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

genome feature 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

24

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_1097686	protein coding gene	Chr1:180628397-180641508 (-)
129S1/SvImJ	ENSMUSG00200022244	protein coding gene	Chr1:178380516-178393628 (-)
A/J	ENSMUSG00195041436	protein coding gene	Chr1:177997044-178010252 (-)
A/J	ENSMUSG00195031190	protein coding gene	Chr11:112983893-112989745 (-)
AKR/J	ENSMUSG00220028991	protein coding gene	Chr11:113087943-113093982 (-)
AKR/J	ENSMUSG00220019067	protein coding gene	Chr1:177233478-177246594 (-)
BALB/cJ	ENSMUSG00180036558	protein coding gene	Chr1:178031739-178044852 (-)
C3H/HeJ	ENSMUSG00175042944	protein coding gene	Chr11:113235680-113241540 (-)
C3H/HeJ	ENSMUSG00175037845	protein coding gene	Chr1:178207543-178220654 (-)
C57BL/6NJ	ENSMUSG00215019719	protein coding gene	Chr1:177432412-177445525 (-)
C57BL/6NJ	ENSMUSG00215041124	protein coding gene	Chr11:112772877-112778927 (-)
CAROLI/EiJ	MGP_CAROLIEiJ_G0014982	protein coding gene	Chr1:170667960-170680805 (-)
CAST/EiJ	no annotation
CBA/J	ENSMUSG00210048785	protein coding gene	Chr11:112955674-112961530 (-)
CBA/J	ENSMUSG00210018480	protein coding gene	Chr1:177868985-177882098 (-)
DBA/2J	ENSMUSG00185035359	protein coding gene	Chr1:182488423-182501537 (-)
FVB/NJ	ENSMUSG00205026822	protein coding gene	Chr1:176927226-176940332 (-)
JF1/MsJ	ENSUMUG00000016342	protein coding gene	Chr1:181467476-181480516 (-)
LP/J	ENSMUSG00230031080	protein coding gene	Chr1:182046360-182059471 (-)
LP/J	ENSMUSG00230046593	protein coding gene	Chr11:114329012-114334868 (-)
NOD/ShiLtJ	ENSMUSG00190023332	protein coding gene	Chr1:177893406-177906517 (-)
NZO/HlLtJ	ENSMUSG00225010986	protein coding gene	Chr1:185800663-185813777 (-)
NZO/HlLtJ	ENSMUSG00225049904	protein coding gene	Chr11:116381640-116387677 (-)
PWK/PhJ	ENSLUMG00010016595	protein coding gene	Chr1:176741056-176754235 (-)
SPRET/EiJ	no annotation
WSB/EiJ	ENSIUOG00005011232	protein coding gene	Chr1:177105391-177118563 (-)

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, H3F3, H3F3A
Links

HGNC:4764

NCBI Gene ID: 3020

UniProt: P84243
Chr Location

1q42.12; chr1:226061571-226073206 (+) GRCh38

Human Ortholog

H3-5, H3.5 histone
Synonyms

H3.3C, H3.5, H3F3C
Links

HGNC:33164

NCBI Gene ID: 440093

UniProt: Q6NXT2
Chr Location

12p11.21; chr12:31791185-31792298 (-) GRCh38

MGI Vertebrate Homology

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

vertebrate homology predictions: H3-3A, H3-5
Gene Tree

H3f3a

Diseases

2 with human H3-3A,H3-3B associations

				Human Disease	Mouse Models
				Bryant-Li-Bhoj neurodevelopmental syndrome 1 IDs Bryant-Li-Bhoj neurodevelopmental syndrome 1 DOID:0051011 OMIM:619720
				Bryant-Li-Bhoj neurodevelopmental syndrome 2 IDs Bryant-Li-Bhoj neurodevelopmental syndrome 2 DOID:0051012 OMIM:619721

Click on a disease name to see all genes associated with that disease.

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Phenotype Summary

7 phenotypes from 3 alleles in 3 genetic backgrounds
28 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

52
Chemically induced (other)

2
Endonuclease-mediated

7
Gene trapped

26
Targeted

17
Genomic Mutations

2 involving H3f3a
Find Mice (IMSR)

33 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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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

751
Tissues

75
cDNA Data

28
Literature Summary

19

Images

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

Other Mouse Links

Allen Institute

GEO

Expression Atlas

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All Sequences

87
RefSeq

2
UniProt

4
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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UniProt

4 Sequences

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All nucleic 37

cDNA 30

Primer pair 5

Other 2

Microarray probesets 9

Summaries

All 127

Developmental Gene Expression 19

Phenotypes 28
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:390413 Chauhan S, et al., Histone H3.3 ensures cell proliferation and genomic stability during myeloid cell development. iScience. 2026 Jul 17;29(7):116501

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 09/08/2026 MGI 6.24