Zcchc13 (zinc finger, CCHC domain containing 13)

Gene: Zcchc13 (zinc finger, CCHC domain containing 13) Mus musculus

Analyze

Symbol:

Zcchc13

Name:

zinc finger, CCHC domain containing 13

RGD ID:

1557292

MGI Page

MGI

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. Is expressed in central nervous system and sensory organ. Orthologous to human ZCCHC13 (zinc finger CCHC-type containing 13).

Type:

protein-coding

RefSeq Status:

VALIDATED

Previously known as:

4930513O09Rik; cellular nucleic acid binding protein 2; cellular nucleic acid binding-like protein; Cnb; Cnbp2; zinc finger CCHC domain-containing protein 13

RGD Orthologs

Alliance Genes

More Info

more info ...

Latest Assembly:

GRCm39 - Mouse Genome Assembly GRCm39

Position:

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	X	102,674,187 - 102,675,277 (+)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	X	102,674,192 - 102,675,276 (+)	Ensembl		GRCm39 Ensembl
GRCm38	X	103,630,586 - 103,631,664 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	X	103,630,586 - 103,631,670 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	X	100,825,925 - 100,827,003 (+)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	X	99,833,305 - 99,834,383 (+)	NCBI		MGSCv36	mm8
Celera	X	90,532,075 - 90,533,153 (+)	NCBI		Celera
Cytogenetic Map	X	D	NCBI
cM Map	X	46.26	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

autistic disorder (ISO)

genetic disease (ISO)

syndromic X-linked intellectual disability Lubs type (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

2,2',4,4',5,5'-hexachlorobiphenyl (EXP)

2,2',5,5'-tetrachlorobiphenyl (EXP)

benzo[a]pyrene (ISO)

bisphenol A (EXP)

choline (EXP)

clothianidin (ISO)

folic acid (EXP)

L-methionine (EXP)

PCB138 (EXP)

rifampicin (ISO)

sodium arsenite (EXP)

titanium dioxide (EXP)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

positive regulation of cytoplasmic translation (IBA)

Cellular Component

cytoplasm (IBA)

Molecular Function

mRNA binding (IBA)

protein binding (ISO)

single-stranded RNA binding (IBA)

translation regulator activity (IBA)

Phenotype Annotations Click to see Annotation Detail View

Mammalian Phenotype

no abnormal phenotype detected (IAGP)

References

References - curated

#	Reference Title	Reference Citation
1.	Functional annotation of a full-length mouse cDNA collection.	Kawai J, etal., Nature. 2001 Feb 8;409(6821):685-90.
2.	MGDs mouse GO annotations	MGD data from the GO Consortium
3.	Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs.	Okazaki Y, etal., Nature. 2002 Dec 5;420(6915):563-73.
4.	Data Import for Chemical-Gene Interactions	RGD automated import pipeline for gene-chemical interactions

Additional References at PubMed

PMID:10349636	PMID:11042159	PMID:11076861	PMID:12045143	PMID:12477932	PMID:16033648	PMID:16141072	PMID:16141073	PMID:21873635	PMID:23940725	PMID:27357688

Genomics

Comparative Map Data

Zcchc13
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	X	102,674,187 - 102,675,277 (+)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	X	102,674,192 - 102,675,276 (+)	Ensembl		GRCm39 Ensembl
GRCm38	X	103,630,586 - 103,631,664 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	X	103,630,586 - 103,631,670 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	X	100,825,925 - 100,827,003 (+)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	X	99,833,305 - 99,834,383 (+)	NCBI		MGSCv36	mm8
Celera	X	90,532,075 - 90,533,153 (+)	NCBI		Celera
Cytogenetic Map	X	D	NCBI
cM Map	X	46.26	NCBI

ZCCHC13
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	X	74,304,180 - 74,305,034 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	X	74,304,180 - 74,305,034 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	X	73,524,015 - 73,524,869 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	X	73,440,750 - 73,441,594 (+)	NCBI	NCBI36	Build 36	hg18	NCBI36
Build 34	X	73,307,045 - 73,307,885	NCBI
Celera	X	73,807,493 - 73,808,337 (+)	NCBI		Celera
Cytogenetic Map	X	q13.2	NCBI
HuRef	X	67,159,428 - 67,160,272 (+)	NCBI		HuRef
CHM1_1	X	73,417,023 - 73,417,867 (+)	NCBI		CHM1_1
T2T-CHM13v2.0	X	72,737,690 - 72,738,544 (+)	NCBI		T2T-CHM13v2.0

