Zic5 (zinc finger protein of the cerebellum 5) - Rat Genome Database

Send us a Message
Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Search RGD Grant Resources Citing RGD About Us Contact Us
Genes Variants Community Projects QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Synteny Browser (VCMap) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) AllianceMine GViewer (Genome Viewer)
Aging & Age-Related Disease Cancer & Neoplastic Disease Cardiovascular Disease Coronavirus Disease Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease
Find Models   new Genetic Models Autism Models Rat PhenoMiner (Quantitative Phenotypes) Chinchilla PhenoMiner Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive
Pathways
Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Presentations Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
Gene: Zic5 (zinc finger protein of the cerebellum 5) Mus musculus
Analyze
Symbol: Zic5
Name: zinc finger protein of the cerebellum 5
RGD ID: 1320900
MGI Page MGI
Description: Enables DNA-binding transcription factor activity and RNA polymerase II transcription regulatory region sequence-specific DNA binding activity. Acts upstream of or within forebrain development; neural crest cell differentiation; and neural tube closure. Located in nucleus. Is expressed in several structures, including central nervous system; early conceptus; limb mesenchyme; sensory organ; and trunk paraxial mesenchyme. Orthologous to human ZIC5 (Zic family member 5).
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: 1700049L20Rik; odd-paired related; Opr; Zic family member 5 (odd-paired homolog, Drosophila); zinc finger protein ZIC 5
RGD Orthologs
Human
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Related Pseudogenes: Gm12241   Gm18801  
Latest Assembly: GRCm39 - Mouse Genome Assembly GRCm39
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3914122,696,572 - 122,703,127 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl14122,694,207 - 122,703,089 (-)EnsemblGRCm39 Ensembl
GRCm3814122,459,160 - 122,465,658 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl14122,456,795 - 122,465,677 (-)EnsemblGRCm38mm10GRCm38
MGSCv3714122,858,382 - 122,864,880 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv3614121,594,340 - 121,600,838 (-)NCBIMGSCv36mm8
Celera14121,021,344 - 121,027,985 (-)NCBICelera
Cytogenetic Map14E5NCBI
cM Map1465.96NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
nucleus  (IBA,IDA)

Phenotype Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Mouse brain organization revealed through direct genome-scale TF expression analysis. Gray PA, etal., Science 2004 Dec 24;306(5705):2255-7.
2. Functional annotation of a full-length mouse cDNA collection. Kawai J, etal., Nature. 2001 Feb 8;409(6821):685-90.
3. MGDs mouse GO annotations MGD data from the GO Consortium
4. MGD IEA MGD IEA
5. Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Okazaki Y, etal., Nature. 2002 Dec 5;420(6915):563-73.
6. Mouse MP Annotation Import Pipeline RGD automated import pipeline
7. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:10349636   PMID:11042159   PMID:11044622   PMID:11076861   PMID:12447396   PMID:15136147   PMID:15465018   PMID:15736266   PMID:15799026   PMID:16141072   PMID:16141073   PMID:17614941  
PMID:18287559   PMID:18298960   PMID:19627984   PMID:20412781   PMID:21873635   PMID:23606270   PMID:24952961   PMID:32499648   PMID:34184034   PMID:34638777   PMID:34921112   PMID:35377797  
PMID:36752150   PMID:37756587   PMID:37973188  


