Zic1 (Zic family member 1) - Rat Genome Database

Name: Zic1
Creator: Rat Genome Database
License: Creative Commons CC BY 4.0
Keywords: Rat Gene RGD Genome

Gene: Zic1 (Zic family member 1) Ictidomys tridecemlineatus

Analyze

Symbol:

Zic1

Name:

Zic family member 1

RGD ID:

12517026

Description:

ENCODES a protein that exhibits DNA-binding transcription activator activity, RNA polymerase II-specific (inferred); DNA-binding transcription factor activity (inferred); DNA-binding transcription factor activity, RNA polymerase II-specific (inferred); INVOLVED IN adult walking behavior (ortholog); central nervous system development (ortholog); ASSOCIATED WITH craniosynostosis (ortholog); Craniosynostosis 6 (ortholog); Dandy-Walker syndrome (ortholog); FOUND IN cytoplasm (inferred); nucleoplasm (inferred); nucleus (inferred)

Type:

protein-coding

RefSeq Status:

MODEL

Previously known as:

zinc finger protein ZIC 1

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):	ZIC1 (Zic family member 1)	NCBI	Ortholog
Mus musculus (house mouse):	Zic1 (zinc finger protein of the cerebellum 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Rattus norvegicus (Norway rat):	Zic1 (Zic family member 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chinchilla lanigera (long-tailed chinchilla):	Zic1 (Zic family member 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	ZIC1 (Zic family member 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	ZIC1 (Zic family member 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	ZIC1 (Zic family member 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	ZIC1 (Zic family member 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Zic1 (Zic family member 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline

Latest Assembly:

SpeTri2.0 - Squirrel SpeTri2.0 Assembly

Position:

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HiC_Itri_2	NW_024405602	81,731,682 - 81,736,232 (+)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936519	7,994,455 - 8,002,487 (-)	Ensembl	SpeTri2.0	SpeTri2.0 Ensembl
SpeTri2.0	NW_004936519	7,997,824 - 8,001,614 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

craniosynostosis (ISO)

Craniosynostosis 6 (ISO)

Dandy-Walker syndrome (ISO)

genetic disease (ISO)

Joubert syndrome (ISO)

STRUCTURAL BRAIN ANOMALIES WITH IMPAIRED INTELLECTUAL DEVELOPMENT AND CRANIOSYNOSTOSIS (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

adult walking behavior (IEA,ISO)

brain development (IEA)

central nervous system development (IEA,ISO)

forebrain development (IEA)

gene expression (IEA)

hippocampus development (IEA)

maintenance of cell number (IEA)

negative regulation of transcription by RNA polymerase II (IEA)

olfactory bulb development (IEA)

pattern specification process (IEA)

positive regulation of DNA-templated transcription (IEA)

positive regulation of protein import into nucleus (IEA)

positive regulation of transcription by RNA polymerase II (IEA)

regulation of smoothened signaling pathway (IEA)

spinal cord development (IEA)

Cellular Component

cytoplasm (IEA)

nucleoplasm (IEA)

nucleus (IEA)

Molecular Function

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

DNA-binding transcription factor activity (IEA)

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

protein binding (ISO)

RNA polymerase II cis-regulatory region sequence-specific DNA binding (IEA)

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

sequence-specific double-stranded DNA binding (IEA)

References

Additional References at PubMed

PMID:30032202

Genomics

Comparative Map Data

Zic1
(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_024405602	81,731,682 - 81,736,232 (+)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936519	7,994,455 - 8,002,487 (-)	Ensembl	SpeTri2.0	SpeTri2.0 Ensembl
SpeTri2.0	NW_004936519	7,997,824 - 8,001,614 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

ZIC1
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	3	147,409,365 - 147,416,719 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	3	147,393,422 - 147,510,293 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	3	147,127,152 - 147,134,506 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	3	148,609,871 - 148,617,196 (+)	NCBI	NCBI36	Build 36	hg18	NCBI36
Build 34	3	148,609,878 - 148,615,046	NCBI
Celera	3	145,539,633 - 145,546,958 (+)	NCBI		Celera
Cytogenetic Map	3	q24	NCBI
HuRef	3	144,503,350 - 144,510,663 (+)	NCBI		HuRef
CHM1_1	3	147,090,188 - 147,097,518 (+)	NCBI		CHM1_1
T2T-CHM13v2.0	3	150,164,618 - 150,171,972 (+)	NCBI		T2T-CHM13v2.0

Zic1
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	9	91,240,111 - 91,250,136 (-)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	9	91,240,111 - 91,247,863 (-)	Ensembl		GRCm39 Ensembl
GRCm38	9	91,358,058 - 91,365,768 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	9	91,358,058 - 91,365,810 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	9	91,255,183 - 91,260,637 (-)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	9	91,158,250 - 91,163,704 (-)	NCBI		MGSCv36	mm8
Celera	9	90,951,458 - 90,959,662 (-)	NCBI		Celera
Cytogenetic Map	9	E3.2	NCBI
cM Map	9	48.26	NCBI

