Zc3h4 MGI Mouse Gene Detail - MGI:2682314 - zinc finger CCCH-type containing 4

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Zc3h4 Gene Detail

Symbol

Zc3h4
Name

zinc finger CCCH-type containing 4
Synonyms

Bwq1, Kiaa1064-hp, LOC330474, MGC:67629, mKIAA1064

Feature Type

protein coding gene
IDs

MGI:2682314
NCBI Gene: 330474
Alliance

gene page
Transcription Start Sites

7 TSS
Candidate for QTL

5 QTL

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Sequence Map

Chr7:16134835-16171621 bp, + strand
From Ensembl annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 7, 9.03 cM
Mapping Data

7 experiments

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SNPs within 2kb

751 from dbSNP Build 142
Strain Annotations

18

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates	Select Strains
C57BL/6J	MGI_C57BL6J_2682314	protein coding gene	Chr7:16132549-16171621 (+)
129S1/SvImJ	MGP_129S1SvImJ_G0031709	protein coding gene	Chr7:14102593-14146563 (+)
A/J	MGP_AJ_G0031681	protein coding gene	Chr7:13873320-13910137 (+)
AKR/J	MGP_AKRJ_G0031606	protein coding gene	Chr7:14192578-14230493 (+)
BALB/cJ	MGP_BALBcJ_G0031688	protein coding gene	Chr7:13981014-14017789 (+)
C3H/HeJ	MGP_C3HHeJ_G0031410	protein coding gene	Chr7:14378390-14416439 (+)
C57BL/6NJ	MGP_C57BL6NJ_G0032154	protein coding gene	Chr7:14854661-14893870 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0029233	protein coding gene	Chr7:15426462-15462728 (+)
CAST/EiJ	MGP_CASTEiJ_G0030761	protein coding gene	Chr7:11135014-11171477 (+)
CBA/J	MGP_CBAJ_G0031369	protein coding gene	Chr7:15318001-15359942 (+)
DBA/2J	MGP_DBA2J_G0031525	protein coding gene	Chr7:13759329-13795860 (+)
FVB/NJ	MGP_FVBNJ_G0031481	protein coding gene	Chr7:13655620-13694840 (+)
LP/J	MGP_LPJ_G0031610	protein coding gene	Chr7:14355657-14394373 (+)
NOD/ShiLtJ	MGP_NODShiLtJ_G0031516	protein coding gene	Chr7:15273817-15311462 (+)
NZO/HlLtJ	MGP_NZOHlLtJ_G0032183	protein coding gene	Chr7:13969537-14006320 (+)
PWK/PhJ	MGP_PWKPhJ_G0030485	protein coding gene	Chr7:11281809-11319165 (+)
SPRET/EiJ	MGP_SPRETEiJ_G0030312	protein coding gene	Chr7:8882171-8922975 (+)
WSB/EiJ	MGP_WSBEiJ_G0030858	protein coding gene	Chr7:14026388-14063818 (+)

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Human Ortholog

ZC3H4, zinc finger CCCH-type containing 4

Vertebrate Orthologs

3

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

ZC3H4, zinc finger CCCH-type containing 4
Synonyms

C19orf7
Links

HGNC:17808

NCBI Gene ID: 23211

neXtProt AC: NX_Q9UPT8

UniProt: Q9UPT8
Chr Location

19q13.32; chr19:47064187-47113776 (-) GRCh38

MGI Vertebrate Homology

Zc3h4 stringent orthology
1 human;1 mouse;1 rat;1 zebrafish
HCOP

vertebrate homology predictions: ZC3H4
Gene Tree

Zc3h4

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Phenotype Summary

28 phenotypes from 2 alleles in 2 genetic backgrounds
1 phenotype from multigenic genotypes
1 images
17 phenotype references

Phenotype Overview

Phenotype Overview

Blue squares indicate phenotypes directly attributed to mutations/alleles of this gene.

adipose tissue	behavior/neurological	cardiovascular system	cellular	craniofacial	digestive/alimentary system	embryo	endocrine/exocrine glands	growth/size/body	hearing/vestibular/ear	hematopoietic system	homeostasis/metabolism	integument	immune system	limbs/digits/tail	liver/biliary system	mortality/aging	muscle	nervous system	pigmentation	renal/urinary system	reproductive system	respiratory system	skeleton	taste/olfaction	neoplasm	vision/eye

Click cells to view annotations.