Zcchc13
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	X	72,709,319 - 72,710,422 (+)	NCBI		GRCr8
mRatBN7.2	X	68,643,568 - 68,644,671 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	X	68,643,549 - 68,665,131 (+)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	X	70,152,748 - 70,153,851 (+)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	X	73,652,985 - 73,654,088 (+)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	X	71,214,169 - 71,215,272 (+)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	X	74,497,127 - 74,498,269 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	X	74,497,262 - 74,497,774 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	X	75,298,484 - 75,299,545 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	X	91,615,417 - 91,615,930 (+)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
Celera	X	70,008,972 - 70,010,114 (+)	NCBI		Celera
Cytogenetic Map	X	q22	NCBI

ZCCHC13
(Pan paniscus - bonobo/pygmy chimpanzee)

Bonobo Assembly	Chr	Position (strand)	Source	Genome Browsers
Bonobo Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
NHGRI_mPanPan1-v2	X	73,988,645 - 73,989,500 (+)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	X	73,992,254 - 73,993,109 (+)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	X	63,557,890 - 63,559,079 (+)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	X	73,676,686 - 73,677,524 (+)	NCBI	panpan1.1	PanPan1.1	panPan2

ZCCHC13
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	X	57,603,420 - 57,604,605 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	X	57,603,525 - 57,604,040 (+)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	X	48,784,012 - 48,784,811 (+)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	X	58,817,782 - 58,818,581 (+)	NCBI		ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	X	58,817,884 - 58,818,399 (+)	Ensembl		ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	X	56,563,956 - 56,564,755 (+)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	X	58,142,090 - 58,142,889 (+)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	X	57,749,379 - 57,750,178 (+)	NCBI		UU_Cfam_GSD_1.0

Zcchc13
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HiC_Itri_2	X	44,284,856 - 44,285,997 (-)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936683	661,870 - 662,382 (+)	Ensembl	SpeTri2.0	SpeTri2.0 Ensembl
SpeTri2.0	NW_004936683	661,870 - 662,382 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

ZCCHC13
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	X	59,613,996 - 59,614,511 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	X	59,613,770 - 59,615,086 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	X	67,536,558 - 67,542,563 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

ZCCHC13
(Chlorocebus sabaeus - green monkey)

Green Monkey Assembly	Chr	Position (strand)	Source	Genome Browsers
Green Monkey Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1	X	63,905,061 - 63,906,244 (+)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	X	63,905,466 - 63,905,978 (+)	Ensembl	ChlSab1.1	ChlSab1.1 Ensembl	chlSab2
Vero_WHO_p1.0	NW_023666067	17,817,254 - 17,818,111 (-)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Variants

Variants in Zcchc13
29 total Variants

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	95
Count of miRNA genes:	91
Interacting mature miRNAs:	91
Transcripts:	ENSMUST00000033692
Prediction methods:	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 (GRCm39)

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
1357433	Dbts2_m	diabetes 2 (mouse)			Not determined		X	7226295	150107038	Mouse
4141630	Gct6_m	granulosa cell tumorigenesis 6 (mouse)			Not determined			47179121	129764756	Mouse
13824980	Ferq1_m	genetic fertility QTL 1 (mouse)					X	54045360	148782996	Mouse
4141665	Mhysq2_m	male hybrid sterility QTL 2 (mouse)			Not determined			71453852	139203212	Mouse
1357500	Mdmsc6_m	modifier of muscularity 6 (mouse)			Not determined		X	75306671	109306758	Mouse
11075102	Modc2_m	modifier of Odc2 (mouse)					X	80189914	114190059	Mouse
4141803	Lmr30_m	leishmaniasis resistance 30 (mouse)			Not determined			85062606	119062720	Mouse
13208552	Wght12_m	weight 12 (mouse)					X	94043606	149782996	Mouse
13208556	Lgth14_m	body length 14 (mouse)					X	94043606	149782996	Mouse
1357823	Spha3_m	sperm head anomaly 3 (mouse)			Not determined		X	102055848	162758941	Mouse

