Zic2 (Zic family member 2) - Rat Genome Database

Name: Zic2
Creator: Rat Genome Database
License: Creative Commons CC BY 4.0
Keywords: Rat Gene RGD Genome

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

Alliance Genes

More Info

more info ...

More Info

Species	Gene symbol and name	Data Source	Assertion derived from	less info ...
Orthologs ¹				less info ...
Homo sapiens (human):	ZIC2 (Zic family member 2)	HGNC	Ensembl, HomoloGene, Inparanoid, NCBI, Panther
Mus musculus (house mouse):	Zic2 (zinc finger protein of the cerebellum 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chinchilla lanigera (long-tailed chinchilla):	Zic2 (Zic family member 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	ZIC2 (Zic family member 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	ZIC2 (Zic family member 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Zic2 (Zic family member 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	ZIC2 (Zic family member 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	ZIC2 (Zic family member 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Zic2 (Zic family member 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Other homologs ²
Homo sapiens (human):	RUFY3 (RUN and FYVE domain containing 3)	HGNC	OMA
Alliance orthologs ³
Homo sapiens (human):	ZIC2 (Zic family member 2)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Mus musculus (house mouse):	Zic2 (zinc finger protein of the cerebellum 2)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Danio rerio (zebrafish):	zic2a (zic family member 2 (odd-paired homolog, Drosophila), a)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Danio rerio (zebrafish):	zic2b (zic family member 2 (odd-paired homolog, Drosophila) b)	Alliance	DIOPT (Ensembl Compara\|OrthoFinder\|PANTHER\|PhylomeDB)
Caenorhabditis elegans (roundworm):	ref-2	Alliance	DIOPT (InParanoid\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Drosophila melanogaster (fruit fly):	opa	Alliance	DIOPT (Hieranoid\|InParanoid\|OrthoInspector\|PANTHER\|SonicParanoid)
Xenopus tropicalis (tropical clawed frog):	zic2	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)

Latest Assembly:

mRatBN7.2 - mRatBN7.2 Assembly

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	15	105,982,711 - 105,988,167 (+)	NCBI		GRCr8
mRatBN7.2	15	99,576,697 - 99,581,522 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	15	99,576,697 - 99,581,522 (+)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	15	103,509,279 - 103,514,110 (+)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	15	104,604,163 - 104,609,002 (+)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	15	101,531,399 - 101,536,238 (+)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	15	108,908,366 - 108,913,812 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	15	108,908,607 - 108,912,737 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	15	112,296,472 - 112,301,371 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	15	107,609,060 - 107,613,169 (+)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	15	107,624,839 - 107,629,424 (+)	NCBI
Celera	15	98,350,700 - 98,355,483 (+)	NCBI		Celera
Cytogenetic Map	15	q25	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

Anal Atresia, Hypospadias, and Penoscrotal Inversion (ISO)

cognitive disorder (ISO)

genetic disease (ISO)

hepatocellular carcinoma (ISO)

holoprosencephaly (ISO)

holoprosencephaly 1 (ISO)

holoprosencephaly 5 (ISO,ISS)

neural tube defect (ISO)

Neurodevelopmental Disorders (ISO)

propionic acidemia (ISO)

Prostatic Neoplasms (ISO)

schizophrenia (ISS)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

17beta-estradiol (EXP,ISO)

2,3,7,8-tetrachlorodibenzodioxine (ISO)

2,3,7,8-Tetrachlorodibenzofuran (EXP)

6-propyl-2-thiouracil (EXP)

aflatoxin B1 (ISO)

aldehydo-D-glucose (ISO)

all-trans-retinoic acid (ISO)

benzo[a]pyrene (ISO)

bis(2-chloroethyl) sulfide (ISO)

bisphenol A (EXP,ISO)

bisphenol F (ISO)

cadmium dichloride (ISO)

carbamazepine (ISO)

cisplatin (ISO)

copper atom (EXP)

copper(0) (EXP)

Cuprizon (EXP)

cyclosporin A (ISO)

D-glucose (ISO)

dorsomorphin (ISO)

enzyme inhibitor (ISO)

fenvalerate (EXP)

fulvestrant (ISO)

glucose (ISO)

lead(0) (ISO)

manganese(II) chloride (EXP)

methamphetamine (EXP)