All Mutations and Alleles

152
Endonuclease-mediated

3
Gene trapped

146
QTL

2
Targeted

1
Incidental Mutations

Mutagenetix , APF
Find Mice (IMSR)

177 strains or lines available
Comparison Matrix

Gene Expression + Phenotype

Embryos homozygous for a knock-out allele do not develop past blastocyst formation, fail to hatch from the zona pellucida or hatch but do not form typical outgrowth colonies, and show peri-implantation lethality, defective epiblast and primitive endoderm lineages, increased embryonic tissue cell apoptosis, and reduced cell proliferation.

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All GO Annotations

22
GO References

6

Molecular Function

carbohydrate derivative binding	cytoskeletal protein binding	DNA binding	enzyme regulator	hydrolase	ligase	lipid binding	oxidoreductase	RNA binding	signaling receptor activity	signaling receptor binding	transcription	transferase	transporter

Biological Process

carbohydrate derivative metabolism	cell differentiation	cell population proliferation	cellular component organization	DNA-templated transcription	establishment of localization	homeostatic process	immune system process	lipid metabolic process	programmed cell death	protein metabolic process	response to stimulus	signaling	system development

Cellular Component

cell projection	cytoplasmic vesicle	cytoskeleton	cytosol	endoplasmic reticulum	endosome	extracellular region	Golgi apparatus	mitochondrion	membraneless organelle	nucleus	organelle envelope	organelle lumen	plasma membrane	protein-containing complex	synapse	vacuole

Click cells to view annotations.

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Expression Overview

Expression Overview

GXD's primary emphasis is on endogenous gene expression during development. Click on grid cells to view annotations.

Blue cells = expressed in wild-type.
Gray triangles = other expression annotations only
(e.g. absence of expression or data from mutants).

early conceptus	embryo ectoderm	embryo endoderm	embryo mesoderm	embryo mesenchyme	extraembryonic component	alimentary system	auditory system	branchial arches	cardiovascular system	connective tissue	endocrine system	exocrine system	hemolymphoid system	integumental system	limbs	liver and biliary system	musculoskeletal system	nervous system	olfactory system	reproductive system	respiratory system	urinary system	visual system

Click cells to view annotations.

Assay Results

739
Tissues

23
cDNA Data

9
Literature Summary

5

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

Other Mouse Links

Allen Institute

GEO

Expression Atlas
Other Vertebrate Links

Xenbase zc3h4

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All Sequences

73
RefSeq

28
UniProt

6
CCDS

CCDS52040.1

Ensembl

ENSMUSG00000059273 (Evidence)
NCBI Gene

330474

Representative Sequences				Length	Strain/Species	Flank
	genomic	ENSMUSG00000059273	Ensembl Gene Model \| MGI Sequence Detail	36787	C57BL/6J	± kb
	transcript	ENSMUST00000098789	Ensembl \| MGI Sequence Detail	6039	Not Applicable
	polypeptide	ENSMUSP00000096386	Ensembl \| MGI Sequence Detail	1255	Not Applicable

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UniProt

6 Sequences
Protein Ontology

PR:000031210 zinc finger CCCH domain-containing protein 4

(term hierarchy)
InterPro Domains

IPR041367 E3 ligase, CCCH-type zinc finger

IPR045124 Protein suppressor of sable-like

IPR000571 Zinc finger, CCCH-type

IPR036855 Zinc finger, CCCH-type superfamily

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All nucleic 14

Genomic 2

cDNA 10

Primer pair 2

Microarray probesets 1

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MGI:1298203, MGI:2389001, MGI:2685614

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Summaries

All 47

Developmental Gene Expression 5

Gene Ontology 6

Phenotypes 17
Earliest

J:48704 Suto J, et al., Genetics of obesity in KK mouse and effects of A(y) allele on quantitative regulation. Mamm Genome. 1998 Jul;9(7):506-10
Latest

