations in ZIC2, a homologue of Drosophila odd-paired. Brown SA, etal., Nat Genet. 1998 Oct;20(2):180-3.
4. Overlapping and distinct expression domains of Zic2 and Zic3 during mouse gastrulation. Elms P, etal., Gene Expr Patterns 2004 Sep;4(5):505-11.
5. 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.
6. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
7. Zic2 hypomorphic mutant mice as a schizophrenia model and ZIC2 mutations identified in schizophrenia patients. Hatayama M, etal., Sci Rep. 2011;1:16. doi: 10.1038/srep00016. Epub 2011 Jun 17.
8. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
9. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
10. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
11. GOA pipeline RGD automated data pipeline
12. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
13. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
14. Comprehensive gene review and curation RGD comprehensive gene curation
15. Comparison of mutation findings in ZIC2 between microform and classical holoprosencephaly in a Brazilian cohort. Ribeiro LA, etal., Birth Defects Res A Clin Mol Teratol. 2012 Nov;94(11):912-7. doi: 10.1002/bdra.23047. Epub 2012 Jul 27.
16. Zic2-associated holoprosencephaly is caused by a transient defect in the organizer region during gastrulation. Warr N, etal., Hum Mol Genet. 2008 Oct 1;17(19):2986-96. doi: 10.1093/hmg/ddn197. Epub 2008 Jul 9.
Additional References at PubMed
PMID:10677508   PMID:10932191   PMID:11053430   PMID:11238441   PMID:11756505   PMID:13678579   PMID:15207726   PMID:15384171   PMID:15465018   PMID:18068128   PMID:18298960   PMID:18755297  
PMID:20676059   PMID:24585447  


Genomics

Comparative Map Data
Zic2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr815105,982,711 - 105,988,167 (+)NCBIGRCr8
mRatBN7.21599,576,697 - 99,581,522 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1599,576,697 - 99,581,522 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx15103,509,279 - 103,514,110 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.015104,604,163 - 104,609,002 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.015101,531,399 - 101,536,238 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.015108,908,366 - 108,913,812 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl15108,908,607 - 108,912,737 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.015112,296,472 - 112,301,371 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.415107,609,060 - 107,613,169 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.115107,624,839 - 107,629,424 (+)NCBI
Celera1598,350,700 - 98,355,483 (+)NCBICelera
Cytogenetic Map15q25NCBI
ZIC2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381399,981,784 - 99,986,765 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1399,981,784 - 99,986,765 (+)EnsemblGRCh38hg38GRCh38
GRCh3713100,634,038 - 100,639,019 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361399,432,320 - 99,437,020 (+)NCBINCBI36Build 36hg18NCBI36
Build 341399,432,319 - 99,437,019NCBI
Celera1381,478,855 - 81,483,555 (+)NCBICelera
Cytogenetic Map13q32.3NCBI
HuRef1381,227,505 - 81,232,531 (+)NCBIHuRef
CHM1_113100,603,892 - 100,608,865 (+)NCBICHM1_1
T2T-CHM13v2.01399,192,694 - 99,197,676 (+)NCBIT2T-CHM13v2.0
Zic2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3914122,712,796 - 122,717,740 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl14122,712,847 - 122,717,264 (+)EnsemblGRCm39 Ensembl
GRCm3814122,475,384 - 122,480,328 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl14122,475,435 - 122,479,852 (+)EnsemblGRCm38mm10GRCm38
MGSCv3714122,874,606 - 122,879,550 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv3614121,610,615 - 121,615,032 (+)NCBIMGSCv36mm8
Celera14121,006,828 - 121,042,740 (+)NCBICelera
Cytogenetic Map14E5NCBI
cM Map1465.97NCBI
Zic2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_00495540410,731,987 - 10,735,599 (-)NCBIChiLan1.0ChiLan1.0
ZIC2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v214101,508,447 - 101,513,428 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan113100,175,671 - 100,180,672 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01381,151,669 - 81,156,648 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.113100,285,212 - 100,289,598 (+)NCBIpanpan1.1PanPan1.1panPan2
ZIC2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12249,948,743 - 49,952,007 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2249,948,778 - 49,950,055 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2249,729,321 - 49,734,051 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02250,390,470 - 50,395,205 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2250,390,481 - 50,394,094 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12250,040,527 - 50,045,249 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02250,074,149 - 50,078,870 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02250,111,170 - 50,115,894 (+)NCBIUU_Cfam_GSD_1.0
Zic2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404945185,347,014 - 185,350,047 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493647210,602,102 - 10,605,191 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493647210,599,717 - 10,605,187 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
ZIC2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1168,840,631 - 68,845,378 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11168,840,802 - 68,845,441 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21176,103,699 - 76,107,978 (+)NCBISscrofa10.2Sscrofa10.2susScr3
ZIC2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1378,631,556 - 78,637,422 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl378,631,530 - 78,636,548 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604635,132,313 - 35,137,417 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Zic2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462479311,163,916 - 11,167,457 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462479311,162,835 - 11,167,497 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Zic2
11 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:105
Count of miRNA genes:72
Interacting mature miRNAs:87
Transcripts:ENSRNOT00000066195
Prediction methods:Miranda, 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
631655Bp126Blood pressure QTL 1264arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1558156477101769107Rat
731177Uae26Urinary albumin excretion QTL 262.40.025urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)1567588667101769107Rat
2300326Plaw1Placental weight QTL 1150.005placenta mass (VT:0004257)placenta wet weight (CMO:0002088)1568327165100062518Rat
1641889Colcr6Colorectal carcinoma resistance QTL 62.90.0126intestine integrity trait (VT:0010554)benign colorectal tumor surface area measurement (CMO:0001799)157369051899794247Rat
2317055Aia10Adjuvant induced arthritis QTL 103.41joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)1575788062101769107Rat
1549844Bss7Bone structure and strength QTL 76.4femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)1575788062101769107Rat
70155Gcs1Gastric cancer susceptibility QTL13.8stomach morphology trait (VT:0000470)stomach tumor susceptibility score (CMO:0002043)1576306099101769107Rat