N-ethyl-N-nitrosourea (ISO)

N-methyl-4-phenylpyridinium (EXP)

nickel sulfate (ISO)

niclosamide (ISO)

paracetamol (ISO)

perfluorohexanesulfonic acid (ISO)

phenylmercury acetate (ISO)

quercetin (ISO)

resorcinol (ISO)

resveratrol (ISO)

SB 431542 (ISO)

SCH 23390 (EXP)

silicon dioxide (ISO)

silver atom (ISO)

silver(0) (ISO)

sirolimus (ISO)

sodium arsenite (ISO)

trichostatin A (ISO)

valproic acid (ISO)

vorinostat (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

axial mesoderm development (ISO)

biological_process (ND)

central nervous system development (IBA,ISO)

central nervous system segmentation (ISO)

cilium organization (ISO)

developmental pigmentation (ISO)

gene expression (ISO)

negative regulation of DNA-templated transcription (ISO)

nervous system development (ISO)

neural crest cell differentiation (ISO)

neural plate development (ISO)

neural tube closure (ISO)

nodal signaling pathway (ISO)

paraxial mesoderm development (ISO)

positive regulation of DNA-templated transcription (ISO)

positive regulation of transcription by RNA polymerase II (ISO)

regulation of transcription by RNA polymerase II (IBA)

retinal ganglion cell axon guidance (ISO)

visual perception (ISO)

Cellular Component

cytoplasm (ISO)

nuclear body (IEA,ISO)

nucleoplasm (ISO)

nucleus (ISO)

Molecular Function

chromatin DNA binding (ISO)

DNA binding (ISO)

DNA-binding transcription activator activity, RNA polymerase II-specific (ISO)

DNA-binding transcription factor activity (ISO)

DNA-binding transcription factor activity, RNA polymerase II-specific (IBA)

protein binding (ISO)

RNA polymerase II cis-regulatory region sequence-specific DNA binding (IBA,ISO)

RNA polymerase II transcription regulatory region sequence-specific DNA binding (ISO)

Molecular Pathway Annotations Click to see Annotation Detail View

Hedgehog signaling pathway (IEA)

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 Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	15	105,982,711 - 105,988,167 (+)	NCBI		GRCr8
mRatBN7.2	15	99,576,697 - 99,581,522 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	15	99,576,697 - 99,581,522 (+)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	15	103,509,279 - 103,514,110 (+)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	15	104,604,163 - 104,609,002 (+)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	15	101,531,399 - 101,536,238 (+)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	15	108,908,366 - 108,913,812 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	15	108,908,607 - 108,912,737 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	15	112,296,472 - 112,301,371 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	15	107,609,060 - 107,613,169 (+)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	15	107,624,839 - 107,629,424 (+)	NCBI
Celera	15	98,350,700 - 98,355,483 (+)	NCBI		Celera
Cytogenetic Map	15	q25	NCBI

ZIC2
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	13	99,981,784 - 99,986,765 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	13	99,981,784 - 99,986,765 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	13	100,634,038 - 100,639,019 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	13	99,432,320 - 99,437,020 (+)	NCBI	NCBI36	Build 36	hg18	NCBI36
Build 34	13	99,432,319 - 99,437,019	NCBI
Celera	13	81,478,855 - 81,483,555 (+)	NCBI		Celera
Cytogenetic Map	13	q32.3	NCBI
HuRef	13	81,227,505 - 81,232,531 (+)	NCBI		HuRef
CHM1_1	13	100,603,892 - 100,608,865 (+)	NCBI		CHM1_1
T2T-CHM13v2.0	13	99,192,694 - 99,197,676 (+)	NCBI		T2T-CHM13v2.0

Zic2
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	14	122,712,796 - 122,717,740 (+)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	14	122,712,847 - 122,717,264 (+)	Ensembl		GRCm39 Ensembl
GRCm38	14	122,475,384 - 122,480,328 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	14	122,475,435 - 122,479,852 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	14	122,874,606 - 122,879,550 (+)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	14	121,610,615 - 121,615,032 (+)	NCBI		MGSCv36	mm8
Celera	14	121,006,828 - 121,042,740 (+)	NCBI		Celera
Cytogenetic Map	14	E5	NCBI
cM Map	14	65.97	NCBI

