Zcchc3 (zinc finger, CCHC domain containing 3) - Rat Genome Database

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Gene: Zcchc3 (zinc finger, CCHC domain containing 3) Mus musculus
Analyze
Symbol: Zcchc3
Name: zinc finger, CCHC domain containing 3
RGD ID: 1621536
MGI Page MGI
Description: Predicted to enable double-stranded DNA binding activity. Involved in several processes, including cellular response to exogenous dsRNA; defense response to virus; and positive regulation of type I interferon production. Predicted to be active in cytoplasm. Is expressed in Meckel's cartilage; medulla oblongata basal plate mantle layer; skeleton; and ventral grey horn. Orthologous to human ZCCHC3 (zinc finger CCHC-type containing 3).
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: 2810406K24Rik; zinc finger CCHC domain-containing protein 3
RGD Orthologs
Human
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: GRCm39 - Mouse Genome Assembly GRCm39
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm392152,253,875 - 152,256,711 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl2152,253,875 - 152,256,947 (-)EnsemblGRCm39 Ensembl
GRCm382152,411,956 - 152,415,044 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl2152,411,955 - 152,415,027 (-)EnsemblGRCm38mm10GRCm38
MGSCv372152,237,692 - 152,240,780 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv362152,104,396 - 152,106,468 (-)NCBIMGSCv36mm8
Celera2158,224,872 - 158,227,955 (-)NCBICelera
Cytogenetic Map2H1NCBI
cM Map274.98NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
cytoplasm  (IBA,ISO)

Molecular Function

Phenotype Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:8889548   PMID:10349636   PMID:10922068   PMID:11042159   PMID:11076861   PMID:11125038   PMID:11217851   PMID:12466851   PMID:12477932   PMID:15172686   PMID:16141072   PMID:16141073  
PMID:21267068   PMID:21873635   PMID:30135424   PMID:30193849   PMID:32133501  