Markers in Region
UniSTS:144841  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21599,580,833 - 99,580,984 (+)MAPPERmRatBN7.2
Rnor_6.015108,913,124 - 108,913,274NCBIRnor6.0
Rnor_5.015112,300,683 - 112,300,833UniSTSRnor5.0
RGSC_v3.415107,612,956 - 107,613,106UniSTSRGSC3.4
Celera1598,354,795 - 98,354,945UniSTS
Cytogenetic Map15q25UniSTS
UniSTS:466092  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21599,579,908 - 99,580,217 (+)MAPPERmRatBN7.2
Rnor_6.015108,911,578 - 108,911,886NCBIRnor6.0
Rnor_5.015112,299,758 - 112,300,066UniSTSRnor5.0
RGSC_v3.415107,612,031 - 107,612,339UniSTSRGSC3.4
Celera1598,353,910 - 98,354,218UniSTS
Cytogenetic Map15q25UniSTS
UniSTS:496749  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21599,580,395 - 99,580,498 (+)MAPPERmRatBN7.2
Rnor_6.015108,912,686 - 108,912,788NCBIRnor6.0
Rnor_5.015112,300,245 - 112,300,347UniSTSRnor5.0
RGSC_v3.415107,612,518 - 107,612,620UniSTSRGSC3.4
Celera1598,354,357 - 98,354,459UniSTS
Cytogenetic Map15q25UniSTS


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

endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 70 1
Low 4 9
Below cutoff 8 7 1 7 3 3 4 19 2 3

Sequence


RefSeq Acc Id: ENSRNOT00000089455   ⟹   ENSRNOP00000069986
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1599,576,697 - 99,581,522 (+)Ensembl
Rnor_6.0 Ensembl15108,908,607 - 108,912,737 (+)Ensembl
RefSeq Acc Id: NM_001108392   ⟹   NP_001101862
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr815105,983,342 - 105,988,167 (+)NCBI
mRatBN7.21599,576,697 - 99,581,522 (+)NCBI
Rnor_6.015108,908,366 - 108,913,812 (+)NCBI
Rnor_5.015112,296,472 - 112,301,371 (+)NCBI
RGSC_v3.415107,609,060 - 107,613,169 (+)RGD
Celera1598,350,700 - 98,355,483 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039093543   ⟹   XP_038949471
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr815105,982,711 - 105,986,882 (+)NCBI
mRatBN7.21599,576,907 - 99,580,238 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001101862 (Get FASTA)   NCBI Sequence Viewer  
  XP_038949471 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDM02583 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000069986
  ENSRNOP00000069986.2
RefSeq Acc Id: NP_001101862   ⟸   NM_001108392
- UniProtKB: A0A0G2JWR6 (UniProtKB/TrEMBL),   A6HUM0 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000069986   ⟸   ENSRNOT00000089455
RefSeq Acc Id: XP_038949471   ⟸   XM_039093543
- Peptide Label: isoform X1
Protein Domains
C2H2-type

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:1311174 AgrOrtholog
BioCyc Gene G2FUF-12339 BioCyc
Ensembl Genes ENSRNOG00000054879 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000089455 ENTREZGENE
  ENSRNOT00000089455.2 UniProtKB/TrEMBL
Gene3D-CATH Classic Zinc Finger UniProtKB/TrEMBL
InterPro Znf_C2H2/integrase_DNA-bd UniProtKB/TrEMBL
  Znf_C2H2_sf UniProtKB/TrEMBL
  Znf_ZIC UniProtKB/TrEMBL
KEGG Report rno:361096 UniProtKB/TrEMBL
NCBI Gene 361096 ENTREZGENE
PANTHER ZINC FINGER PROTEIN ZIC 2 UniProtKB/TrEMBL
  ZINC FINGER PROTEIN ZIC AND GLI UniProtKB/TrEMBL
Pfam zf-C2H2 UniProtKB/TrEMBL
  zf_ZIC UniProtKB/TrEMBL
PhenoGen Zic2 PhenoGen
PROSITE ZINC_FINGER_C2H2_1 UniProtKB/TrEMBL
  ZINC_FINGER_C2H2_2 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000054879 RatGTEx
SMART ZnF_C2H2 UniProtKB/TrEMBL
Superfamily-SCOP SSF57667 UniProtKB/TrEMBL
UniProt A0A0G2JWR6 ENTREZGENE, UniProtKB/TrEMBL
  A6HUM0 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2011-08-01 Zic2  Zic family member 2  Zic2  Zic family member 2 (odd-paired homolog, Drosophila)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-09-25 Zic2  Zic family member 2 (odd-paired homolog, Drosophila)  Zic2  zinc finger protein of the cerebellum 2  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-03 Zic2  zinc finger protein of the cerebellum 2  Zic2_predicted  Zic family member 2 (odd-paired homolog, Drosophila) (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-01-12 Zic2_predicted  Zic family member 2 (odd-paired homolog, Drosophila) (predicted)      Symbol and Name status set to approved 70820 APPROVED