XLOC_007965 (zic3)


Basic Information

Item Value
gene id XLOC_007965
gene name zic3
gene type coding
species zebrafish (Danio rerio)
category of species model fish

Chromosome Information

Item Value
chromosome id NC_007125.7
NCBI id CM002898.2
chromosome length 52660232
location 32011689 ~ 32016615 (-)
genome version GRCz11_2017_zebrafish_Genome

Sequence

>TCONS_00015560
ATCAGTCCAAGGACATCATTCGTCTGGAAAGGGGGGGAAGTTTGATCCTCTTTCTCACGGATCCCAGTTGCGGGAGTTTTTCTCCCGTTTACCGAGACCCGGGATTAtcatttcgtttttttttcaattgaagaTTTCTTTTTTCAAGCTTACGTGAAATTGCGCTCAATTTCCCGGTACCCGTTCACTCCACTAACCTGGGGTTtccctctttttttatttttcatttgtttttctcgATTGAGCCCAATGACTATGCTCCTTGATAGCGCTCCTCAGTTCCCGTCACTAGGAGTAGGGGGCTTCGGAACGCCTAGACACCATGAGTTAGGAAACAGAGACCCTGGGCTGGGACTCAGTCCCTTCGCAGATTCATCTCACTCGGCTGCCTTCAAGATTAGTCCCGTTACTCACGACATCGCCTCCAGCCAGACATCAGCGTTCACACCGCAAGCAACTGGATACGCAGCAGCGCTCGGACACCACCACGGAGGACAAGTTGGTTCTTACGCCGGTGGAGCATTCAATTCGACCAGGGACTTTCTCTTCAGAAACAGGGGCGCAGGCATCGGAGAGACCGCACCGCCGAGTGCCCAGCATGGAATCTTTGCCGCTTCTGCTGGGAGTCTACACGGGCCCCCCGGAATTTCGGACAACCCGGGACATCTGTTGTTTCCTGGACTTCACGATCAGAGCGTGAGCCACACATCACCAGGAGGACATGTTGTAAACAGTCAAATGCACCTGGGTTTACGCGGGGACATTTTTGGCCGTCCAGATCCATATCGACCTGTGGCGAGCCCTCGTACGGAACCTTATGGCGCCGCTCCGCTGCATAACTATAACCATCCCATTAATATGAACATGGGAATGAACGTACCCACACACCATGGTCCGGGGGCCTTCTTCAGATACATGCGGCAGCCTATAAAGCAAGAATTGTCTTGTAAGTGGATAGATGAGAATCAGATGAACAGACCTAAAAAGACTTGTGACAGAACTTTCAGCACAATGCATGAAATGGTGACACATGTTTCGATGGAACACGTTGGCGGCCCAGAGCAGAGTAATCATGTTTGCTACTGGGAGGATTGCCCGAGAGAGGGGAAATCCTTTAAGGCCAAATACAAACTCGTGAACCACATCCGagtacacactggagagaaaccgttcccTTGTCCGTTTCCTGGTTGTGGTAAAATTTTCGCAAGATCAGAAAATCTTAAAATTCACAAAAGAACTCACACAGGTGAGAAGCCATTTAAATGCGAGTTCGATGGCTGCGACAGGCGATTTGCAAACAGCAGCGACAGGAAAAAGCACATGCACGTGCACACATCTGACAAGCCATATATCTGCAAAGTGTGTGACAAGTCCTACACACATCCCAGCTCTCTCAGGAAACATATGAAGGTACACGAATCACAAGGCTCAGAGTCGTCTCCGGCTGCGAGCTCTGGATACGAGTCGTCCACGCCGCCAGTGCTGGTTTCTGCGAACACTGAAGACCCGACAAAAACACCCACGTCCGCGGTGCAAAATTCATCAGCACACAGCGATGGACTACCACCTAATTTTAACGAATGGTACGTTTGAAGCTCCAAGCAGACTCTCAAATGGTGGACCAAAAGGTTGAAGTAacctttaaaaactatttacGCTATGGCGTACAAAATGGCATTGAAACAACAGGAAAAGATGAGAGTTCGCCAGCAGGCCTCGTCCATTCTCAGGATTCGAAATTTGACTTTATTCCGAGTTCGAAGAAAACTAGCaagacataaaataacaaaataacactttCTAAGAATAAATGGTTTTCCTTTAGTTTTCAGATTtcagatgattattttatttttcattttatgtattttctgaaaaaaatatttaaaaataatggcaAAGAAAGAATATTTCACGGTGTTTTATATTAAGGTGACACTCACATCACCTTTGATTGATTGTTAAAACTTCAGACAGTCTTAAGAAACGTGCCAAAGTCTTTGTCTTGaacttgaacaaaaaataaatcataaataagtaTATAGCCTACTCGTGAATGTATTTCCTTGTTTGATGGAGTCAAATCTGTTGTCCAAGTCCGTTTTCAGGTGGAGAAATGTGGTATTAGCTTACGATTGTTACCTTTGATTATAACGTTGCCTTTGTTAATAATGATGTAAATACATATCCATGATGCCATATTTAtcaatttgtaatttaattatcGGCGAAAAAGCCGAATCTTAAATGATATTTATGGAAATGTTTTCTAACAAGACTGTACAGTTTTGAGTCAACCAGTTTTAACGATGAAAAGGGAGTCAGTTCTAAAGTTCCCACGATACGATTGTATCTTTTTTAACCAATGTATGTGTCTTATCTGGGTCGTAaagtattaattatattaataatatgacaAGACATGCTCTATAGTTTAAAGTTTGCATTTTGCAACATAAGCTGATGTAAGGATCggtataaaaagtaataaaacaatGGGTTCTTTCCCCCCTTTATATCACTGATGAATCAGCCATATATGTGAGTTATACAGAGGCATTCTGGTTATCGAAAtttcttattttgtatttttctttactCTTACCATTCGAGTATAGACTACACCTAAGGATCACTTACAAATTCGAGATGCCCACTGACCAGTATTTTCATCGAAACGCCACTTTTTGATCAGATACACCATGCAATAGCATAGCTTTCATTCATGCATCAACTTTGAAACCGTGTGACAGTGTTAAAGAAGTTAACCAATATTCCTGGGTTTAAGGTCCATTTGAATCAGTATGGTATTCCATTTTTGATAGTTCCAGAACTGTCTTTGTGGATGCAAGTCTGTGTTTAATGTGTCAAAGAGGAGCAATGATCTGTCACAACAGTAATctcaaaataaaactttctgtCTGTCAGTTTGCATTGTTTTAAATGTAGTTCTTCTGTGAATATAGCGTGTTGTTTGTTATGAGTACTGTGGTATAACATATAGAAAACTTTGATTACACATTTGCTTGTTTTATGTGAATAACTTTTCCAGATGTGGAACTGTATGTGTGAATGAAATTTAGTATTAAGAATACTACAACTTTTTAAGATGGAAAAGTGAGGGGAAATATGTGTTCAGTGACACCGAGAGTTACAGCATTGCATTGTTACATATTTTTTAAGAGACTAAAattatgcatataaatatattgtGCTTATGAACATGATTTCAAACCACCAGCACTACTTTTGAAAACAAACGTAAAAAAACAGTACCTCGTAACGGTGATATATAAAAacgtttatttaaataatttaatgaatatatgttttatatactaTTTTCTATACGTTAagttaaagaaaataaagatttatttcaGCCACATTCGATGTTTCTTCAACCCTGATCTCAGACAGATCTAATGTACAAATGGAGCTTGAATGTGATTCTGTGACATTTTCTCGTGGAAATGGGTCACGCATCAAGTTATTCCTGAAAAGCATATGTTTAACTGATGAACTGTGTCACTGTGCCATTTTCGAGGCAAGCGATGTTACTGCAACATACCCTATTCAAAATTCAGCAGAATCTTGTACTTTCTTCCGAAGTAGGGttattgtttgttggtttgtttaacAAACTATTTATGACAAAATGTGAACAAGTTTTGACTGGAATTAAAACAAATCCTGAAATGTCACAAA

Function

symbol description
zic3 Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Acts upstream of or within anterior/posterior axis specification and determination of left/right symmetry. Predicted to be active in nucleus. Is expressed in several structures, including central nervous system; mesoderm; neural keel; neural plate; and presumptive structure. Used to study right atrial isomerism; spina bifida; and visceral heterotaxy. 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).