Genomics

Comparative Map Data
Zic5
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3914122,696,572 - 122,703,127 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl14122,694,207 - 122,703,089 (-)EnsemblGRCm39 Ensembl
GRCm3814122,459,160 - 122,465,658 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl14122,456,795 - 122,465,677 (-)EnsemblGRCm38mm10GRCm38
MGSCv3714122,858,382 - 122,864,880 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv3614121,594,340 - 121,600,838 (-)NCBIMGSCv36mm8
Celera14121,021,344 - 121,027,985 (-)NCBICelera
Cytogenetic Map14E5NCBI
cM Map1465.96NCBI
ZIC5
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381399,962,964 - 99,971,909 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1399,962,964 - 99,971,767 (-)EnsemblGRCh38hg38GRCh38
GRCh3713100,615,218 - 100,624,163 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361399,413,276 - 99,422,179 (-)NCBINCBI36Build 36hg18NCBI36
Build 341399,415,451 - 99,422,179NCBI
Celera1381,459,810 - 81,468,714 (-)NCBICelera
Cytogenetic Map13q32.3NCBI
HuRef1381,209,062 - 81,217,860 (-)NCBIHuRef
CHM1_113100,585,230 - 100,594,123 (-)NCBICHM1_1
T2T-CHM13v2.01399,173,877 - 99,182,820 (-)NCBIT2T-CHM13v2.0
Zic5
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr815105,964,932 - 105,973,669 (-)NCBIGRCr8
mRatBN7.21599,558,285 - 99,567,023 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1599,560,323 - 99,567,035 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx15103,490,858 - 103,499,612 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.015104,585,736 - 104,594,463 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.015101,512,984 - 101,521,711 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.015108,891,992 - 108,907,601 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl15108,891,992 - 108,898,703 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.015112,280,174 - 112,286,885 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.415107,592,742 - 107,598,927 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.115107,608,864 - 107,614,354 (-)NCBI
Celera1598,334,362 - 98,341,135 (-)NCBICelera
Cytogenetic Map15q25NCBI
Zic5
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540410,745,620 - 10,751,872 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495540410,745,551 - 10,752,006 (+)NCBIChiLan1.0ChiLan1.0
ZIC5
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v214101,489,625 - 101,506,323 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan113100,156,868 - 100,173,568 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01381,132,841 - 81,149,539 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.113100,266,163 - 100,273,498 (-)NCBIpanpan1.1PanPan1.1panPan2
ZIC5
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12249,929,198 - 49,938,002 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2249,931,460 - 49,937,853 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2249,709,996 - 49,718,800 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02250,371,040 - 50,379,856 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2250,373,332 - 50,379,707 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12250,021,233 - 50,030,020 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02250,054,753 - 50,063,553 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02250,091,841 - 50,100,649 (-)NCBIUU_Cfam_GSD_1.0
Zic5
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404945185,327,425 - 185,336,209 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493647210,616,122 - 10,622,338 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493647210,615,843 - 10,623,221 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
ZIC5
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1168,821,735 - 68,830,540 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11168,821,733 - 68,830,472 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21176,085,623 - 76,093,461 (-)NCBISscrofa10.2Sscrofa10.2susScr3
ZIC5
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1378,611,133 - 78,629,616 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl378,615,177 - 78,621,446 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604635,113,604 - 35,122,540 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Zic5
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462479311,176,946 - 11,189,003 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462479311,171,431 - 11,186,415 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Zic5
121 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:955
Count of miRNA genes:500
Interacting mature miRNAs:616
Transcripts:ENSMUST00000039118, ENSMUST00000143084
Prediction methods:Miranda, 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 (GRCm39)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
12792981Fbmd5_mfemoral bone mineral density 5, females only (mouse)1499838217125033054Mouse
10755523Hgb2_mhemoglobin 2 (mouse)14105884654125139656Mouse

Markers in Region
BB391594  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm381156,462,285 - 56,462,413UniSTSGRCm38
GRCm3814122,456,975 - 122,457,103UniSTSGRCm38
MGSCv3714122,856,197 - 122,856,325UniSTSGRCm37
MGSCv371156,275,787 - 56,275,915UniSTSGRCm37
Celera14121,019,159 - 121,019,287UniSTS
Celera1161,229,647 - 61,229,775UniSTS
Cytogenetic Map11B1.3UniSTS
Cytogenetic Map14E5UniSTS
cM Map1462.0UniSTS
Whitehead/MRC_RH11743.24UniSTS
Zic5  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm3814122,459,254 - 122,459,359UniSTSGRCm38
GRCm381156,460,048 - 56,460,153UniSTSGRCm38
MGSCv3714122,858,476 - 122,858,581UniSTSGRCm37
MGSCv371156,273,550 - 56,273,655UniSTSGRCm37
Celera14121,021,438 - 121,021,543UniSTS
Celera1161,227,356 - 61,227,461UniSTS
Cytogenetic Map14E5UniSTS
Cytogenetic Map11B1.3UniSTS
cM Map14 UniSTS


