Zgpat (zinc finger CCCH-type and G-patch domain containing) - Rat Genome Database

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Gene: Zgpat (zinc finger CCCH-type and G-patch domain containing) Rattus norvegicus
Analyze
Symbol: Zgpat
Name: zinc finger CCCH-type and G-patch domain containing
RGD ID: 1310801
Description: Predicted to enable DNA-binding transcription repressor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in negative regulation of epidermal growth factor-activated receptor activity and negative regulation of transcription by RNA polymerase II. Predicted to be located in nucleoplasm and plasma membrane. Predicted to be active in nucleus. Orthologous to human ZGPAT (zinc finger CCCH-type and G-patch domain containing); INTERACTS WITH 2,4-dinitrotoluene; bisphenol A; vinclozolin.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC296478; MGC105627; RGD1310801; similar to cDNA sequence BC021513; zinc finger CCCH-type with G patch domain-containing protein; zinc finger, CCCH-type with G patch domain
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.23168,473,836 - 168,490,380 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl3168,473,981 - 168,490,380 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx3172,854,524 - 172,870,932 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.03181,813,625 - 181,830,033 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.03178,475,020 - 178,491,313 (+)NCBIRnor_WKY
Rnor_6.03176,865,078 - 176,881,603 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl3176,865,156 - 176,881,549 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.03180,575,280 - 180,591,735 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.43170,505,701 - 170,521,996 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.13170,411,736 - 170,428,030 (+)NCBI
Celera3164,096,159 - 164,112,380 (-)NCBICelera
Cytogenetic Map3q43NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


References

References - curated
# Reference Title Reference Citation
1. 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.
2. GOA pipeline RGD automated data pipeline
3. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:12477932   PMID:19644445  