J:345621 Adams DJ, et al., Genetic determinants of micronucleus formation in vivo. Nature. 2024 Mar;627(8002):130-136

TSS for Zc3h4:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr64607	Chr7:16134182-16134226 (+)	-631 bp
Tssr64608	Chr7:16134229-16134256 (+)	-592 bp
Tssr2083	Chr7:16134818-16134857 (+)	3 bp
Tssr64609	Chr7:16135112-16135158 (+)	300 bp
Tssr64610	Chr7:16135193-16135208 (+)	366 bp
Tssr64611	Chr7:16149596-16149600 (+)	14,763 bp
Tssr64612	Chr7:16154878-16154921 (+)	20,065 bp

Zc3h4 is Candidate Gene for:

QTL	Genetic Location*	Genome Location (GRCm39)	Reference	QTL Note
Bglq4	Chr4, 33.96 cM		J:99477	Authors used novel data mining tool ExQuest to identify novel candidate genes for existing diabesity QTLs. Next, candidate gene expression in the liver, adipose, and pancreas of diabesity-prone Tally Ho mice and diabesity-resistant C57BL/6J mice was assessed by quantitative PCR analysis. Several potential candidate genes, some with no previous association to diabesity QTLs, were identified. Since QTL intervals may be large and could contain hundreds or thousands of potential candidate genes, this method allows researchers to focus on those with strong potential as well as identify novel candidate genes. Potential candidate genes for Tafat (80 cM) on mouse Chromosome 4 as identified by ExQuest are Ela2, Ela3b, and Dvl1 (82 cM). Chr 10 locus Ela2 exhibits 55-fold decreased expression in the pancreas of Tally Ho animals compared to C57BL/6J. For QTL Bwq1 (6.3 cM), potential candidate gene Decr1 was identified. For QTLs Triglq1 (6.5 cM) and Bglq4 (6.5 cM), potential candidate genes Ttpa, Bhmt(Chr 13), Baat(22.7 cM), and Aldob (22.3 cM) were identified. For QTLs Nidd1 (48 cM) and Dob1 (50 cM), potential candidate genes Lepr (46.7 cM), Dio1 (48.7 cM), Scp2 (52 cM), Faah (56.5 cM), and Usp1 were identified.
Dob1	Chr4, syntenic	Chr4:101574601-123127211	J:99477	Authors used novel data mining tool ExQuest to identify novel candidate genes for existing diabesity QTLs. Next, candidate gene expression in the liver, adipose, and pancreas of diabesity-prone Tally Ho mice and diabesity-resistant C57BL/6J mice was assessed by quantitative PCR analysis. Several potential candidate genes, some with no previous association to diabesity QTLs, were identified. Since QTL intervals may be large and could contain hundreds or thousands of potential candidate genes, this method allows researchers to focus on those with strong potential as well as identify novel candidate genes. Potential candidate genes for Tafat (80 cM) on mouse Chromosome 4 as identified by ExQuest are Ela2, Ela3b, and Dvl1 (82 cM). Chr 10 locus Ela2 exhibits 55-fold decreased expression in the pancreas of Tally Ho animals compared to C57BL/6J. For QTL Bwq1 (6.3 cM), potential candidate gene Decr1 was identified. For QTLs Triglq1 (6.5 cM) and Bglq4 (6.5 cM), potential candidate genes Ttpa, Bhmt(Chr 13), Baat(22.7 cM), and Aldob (22.3 cM) were identified. For QTLs Nidd1 (48 cM) and Dob1 (50 cM), potential candidate genes Lepr (46.7 cM), Dio1 (48.7 cM), Scp2 (52 cM), Faah (56.5 cM), and Usp1 were identified.