Genomics

Comparative Map Data
Zcchc3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm392152,253,875 - 152,256,711 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl2152,253,875 - 152,256,947 (-)EnsemblGRCm39 Ensembl
GRCm382152,411,956 - 152,415,044 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl2152,411,955 - 152,415,027 (-)EnsemblGRCm38mm10GRCm38
MGSCv372152,237,692 - 152,240,780 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv362152,104,396 - 152,106,468 (-)NCBIMGSCv36mm8
Celera2158,224,872 - 158,227,955 (-)NCBICelera
Cytogenetic Map2H1NCBI
cM Map274.98NCBI
ZCCHC3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh3820297,570 - 300,321 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl20297,570 - 300,321 (+)EnsemblGRCh38hg38GRCh38
GRCh3720278,211 - 280,965 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 3620226,204 - 228,965 (+)NCBINCBI36Build 36hg18NCBI36
Build 3420226,203 - 228,961NCBI
Celera20373,047 - 375,805 (+)NCBICelera
Cytogenetic Map20p13NCBI
HuRef20229,449 - 232,207 (+)NCBIHuRef
CHM1_120278,201 - 280,959 (+)NCBICHM1_1
T2T-CHM13v2.020340,752 - 343,503 (+)NCBIT2T-CHM13v2.0
Zcchc3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr83161,332,760 - 161,335,591 (-)NCBIGRCr8
mRatBN7.23140,872,460 - 140,875,292 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl3140,872,460 - 140,882,408 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx3144,777,641 - 144,780,474 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.03153,361,487 - 153,364,319 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.03151,101,349 - 151,104,179 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.03147,877,321 - 147,881,434 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl3147,878,936 - 147,880,138 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.03154,225,218 - 154,228,259 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.43142,727,648 - 142,730,465 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera3139,624,087 - 139,628,200 (-)NCBICelera
Cytogenetic Map3q41NCBI
Zcchc3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955597195,002 - 196,231 (+)EnsemblChiLan1.0
ChiLan1.0NW_004955597194,912 - 197,697 (+)NCBIChiLan1.0ChiLan1.0
ZCCHC3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2211,376,883 - 1,388,569 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1201,381,953 - 1,385,396 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v020504,967 - 508,354 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.120274,522 - 277,493 (+)NCBIpanpan1.1PanPan1.1panPan2
ZCCHC3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12420,537,849 - 20,540,098 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2420,190,822 - 20,193,772 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02421,231,074 - 21,234,025 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2421,232,594 - 21,234,183 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12420,506,754 - 20,509,706 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02420,612,306 - 20,615,248 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02421,043,099 - 21,046,051 (-)NCBIUU_Cfam_GSD_1.0
Zcchc3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494472,532,832 - 72,547,892 (+)NCBIHiC_Itri_2
SpeTri2.0NW_0049366703,048,914 - 3,049,809 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
ZCCHC3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1734,882,816 - 34,885,505 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11734,882,812 - 34,885,632 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21739,662,491 - 39,665,335 (-)NCBISscrofa10.2Sscrofa10.2susScr3
ZCCHC3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1235,422,903 - 35,426,145 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl235,423,430 - 35,424,638 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660787,594,906 - 7,598,250 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Zcchc3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247411,399,481 - 1,400,701 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247411,399,405 - 1,400,980 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Zcchc3
56 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:657
Count of miRNA genes:396
Interacting mature miRNAs:451
Transcripts:ENSMUST00000099207
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 (GRCm39)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
5491197Mobq5_mmultigenic obesity QTL 5 (mouse)Not determined265269746162518926Mouse
5491196Mobq6_mmultigenic obesity QTL 6 (mouse)Not determined285724269180896594Mouse
27226761Feml18_mfemur length 18, 16 week (mouse)294230345154241920Mouse
27226788Feml13_mfemur length 13, 10 week (mouse)2102630345159941920Mouse
11038702Ltpr2_mLeishmania tropica response 2 (mouse)2103095716167212356Mouse
10045885Cplaq15_mcircadian period of locomotor activity 15 (mouse)Not determined2110916118154354667Mouse
1301618Bglu1_mblood glucose level 1 (mouse)Not determined2117942930174324863Mouse
12910795Pwbwq5_mpost-weaning body weight QTL 5 (mouse)2118589253160611165Mouse
12910799Pwgrq2_mpre-weaning growth rate QTL 2 (mouse)2118589253160611165Mouse
12910812Pwgrq1_mpre-weaning growth rate QTL 1 (mouse)2118589253160611165Mouse
12910814Pwbwq1_mpre-weaning body weight QTL 1 (mouse)2118589253160611165Mouse
1301294Hrtfm5_mheart failure modifier 5 (mouse)Not determined2122883015156883131Mouse
1301822Pgia2_mproteoglycan induced arthritis 2 (mouse)Not determined2123937311157937424Mouse
27226749Femd10_mfemur midshaft diameter 10, 16 week (mouse)2124441920168241920Mouse
1302143Bwq5_mbody weight (mouse)Not determined2127664019161664118Mouse
1301031Bdln3_mbody length 3 (mouse)Not determined2127664019161664118Mouse
12880427V25Dq3_mvitamin D inactive form serum level QTL 3 (mouse)2129341920163341920Mouse
1301961Bts1_mbladder tumor susceptibility 1 (mouse)Not determined2132024159166024330Mouse
11049567Lmr28f_mleishmaniasis resistance 28f (mouse)2133144911167145058Mouse
11049566Lmr28e_mleishmaniasis resistance 28e (mouse)2133144911167145058Mouse
11341717Rvfs1_mRift Valley fever susceptibility 1 (mouse)2135432544173449616Mouse
4141703Chlq13_mcirculating hormone level QTL 13 (mouse)Not determined2135699221169699361Mouse
1301907Rends_mrenal disease susceptibility (mouse)Not determined2135699221169699361Mouse
10043956Gnf5_mgrowth and fatness 5 (mouse)Not determined2135699221169699361Mouse
10054066Bwq9_mbody weight QTL 9 (mouse)Not determined2135699221169699361Mouse
1300846Pbwg11_mpostnatal body weight growth 11 (mouse)Not determined2138966600172966729Mouse
11353826Bdln10_mbody length 10 (mouse)2140441482174441482Mouse
12801461Intim1_mintima modifier 1 (mouse)2142428347176428450Mouse
12801456Intmrm1_mintima/media ratio modifier 1 (mouse)2142428347176428450Mouse
1301783Bhr1_mbronchial hyperresponsiveness 1 (mouse)Not determined2142593476178442452Mouse
4141033Wg2d_mweight gain in high growth mice 2d (mouse)Not determined143773445160303008Mouse
1357484Bsbob_mBSB obesity (mouse)Not determined2143773445165665019Mouse
1558939Gnf1_mgrowth and fatness 1 (mouse)Not determined2143773445169117924Mouse
1300867Lore2_mloss of righting induced by ethanol 2 (mouse)Not determined2144515861180896594Mouse
1302013Tbbmd3_mtotal body bone mineral density 3 (mouse)Not determined2145196949179197085Mouse
1300806Aod4_mautoimmune ovarian dysgenesis 4 (mouse)Not determined2145228719179228841Mouse
1301865Hdlq19_mHDL QTL 19 (mouse)Not determined2145518775179518926Mouse
13504830Bacsq1_mbaculum shape QTL 1 (mouse)2145716184161016184Mouse
12790983Bwq12_mbody weight QTL 12 (mouse)2148238204181755017Mouse
4142211Nilac3_mnicotine induced locomotor activity 3 (mouse)Not determined2148664893181755017Mouse
1558917Gct8_mgranulosa cell tumorigenesis 8 (mouse)Not determined2149236907181755017Mouse
1300751Bdt1_mbone density traits 1 (mouse)Not determined2149988902181755017Mouse
1301085Lrnx10_mlearning-contextual 10 (mouse)Not determined2150212221181755017Mouse
11038701Ltpr2e_mLeishmania tropica response 2e (mouse)2150212221181755017Mouse
4142450Lmr16_mleishmaniasis resistance 16 (mouse)Not determined2150212221181755017Mouse
1357862Epfq1_mepididymal fat pad weight QTL 1 (mouse)Not determined2151640941162737074Mouse
1357772Scfq1_msubcutaneous fat pad weight QTL 1 (mouse)Not determined2151640941162737074Mouse
1558842Tailq2_mtail length QTL 2 (mouse)Not determined2151640941162737074Mouse
10412080Hylaq2_mHyperlocomotor activity related QTL 2 (mouse)Not determined2151640941164119146Mouse
12910520Scgq3_mspontaneous crescentic glomerulonephritis QTL 3 (mouse)2151709273174389124Mouse
1301019Bmd6_mbone mineral density 6 (mouse)Not determined2151778297181755017Mouse
13825247Agoc2_magouti coat color QTL 2 (mouse)2151841920159841920Mouse