Zic1
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	8	100,785,282 - 100,797,716 (-)	NCBI		GRCr8
mRatBN7.2	8	91,908,548 - 91,918,020 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	8	91,908,576 - 91,912,731 (-)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	8	97,587,773 - 97,591,212 (-)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	8	95,787,021 - 95,790,460 (-)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	8	93,600,935 - 93,604,373 (-)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	8	98,733,715 - 98,738,960 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	8	98,734,295 - 98,738,446 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	8	98,226,542 - 98,229,980 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	8	96,314,692 - 96,318,130 (-)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	8	96,334,146 - 96,337,585 (-)	NCBI
Celera	8	91,436,069 - 91,439,507 (-)	NCBI		Celera
Cytogenetic Map	8	q31	NCBI

Zic1
(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 Ensembl	NW_004955474	10,029,174 - 10,033,380 (-)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955474	10,029,226 - 10,033,104 (-)	NCBI	ChiLan1.0	ChiLan1.0

ZIC1
(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	2	145,305,012 - 145,312,262 (+)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	3	145,310,546 - 145,316,993 (+)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	3	144,437,075 - 144,443,516 (+)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	3	152,019,288 - 152,024,497 (+)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	3	152,019,013 - 152,024,502 (+)	Ensembl	panpan1.1		panPan2

ZIC1
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Dog10K_Boxer_Tasha	23	42,405,942 - 42,410,126 (+)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	23	43,154,161 - 43,158,357 (+)	NCBI		ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	23	43,154,177 - 43,162,933 (+)	Ensembl		ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	23	42,751,244 - 42,755,412 (+)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	23	42,803,713 - 42,807,873 (+)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	23	43,055,395 - 43,059,590 (+)	NCBI		UU_Cfam_GSD_1.0

ZIC1
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	13	87,745,552 - 87,750,192 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	13	87,740,769 - 87,750,258 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	13	95,427,405 - 95,431,044 (-)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

ZIC1
(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	15	43,280,429 - 43,285,674 (-)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	15	43,281,433 - 43,284,948 (-)	Ensembl	ChlSab1.1	ChlSab1.1 Ensembl	chlSab2
Vero_WHO_p1.0	NW_023666041	16,147,496 - 16,153,069 (-)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Zic1
(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_004624730	24,440,192 - 24,448,421 (+)	Ensembl	HetGla_female_1.0	HetGla_female_1.0 Ensembl	hetGla2
HetGla 1.0	NW_004624730	24,440,717 - 24,444,663 (+)	NCBI	HetGla_female_1.0	HetGla 1.0	hetGla2

Expression

Sequence

Nucleotide Sequences


RefSeq Transcripts	XM_005325722	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	JAESOR010000662	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

RefSeq Acc Id:

ENSSTOT00000000949 ⟹ ENSSTOP00000000849

Type:

CODING

Position:

Squirrel Assembly	Chr	Position (strand)	Source
SpeTri2.0 Ensembl	NW_004936519	7,994,455 - 8,002,487 (-)	Ensembl

RefSeq Acc Id:

XM_005325722 ⟹ XP_005325779

Type:

CODING

Position:

Squirrel Assembly	Chr	Position (strand)	Source
HiC_Itri_2	NW_024405602	81,731,682 - 81,736,232 (+)	NCBI
SpeTri2.0	NW_004936519	7,997,824 - 8,001,614 (-)	NCBI

Sequence:

show sequence

TTTTCCCTCCTCGGCGGGCGAGGGTGGGGGGGGCGGGGGAGGCCGGGGCTTGCCCGGAGCAGCC
ACGATGCTCCTGGACGCCGGCCCCCAGTATCCTGCGATCGGTGTGACCACCTTTGGCGCATCCC
GCCACCATTCGGCGGGAGACGTGGCCGAGCGAGACGTGGGCCTGGGCATCAACCCGTTCGCCGA
CGGCATGGGCGCCTTCAAGCTCAACCCCAGTTCGCACGAGCTGGCTTCGGCCGGCCAGACGGCC
TTCACGTCTCAGGCACCCGGCTATGCGGCTGCTGCGGCCCTGGGTCATCACCACCACCCGGGCC
ACGTCGGCTCCTATTCCAGTGCAGCTTTCAATTCTACGCGGGACTTTCTGTTTCGCAACCGGGG
TTTTGGAGACGCGGCGGCGGCAGCCAGCGCGCAGCATAGCCTCTTCGCTGCTTCAGCCGGCGGC
TTCGGGGGCCCACACGGCCATACGGACGCCGCGGGCCACCTCCTTTTTCCCGGGCTTCACGAGC
AGGCGGCGGGCCACGCTTCGCCCAACGTGGTCAACGGGCAAATGAGGCTCGGCTTCTCTGGGGA
CATGTACCCGCGGCCCGAACAGTACGGCCAGGTGACCAGCCCGCGATCCGAGCACTATGCCGCC
CCGCAGCTGCACGGGTACGGGCCCATGAACGTGAACATGGCCGCGCATCACGGCGCCGGCGCCT
TCTTCCGCTATATGCGCCAACCCATCAAGCAAGAGCTCATCTGTAAGTGGATCGAGCCAGAGCA
GCTGGCCAACCCCAAAAAGTCGTGCAACAAAACTTTCAGCACCATGCATGAGCTGGTCACGCAC
GTCACTGTGGAACACGTCGGCGGCCCAGAGCAGAGTAACCACATCTGCTTCTGGGAGGAGTGTC
CACGCGAGGGCAAGCCCTTCAAAGCCAAATACAAACTGGTCAACCACATCCGCGTGCACACGGG
CGAAAAACCCTTCCCCTGCCCTTTCCCTGGCTGCGGCAAGGTCTTCGCGCGCTCAGAAAACCTA
AAGATCCACAAAAGGACGCACACAGGGGAGAAGCCCTTCAAGTGCGAATTCGAGGGCTGCGACC
GGCGCTTTGCTAACAGCAGCGACCGCAAGAAGCACATGCACGTGCATACGAGTGATAAACCCTA
TCTTTGCAAGATGTGCGACAAGTCCTACACGCACCCCAGCTCGCTGCGCAAACACATGAAGGTC
CACGAATCCTCCTCGCAGGGCTCCCAGCCTTCGCCCGCCGCCAGCTCGGGCTACGAGTCCTCCA
CGCCGCCCACCATCGTGTCTCCCTCCACAGAGAACCCGACCACCAGCTCCCTGTCGCCCTCCTC
CTCCGCGGTCCACCACACAGCCGGCCACAGCGCGCTCTCTTCCAATTTTAACGAATGGTACGTT
TAAAATCAGAAACAAAACACCGAACAAAACCCTATTTAAGAGACTGAACACACACGTATACACC
ATATTATTGAACGAACCCTGAACCCTGCGAATCCGAAACAACCCCTCCCAGACCCCAGTGTCCT
TTTTTTTTTTTTTTTTTTTTAAATCTGCCAATAGGCCCAGGACTGAGTCAGAGAGAGGAAGTAT
CAAACCTTCTTAAAATTTCCTTCACTACATTTTCTTTCTTT

hide sequence

Protein Sequences


Protein RefSeqs	XP_005325779	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSSTOP00000000849.3

RefSeq Acc Id:

XP_005325779 ⟸ XM_005325722

- UniProtKB:

I3LXN1 (UniProtKB/TrEMBL)

- Sequence:

show sequence

MLLDAGPQYPAIGVTTFGASRHHSAGDVAERDVGLGINPFADGMGAFKLNPSSHELASAGQTAF
TSQAPGYAAAAALGHHHHPGHVGSYSSAAFNSTRDFLFRNRGFGDAAAAASAQHSLFAASAGGF
GGPHGHTDAAGHLLFPGLHEQAAGHASPNVVNGQMRLGFSGDMYPRPEQYGQVTSPRSEHYAAP
QLHGYGPMNVNMAAHHGAGAFFRYMRQPIKQELICKWIEPEQLANPKKSCNKTFSTMHELVTHV
TVEHVGGPEQSNHICFWEECPREGKPFKAKYKLVNHIRVHTGEKPFPCPFPGCGKVFARSENLK
IHKRTHTGEKPFKCEFEGCDRRFANSSDRKKHMHVHTSDKPYLCKMCDKSYTHPSSLRKHMKVH
ESSSQGSQPSPAASSGYESSTPPTIVSPSTENPTTSSLSPSSSAVHHTAGHSALSSNFNEWYV

hide sequence

RefSeq Acc Id:

ENSSTOP00000000849 ⟸ ENSSTOT00000000949

Protein Domains

C2H2-type

Additional Information

External Database Links

Database	Acc Id	Source(s)
Ensembl Genes	ENSSTOG00000000952	Ensembl, UniProtKB/TrEMBL
Ensembl Transcript	ENSSTOT00000000949.3	UniProtKB/TrEMBL
Gene3D-CATH	Classic Zinc Finger	UniProtKB/TrEMBL
InterPro	Znf_C2H2_sf	UniProtKB/TrEMBL
	Znf_C2H2_type	UniProtKB/TrEMBL
	Znf_ZIC	UniProtKB/TrEMBL
NCBI Gene	Zic1	ENTREZGENE
PANTHER	ZINC FINGER PROTEIN ZIC 1	UniProtKB/TrEMBL
	ZINC FINGER PROTEIN ZIC AND GLI	UniProtKB/TrEMBL
Pfam	zf-C2H2	UniProtKB/TrEMBL
	zf_ZIC	UniProtKB/TrEMBL
PROSITE	ZINC_FINGER_C2H2_1	UniProtKB/TrEMBL
	ZINC_FINGER_C2H2_2	UniProtKB/TrEMBL
SMART	ZnF_C2H2	UniProtKB/TrEMBL
Superfamily-SCOP	SSF57667	UniProtKB/TrEMBL
UniProt	I3LXN1	ENTREZGENE, UniProtKB/TrEMBL

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)

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