Nidd1	Chr4, syntenic		J:99477	Authors used novel data mining tool ExQuest to identify novel candidate genes for existing diabesity QTLs. Next, candidate gene expression in the liver, adipose, and pancreas of diabesity-prone Tally Ho mice and diabesity-resistant C57BL/6J mice was assessed by quantitative PCR analysis. Several potential candidate genes, some with no previous association to diabesity QTLs, were identified. Since QTL intervals may be large and could contain hundreds or thousands of potential candidate genes, this method allows researchers to focus on those with strong potential as well as identify novel candidate genes. Potential candidate genes for Tafat (80 cM) on mouse Chromosome 4 as identified by ExQuest are Ela2, Ela3b, and Dvl1 (82 cM). Chr 10 locus Ela2 exhibits 55-fold decreased expression in the pancreas of Tally Ho animals compared to C57BL/6J. For QTL Bwq1 (6.3 cM), potential candidate gene Decr1 was identified. For QTLs Triglq1 (6.5 cM) and Bglq4 (6.5 cM), potential candidate genes Ttpa, Bhmt(Chr 13), Baat(22.7 cM), and Aldob (22.3 cM) were identified. For QTLs Nidd1 (48 cM) and Dob1 (50 cM), potential candidate genes Lepr (46.7 cM), Dio1 (48.7 cM), Scp2 (52 cM), Faah (56.5 cM), and Usp1 were identified.
Tafat	Chr4, 74.75 cM	Chr4:141621281-141621387	J:99477	Authors used novel data mining tool ExQuest to identify novel candidate genes for existing diabesity QTLs. Next, candidate gene expression in the liver, adipose, and pancreas of diabesity-prone Tally Ho mice and diabesity-resistant C57BL/6J mice was assessed by quantitative PCR analysis. Several potential candidate genes, some with no previous association to diabesity QTLs, were identified. Since QTL intervals may be large and could contain hundreds or thousands of potential candidate genes, this method allows researchers to focus on those with strong potential as well as identify novel candidate genes. Potential candidate genes for Tafat (80 cM) on mouse Chromosome 4 as identified by ExQuest are Ela2, Ela3b, and Dvl1 (82 cM). Chr 10 locus Ela2 exhibits 55-fold decreased expression in the pancreas of Tally Ho animals compared to C57BL/6J. For QTL Bwq1 (6.3 cM), potential candidate gene Decr1 was identified. For QTLs Triglq1 (6.5 cM) and Bglq4 (6.5 cM), potential candidate genes Ttpa, Bhmt(Chr 13), Baat(22.7 cM), and Aldob (22.3 cM) were identified. For QTLs Nidd1 (48 cM) and Dob1 (50 cM), potential candidate genes Lepr (46.7 cM), Dio1 (48.7 cM), Scp2 (52 cM), Faah (56.5 cM), and Usp1 were identified.
Triglq1	Chr4, 10.61 cM	Chr4:25683240-25683429	J:99477	Authors used novel data mining tool ExQuest to identify novel candidate genes for existing diabesity QTLs. Next, candidate gene expression in the liver, adipose, and pancreas of diabesity-prone Tally Ho mice and diabesity-resistant C57BL/6J mice was assessed by quantitative PCR analysis. Several potential candidate genes, some with no previous association to diabesity QTLs, were identified. Since QTL intervals may be large and could contain hundreds or thousands of potential candidate genes, this method allows researchers to focus on those with strong potential as well as identify novel candidate genes. Potential candidate genes for Tafat (80 cM) on mouse Chromosome 4 as identified by ExQuest are Ela2, Ela3b, and Dvl1 (82 cM). Chr 10 locus Ela2 exhibits 55-fold decreased expression in the pancreas of Tally Ho animals compared to C57BL/6J. For QTL Bwq1 (6.3 cM), potential candidate gene Decr1 was identified. For QTLs Triglq1 (6.5 cM) and Bglq4 (6.5 cM), potential candidate genes Ttpa, Bhmt(Chr 13), Baat(22.7 cM), and Aldob (22.3 cM) were identified. For QTLs Nidd1 (48 cM) and Dob1 (50 cM), potential candidate genes Lepr (46.7 cM), Dio1 (48.7 cM), Scp2 (52 cM), Faah (56.5 cM), and Usp1 were identified.

*cM position of peak correlated region/marker

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