Markers in Region

Cnbp2

Mouse Assembly	Chr	Position (strand)	Source	JBrowse
GRCm38	X	103,631,006 - 103,631,659	UniSTS	GRCm38
MGSCv37	X	100,826,345 - 100,826,998	UniSTS	GRCm37
Celera	X	90,532,495 - 90,533,148	UniSTS
Cytogenetic Map	X	D	UniSTS
cM Map	X	42.0	UniSTS

Expression

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_029158	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AJ421478	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AK015789	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AL683845	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BC145772	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BC145774	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH466564	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

RefSeq Acc Id:

ENSMUST00000033692 ⟹ ENSMUSP00000033692

Type:

CODING

Position:

Mouse Assembly	Chr	Position (strand)	Source
GRCm39 Ensembl	X	102,674,192 - 102,675,276 (+)	Ensembl
GRCm38.p6 Ensembl	X	103,630,586 - 103,631,670 (+)	Ensembl

RefSeq Acc Id:

NM_029158 ⟹ NP_083434

RefSeq Status:

VALIDATED

Type:

CODING

Position:

Mouse Assembly	Chr	Position (strand)	Source
GRCm39	X	102,674,187 - 102,675,277 (+)	NCBI
GRCm38	X	103,630,586 - 103,631,664 (+)	ENTREZGENE
MGSCv37	X	100,825,925 - 100,827,003 (+)	RGD
Celera	X	90,532,075 - 90,533,153 (+)	RGD
cM Map	X		ENTREZGENE

Sequence:

show sequence

TTTCCATCTAAGCCATCCTAGGCAGGTAGCCTCGGGGCCCGTGGCAGTGGGGTGTGGGCCTGCT
CACCGGAAGATCTCACCGTACCCATGAGCAGTAAAAGTTGCTTCAAGTGTGGACACTCTGGCCA
CTGGGCCCGGGAGTGTCCTAAGGGAGGAACCCGAGGGCGAACAGCAAGAGGTCGTACCAGAGGT
CCCCAGTGCAGCACCGCCAACCAGTCCGATGTTTGTTATCGCTGTGGTGAAACTGGTCACTACG
CCAAGGACTGTGATCTTCTCCAGGATACCTGCTACAACTGCGGGAGAAGAGGACACATAGCTAA
GGACTGTACCCAGGCTAAACGAGAGAGGGAGCAGTGCTGTTACATCTGCAGTCAGCCTGGTCAT
CTGGCTCGGGACTGCAACCGGCAAGAAGAACAGAAATGCTACACTTGTGGTGAATTTGGGCACA
TCCAGAAAGATTGTACCCAAATTAAGTGCTACAGATGTGGTGAGAATGGCCACATGGCGGTGAA
CTGCAGCAAGACGAGCGAAGTCAGCTGCTACCGCTGTGGAGAGTCTGGACATCTGGCTCGGGAA
TGCCCCATTGAGGCTACCGCTTAGTAACCCCCTTAAACGCCATCCTTTACTAAGTACGCTGTTT
CTAACATTTCTTTGCTAATCAAAAACGTGATAGATGGAAGCTACTCCTATACCATTATAATTAT
CATCTTAAAGCAAGAAAAGACTGGGGGGGAAACATGTCAAAAATGTTATAATCAATATGCTATT
TGGTTGCCATGAGGAAGTTCAGATAGGGCACAGCCATTTTTGAATTGGACACTAGTGGATCCTT
TGAGTACGGTTCGTTTTGACACACTAAATTAGAAATTGATAGTGAAAAATTACAGCAAGCTTGG
AACATCGTCTTTGAATTTACTAACAAATACTATATATGTATGTCAGATAGAGATAAACTGCTTT
GAAGCGAGAGACAACTGACTAAAATAAGAAGAGAAACTACTTCCTTGGTGGTGGGGGCAAGAAC
ATTTTGAGGAAGTAACATTTCTTCAGAGACTTTTAGAGCAAATAAAAGTGTTTCT

hide sequence

Protein Sequences


Protein RefSeqs	NP_083434	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAI45773	(Get FASTA)	NCBI Sequence Viewer
	AAI45775	(Get FASTA)	NCBI Sequence Viewer
	BAB29977	(Get FASTA)	NCBI Sequence Viewer
	CAD33940	(Get FASTA)	NCBI Sequence Viewer
	EDL14094	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSMUSP00000033692
	ENSMUSP00000033692.8