Genomics

Comparative Map Data
Zgpat
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.23168,473,836 - 168,490,380 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl3168,473,981 - 168,490,380 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx3172,854,524 - 172,870,932 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.03181,813,625 - 181,830,033 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.03178,475,020 - 178,491,313 (+)NCBIRnor_WKY
Rnor_6.03176,865,078 - 176,881,603 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl3176,865,156 - 176,881,549 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.03180,575,280 - 180,591,735 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.43170,505,701 - 170,521,996 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.13170,411,736 - 170,428,030 (+)NCBI
Celera3164,096,159 - 164,112,380 (-)NCBICelera
Cytogenetic Map3q43NCBI
ZGPAT
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382063,707,442 - 63,736,142 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl2063,707,465 - 63,736,142 (+)EnsemblGRCh38hg38GRCh38
GRCh372062,338,794 - 62,367,494 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 362061,809,238 - 61,837,938 (+)NCBINCBI36Build 36hg18NCBI36
Celera2059,023,048 - 59,051,759 (+)NCBICelera
Cytogenetic Map20q13.33NCBI
HuRef2059,071,764 - 59,099,837 (+)NCBIHuRef
CHM1_12062,240,675 - 62,269,377 (+)NCBICHM1_1
T2T-CHM13v2.02065,527,749 - 65,556,418 (+)NCBIT2T-CHM13v2.0
Zgpat
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm392181,006,724 - 181,022,586 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl2181,006,721 - 181,025,421 (+)EnsemblGRCm39 Ensembl
GRCm382181,364,931 - 181,380,793 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl2181,364,928 - 181,383,628 (+)EnsemblGRCm38mm10GRCm38
MGSCv372181,099,636 - 181,115,498 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv362181,294,335 - 181,310,189 (+)NCBIMGSCv36mm8
Celera2185,447,199 - 185,463,092 (+)NCBICelera
Cytogenetic Map2H4NCBI
Zgpat
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955528493,051 - 519,780 (-)EnsemblChiLan1.0
ChiLan1.0NW_004955528493,051 - 519,780 (-)NCBIChiLan1.0ChiLan1.0
ZGPAT
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12061,630,274 - 61,662,967 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2061,630,271 - 61,662,967 (+)Ensemblpanpan1.1panPan2
ZGPAT
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12447,257,396 - 47,269,742 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2447,175,277 - 47,272,281 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2446,400,813 - 46,403,692 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02448,396,016 - 48,408,659 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2448,396,292 - 48,408,656 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12447,240,925 - 47,253,546 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02447,365,768 - 47,378,411 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02448,103,882 - 48,116,507 (+)NCBIUU_Cfam_GSD_1.0
Zgpat
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024408640195,511,577 - 195,526,655 (+)NCBIHiC_Itri_2
SpeTri2.0NW_00493651410,965,220 - 10,980,298 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
ZGPAT
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1762,635,018 - 62,652,483 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11762,640,988 - 62,652,478 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
ZGPAT
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12494,547 - 520,081 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2494,771 - 519,519 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366605048,048,248 - 48,074,527 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Zgpat
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462474129,356,260 - 29,390,300 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462474129,355,960 - 29,390,543 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Zgpat
33 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:41
Count of miRNA genes:33
Interacting mature miRNAs:39
Transcripts:ENSRNOT00000019084
Prediction methods:Miranda, 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.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1559282Emca5Estrogen-induced mammary cancer QTL 53.9mammary gland integrity trait (VT:0010552)percentage of study population developing mammary tumors during a period of time (CMO:0000948)343827364169034231Rat
631541Bp81Blood pressure QTL 814arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3124122556169034231Rat
1578656Vnigr2Vascular neointimal growth QTL 24.2artery morphology trait (VT:0002191)lesioned artery residual lumen area (CMO:0001417)3130656562169034231Rat
1578653Vnigr3Vascular neointimal growth QTL 33.1artery morphology trait (VT:0002191)artery neointimal hyperplastic lesion area (CMO:0001414)3130656562169034231Rat
9589106Insul23Insulin level QTL 2313.860.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)3131635904169034231Rat
2298477Eau4Experimental allergic uveoretinitis QTL 40.0011uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)3137398739169034231Rat
8552952Pigfal13Plasma insulin-like growth factor 1 level QTL 13blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)3138799500169034231Rat
1298068Bp167Blood pressure QTL 1670.004arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3141074471169034231Rat
2317883Alcrsp26Alcohol response QTL 261.80.63response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)3145526770169034231Rat
8552791Vie2Viral induced encephalitis QTL 24.1brain integrity trait (VT:0010579)encephalitis incidence/prevalence measurement (CMO:0002361)3145956084169034231Rat
1300161Rf10Renal function QTL 103.57renal blood flow trait (VT:2000006)absolute change in renal vascular resistance (CMO:0001900)3161192952169034231Rat

Markers in Region
RH128332  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.23168,490,188 - 168,490,340 (+)MAPPERmRatBN7.2
Rnor_6.03176,881,412 - 176,881,563NCBIRnor6.0
Rnor_5.03180,591,544 - 180,591,695UniSTSRnor5.0
RGSC_v3.43170,521,805 - 170,521,956UniSTSRGSC3.4
Celera3164,096,199 - 164,096,350UniSTS
Cytogenetic Map3q43UniSTS


