Zcchc13 (zinc finger CCHC-type containing 13) - Rat Genome Database

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Gene: Zcchc13 (zinc finger CCHC-type containing 13) Rattus norvegicus
Analyze
Symbol: Zcchc13
Name: zinc finger CCHC-type containing 13 (Ensembl:zinc finger, CCHC domain containing 13)
RGD ID: 1589760
Description: Predicted to enable mRNA binding activity; single-stranded RNA binding activity; and translation regulator activity. Predicted to be involved in positive regulation of cytoplasmic translation. Predicted to be active in cytoplasm. Orthologous to human ZCCHC13 (zinc finger CCHC-type containing 13); INTERACTS WITH 2,2',4,4',5,5'-hexachlorobiphenyl (ortholog); 2,2',5,5'-tetrachlorobiphenyl (ortholog); benzo[a]pyrene (ortholog).
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC302399; similar to cellular nucleic acid binding protein 2; zinc finger CCHC domain-containing protein 13; zinc finger, CCHC domain containing 13
RGD Orthologs
Human
Mouse
Bonobo
Dog
Squirrel
Pig
Green Monkey
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2X68,643,554 - 68,644,646 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX68,643,549 - 68,665,131 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_UtxX70,152,748 - 70,153,851 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0X73,652,985 - 73,654,088 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0X71,214,169 - 71,215,272 (+)NCBIRnor_WKY
Rnor_6.0X74,497,127 - 74,498,269 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX74,497,262 - 74,497,774 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X75,298,484 - 75,299,545 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X91,615,417 - 91,615,930 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
CeleraX70,008,972 - 70,010,114 (+)NCBICelera
Cytogenetic MapXq22NCBI
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
cytoplasm  (IBA)

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. GOA pipeline RGD automated data pipeline
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions

Genomics

Comparative Map Data
Zcchc13
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2X68,643,554 - 68,644,646 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX68,643,549 - 68,665,131 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_UtxX70,152,748 - 70,153,851 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0X73,652,985 - 73,654,088 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0X71,214,169 - 71,215,272 (+)NCBIRnor_WKY
Rnor_6.0X74,497,127 - 74,498,269 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX74,497,262 - 74,497,774 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X75,298,484 - 75,299,545 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X91,615,417 - 91,615,930 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
CeleraX70,008,972 - 70,010,114 (+)NCBICelera
Cytogenetic MapXq22NCBI
ZCCHC13
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38X74,304,180 - 74,305,034 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 EnsemblX74,304,180 - 74,305,034 (+)EnsemblGRCh38hg38GRCh38
GRCh37X73,524,015 - 73,524,869 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36X73,440,750 - 73,441,594 (+)NCBINCBI36Build 36hg18NCBI36
Build 34X73,307,045 - 73,307,885NCBI
CeleraX73,807,493 - 73,808,337 (+)NCBICelera
Cytogenetic MapXq13.2NCBI
HuRefX67,159,428 - 67,160,272 (+)NCBIHuRef
CHM1_1X73,417,023 - 73,417,867 (+)NCBICHM1_1
T2T-CHM13v2.0X72,737,690 - 72,738,544 (+)NCBIT2T-CHM13v2.0
Zcchc13
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X102,674,192 - 102,675,270 (+)NCBIGRCm39GRCm39mm39
GRCm39 EnsemblX102,674,192 - 102,675,276 (+)EnsemblGRCm39 Ensembl
GRCm38X103,630,586 - 103,631,664 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX103,630,586 - 103,631,670 (+)EnsemblGRCm38mm10GRCm38
MGSCv37X100,825,925 - 100,827,003 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36X99,833,305 - 99,834,383 (+)NCBIMGSCv36mm8
CeleraX90,532,075 - 90,533,153 (+)NCBICelera
Cytogenetic MapXDNCBI
cM MapX46.26NCBI
ZCCHC13
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1X73,676,686 - 73,677,524 (+)NCBIpanpan1.1PanPan1.1panPan2
Mhudiblu_PPA_v0X63,557,890 - 63,559,079 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
ZCCHC13
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X57,603,420 - 57,604,605 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 EnsemblX57,603,525 - 57,604,040 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_TashaX48,784,012 - 48,784,811 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0X58,817,782 - 58,818,581 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 EnsemblX58,817,884 - 58,818,399 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1X56,563,956 - 56,564,755 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0X58,142,090 - 58,142,889 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0X57,749,379 - 57,750,178 (+)NCBIUU_Cfam_GSD_1.0
Zcchc13
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X44,284,856 - 44,285,997 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936683661,870 - 662,382 (+)EnsemblSpeTri2.0
SpeTri2.0NW_004936683661,870 - 662,382 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
ZCCHC13
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX59,613,996 - 59,614,511 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1X59,613,770 - 59,615,086 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X67,536,558 - 67,542,563 (+)NCBISscrofa10.2Sscrofa10.2susScr3
ZCCHC13
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X63,905,061 - 63,906,244 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 EnsemblX63,905,466 - 63,905,978 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366606717,817,254 - 17,818,111 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0