Markers in Region
AI173521  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm3844,977,936 - 4,978,083UniSTSGRCm38
GRCm382152,412,989 - 152,413,136UniSTSGRCm38
MGSCv3744,905,083 - 4,905,230UniSTSGRCm37
MGSCv372152,238,725 - 152,238,872UniSTSGRCm37
Celera44,899,662 - 4,899,809UniSTS
Celera2158,225,900 - 158,226,047UniSTS
Cytogenetic Map2H1UniSTS
Whitehead/MRC_RH41.21UniSTS
Whitehead/MRC_RH40.68UniSTS
UniSTS:234862  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm3844,977,419 - 4,977,539UniSTSGRCm38
GRCm382152,412,486 - 152,412,606UniSTSGRCm38
MGSCv3744,904,566 - 4,904,686UniSTSGRCm37
MGSCv372152,238,222 - 152,238,342UniSTSGRCm37
Celera44,899,145 - 4,899,265UniSTS
Celera2158,225,397 - 158,225,517UniSTS
Cytogenetic Map2H1UniSTS
WI-15102  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm3844,978,478 - 4,978,599UniSTSGRCm38
GRCm382152,413,546 - 152,413,677UniSTSGRCm38
MGSCv3744,905,625 - 4,905,746UniSTSGRCm37
MGSCv372152,239,282 - 152,239,413UniSTSGRCm37
Celera44,900,203 - 4,900,324UniSTS
Celera2158,226,457 - 158,226,588UniSTS
Cytogenetic Map2H1UniSTS
Cytogenetic Map4A1UniSTS