RefSeq Acc Id:	NP_083434 ⟸ NM_029158
- UniProtKB:	Q9D548 (UniProtKB/TrEMBL)
- Sequence:	show sequence MSSKSCFKCGHSGHWARECPKGGTRGRTARGRTRGPQCSTANQSDVCYRCGETGHYAKDCDLLQ DTCYNCGRRGHIAKDCTQAKREREQCCYICSQPGHLARDCNRQEEQKCYTCGEFGHIQKDCTQI KCYRCGENGHMAVNCSKTSEVSCYRCGESGHLARECPIEATA hide sequence

RefSeq Acc Id:

ENSMUSP00000033692 ⟸ ENSMUST00000033692

Protein Domains

CCHC-type

Protein Structures

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-Q9D548-F1-model_v2	AlphaFold	Q9D548	1-170	view protein structure

Promoters

RGD ID:

6846534

Promoter ID:

MM_KWN:61447

Type:

Non-CpG

SO ACC ID:

SO:0000170

Source:

MPROMDB

Tissues & Cell Lines:

Brain, Kidney

Transcripts:

NM_029158

Position:

Mouse Assembly	Chr	Position (strand)	Source
MGSCv36	X	100,826,054 - 100,826,554 (+)	MPROMDB

RGD ID:

13681140

Promoter ID:

EPDNEW_M24719

Type:

initiation region

Name:

Zcchc13_1

Description:

Mus musculus zinc finger, CCHC domain containing 13 , mRNA.

SO ACC ID:

SO:0000170

Source:

EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)

Experiment Methods:

Single-end sequencing.

Position:

Mouse Assembly	Chr	Position (strand)	Source
GRCm38	X	103,630,657 - 103,630,717	EPDNEW

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	MGI:1922314	AgrOrtholog
Ensembl Genes	ENSMUSG00000031330	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript	ENSMUST00000033692	ENTREZGENE
	ENSMUST00000033692.9	UniProtKB/TrEMBL
Gene3D-CATH	Zinc finger, CCHC-type	UniProtKB/TrEMBL
InterPro	Znf_CCHC	UniProtKB/TrEMBL
	Znf_CCHC_sf	UniProtKB/TrEMBL
KEGG Report	mmu:75064	UniProtKB/TrEMBL
MGD	MGI:1922314	ENTREZGENE
NCBI Gene	75064	ENTREZGENE
PANTHER	CELLULAR NUCLEIC ACID BINDING-LIKE PROTEIN	UniProtKB/TrEMBL
	ZINC FINGER CCHC DOMAIN CONTAINING PROTEIN	UniProtKB/TrEMBL
Pfam	zf-CCHC	UniProtKB/TrEMBL
PhenoGen	Zcchc13	PhenoGen
PROSITE	ZF_CCHC	UniProtKB/TrEMBL
SMART	ZnF_C2HC	UniProtKB/TrEMBL
Superfamily-SCOP	SSF57756	UniProtKB/TrEMBL
UniProt	Q9D548	ENTREZGENE, UniProtKB/TrEMBL

Gene Annotator (Functional Annotation) unavailable	Gene Annotator (Annotation Distribution) unavailable	Variant Visualizer (Genomic Variants) unavailble Variant Visualizer (Genomic Variants) unavailable
Gene Annotator (Functional Annotation)	Gene Annotator (Annotation Distribution)	Variant Visualizer (Genomic Variants)

InterViewer (Protein-Protein Interactions) unavailable	Gviewer (Genome Viewer) unavailable	Variant Visualizer (Damaging Variants) unavailble Variant Visualizer (Damaging Variants) unavailable
InterViewer (Protein-Protein Interactions)	GViewer (Genome Viewer)	Variant Visualizer (Damaging Variants)

Gene Annotator (Annotation Comparison) unavailable	OLGA (Gene List Generator) unavailable
Gene Annotator (Annotation Comparison)	OLGA (Gene List Generator)	Excel (Download)

MOET (Multi-Ontology Enrichement) unavailable	GOLF (Gene-Ortholog Location Finder) unavailable
MOET (Multi-Ontology Enrichement)	GOLF (Gene-Ortholog Location Finder)

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Imported Disease Annotations - ClinVar

Mammalian Phenotype