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
RGD ID: 1561261
Description: Predicted to have DNA-binding transcription activator activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in several processes, including determination of left/right symmetry; lung development; and positive regulation of transcription by RNA polymerase II. Predicted to localize to cytoplasm and nucleoplasm. 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: PROVISIONAL
Also 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: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
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 (+)NCBIRGSC3.4rn4RGSC3.4
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

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

References

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
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 (+)NCBIRGSC3.4rn4RGSC3.4
CeleraX132,262,545 - 132,272,607 (+)NCBICelera
Cytogenetic MapXq36NCBI
ZIC3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 EnsemblX137,566,127 - 137,577,691 (+)EnsemblGRCh38hg38GRCh38
GRCh38X137,566,127 - 137,577,691 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37X136,648,346 - 136,654,259 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36X136,476,012 - 136,481,925 (+)NCBINCBI36hg18NCBI36
Build 34X136,373,865 - 136,379,777NCBI
CeleraX137,014,356 - 137,020,269 (+)NCBI
Cytogenetic MapXq26.3NCBI
HuRefX125,916,990 - 125,922,902 (+)NCBIHuRef
CHM1_1X136,559,744 - 136,565,657 (+)NCBICHM1_1
Zic3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X57,075,988 - 57,081,990 (+)NCBIGRCm39mm39
GRCm38X58,030,628 - 58,036,630 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX58,022,700 - 58,041,736 (+)EnsemblGRCm38mm10GRCm38
MGSCv37X55,283,805 - 55,289,807 (+)NCBIGRCm37mm9NCBIm37
MGSCv36X54,377,427 - 54,382,686 (+)NCBImm8
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_v0panPan3
ZIC3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 EnsemblX107,821,948 - 107,833,597 (+)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.1X107,822,002 - 107,833,582 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Zic3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049365139,780,895 - 9,792,865 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
ZIC3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX112,592,953 - 112,604,068 (+)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 - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X112,597,329 - 112,609,411 (+)NCBI
ChlSab1.1 EnsemblX112,598,466 - 112,601,803 (+)Ensembl
Zic3
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248089,201,025 - 9,212,192 (-)NCBI

Position Markers
RH130454  
Rat AssemblyChrPosition (strand)SourceJBrowse
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
Cytogenetic MapXq36UniSTS
RH 3.4 MapX971.3UniSTS
ZIC3  
Rat AssemblyChrPosition (strand)SourceJBrowse
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


QTLs in Region (Rnor_6.0)
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)X44320616158345622Rat
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)X101333032146333032Rat
738025Stresp3Stress response QTL 34.610.0066stress-related behavior trait (VT:0010451)defensive burying - approachX107886746152409805Rat
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)X110957467155957467Rat
1598856Memor1Memory QTL 11.9exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)X110957467155957467Rat
10059603Bw174Body weight QTL 1743.40.025body mass (VT:0001259)body weight (CMO:0000012)X118715462159970021Rat
738029Stresp2Stress response QTL 23.40.0004stress-related behavior trait (VT:0010451)defensive burying - approachX120045041143145818Rat
634346Insul4Insulin level QTL 40blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)X134627816159970021Rat

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.


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
Rnor_6.0 EnsemblX140,878,216 - 140,883,816 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000077026   ⟹   ENSRNOP00000068130
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX140,878,216 - 140,888,795 (+)Ensembl
RefSeq Acc Id: NM_001109019   ⟹   NP_001102489
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
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_006257586   ⟹   XP_006257648
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0X140,877,753 - 140,883,816 (+)NCBI
Rnor_5.0X140,918,894 - 140,931,861 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017602125   ⟹   XP_017457614
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0X140,875,191 - 140,883,816 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001102489 (Get FASTA)   NCBI Sequence Viewer  
  XP_006257648 (Get FASTA)   NCBI Sequence Viewer  
  XP_017457614 (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: XP_006257648   ⟸   XM_006257586
- Peptide Label: isoform X2
- UniProtKB: A0A096MIX7 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017457614   ⟸   XM_017602125
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000068130   ⟸   ENSRNOT00000077026
RefSeq Acc Id: ENSRNOP00000067915   ⟸   ENSRNOT00000075840
Protein Domains
C2H2-type

Transcriptome

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


Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1561261 AgrOrtholog
Ensembl Genes ENSRNOG00000000861 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000067915 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000068130 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000075840 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000077026 ENTREZGENE, 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
UniGene Rn.64713 ENTREZGENE
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