Zic2
(Chinchilla lanigera - long-tailed chinchilla)

Chinchilla Assembly	Chr	Position (strand)	Source	Genome Browsers
Chinchilla Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChiLan1.0	NW_004955404	10,731,987 - 10,735,599 (-)	NCBI	ChiLan1.0	ChiLan1.0

ZIC2
(Pan paniscus - bonobo/pygmy chimpanzee)

Bonobo Assembly	Chr	Position (strand)	Source	Genome Browsers
Bonobo Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
NHGRI_mPanPan1-v2	14	101,508,447 - 101,513,428 (+)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	13	100,175,671 - 100,180,672 (+)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	13	81,151,669 - 81,156,648 (+)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	13	100,285,212 - 100,289,598 (+)	NCBI	panpan1.1	PanPan1.1	panPan2

ZIC2
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	22	49,948,743 - 49,952,007 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	22	49,948,778 - 49,950,055 (+)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	22	49,729,321 - 49,734,051 (+)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	22	50,390,470 - 50,395,205 (+)	NCBI		ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	22	50,390,481 - 50,394,094 (+)	Ensembl		ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	22	50,040,527 - 50,045,249 (+)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	22	50,074,149 - 50,078,870 (+)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	22	50,111,170 - 50,115,894 (+)	NCBI		UU_Cfam_GSD_1.0

Zic2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HiC_Itri_2	NW_024404945	185,347,014 - 185,350,047 (+)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936472	10,602,102 - 10,605,191 (-)	Ensembl	SpeTri2.0	SpeTri2.0 Ensembl
SpeTri2.0	NW_004936472	10,599,717 - 10,605,187 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

ZIC2
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	11	68,840,631 - 68,845,378 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	11	68,840,802 - 68,845,441 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	11	76,103,699 - 76,107,978 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

ZIC2
(Chlorocebus sabaeus - green monkey)

Green Monkey Assembly	Chr	Position (strand)	Source	Genome Browsers
Green Monkey Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1	3	78,631,556 - 78,637,422 (+)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	3	78,631,530 - 78,636,548 (+)	Ensembl	ChlSab1.1	ChlSab1.1 Ensembl	chlSab2
Vero_WHO_p1.0	NW_023666046	35,132,313 - 35,137,417 (+)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Zic2
(Heterocephalus glaber - naked mole-rat)

Naked Mole-Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Naked Mole-Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HetGla_female_1.0 Ensembl	NW_004624793	11,163,916 - 11,167,457 (-)	Ensembl	HetGla_female_1.0	HetGla_female_1.0 Ensembl	hetGla2
HetGla 1.0	NW_004624793	11,162,835 - 11,167,497 (-)	NCBI	HetGla_female_1.0	HetGla 1.0	hetGla2

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.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
631655	Bp126	Blood pressure QTL 126	4		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	15	58156477	101769107	Rat
731177	Uae26	Urinary albumin excretion QTL 26	2.4	0.025	urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	15	67588667	101769107	Rat
2300326	Plaw1	Placental weight QTL 1	15	0.005	placenta mass (VT:0004257)	placenta wet weight (CMO:0002088)	15	68327165	100062518	Rat
1641889	Colcr6	Colorectal carcinoma resistance QTL 6	2.9	0.0126	intestine integrity trait (VT:0010554)	benign colorectal tumor surface area measurement (CMO:0001799)	15	73690518	99794247	Rat
2317055	Aia10	Adjuvant induced arthritis QTL 10	3.41		joint integrity trait (VT:0010548)	left rear ankle joint diameter (CMO:0002149)	15	75788062	101769107	Rat
1549844	Bss7	Bone structure and strength QTL 7	6.4		femur strength trait (VT:0010010)	femur midshaft polar moment of inertia (CMO:0001669)	15	75788062	101769107	Rat
70155	Gcs1	Gastric cancer susceptibility QTL1	3.8		stomach morphology trait (VT:0000470)	stomach tumor susceptibility score (CMO:0002043)	15	76306099	101769107	Rat

