Zic5 (Zic family member 5) - Rat Genome Database

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Gene: Zic5 (Zic family member 5) Rattus norvegicus
Analyze
Symbol: Zic5
Name: Zic family member 5
RGD ID: 1310160
Description: Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in central nervous system development and regulation of transcription by RNA polymerase II. Predicted to act upstream of or within forebrain development; neural crest cell differentiation; and neural tube closure. Predicted to be active in nucleus. Orthologous to human ZIC5 (Zic family member 5); INTERACTS WITH 4,4'-sulfonyldiphenol; 6-propyl-2-thiouracil; bis(2-ethylhexyl) phthalate.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC361095; Zic family member 5 (odd-paired homolog, Drosophila); zinc finger protein of the cerebellum 5; zinc finger protein ZIC 5
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
GRCr815105,964,932 - 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
JBrowse: View Region in Genome Browser (JBrowse)
Model


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. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
3. GOA pipeline RGD automated data pipeline
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:15136147   PMID:15465018   PMID:15736266   PMID:18298960  


Genomics

Comparative Map Data
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
(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
(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
(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
35 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:621
Count of miRNA genes:284
Interacting mature miRNAs:349
Transcripts:ENSRNOT00000048143, ENSRNOT00000067577
Prediction methods:Microtar, 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 (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:496750  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21599,560,759 - 99,560,862 (+)MAPPERmRatBN7.2
Rnor_6.015108,892,429 - 108,892,531NCBIRnor6.0
Rnor_5.015112,280,611 - 112,280,713UniSTSRnor5.0
RGSC_v3.415107,593,179 - 107,593,281UniSTSRGSC3.4
Celera1598,334,799 - 98,334,901UniSTS
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

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 47
Low 1 27 5
Below cutoff 4 4 4 1 4 2 3 1 21 7 2

Sequence


RefSeq Acc Id: ENSRNOT00000067577   ⟹   ENSRNOP00000063030
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1599,560,323 - 99,567,035 (-)Ensembl
Rnor_6.0 Ensembl15108,891,992 - 108,898,703 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000111883   ⟹   ENSRNOP00000077057
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1599,560,323 - 99,566,682 (-)Ensembl
RefSeq Acc Id: NM_001395664   ⟹   NP_001382593
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr815105,964,932 - 105,973,669 (-)NCBI
mRatBN7.21599,558,285 - 99,567,023 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001382593 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDM02581 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000063030.2
  ENSRNOP00000077057
  ENSRNOP00000077057.1
RefSeq Acc Id: ENSRNOP00000063030   ⟸   ENSRNOT00000067577
RefSeq Acc Id: ENSRNOP00000077057   ⟸   ENSRNOT00000111883
RefSeq Acc Id: NP_001382593   ⟸   NM_001395664
- UniProtKB: A0A8I5ZJD4 (UniProtKB/TrEMBL)
Protein Domains
C2H2-type

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-F1M349-F1-model_v2 AlphaFold F1M349 1-265 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:1310160 AgrOrtholog
BioCyc Gene G2FUF-12343 BioCyc
Ensembl Genes ENSRNOG00000014358 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000067577.5 UniProtKB/TrEMBL
  ENSRNOT00000111883 ENTREZGENE
  ENSRNOT00000111883.1 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:361095 UniProtKB/TrEMBL
NCBI Gene 361095 ENTREZGENE
PANTHER ZINC FINGER PROTEIN ZIC 5 UniProtKB/TrEMBL
  ZINC FINGER PROTEIN ZIC AND GLI UniProtKB/TrEMBL
Pfam zf-C2H2 UniProtKB/TrEMBL
  zf_ZIC UniProtKB/TrEMBL
PhenoGen Zic5 PhenoGen
PROSITE ZINC_FINGER_C2H2_1 UniProtKB/TrEMBL
  ZINC_FINGER_C2H2_2 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000014358 RatGTEx
SMART ZnF_C2H2 UniProtKB/TrEMBL
Superfamily-SCOP SSF57667 UniProtKB/TrEMBL
UniProt A0A8I5ZJD4 ENTREZGENE, UniProtKB/TrEMBL
  F1M349_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2011-08-01 Zic5  Zic family member 5  Zic5  Zic family member 5 (odd-paired homolog, Drosophila)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-09-25 Zic5  Zic family member 5 (odd-paired homolog, Drosophila)  Zic5  zinc finger protein of the cerebellum 5   Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Zic5  zinc finger protein of the cerebellum 5   Zic5_predicted  zinc finger protein of the cerebellum 5 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Zic5_predicted  zinc finger protein of the cerebellum 5 (predicted)      Symbol and Name status set to approved 70820 APPROVED