H3f3a MGI Mouse Gene Detail - MGI:1097686

Symbol

H3f3a
Name

H3.3 histone A
Synonyms

H3-3a, H3.3A

Feature Type

protein coding gene
IDs

MGI:1097686
NCBI Gene: 15078
Alliance

gene page
Transcription Start Sites

6 TSS

Sequence Map

Chr1:180630125-180641127 bp, - strand
From NCBI annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 1, 84.46 cM, cytoband D2.3
Mapping Data

2 experiments

SNPs within 2kb

349 from dbSNP Build 142
Strain Annotations

18

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_1097686	protein coding gene	Chr1:180628397-180641508 (-)
129S1/SvImJ	MGP_129S1SvImJ_G0016874	protein coding gene	Chr1:187260176-187275877 (-)
A/J	MGP_AJ_G0016853	protein coding gene	Chr1:179683855-179702144 (-)
AKR/J	MGP_AKRJ_G0016819	protein coding gene	Chr1:185024579-185040759 (-)
BALB/cJ	MGP_BALBcJ_G0016811	protein coding gene	Chr1:180309955-180324292 (-)
C3H/HeJ	MGP_C3HHeJ_G0016636	protein coding gene	Chr1:185795739-185810240 (-)
C57BL/6NJ	MGP_C57BL6NJ_G0017274	protein coding gene	Chr1:193292963-193298088 (-)
CAROLI/EiJ	MGP_CAROLIEiJ_G0014982	protein coding gene	Chr1:170667960-170680805 (-)
CAST/EiJ	MGP_CASTEiJ_G0016217	protein coding gene	Chr1:185143702-185159821 (-)
CBA/J	MGP_CBAJ_G0016610	protein coding gene	Chr1:200468560-200483951 (-)
DBA/2J	MGP_DBA2J_G0016716	protein coding gene	Chr1:178519654-178532444 (-)
FVB/NJ	MGP_FVBNJ_G0016712	protein coding gene	Chr1:176616991-176629725 (-)
LP/J	MGP_LPJ_G0016790	protein coding gene	Chr1:188518849-188536264 (-)
NOD/ShiLtJ	MGP_NODShiLtJ_G0016743	protein coding gene	Chr1:207648358-207661034 (-)
NZO/HlLtJ	MGP_NZOHlLtJ_G0017311	protein coding gene	Chr1:184808925-184823154 (-)
PWK/PhJ	MGP_PWKPhJ_G0016005	protein coding gene	Chr1:177634167-177647075 (-)
SPRET/EiJ	MGP_SPRETEiJ_G0015781	protein coding gene	Chr1:183744359-183756903 (-)
WSB/EiJ	MGP_WSBEiJ_G0016280	protein coding gene	Chr1:184999545-185012240 (-)

Human Ortholog

H3-3A, H3.3 histone A

Vertebrate Orthologs

9

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

H3-3A, H3.3 histone A
Synonyms

BRYLIB1, H3.3A, H3-3B, H3F3, H3F3A
Links

HGNC:4764

NCBI Gene ID: 3020

neXtProt AC: NX_P84243

UniProt: P84243
Chr Location

1q42.12; chr1:226061831-226072019 (+) GRCh38

Human Ortholog

H3-3B, H3.3 histone B
Synonyms

BRYLIB2, H3-3A, H3.3B, H3F3B
Links

HGNC:4765

NCBI Gene ID: 3021

neXtProt AC: NX_P84243

UniProt: P84243
Chr Location

17q25.1; chr17:75776434-75785893 (-) GRCh38

MGI Vertebrate Homology

H3f3a stringent orthology
2 human;1 mouse;2 rat;5 zebrafish
HCOP

vertebrate homology predictions: H3-3A, H3-3B
Gene Tree

H3f3a

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Phenotype Summary

7 phenotypes from 3 alleles in 3 genetic backgrounds
23 phenotype references

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

46
Chemically induced (other)

2
Endonuclease-mediated

5
Gene trapped

26
Targeted

13
Genomic Mutations

2 involving H3f3a
Find Mice (IMSR)

29 strains or lines available
Comparison Matrix

Gene Expression + Phenotype

Homozygous mutants for a hypomorphic gene trap allele display partial neonatal lethality, reduced fertility, growth abnormalities and neuromuscular defects. Mice homozygous for a reporter allele exhibit reduced body size and male fertility.

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All GO Annotations

29
GO References

8

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

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

858
Tissues

74
cDNA Data

28
Literature Summary

19

Images

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

Other Mouse Links

Allen Institute

GEO

Expression Atlas
Other Vertebrate Links

Xenbase h3-3a

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All Sequences

77
RefSeq

2
CCDS

CCDS15573.1

Ensembl

ENSMUSG00000060743 (Evidence)
NCBI Gene

15078

			Length	Strain/Species	Flank
genomic	15078	NCBI Gene Model \| MGI Sequence Detail	11003	C57BL/6J	± kb
transcript	NM_008210	RefSeq \| MGI Sequence Detail	1043	C57BL/6
polypeptide	NP_032236	RefSeq \| MGI Sequence Detail	136	C57BL/6

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All nucleic 36

cDNA 30

Primer pair 4

Other 2

Microarray probesets 9

Summaries

All 100

Developmental Gene Expression 19

Gene Ontology 8

Phenotypes 23
Earliest

J:42392 Hraba-Renevey S, et al., Expression of a mouse replacement histone H3.3 gene with a highly conserved 3' noncoding region during SV40- and polyoma-induced Go to S-phase transition. Nucleic Acids Res. 1989 Apr 11;17(7):2449-61
Latest

J:353083 Khazaei S, et al., Single substitution in H3.3G34 alters DNMT3A recruitment to cause progressive neurodegeneration. Cell. 2023 Mar 16;186(6):1162-1178.e20

TSS for H3f3a:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr15550	Chr1:180641430-180641447 (-)	-312 bp
Tssr15549	Chr1:180641156-180641170 (-)	-36 bp
Tssr15548	Chr1:180641114-180641148 (-)	-4 bp
Tssr15547	Chr1:180639893-180639897 (-)	1,232 bp
Tssr15546	Chr1:180636238-180636241 (-)	4,887 bp
Tssr15545	Chr1:180635806-180635811 (-)	5,318 bp

Contributing Projects: Mouse Genome Database (MGD), Gene Expression Database (GXD), Mouse Models of Human Cancer database (MMHCdb) (formerly Mouse Tumor Biology (MTB)), Gene Ontology (GO)
Citing These Resources Funding Information Warranty Disclaimer, Privacy Notice, Licensing, & Copyright Send questions and comments to User Support.	last database update 11/12/2024 MGI 6.24