Variants

.
Variants in Zcchc13
1 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:16
Count of miRNA genes:16
Interacting mature miRNAs:16
Transcripts:ENSRNOT00000003899
Prediction methods:Miranda, Pita, 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
61430Cia18Collagen induced arthritis QTL 183.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X14843113120568734Rat
1598837Memor13Memory QTL 133.2exploratory behavior trait (VT:0010471)difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)X41052407146860749Rat
738035Stresp1Stress response QTL 14.960.000011stress-related behavior trait (VT:0010451)defensive burying - copingX41304447112935181Rat
61431Cia19Collagen induced arthritis QTL 194.4joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X65612192120568734Rat

Markers in Region
UniSTS:478993  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X68,643,993 - 68,644,659 (+)MAPPERmRatBN7.2
Rnor_6.0X74,497,595 - 74,498,260NCBIRnor6.0
Rnor_5.0X75,298,904 - 75,299,569UniSTSRnor5.0
RGSC_v3.4X91,615,751 - 91,616,416UniSTSRGSC3.4
CeleraX70,009,440 - 70,010,105UniSTS
Cytogenetic MapXq31UniSTS


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 7
Low 2 1 1 1 2 1
Below cutoff 1 2 14 2 11 2 2 3 1 4 10 1 2

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000003899   ⟹   ENSRNOP00000065246
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX68,643,549 - 68,665,131 (+)Ensembl
Rnor_6.0 EnsemblX74,497,262 - 74,497,774 (+)Ensembl
RefSeq Acc Id: XM_003752085   ⟹   XP_003752133
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X68,643,554 - 68,644,646 (+)NCBI
Rnor_6.0X74,497,127 - 74,498,269 (+)NCBI
Rnor_5.0X75,298,484 - 75,299,545 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001388052 (Get FASTA)   NCBI Sequence Viewer  
  XP_003752133 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDM07175 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: XP_003752133   ⟸   XM_003752085
- UniProtKB: M0R729 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000065246   ⟸   ENSRNOT00000003899
Protein Domains
CCHC-type

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-M0R729-F1-model_v2 AlphaFold M0R729 1-170 view protein structure

Transcriptome

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

Promoters
RGD ID:13701895
Promoter ID:EPDNEW_R12416
Type:single initiation site
Name:Zcchc13_1
Description:zinc finger CCHC-type containing 13
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_6.0X74,497,170 - 74,497,230EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1589760 AgrOrtholog
BioCyc Gene G2FUF-2007 BioCyc
Ensembl Genes ENSRNOG00000002923 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000065246 ENTREZGENE
  ENSRNOP00000065246.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000003899 ENTREZGENE
  ENSRNOT00000003899.4 UniProtKB/TrEMBL
InterPro Znf_CCHC UniProtKB/TrEMBL
  Znf_CCHC_sf UniProtKB/TrEMBL
KEGG Report rno:302399 UniProtKB/TrEMBL
NCBI Gene 302399 ENTREZGENE
Pfam zf-CCHC UniProtKB/TrEMBL
PhenoGen Zcchc13 PhenoGen
PROSITE ZF_CCHC UniProtKB/TrEMBL
SMART ZnF_C2HC UniProtKB/TrEMBL
Superfamily-SCOP SSF57756 UniProtKB/TrEMBL
UniProt M0R729 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-02-17 Zcchc13  zinc finger CCHC-type containing 13  Zcchc13  zinc finger, CCHC domain containing 13  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2013-08-09 Zcchc13  zinc finger, CCHC domain containing 13  LOC302399  similar to cellular nucleic acid binding protein 2  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-11-19 LOC302399  similar to cellular nucleic acid binding protein 2      Symbol and Name status set to provisional 70820 PROVISIONAL