Zc3h18 (zinc finger CCCH-type containing 18) - Rat Genome Database

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Gene: Zc3h18 (zinc finger CCCH-type containing 18) Rattus norvegicus
Analyze
Symbol: Zc3h18
Name: zinc finger CCCH-type containing 18
RGD ID: 1303257
Description: Predicted to enable mRNA cap binding complex binding activity and protein-macromolecule adaptor activity. Predicted to be involved in RNA destabilization. Predicted to be located in nuclear speck. Predicted to be part of ribonucleoprotein complex. Orthologous to human ZC3H18 (zinc finger CCCH-type containing 18); INTERACTS WITH 2,4-dinitrotoluene; 2,6-dinitrotoluene; atrazine.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: conserved nuclear protein Nhn1; Nhn1; nuclear protein NHN1; zinc finger CCCH domain-containing protein 18
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
mRatBN7.21950,434,864 - 50,479,855 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1950,434,903 - 50,479,854 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1957,239,392 - 57,274,732 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.01957,918,922 - 57,954,497 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.01960,138,009 - 60,173,350 (+)NCBIRnor_WKY
Rnor_6.01955,197,348 - 55,241,800 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1955,197,704 - 55,241,851 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01965,908,164 - 65,952,662 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41952,654,167 - 52,691,342 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11952,659,047 - 52,696,223 (+)NCBI
Celera1949,683,661 - 49,719,107 (+)NCBICelera
Cytogenetic Map19q12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. GOA pipeline RGD automated data pipeline
2. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:22658674   PMID:22681889   PMID:23793891  


Genomics

Comparative Map Data
Zc3h18
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21950,434,864 - 50,479,855 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1950,434,903 - 50,479,854 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1957,239,392 - 57,274,732 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.01957,918,922 - 57,954,497 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.01960,138,009 - 60,173,350 (+)NCBIRnor_WKY
Rnor_6.01955,197,348 - 55,241,800 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1955,197,704 - 55,241,851 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01965,908,164 - 65,952,662 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41952,654,167 - 52,691,342 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11952,659,047 - 52,696,223 (+)NCBI
Celera1949,683,661 - 49,719,107 (+)NCBICelera
Cytogenetic Map19q12NCBI
ZC3H18
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381688,570,403 - 88,631,964 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl1688,570,403 - 88,631,964 (+)EnsemblGRCh38hg38GRCh38
GRCh371688,636,811 - 88,698,372 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361687,164,343 - 87,225,761 (+)NCBINCBI36Build 36hg18NCBI36
Celera1673,707,153 - 73,768,044 (+)NCBICelera
Cytogenetic Map16q24.2NCBI
HuRef1674,330,774 - 74,392,389 (+)NCBIHuRef
CHM1_11690,048,070 - 90,109,663 (+)NCBICHM1_1
T2T-CHM13v2.01694,638,009 - 94,699,796 (+)NCBIT2T-CHM13v2.0
Zc3h18
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm398123,103,298 - 123,144,104 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl8123,103,348 - 123,144,099 (+)EnsemblGRCm39 Ensembl
GRCm388122,376,564 - 122,417,365 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl8122,376,609 - 122,417,360 (+)EnsemblGRCm38mm10GRCm38
MGSCv378124,900,516 - 124,941,260 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv368125,262,706 - 125,303,450 (+)NCBIMGSCv36mm8
Celera8126,605,738 - 126,646,471 (+)NCBICelera
Cytogenetic Map8E1NCBI
Zc3h18
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555412,524,499 - 2,567,203 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049555412,531,230 - 2,566,959 (+)NCBIChiLan1.0ChiLan1.0
ZC3H18
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11688,944,521 - 89,005,199 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1688,944,517 - 89,005,199 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01669,282,652 - 69,345,077 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
ZC3H18
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1564,708,472 - 64,774,098 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl564,704,083 - 64,766,994 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha564,719,012 - 64,784,545 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0564,927,749 - 64,993,499 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl564,927,666 - 64,993,513 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1564,953,769 - 65,018,478 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0564,785,557 - 64,851,107 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0565,191,670 - 65,257,423 (-)NCBIUU_Cfam_GSD_1.0
Zc3h18
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934925,300,104 - 25,351,109 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366411,053,624 - 1,104,670 (-)EnsemblSpeTri2.0
SpeTri2.0NW_0049366411,053,650 - 1,104,664 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
ZC3H18
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl61,030,418 - 1,081,538 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.161,030,416 - 1,081,541 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
ZC3H18
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1573,944,502 - 74,010,379 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl573,944,574 - 74,009,714 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660471,674,938 - 1,742,167 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Zc3h18
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_004624746919,636 - 960,533 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_004624746923,734 - 964,965 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Zc3h18
207 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:210
Count of miRNA genes:116
Interacting mature miRNAs:125
Transcripts:ENSRNOT00000039273, ENSRNOT00000045657
Prediction methods:Microtar, Miranda, Rnahybrid
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
724566Uae12Urinary albumin excretion QTL 125urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19218792756457239Rat
1331737Uae29Urinary albumin excretion QTL 295.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19409615555283277Rat
7411549Bw130Body weight QTL 13050.001body mass (VT:0001259)body weight gain (CMO:0000420)191545586057337602Rat
1578764Stresp19Stress response QTL 193.60.001blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)191563020157337602Rat
2298478Eau8Experimental allergic uveoretinitis QTL 80.0163uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)191715443357337602Rat
61350Bp32Blood pressure QTL 320.012arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)192048357557337602Rat
724546Kidm3Kidney mass QTL 33.1kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)192932249057337602Rat
1358200Insglur2Insulin/glucose ratio QTL 24.1blood glucose amount (VT:0000188)serum insulin level (CMO:0000358)193383821455283146Rat
1358200Insglur2Insulin/glucose ratio QTL 24.1blood glucose amount (VT:0000188)serum glucose level (CMO:0000543)193383821455283146Rat
5135224Leukc1Leukocyte quantity QTL 1eosinophil quantity (VT:0002602)blood eosinophil count (CMO:0000033)194434021455283277Rat
2313395Anxrr26Anxiety related response QTL 26aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)194997648153225766Rat

Markers in Region
RH132879  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21950,466,029 - 50,466,247 (+)MAPPERmRatBN7.2
Rnor_6.01955,227,977 - 55,228,194NCBIRnor6.0
Rnor_5.01965,938,839 - 65,939,056UniSTSRnor5.0
RGSC_v3.41952,677,810 - 52,678,027UniSTSRGSC3.4
Celera1949,705,575 - 49,705,792UniSTS
RH 3.4 Map19698.1UniSTS
Cytogenetic Map19q12UniSTS


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 30 55 39 19 39 1 4 73 35 41 11 1
Low 13 2 2 2 7 7 1 7
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000039273   ⟹   ENSRNOP00000035933
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1950,434,903 - 50,479,854 (+)Ensembl
Rnor_6.0 Ensembl1955,206,455 - 55,241,509 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000045657   ⟹   ENSRNOP00000048376
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1950,435,351 - 50,479,854 (+)Ensembl
Rnor_6.0 Ensembl1955,197,704 - 55,241,851 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000101747   ⟹   ENSRNOP00000093359
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1950,435,351 - 50,479,564 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000104719   ⟹   ENSRNOP00000088629
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1950,435,351 - 50,479,564 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000106092   ⟹   ENSRNOP00000082197
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1950,434,903 - 50,479,627 (+)Ensembl
RefSeq Acc Id: NM_201416   ⟹   NP_958819
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21950,443,991 - 50,479,564 (+)NCBI
Rnor_6.01955,206,455 - 55,241,509 (+)NCBI
Rnor_5.01965,908,164 - 65,952,662 (+)NCBI
RGSC_v3.41952,654,167 - 52,691,342 (+)RGD
Celera1949,683,661 - 49,719,107 (+)RGD
Sequence:
RefSeq Acc Id: XM_006255758   ⟹   XP_006255820
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21950,435,165 - 50,479,855 (+)NCBI
Rnor_6.01955,197,822 - 55,241,800 (+)NCBI
Rnor_5.01965,908,164 - 65,952,662 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006255759   ⟹   XP_006255821
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21950,435,162 - 50,479,855 (+)NCBI
Rnor_6.01955,197,821 - 55,241,800 (+)NCBI
Rnor_5.01965,908,164 - 65,952,662 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006255760   ⟹   XP_006255822
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21950,435,167 - 50,479,855 (+)NCBI
Rnor_6.01955,197,825 - 55,241,800 (+)NCBI
Rnor_5.01965,908,164 - 65,952,662 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006255761   ⟹   XP_006255823
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21950,434,864 - 50,479,855 (+)NCBI
Rnor_6.01955,197,348 - 55,241,800 (+)NCBI
Rnor_5.01965,908,164 - 65,952,662 (+)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_958819   ⟸   NM_201416
- UniProtKB: Q6TQE1 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006255823   ⟸   XM_006255761
- Peptide Label: isoform X4
- UniProtKB: Q6TQE1 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006255820   ⟸   XM_006255758
- Peptide Label: isoform X1
- UniProtKB: A0A140TAG3 (UniProtKB/TrEMBL),   A0A8I6AKJ5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006255821   ⟸   XM_006255759
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_006255822   ⟸   XM_006255760
- Peptide Label: isoform X3
- UniProtKB: A0A140TAG3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000048376   ⟸   ENSRNOT00000045657
RefSeq Acc Id: ENSRNOP00000035933   ⟸   ENSRNOT00000039273
RefSeq Acc Id: ENSRNOP00000088629   ⟸   ENSRNOT00000104719
RefSeq Acc Id: ENSRNOP00000082197   ⟸   ENSRNOT00000106092
RefSeq Acc Id: ENSRNOP00000093359   ⟸   ENSRNOT00000101747
Protein Domains
C3H1-type   zf-CCCH_4

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q6TQE1-F1-model_v2 AlphaFold Q6TQE1 1-947 view protein structure

Transcriptome

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

Promoters
RGD ID:13701204
Promoter ID:EPDNEW_R11726
Type:single initiation site
Name:Zc3h18_1
Description:zinc finger CCCH-type containing 18
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R11727  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01955,197,650 - 55,197,710EPDNEW
RGD ID:13701224
Promoter ID:EPDNEW_R11727
Type:single initiation site
Name:Zc3h18_2
Description:zinc finger CCCH-type containing 18
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R11726  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01955,206,429 - 55,206,489EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1303257 AgrOrtholog
BioCyc Gene G2FUF-5400 BioCyc
Ensembl Genes ENSRNOG00000028501 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000035933 ENTREZGENE
  ENSRNOP00000035933.6 UniProtKB/TrEMBL
  ENSRNOP00000048376 ENTREZGENE
  ENSRNOP00000048376.6 UniProtKB/TrEMBL
  ENSRNOP00000082197.1 UniProtKB/TrEMBL
  ENSRNOP00000088629.1 UniProtKB/TrEMBL
  ENSRNOP00000093359 ENTREZGENE
  ENSRNOP00000093359.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000039273 ENTREZGENE
  ENSRNOT00000039273.6 UniProtKB/TrEMBL
  ENSRNOT00000045657 ENTREZGENE
  ENSRNOT00000045657.7 UniProtKB/TrEMBL
  ENSRNOT00000101747 ENTREZGENE
  ENSRNOT00000101747.1 UniProtKB/TrEMBL
  ENSRNOT00000104719.1 UniProtKB/TrEMBL
  ENSRNOT00000106092.1 UniProtKB/TrEMBL
InterPro Znf-CCCH_4 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Znf_CCCH UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Znf_CCCH_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:292067 UniProtKB/Swiss-Prot
NCBI Gene 292067 ENTREZGENE
Pfam zf-CCCH_4 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Zc3h18 PhenoGen
PROSITE ZF_C3H1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART ZnF_C3H1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF90229 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A140TAG3 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I5ZUH8_RAT UniProtKB/TrEMBL
  A0A8I6AKJ5 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I6GGF2_RAT UniProtKB/TrEMBL
  A0A8L2QI36_RAT UniProtKB/TrEMBL
  Q6TQE1 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary Q6TQE2 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-05-15 Zc3h18  zinc finger CCCH-type containing 18  Nhn1  conserved nuclear protein Nhn1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-09-30 Nhn1        Symbol and Name status set to provisional 70820 PROVISIONAL