GO:

id name namespace
GO:0006357 regulation of transcription by RNA polymerase II biological_process
GO:0009948 anterior/posterior axis specification biological_process
GO:0009952 anterior/posterior pattern specification biological_process
GO:0007368 determination of left/right symmetry biological_process
GO:0045944 positive regulation of transcription by RNA polymerase II biological_process
GO:0007417 central nervous system development biological_process
GO:0005634 nucleus cellular_component
GO:0046872 metal ion binding molecular_function
GO:0003676 nucleic acid binding molecular_function
GO:0000978 RNA polymerase II cis-regulatory region sequence-specific DNA binding molecular_function
GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific molecular_function

KEGG:

id description
ko04550 Signaling pathways regulating pluripotency of stem cells
ko03000 Transcription factors

ZFIN:

id description
ZDB-GENE-030708-2 Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Acts upstream of or within anterior/posterior axis specification and determination of left/right symmetry. Predicted to be active in nucleus. Is expressed in several structures, including central nervous system; mesoderm; neural keel; neural plate; and presumptive structure. Used to study right atrial isomerism; spina bifida; and visceral heterotaxy. 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).

Ensembl:

ensembl_id ENSDARG00000071497

RNA

RNA id representative length rna type GC content exon number start site end site
TCONS_00015560 True 3711 mRNA 0.40 3 32011689 32016615

Neighbor

gene id symbol gene type direction distance location
XLOC_007964 gpr101 coding downstream 117693 31890001 ~ 31893996 (-)
XLOC_007963 NA coding downstream 122429 31881282 ~ 31889260 (-)
XLOC_007959 arhgef6 coding downstream 148969 31799787 ~ 31862720 (-)
XLOC_007966 NA coding upstream 52189 32068804 ~ 32134037 (-)
XLOC_007967 fgf13a coding upstream 167363 32183978 ~ 32428689 (-)
XLOC_007968 NA coding upstream 415833 32432448 ~ 32435306 (-)
XLOC_007969 mcf2a coding upstream 424024 32440639 ~ 32503363 (-)
XLOC_007970 atp11c coding upstream 491196 32507811 ~ 32631519 (-)
XLOC_007641 CU855896.1 misc downstream 29603849 2407736 ~ 2407840 (-)
XLOC_007640 CU855896.2 misc downstream 29604258 2407328 ~ 2407431 (-)
XLOC_007639 CU855896.3 misc downstream 29604617 2406945 ~ 2407072 (-)
XLOC_007962 AL929434.2 non-coding downstream 150862 31860750 ~ 31860827 (-)
XLOC_007961 AL929434.3 non-coding downstream 151219 31860408 ~ 31860470 (-)
XLOC_007960 AL929434.1 non-coding downstream 152183 31859430 ~ 31859506 (-)
XLOC_007957 BX511227.4 non-coding downstream 376256 31633146 ~ 31635433 (-)
XLOC_007971 NA non-coding upstream 648014 32664629 ~ 32755070 (-)
XLOC_007973 AL590151.1 non-coding upstream 757057 32773672 ~ 32789588 (-)
XLOC_007979 BX247946.1 non-coding upstream 897065 32913680 ~ 32918834 (-)

Expression


Co-expression Network

Homologous

species gene id symbol gene type chromosome NCBI id location
eurasian perch (Perca fluviatilis) G79510 NA non-coding NC_053118.1 CM020915.1 38250106 ~ 38255038 (-)
bowfin (Amia calva) G85332 zic3,LOC107744514,LOC107601137,LOC107658104,LOC102782288 non-coding CM030130.1 CM030130.1 15041063 ~ 15043903 (-)