Zcchc9 (zinc finger CCHC-type containing 9) - Rat Genome Database

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Gene: Zcchc9 (zinc finger CCHC-type containing 9) Rattus norvegicus
Analyze
Symbol: Zcchc9
Name: zinc finger CCHC-type containing 9
RGD ID: 1307450
Description: Predicted to enable nucleic acid binding activity and zinc ion binding activity. Predicted to be located in nucleoplasm. Predicted to be active in nucleolus. Orthologous to human ZCCHC9 (zinc finger CCHC-type containing 9); INTERACTS WITH 2,4-dinitrotoluene; bisphenol A; flutamide.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC309986; zinc finger CCHC domain-containing protein 9; zinc finger, CCHC domain containing 9
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8224,773,319 - 24,783,339 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl224,773,319 - 24,781,999 (-)EnsemblGRCr8
mRatBN7.2223,038,156 - 23,048,249 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl223,038,317 - 23,048,217 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx230,079,173 - 30,087,877 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0228,179,514 - 28,188,218 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0222,998,647 - 23,013,999 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0220,909,764 - 20,919,848 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl220,909,761 - 20,919,824 (-)Ensemblrn6Rnor6.0
Rnor_5.0248,034,186 - 48,044,270 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4222,045,797 - 22,054,476 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera219,141,504 - 19,150,191 (-)NCBICelera
RGSC_v3.1221,966,165 - 21,974,846 (-)NCBI
Cytogenetic Map2q12NCBI
JBrowse:




Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
nucleolus  (IBA,IEA,ISO)
nucleoplasm  (IEA,ISO)

Molecular Function

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. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
3. GOA pipeline RGD automated data pipeline
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
5. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
Additional References at PubMed
PMID:19389623   PMID:22658674  


Genomics

Comparative Map Data
Zcchc9
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8224,773,319 - 24,783,339 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl224,773,319 - 24,781,999 (-)EnsemblGRCr8
mRatBN7.2223,038,156 - 23,048,249 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl223,038,317 - 23,048,217 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx230,079,173 - 30,087,877 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0228,179,514 - 28,188,218 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0222,998,647 - 23,013,999 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0220,909,764 - 20,919,848 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl220,909,761 - 20,919,824 (-)Ensemblrn6Rnor6.0
Rnor_5.0248,034,186 - 48,044,270 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4222,045,797 - 22,054,476 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera219,141,504 - 19,150,191 (-)NCBICelera
RGSC_v3.1221,966,165 - 21,974,846 (-)NCBI
Cytogenetic Map2q12NCBI
ZCCHC9
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38581,301,587 - 81,313,297 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl581,301,583 - 81,313,766 (+)Ensemblhg38GRCh38
GRCh37580,597,406 - 80,609,116 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36580,633,178 - 80,644,872 (+)NCBIBuild 36Build 36hg18NCBI36
Build 34580,633,177 - 80,644,871NCBI
Celera576,501,670 - 76,513,252 (+)NCBICelera
Cytogenetic Map5q14.1NCBI
HuRef575,806,323 - 75,817,895 (+)NCBIHuRef
CHM1_1580,030,202 - 80,041,775 (+)NCBICHM1_1
T2T-CHM13v2.0581,786,162 - 81,797,883 (+)NCBIT2T-CHM13v2.0
Zcchc9
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391391,944,652 - 91,955,824 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1391,944,652 - 91,955,824 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm381391,796,519 - 91,807,718 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1391,796,533 - 91,807,705 (-)Ensemblmm10GRCm38
MGSCv371391,936,138 - 91,947,301 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv361392,270,772 - 92,280,400 (-)NCBIMGSCv36mm8
Celera1395,430,508 - 95,441,604 (-)NCBICelera
Cytogenetic Map13C3NCBI
cM Map1347.43NCBI
Zcchc9
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541828,886,032 - 28,896,569 (-)Ensembl
ChiLan1.0NW_00495541828,886,738 - 28,896,012 (-)NCBIChiLan1.0ChiLan1.0
ZCCHC9
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2433,989,149 - 34,000,714 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1532,142,771 - 32,154,339 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0533,966,502 - 33,978,069 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1534,277,568 - 34,289,261 (-)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl534,277,568 - 34,289,261 (-)EnsemblpanPan2panpan1.1
ZCCHC9
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1325,973,874 - 25,983,132 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl325,963,700 - 25,983,062 (-)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha327,174,393 - 27,219,241 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0325,852,637 - 25,897,603 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl325,888,507 - 25,897,489 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1325,804,565 - 25,849,472 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0325,774,099 - 25,819,040 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0326,053,877 - 26,098,725 (-)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Zcchc9
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024407213182,000,064 - 182,008,394 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936469617,131 - 627,776 (+)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_004936469617,320 - 625,738 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
ZCCHC9
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl289,840,012 - 89,849,064 (+)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1289,840,012 - 89,849,066 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2291,735,398 - 91,744,477 (-)NCBISscrofa10.2Sscrofa10.2susScr3
ZCCHC9
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1475,442,015 - 75,453,203 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl475,445,195 - 75,452,715 (+)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366604924,315,594 - 24,326,878 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Zcchc9
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247431,836,550 - 1,845,195 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
Zcchc9
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v13204,419,500 - 204,429,424 (+)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Zcchc9
53 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:341
Count of miRNA genes:207
Interacting mature miRNAs:249
Transcripts:ENSRNOT00000020111
Prediction methods:Microtar, Miranda
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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1331764Bp205Blood pressure QTL 2053.476arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)21436870759368707Rat
10755430Coatc6Coat color QTL 60.02576coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)21332504158325041Rat
1600379Mcs18Mammary carcinoma susceptibility QTL 182.6mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)2962358144538110Rat
1331760Bp206Blood pressure QTL 2063.62454arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)24265106205135428Rat
7387318Stl32Serum triglyceride level QTL 323.20.0003blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)22411781369117813Rat
61355Bp36Blood pressure QTL 362.9blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)27605533104774005Rat
10755499Bp389Blood pressure QTL 3892.61arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)220695736231474293Rat
1578664Bmd9Bone mineral QTL density 95femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)2573632550736325Rat
738010Lnnr3Liver neoplastic nodule remodeling QTL 32.94liver integrity trait (VT:0010547)liver remodeling tumorous lesion number (CMO:0001461)2142977529Rat
9590080Insglur4Insulin/glucose ratio QTL 428.70.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)2615276751152767Rat
1579916Bp270Blood pressure QTL 2700.003arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)21605188361051883Rat
731167Glom4Glomerulus QTL 42.40.0082kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)22203804467038044Rat
731166Mamtr2Mammary tumor resistance QTL 20.0001mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)2962358154623581Rat
61368Mcs1Mammary carcinoma susceptibility QTL 14.4mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)2962358125054526Rat
731184Mamtr4Mammary tumor resistance QTL 40.0003mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)21822713763227137Rat

Markers in Region
RH137389  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2223,038,755 - 23,038,917 (+)MAPPERmRatBN7.2
Rnor_6.0220,910,364 - 20,910,525NCBIRnor6.0
Rnor_5.0248,043,509 - 48,043,670UniSTSRnor5.0
RGSC_v3.4222,046,324 - 22,046,485UniSTSRGSC3.4
Celera219,142,039 - 19,142,200UniSTS
Cytogenetic Map2q12UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
16 12 67 165 91 90 59 92 59 6 356 192 11 144 81 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000086300   ⟹   ENSRNOP00000073298
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl224,773,319 - 24,781,999 (-)Ensembl
mRatBN7.2 Ensembl223,038,317 - 23,048,217 (-)Ensembl
Rnor_6.0 Ensembl220,909,761 - 20,919,824 (-)Ensembl
RefSeq Acc Id: NM_001013156   ⟹   NP_001013174
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8224,773,319 - 24,781,998 (-)NCBI
mRatBN7.2223,038,229 - 23,046,908 (-)NCBI
Rnor_6.0220,909,837 - 20,918,516 (-)NCBI
Rnor_5.0248,034,186 - 48,044,270 (+)NCBI
RGSC_v3.4222,045,797 - 22,054,476 (-)RGD
Celera219,141,504 - 19,150,191 (-)RGD
Sequence:
RefSeq Acc Id: XM_006231841   ⟹   XP_006231903
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8224,773,323 - 24,783,339 (-)NCBI
mRatBN7.2223,038,156 - 23,048,249 (-)NCBI
Rnor_6.0220,909,764 - 20,919,848 (-)NCBI
Rnor_5.0248,034,186 - 48,044,270 (+)NCBI
Sequence:
RefSeq Acc Id: XM_063281709   ⟹   XP_063137779
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8224,773,323 - 24,783,238 (-)NCBI
RefSeq Acc Id: NP_001013174   ⟸   NM_001013156
- UniProtKB: Q5XII6 (UniProtKB/TrEMBL),   A0A0G2K555 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006231903   ⟸   XM_006231841
- Peptide Label: isoform X1
- Sequence:
Ensembl Acc Id: ENSRNOP00000073298   ⟸   ENSRNOT00000086300
RefSeq Acc Id: XP_063137779   ⟸   XM_063281709
- Peptide Label: isoform X1
- UniProtKB: Q5XII6 (UniProtKB/TrEMBL),   A0A0G2K555 (UniProtKB/TrEMBL)
Protein Domains
CCHC-type

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q5XII6-F1-model_v2 AlphaFold Q5XII6 1-271 view protein structure

Transcriptome

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

Promoters
RGD ID:13691055
Promoter ID:EPDNEW_R1580
Type:multiple initiation site
Name:Zcchc9_1
Description:zinc finger CCHC-type containing 9
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_6.0220,919,827 - 20,919,887EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1307450 AgrOrtholog
BioCyc Gene G2FUF-54877 BioCyc
Ensembl Genes ENSRNOG00000051682 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000086300 ENTREZGENE
  ENSRNOT00000086300.3 UniProtKB/TrEMBL
Gene3D-CATH Zinc finger, CCHC-type UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7189545 IMAGE-MGC_LOAD
InterPro ZCCHC9 UniProtKB/TrEMBL
  Znf_CCHC UniProtKB/TrEMBL
  Znf_CCHC_sf UniProtKB/TrEMBL
KEGG Report rno:309986 UniProtKB/TrEMBL
MGC_CLONE MGC:94562 IMAGE-MGC_LOAD
NCBI Gene 309986 ENTREZGENE
PANTHER PTHR46242 UniProtKB/TrEMBL
  ZINC FINGER CCHC DOMAIN-CONTAINING PROTEIN 9 UniProtKB/TrEMBL
Pfam zf-CCHC UniProtKB/TrEMBL
PhenoGen Zcchc9 PhenoGen
PROSITE ZF_CCHC UniProtKB/TrEMBL
RatGTEx ENSRNOG00000051682 RatGTEx
SMART ZnF_C2HC UniProtKB/TrEMBL
Superfamily-SCOP SSF57756 UniProtKB/TrEMBL
UniProt A0A0G2K555 ENTREZGENE, UniProtKB/TrEMBL
  A6I4Q0_RAT UniProtKB/TrEMBL
  Q5XII6 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-02-17 Zcchc9  zinc finger CCHC-type containing 9  Zcchc9  zinc finger, CCHC domain containing 9  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-12-06 Zcchc9  zinc finger, CCHC domain containing 9  Zcchc9_predicted  zinc finger, CCHC domain containing 9 (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-12 Zcchc9_predicted  zinc finger, CCHC domain containing 9 (predicted)      Symbol and Name status set to approved 70820 APPROVED