Expression


Sequence


Reference Sequences
RefSeq Acc Id: ENSMUST00000099207   ⟹   ENSMUSP00000096813
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl2152,253,875 - 152,256,947 (-)Ensembl
GRCm38.p6 Ensembl2152,411,955 - 152,415,027 (-)Ensembl
RefSeq Acc Id: NM_175126   ⟹   NP_780335
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm392152,253,875 - 152,256,711 (-)NCBI
GRCm382152,411,956 - 152,415,044 (-)ENTREZGENE
MGSCv372152,237,692 - 152,240,780 (-)RGD
Celera2158,224,872 - 158,227,955 (-)RGD
cM Map2 ENTREZGENE
Sequence:
Protein Sequences
Protein RefSeqs NP_780335 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH55755 (Get FASTA)   NCBI Sequence Viewer  
  BAC35560 (Get FASTA)   NCBI Sequence Viewer  
  EDL05966 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSMUSP00000096813
  ENSMUSP00000096813.4
GenBank Protein Q8BPK2 (Get FASTA)   NCBI Sequence Viewer  
Reference Protein Sequences
RefSeq Acc Id: NP_780335   ⟸   NM_175126
- UniProtKB: Q8BPK2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSMUSP00000096813   ⟸   ENSMUST00000099207

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q8BPK2-F1-model_v2 AlphaFold Q8BPK2 1-400 view protein structure

Promoters
RGD ID:6833101
Promoter ID:MM_KWN:32361
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:3T3L1_Day0,   3T3L1_Day1,   3T3L1_Day2,   BoneMarrow_0Hour,   BoneMarrow_2Hour,   BoneMarrow_4Hour,   Brain,   ES_Cell,   Kidney,   Lung,   MEF_B4,   MEF_B6
Transcripts:NM_175126
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv362152,239,506 - 152,240,697 (-)MPROMDB
RGD ID:6879182
Promoter ID:EPDNEW_M3042
Type:initiation region
Name:Zcchc3_1
Description:Mus musculus zinc finger, CCHC domain containing 3 , mRNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm382152,414,789 - 152,414,849EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:1915167 AgrOrtholog
Ensembl Genes ENSMUSG00000074682 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSMUST00000099207 ENTREZGENE
  ENSMUST00000099207.5 UniProtKB/Swiss-Prot
Gene3D-CATH Zinc finger, CCHC-type UniProtKB/Swiss-Prot
InterPro ZCCHC3 UniProtKB/Swiss-Prot
  Znf_CCHC UniProtKB/Swiss-Prot
  Znf_CCHC_sf UniProtKB/Swiss-Prot
KEGG Report mmu:67917 UniProtKB/Swiss-Prot
MGD MGI:1915167 ENTREZGENE
NCBI Gene 67917 ENTREZGENE
PANTHER PTHR22639 UniProtKB/Swiss-Prot
  ZINC FINGER CCHC DOMAIN-CONTAINING PROTEIN 3 UniProtKB/Swiss-Prot
Pfam zf-CCHC UniProtKB/Swiss-Prot
PhenoGen Zcchc3 PhenoGen
PROSITE ZF_CCHC UniProtKB/Swiss-Prot
SMART ZnF_C2HC UniProtKB/Swiss-Prot
Superfamily-SCOP SSF57756 UniProtKB/Swiss-Prot
UniProt Q8BPK2 ENTREZGENE, UniProtKB/Swiss-Prot