Markers in Region

UniSTS:144841

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	15	99,580,833 - 99,580,984 (+)	MAPPER	mRatBN7.2
Rnor_6.0	15	108,913,124 - 108,913,274	NCBI	Rnor6.0
Rnor_5.0	15	112,300,683 - 112,300,833	UniSTS	Rnor5.0
RGSC_v3.4	15	107,612,956 - 107,613,106	UniSTS	RGSC3.4
Celera	15	98,354,795 - 98,354,945	UniSTS
Cytogenetic Map	15	q25	UniSTS

UniSTS:466092

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	15	99,579,908 - 99,580,217 (+)	MAPPER	mRatBN7.2
Rnor_6.0	15	108,911,578 - 108,911,886	NCBI	Rnor6.0
Rnor_5.0	15	112,299,758 - 112,300,066	UniSTS	Rnor5.0
RGSC_v3.4	15	107,612,031 - 107,612,339	UniSTS	RGSC3.4
Celera	15	98,353,910 - 98,354,218	UniSTS
Cytogenetic Map	15	q25	UniSTS

UniSTS:496749

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	15	99,580,395 - 99,580,498 (+)	MAPPER	mRatBN7.2
Rnor_6.0	15	108,912,686 - 108,912,788	NCBI	Rnor6.0
Rnor_5.0	15	112,300,245 - 112,300,347	UniSTS	Rnor5.0
RGSC_v3.4	15	107,612,518 - 107,612,620	UniSTS	RGSC3.4
Celera	15	98,354,357 - 98,354,459	UniSTS
Cytogenetic Map	15	q25	UniSTS

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

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001108392	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039093543	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AC123185	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473951	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JAXUCZ010000015	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

RefSeq Acc Id:

ENSRNOT00000089455 ⟹ ENSRNOP00000069986

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	15	99,576,697 - 99,581,522 (+)	Ensembl
Rnor_6.0 Ensembl	15	108,908,607 - 108,912,737 (+)	Ensembl

RefSeq Acc Id:

NM_001108392 ⟹ NP_001101862

RefSeq Status:

VALIDATED

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	15	105,983,342 - 105,988,167 (+)	NCBI
mRatBN7.2	15	99,576,697 - 99,581,522 (+)	NCBI
Rnor_6.0	15	108,908,366 - 108,913,812 (+)	NCBI
Rnor_5.0	15	112,296,472 - 112,301,371 (+)	NCBI
RGSC_v3.4	15	107,609,060 - 107,613,169 (+)	RGD
Celera	15	98,350,700 - 98,355,483 (+)	NCBI

Sequence:

show sequence

CGCGCCTCCTCCGCCGCCGCCTCCTCTTCCTCTCCGCGCCTTCGCTCGGCGCCCGGCCGCCTGA
GGCAGATACAGGCGGCGGCGGCCGGCGCAGTAGCCCGGCTCCCGAGGCTGCAGTCGCCAGTGTT
TCCACCGCCGGTTCGCGGAGCCCGGCGTCCAGAGGACGCGCCTCGCCGATCAGGAGGGGAAATC
CAGGCAGCAGGGCTCACCGGGGCCGGCGGGGCGGCCGGGCGCGCTGGCCATGCTTCTGGACGCG
GGGCCGCAGTTCCCGGCCATCGGGGTGGGCAGCTTCGCGCGCCACCACCACCACTCGGCCGCGG
CAGCGGCGGCTGCGGCGGCCGAGATGCAGGACCGGGAGCTGAGCCTGGCGGCGGCACAGAACGG
CTTCGTGGACTCGGCCGCAGCGCACATGGGCGCCTTCAAGCTCAACCCCGGGGCACACGAACTG
TCTCCTGGTCAGAGTTCGGCGTTCACGTCGCAAGGTCCGGGCGCCTACCCGGGTTCGGCTGCAG
CGGCCGCTGCAGCCGCGGCTCTAGGGCCCCACGCCGCTCACGTTGGCTCTTATTCGGGGCCTCC
CTTTAATTCCACCCGGGACTTCCTGTTCCGTAGCCGGGGCTTCGGGGACTCGGCGCCGGGAGGC
GGCCAGCACGGGCTCTTCGGACCCGGCGCCGGCGGCCTCCACCATGCGCACTCGGACGCGCAGG
GCCACCTTCTCTTCCCTGGCCTCCCGGAACAGCACGGGCCGCACGCCTCGCAGAACGTGCTCAA
TGGGCAAATGCGCCTAGGGCTGCCGGGCGAAGTGTTCGGGCGCTCAGAGCAATACCGCCAAGTG
GCCAGCCCGCGGACCGACCCTTACTCGGCGGCGCAGCTCCACAACCAGTACGGCCCTATGAATA
TGAACATGGGGATGAACATGGCAGCGGCCGCAGCCCACCACCACCACCACCATCACCACCCTGG
TGCCTTTTTCCGCTACATGCGGCAGCAGTGCATCAAGCAAGAGCTCATCTGCAAGTGGATCGAC
CCGGAGCAGCTAAGCAATCCCAAGAAAAGCTGCAACAAAACTTTCAGCACCATGCACGAGCTGG
TGACCCACGTCTCTGTAGAGCATGTCGGCGGCCCGGAACAGAGCAACCACGTCTGCTTCTGGGA
GGAGTGTCCACGCGAGGGCAAACCCTTTAAGGCCAAATACAAACTGGTCAACCACATCCGCGTG
CACACGGGCGAGAAACCCTTCCCTTGTCCTTTCCCGGGTTGTGGCAAGGTCTTCGCACGCTCCG
AGAACCTCAAGATCCACAAAAGAACTCACACAGGGGAGAAACCTTTCCAGTGTGAGTTCGAGGG
CTGTGACCGACGCTTCGCCAACAGCAGCGACAGGAAGAAGCACATGCACGTCCACACCTCAGAT
AAGCCCTATCTCTGCAAGATGTGCGACAAGTCCTACACGCATCCCAGCTCCTTGCGGAAGCACA
TGAAGGTCCATGAGTCCTCCCCTCAGGGCTCCGAGTCCTCCCCGGCTGCCAGCTCTGGCTACGA
GTCGTCCACACCCCCAGGGTTGGTGTCCCCCAGCGCAGAGCCACAAAGCAGCTCCAACCTGTCC
CCAGCAGCGGCAGCGGCGGCGGCAGCGGCTGCAGCAGCGGCGGCCGCGGTGTCCGCAGTGCACC
GAGGCGCGGGTTCTGGCAGTAGCGGCTCCGGAGGGGGCTCGGCGGCCGGCAGCGGTGGGGGCGG
CGGCGGGGCGGGCGGCGGGGGCGGCGGCAGCTCTGGCGGGGGCAGCGGGACAGCCGGAGGCCAT
AGCGGCCTCTCCTCCAACTTCAATGAATGGTACGTGTGAAGGGCCAGGCCTTTCTCCCATTCCC
TGTTCCCTTATCCACCGTCGCCCTCCCAAAAACCCACCGAGGGCACCTTAGGATCATCTTACTA
AAATTATGAGTCTGATTTTTATGGTGAAAAAAATTTTACCAGCAGAAGGATTTTTAAAAGTTTT
TTTTTCTTTTTAAAGAAAACAATCTAGGCATGAAAAGCAACATCTCTCTGTATCTCTGAAGCTG
AAAACATAAAAAAAATTTTTTGAAGAAAGTAAACTCCACAAAAATATCGAGCCAAACTTCCCTA
GCAACCCCCAGCCCACTTTCCTTCCCATATGCTTCCCAGTCTTTTTGACAAACTGTACATAGCG
GACTCCTTCCTTTTCCACGGTGATTTTAATGGCTTATTGGTGGATAGAAGTTTGTCCATTTGTA
AACTCCGGATTGCGTTCCCTCCTGCCTTTCTCCCATTCCCCTTCCCCAAGTGACGGACCTTTTC
TTTTTTCCTTTTAGTTTACCCAGTCTTTTTTTTTTTAAAGTAATGTGGAAGAAAATGGTTTATT
TTGTATTGTGGTATTAAATATTGTGTTCCTTTTAAATGAGGCAACTTGATTGTAAACTTCATGC
GACTATAGACTGGAAAATATGAGCCGTGCCAAAGTTTCCCTTCTGTTTCTTCAACACACCAACC
CATAGCACACATCACCACCACCACCAACGCTTGTGAATGTATTTTTCTGTTAGCTGGGTTTACA
TGTGATGTTTCAGTGCTTTTGCGAGTTCGATTTGTTAGTTCTTGTATGAAAGTTTGGGGGTGGG
GTGGGTGGGAGTAAACGTTGTGCCGTTAGCTTTTTCCGAAATAACACCCTTCTGTAAATATCCG
TTGCCATATTTATCCATTTGTAATTAAATTATGGTATTAACTTGCTACAGAGGAAACAATATTT
ATAAAGAATGTTTCTTAACTATAAATATGTACAATTGTGGGCATAAACTGTTTCAGATTTTTTT
ATTTGAAGGTTTAAGTGGTTTGATCATTTCTTGTGATGTTTTGAGAGTAATGCATACAGAAATA
TAATAAAATGTGTTGAAACTGCA