Expression


Sequence


Reference Sequences
RefSeq Acc Id: ENSMUST00000039118   ⟹   ENSMUSP00000035754
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl14122,694,207 - 122,703,089 (-)Ensembl
GRCm38.p6 Ensembl14122,456,795 - 122,465,677 (-)Ensembl
RefSeq Acc Id: ENSMUST00000143084
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl14122,696,605 - 122,697,433 (-)Ensembl
GRCm38.p6 Ensembl14122,459,193 - 122,460,021 (-)Ensembl
RefSeq Acc Id: NM_022987   ⟹   NP_075363
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm3914122,696,572 - 122,703,070 (-)NCBI
GRCm3814122,459,160 - 122,465,658 (-)NCBI
MGSCv3714122,858,382 - 122,864,880 (-)RGD
Celera14121,021,344 - 121,027,985 (-)RGD
cM Map14 ENTREZGENE
Sequence:
RefSeq Acc Id: XM_006519357   ⟹   XP_006519420
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm3914122,701,050 - 122,703,127 (-)NCBI
GRCm3814122,463,659 - 122,465,471 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_075363 (Get FASTA)   NCBI Sequence Viewer  
  XP_006519420 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein BAB18579 (Get FASTA)   NCBI Sequence Viewer  
  BAB24726 (Get FASTA)   NCBI Sequence Viewer  
  BAC79075 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSMUSP00000035754
  ENSMUSP00000035754.7
GenBank Protein Q7TQ40 (Get FASTA)   NCBI Sequence Viewer  
Reference Protein Sequences
RefSeq Acc Id: NP_075363   ⟸   NM_022987
- UniProtKB: Q9EQW1 (UniProtKB/Swiss-Prot),   Q7TQ40 (UniProtKB/Swiss-Prot),   A0A0R4J0E2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006519420   ⟸   XM_006519357
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSMUSP00000035754   ⟸   ENSMUST00000039118
Protein Domains
C2H2-type

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q7TQ40-F1-model_v2 AlphaFold Q7TQ40 1-622 view protein structure

Promoters
RGD ID:6825551
Promoter ID:MM_KWN:17868
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:Brain,   ES_Cell
Transcripts:OTTMUST00000049605
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv3614122,863,281 - 122,865,562 (-)MPROMDB

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:1929518 AgrOrtholog
Ensembl Genes ENSMUSG00000041703 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSMUST00000039118 ENTREZGENE
  ENSMUST00000039118.7 UniProtKB/TrEMBL
Gene3D-CATH Classic Zinc Finger UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro Znf_C2H2_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Znf_C2H2_type UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Znf_ZIC UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report mmu:65100 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
MGD MGI:1929518 ENTREZGENE
NCBI Gene 65100 ENTREZGENE
PANTHER ZINC FINGER PROTEIN ZIC 5 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ZINC FINGER PROTEIN ZIC AND GLI UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam zf-C2H2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  zf_ZIC UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Zic5 PhenoGen
PROSITE ZINC_FINGER_C2H2_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ZINC_FINGER_C2H2_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART ZnF_C2H2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF57667 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0R4J0E2 ENTREZGENE, UniProtKB/TrEMBL
  Q7TQ40 ENTREZGENE
  Q9CVS3_MOUSE UniProtKB/TrEMBL
  Q9EQW1 ENTREZGENE
  ZIC5_MOUSE UniProtKB/Swiss-Prot
UniProt Secondary Q9EQW1 UniProtKB/Swiss-Prot