ZIC5 (Zic family member 5) - Rat Genome Database

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Gene: ZIC5 (Zic family member 5) Sus scrofa
Analyze
Symbol: ZIC5
Name: Zic family member 5
RGD ID: 13907262
Description: ENCODES a protein that exhibits DNA binding (ortholog); DNA-binding transcription factor activity (ortholog); RNA polymerase II transcription regulatory region sequence-specific DNA binding (ortholog); INVOLVED IN forebrain development (ortholog); neural crest cell differentiation (ortholog); neural tube closure (ortholog); ASSOCIATED WITH Anal Atresia, Hypospadias, and Penoscrotal Inversion (ortholog); Craniofacial Abnormalities (ortholog); genetic disease (ortholog); FOUND IN nucleus (inferred)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: zinc finger protein ZIC 5
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Sscrofa11.1 - Pig Sscrofa11.1 Assembly
Position:
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
JBrowse: View Region in Genome Browser (JBrowse)
Model


References
Additional References at PubMed
PMID:30032202  


Genomics

Comparative Map Data
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
(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
(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
(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
(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
145 total Variants

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 nervous system
High
Medium 2
Low 14
Below cutoff 1 5

Sequence


Reference Sequences
RefSeq Acc Id: ENSSSCT00000010439   ⟹   ENSSSCP00000010168
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1 Ensembl1168,821,735 - 68,830,540 (-)Ensembl
RefSeq Acc Id: XM_005653825   ⟹   XP_005653882
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.11168,821,733 - 68,830,472 (-)NCBI
Sequence:
Reference Protein Sequences
RefSeq Acc Id: XP_005653882   ⟸   XM_005653825
- UniProtKB: F1RP23 (UniProtKB/TrEMBL),   A0A8D1RJ23 (UniProtKB/TrEMBL),   A0A4X1UHP1 (UniProtKB/TrEMBL),   A0A8D1KDD9 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSSSCP00000010168   ⟸   ENSSSCT00000010439
Protein Domains
C2H2-type


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSSSCG00000009521 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
  ENSSSCG00025018767 UniProtKB/TrEMBL
  ENSSSCG00030073522 UniProtKB/TrEMBL
  ENSSSCG00035075380 UniProtKB/TrEMBL
  ENSSSCG00040049232 UniProtKB/TrEMBL
  ENSSSCG00045037939 UniProtKB/TrEMBL
  ENSSSCG00050052750 UniProtKB/TrEMBL
  ENSSSCG00055021578 UniProtKB/TrEMBL
  ENSSSCG00060028190 UniProtKB/TrEMBL
  ENSSSCG00065077632 UniProtKB/TrEMBL
  ENSSSCG00070016748 UniProtKB/TrEMBL
Ensembl Transcript ENSSSCT00000010439 ENTREZGENE
  ENSSSCT00000010439.5 UniProtKB/TrEMBL
  ENSSSCT00025025432.1 UniProtKB/TrEMBL
  ENSSSCT00030102954.1 UniProtKB/TrEMBL
  ENSSSCT00035102430.1 UniProtKB/TrEMBL
  ENSSSCT00040066340.1 UniProtKB/TrEMBL
  ENSSSCT00045065591.1 UniProtKB/TrEMBL
  ENSSSCT00050071829.1 UniProtKB/TrEMBL
  ENSSSCT00055042391.1 UniProtKB/TrEMBL
  ENSSSCT00060038130.1 UniProtKB/TrEMBL
  ENSSSCT00065107425.1 UniProtKB/TrEMBL
  ENSSSCT00070032992.1 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 ZIC5 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
PROSITE ZINC_FINGER_C2H2_1 UniProtKB/TrEMBL
  ZINC_FINGER_C2H2_2 UniProtKB/TrEMBL
SMART ZnF_C2H2 UniProtKB/TrEMBL
Superfamily-SCOP SSF57667 UniProtKB/TrEMBL
UniProt A0A4X1UHP1 ENTREZGENE, UniProtKB/TrEMBL
  A0A8D1KDD9 ENTREZGENE, UniProtKB/TrEMBL
  A0A8D1RJ23 ENTREZGENE, UniProtKB/TrEMBL
  F1RP23 ENTREZGENE, UniProtKB/TrEMBL
VGNC ID VGNC:95170 ENTREZGENE