hide sequence

RefSeq Acc Id:

XM_039093543 ⟹ XP_038949471

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	15	105,982,711 - 105,986,882 (+)	NCBI
mRatBN7.2	15	99,576,907 - 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:

show sequence

MLLDAGPQFPAIGVGSFARHHHHSAAAAAAAAAEMQDRELSLAAAQNGFVDSAAAHMGAFKLNP
GAHELSPGQSSAFTSQGPGAYPGSAAAAAAAAALGPHAAHVGSYSGPPFNSTRDFLFRSRGFGD
SAPGGGQHGLFGPGAGGLHHAHSDAQGHLLFPGLPEQHGPHASQNVLNGQMRLGLPGEVFGRSE
QYRQVASPRTDPYSAAQLHNQYGPMNMNMGMNMAAAAAHHHHHHHHPGAFFRYMRQQCIKQELI
CKWIDPEQLSNPKKSCNKTFSTMHELVTHVSVEHVGGPEQSNHVCFWEECPREGKPFKAKYKLV
NHIRVHTGEKPFPCPFPGCGKVFARSENLKIHKRTHTGEKPFQCEFEGCDRRFANSSDRKKHMH
VHTSDKPYLCKMCDKSYTHPSSLRKHMKVHESSPQGSESSPAASSGYESSTPPGLVSPSAEPQS
SSNLSPAAAAAAAAAAAAAAAVSAVHRGAGSGSSGSGGGSAAGSGGGGGGAGGGGGGSSGGGSG
TAGGHSGLSSNFNEWYV

hide 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

External Database Links

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

Gene Annotator (Functional Annotation) unavailable	Gene Annotator (Annotation Distribution) unavailable	Variant Visualizer (Genomic Variants) unavailble Variant Visualizer (Genomic Variants) unavailable
Gene Annotator (Functional Annotation)	Gene Annotator (Annotation Distribution)	Variant Visualizer (Genomic Variants)

InterViewer (Protein-Protein Interactions) unavailable	Gviewer (Genome Viewer) unavailable	Variant Visualizer (Damaging Variants) unavailble Variant Visualizer (Damaging Variants) unavailable
InterViewer (Protein-Protein Interactions)	GViewer (Genome Viewer)	Variant Visualizer (Damaging Variants)

Gene Annotator (Annotation Comparison) unavailable	OLGA (Gene List Generator) unavailable
Gene Annotator (Annotation Comparison)	OLGA (Gene List Generator)	Excel (Download)

MOET (Multi-Ontology Enrichement) unavailable	GOLF (Gene-Ortholog Location Finder) unavailable
MOET (Multi-Ontology Enrichement)	GOLF (Gene-Ortholog Location Finder)

Imported Disease Annotations - ClinVar

Imported Disease Annotations - CTD

Imported Disease Annotations - GAD

Imported Disease Annotations - MGI

Imported Disease Annotations - OMIM

Imported Annotations - KEGG (archival)

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Imported Disease Annotations - MGI

Imported Disease Annotations - OMIM

Imported Annotations - KEGG (archival)