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 integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 3 35 48 32 19 32 1 1 74 35 39 11 1
Low 8 9 9 9 7 10 2 7
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000019084   ⟹   ENSRNOP00000019084
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl3168,473,981 - 168,490,380 (+)Ensembl
Rnor_6.0 Ensembl3176,865,156 - 176,881,549 (+)Ensembl
RefSeq Acc Id: NM_001009656   ⟹   NP_001009656
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.23168,474,084 - 168,490,380 (+)NCBI
Rnor_6.03176,865,273 - 176,881,603 (+)NCBI
Rnor_5.03180,575,280 - 180,591,735 (+)NCBI
RGSC_v3.43170,505,701 - 170,521,996 (+)RGD
Celera3164,096,159 - 164,112,380 (-)RGD
Sequence:
RefSeq Acc Id: XM_006235749   ⟹   XP_006235811
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.23168,473,938 - 168,490,380 (+)NCBI
Rnor_6.03176,865,141 - 176,881,603 (+)NCBI
Rnor_5.03180,575,280 - 180,591,735 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006235750   ⟹   XP_006235812
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.23168,473,848 - 168,490,380 (+)NCBI
Rnor_6.03176,865,078 - 176,881,603 (+)NCBI
Rnor_5.03180,575,280 - 180,591,735 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006235751   ⟹   XP_006235813
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.23168,473,921 - 168,490,380 (+)NCBI
Rnor_6.03176,865,137 - 176,881,603 (+)NCBI
Rnor_5.03180,575,280 - 180,591,735 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006235752   ⟹   XP_006235814
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.23168,473,836 - 168,490,380 (+)NCBI
Rnor_6.03176,865,082 - 176,881,603 (+)NCBI
Rnor_5.03180,575,280 - 180,591,735 (+)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_001009656   ⟸   NM_001009656
- UniProtKB: Q5PPF5 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006235812   ⟸   XM_006235750
- Peptide Label: isoform X1
- UniProtKB: Q5PPF5 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006235811   ⟸   XM_006235749
- Peptide Label: isoform X1
- UniProtKB: Q5PPF5 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006235813   ⟸   XM_006235751
- Peptide Label: isoform X1
- UniProtKB: Q5PPF5 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006235814   ⟸   XM_006235752
- Peptide Label: isoform X1
- UniProtKB: Q5PPF5 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000019084   ⟸   ENSRNOT00000019084
Protein Domains
G-patch

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q5PPF5-F1-model_v2 AlphaFold Q5PPF5 1-507 view protein structure

Transcriptome

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

Promoters
RGD ID:13692754
Promoter ID:EPDNEW_R3279
Type:initiation region
Name:Zgpat_1
Description:zinc finger CCCH-type and G-patch domain containing
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.03176,865,143 - 176,865,203EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1310801 AgrOrtholog
BioCyc Gene G2FUF-46289 BioCyc
Ensembl Genes ENSRNOG00000014235 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000019084 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000019084 ENTREZGENE, UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7318724 IMAGE-MGC_LOAD
InterPro G_patch_dom UniProtKB/Swiss-Prot
  Tudor UniProtKB/Swiss-Prot
  ZGPAT UniProtKB/Swiss-Prot
  Znf-CCCH_4 UniProtKB/Swiss-Prot
  Znf_CCCH UniProtKB/Swiss-Prot
  Znf_CCCH_sf UniProtKB/Swiss-Prot
KEGG Report rno:296478 UniProtKB/Swiss-Prot
MGC_CLONE MGC:105627 IMAGE-MGC_LOAD
NCBI Gene 296478 ENTREZGENE
PANTHER PTHR46297 UniProtKB/Swiss-Prot
Pfam G-patch UniProtKB/Swiss-Prot
  zf-CCCH_4 UniProtKB/Swiss-Prot
PhenoGen Zgpat PhenoGen
PROSITE G_PATCH UniProtKB/Swiss-Prot
  ZF_C3H1 UniProtKB/Swiss-Prot
SMART G_patch UniProtKB/Swiss-Prot
  ZnF_C3H1 UniProtKB/Swiss-Prot
Superfamily-SCOP SSF90229 UniProtKB/Swiss-Prot
UniProt Q5PPF5 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-02-17 Zgpat  zinc finger CCCH-type and G-patch domain containing  Zgpat  zinc finger, CCCH-type with G patch domain  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-30 Zgpat  zinc finger, CCCH-type with G patch domain  RGD1310801  similar to cDNA sequence BC021513  Symbol and Name updated 1299863 APPROVED
2005-12-06 RGD1310801  similar to cDNA sequence BC021513  RGD1310801_predicted  similar to cDNA sequence BC021513 (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-20 RGD1310801_predicted  similar to cDNA sequence BC021513 (predicted)  LOC296478_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC296478_predicted  similar to cDNA sequence BC021513 (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL