H3f4 (H3.4 histone, cluster member) - Rat Genome Database

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Gene: H3f4 (H3.4 histone, cluster member) Mus musculus
Analyze
Symbol: H3f4
Name: H3.4 histone, cluster member
RGD ID: 2295243
MGI Page MGI
Description: Histones are basic nuclear proteins that are responsible for the nucleosome structure of the chromosomal fiber in eukaryotes. Nucleosomes consist of approximately 146 bp of DNA wrapped around a histone octamer composed of pairs of each of the four core histones (H2A, H2B, H3, and H4). The chromatin fiber is further compacted through the interaction of a linker histone, H1, with the DNA between the nucleosomes to form higher order chromatin structures. This gene is intronless and encodes a replication-dependent histone that is a member of the histone H3 family. [provided by RefSeq, Dec 2015]
Type: protein-coding
RefSeq Status: REVIEWED
Previously known as: Gm12260; H3.4 histone; H304; H3mmT; H3t; histone cluster 1, H3 pseudogene; predicted gene 12260; uncharacterized protein LOC382523
RGD Orthologs
Human
Rat
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: GRCm39 - Mouse Genome Assembly GRCm39
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391158,852,537 - 58,853,099 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1158,852,599 - 58,853,364 (+)EnsemblGRCm39 Ensembl
GRCm381158,961,711 - 58,962,273 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1158,961,812 - 58,962,222 (+)EnsemblGRCm38mm10GRCm38
MGSCv371158,775,313 - 58,775,723 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361158,778,007 - 58,778,417 (+)NCBIMGSCv36mm8
Celera1163,728,149 - 63,728,559 (+)NCBICelera
Cytogenetic Map11B1.3NCBI
cM Map1136.39NCBI
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
17beta-estradiol  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2-amino-2-deoxy-D-galactopyranose  (ISO)
4,4'-sulfonyldiphenol  (EXP)
4-(N-nitrosomethylamino)-1-(3-pyridyl)butan-1-one  (ISO)
5-aza-2'-deoxycytidine  (EXP,ISO)
5-azacytidine  (ISO)
9-cis-retinoic acid  (ISO)
aflatoxin B1  (ISO)
aldehydo-D-glucose  (ISO)
all-trans-retinoic acid  (EXP,ISO)
all-trans-retinol  (EXP)
anthra[1,9-cd]pyrazol-6(2H)-one  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenite(3-)  (EXP)
arsenous acid  (EXP,ISO)
benzo[a]pyrene  (EXP,ISO)
berberine  (ISO)
biguanides  (ISO)
biphenyl-4-amine  (ISO)
bisphenol A  (ISO)
butyric acid  (ISO)
CGP 52608  (ISO)
chromium atom  (EXP)
copper atom  (ISO)
copper(0)  (ISO)
crocidolite asbestos  (EXP)
curcumin  (ISO)
D-glucose  (ISO)
diarsenic trioxide  (EXP,ISO)
dimethyl sulfoxide  (ISO)
disodium selenite  (ISO)
disulfiram  (ISO)
entinostat  (EXP,ISO)
furan  (ISO)
genistein  (ISO)
glucose  (ISO)
homocysteine  (ISO)
hydrogen peroxide  (EXP)
iron atom  (ISO)
iron(0)  (ISO)
lipopolysaccharide  (ISO)
LY294002  (EXP)
methoxyacetic acid  (ISO)
mocetinostat  (ISO)
N-methyl-4-phenylpyridinium  (ISO)
N-nitrosodiethylamine  (EXP)
nickel atom  (ISO)
nickel dichloride  (ISO)
nickel sulfate  (ISO)
panobinostat  (ISO)
PhIP  (ISO)
potassium chromate  (ISO)
quercetin  (ISO)
quizartinib  (ISO)
romidepsin  (ISO)
silicon dioxide  (ISO)
sodium arsenite  (EXP,ISO)
sunitinib  (ISO)
tert-butyl hydroperoxide  (ISO)
trichostatin A  (EXP,ISO)
triptonide  (EXP)
valproic acid  (EXP,ISO)
vorinostat  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
nucleoplasm  (ISO)
nucleosome  (ISO)

Molecular Function

References
Additional References at PubMed
PMID:17261847   PMID:26388943   PMID:28099840  


Genomics

Comparative Map Data
H3f4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391158,852,537 - 58,853,099 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1158,852,599 - 58,853,364 (+)EnsemblGRCm39 Ensembl
GRCm381158,961,711 - 58,962,273 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1158,961,812 - 58,962,222 (+)EnsemblGRCm38mm10GRCm38
MGSCv371158,775,313 - 58,775,723 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361158,778,007 - 58,778,417 (+)NCBIMGSCv36mm8
Celera1163,728,149 - 63,728,559 (+)NCBICelera
Cytogenetic Map11B1.3NCBI
cM Map1136.39NCBI
H3-4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381228,424,845 - 228,425,360 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1228,424,845 - 228,425,360 (-)EnsemblGRCh38hg38GRCh38
GRCh371228,612,546 - 228,613,061 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361226,679,169 - 226,679,649 (-)NCBINCBI36Build 36hg18NCBI36
Build 341224,919,280 - 224,919,761NCBI
Celera1201,802,501 - 201,802,981 (-)NCBICelera
Cytogenetic Map1q42.13NCBI
HuRef1199,127,141 - 199,127,621 (-)NCBIHuRef
CHM1_11229,884,858 - 229,885,338 (-)NCBICHM1_1
T2T-CHM13v2.01227,613,357 - 227,613,872 (-)NCBIT2T-CHM13v2.0
H3f4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81044,240,282 - 44,240,842 (+)NCBIGRCr8
mRatBN7.21043,740,702 - 43,741,262 (+)NCBImRatBN7.2mRatBN7.2
UTH_Rnor_SHR_Utx1048,436,208 - 48,436,618 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01047,926,550 - 47,926,960 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01043,430,149 - 43,430,559 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01045,304,696 - 45,305,106 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01045,061,326 - 45,061,736 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41045,252,993 - 45,253,403 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1043,007,140 - 43,007,550 (+)NCBICelera
Cytogenetic Map10q22NCBI
H3-4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2121,179,580 - 21,185,987 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1121,116,631 - 21,127,563 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01203,826,506 - 203,827,872 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11209,037,808 - 209,038,461 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1209,038,009 - 209,038,419 (-)Ensemblpanpan1.1panPan2
H3-4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.114627,178 - 627,587 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl14627,190 - 627,581 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha14531,238 - 531,641 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.014343,173 - 343,582 (+)NCBIROS_Cfam_1.0
UMICH_Zoey_3.114530,366 - 530,769 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.014291,015 - 291,418 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.014300,401 - 300,810 (+)NCBIUU_Cfam_GSD_1.0
H3-4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440721387,066,284 - 87,066,991 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493713530,455 - 30,865 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493713530,302 - 30,865 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
H3-4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1251,709,942 - 51,710,952 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
H3-4
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1251,304,447 - 1,305,991 (+)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_0236660551,183,647 - 1,184,210 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
H3-4
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046249371,122,707 - 1,123,114 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046249371,122,586 - 1,123,425 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in H3f4
29 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:165
Count of miRNA genes:148
Interacting mature miRNAs:163
Transcripts:ENSMUST00000122447
Prediction methods:Miranda, Rnahybrid, Targetscan
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.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
27226798Scvln18_msacral vertebrae length 2, 16 week (mouse)11325000060690826Mouse
26884446Sklq10_mskull length QTL 10, 10 week (mouse)11325000062890826Mouse
26884453Sklq16_mskull length QTL 16, 16 week (mouse)11325000072690826Mouse
13208559Wght10_mweight 10 (mouse)11395000088890826Mouse
13208558Lgth12_mbody length 12 (mouse)11395000094890826Mouse
1300905Scc6_mcolon tumor susceptibility 6 (mouse)Not determined11688027789019734Mouse
27226738Metcl11_mmetatarsal-calcaneal length 11, 10 week (mouse)11885000061390826Mouse
26884401Huml4_mhumerus length 4, 10 week (mouse)111155000068490826Mouse
27226762Feml21_mfemur length 21, 16 week (mouse)111175000065990826Mouse
1357640Orq2_movulation rate QTL 2 (mouse)Not determined111226863768500330Mouse
4141127W3q4_mweight 3 weeks QTL 4 (mouse)Not determined1226863768500330Mouse
4141470Egq4_mearly growth QTL 4 (mouse)Not determined1226863768500330Mouse
4142109W10q2_mweight 10 weeks QTL 2 (mouse)Not determined1226863768500330Mouse
4141582Lgaq1_mlate growth adjusted QTL 1 (mouse)Not determined1226863768500330Mouse
4142308W6q3_mweight 6 weeks QTL 3 (mouse)Not determined111226863768500330Mouse
4142216Lgq1_mlate growth QTL 1 (mouse)Not determined1226863768500330Mouse
4141966Tailq1_mtail length QTL 1 (mouse)Not determined1226863768500330Mouse
1357851Scfq3_msubcutaneous fat pad weight QTL 3 (mouse)Not determined111226863768500330Mouse
1357720Kidpq1_mkidney weight percentage QTL 1 (mouse)Not determined111226863768500330Mouse
1357437Epfq4_mepididymal fat pad weight QTL 4 (mouse)Not determined111226863768500330Mouse
1559002Lmrq4_mLeishmania major resistance QTL 4 (mouse)Not determined111226863769684947Mouse
39128214Lwq20_mliver weight QTL 20 (mouse)1112268637118022724Mouse
1558945Orgwq8_morgan weight QTL 8 (mouse)Not determined111705617567078411Mouse
10053687Eae6_msusceptibility to experimental allergic encephalomyelitis 6 (mouse)Not determined111778196668500330Mouse
4141894Nidd6k_mNidd6 on KK-A (mouse)Not determined1912420496897826Mouse
10412246Dfs2_mdental fluorosis suseptibility 2 (mouse)Not determined112180736495881231Mouse
10044006Hbnr13_mHeligmosomoides bakeri nematode resistance 13 (mouse)Not determined112577262659772741Mouse
1357844Si5lq5_mserum IGFBP-5 level QTL 5 (mouse)Not determined112816587362165976Mouse
13524848Ppiq7_mprepulse inhibition QTL 7 (mouse)112856914762569147Mouse
1301426Desp2_mdespair 2 (mouse)Not determined112870858162708700Mouse
11522752Cocia18_mcocaine-induced activity, QTL 18 (mouse)113100820965008209Mouse
11059563Lmr31_mleishmaniasis resistance 31 (mouse)113210057766100694Mouse
1357782Char8_mP. chabaudi malaria resistance QTL 8 (mouse)Not determined113557861669684987Mouse
13208569Bmiq10_mbody mass index QTL 10 (mouse)113589082784890826Mouse
1301328Mol4_mmodifier of LPS-response 4 (mouse)Not determined113628257783481356Mouse
1301788Lbw8_mlupus NZB x NZW 8 (mouse)Not determined113650328770509492Mouse
1301896Tria1_mT-cell receptor induced activation 1 (mouse)Not determined113661356570613855Mouse
4141853Skmw17_mskeletal muscle weight 17 (mouse)Not determined113708094171081064Mouse
4142475Ity2a_mimmunity to S. typhimurium 2a (mouse)Not determined113776858060402716Mouse
10766457Nwa3_mNew Zealand White autoimmunity 3 (mouse)113801611572016209Mouse
11532698Sluc36a_msusceptibility to lung cancer 36a (mouse)114225661776256730Mouse
11532699Sluc36b_msusceptibility to lung cancer 36b (mouse)114225661776256730Mouse
4142300Ctrq3_mC. trachomatis resistance QTL 3 (mouse)Not determined114463003876854757Mouse
4141367Inf1_macute ozone induced inflammation (mouse)Not determined44630038113058009Mouse
1302021Nidd1n_mnon-insulin-dependent diabetes mellitus 1 in NSY (mouse)Not determined114516587379978324Mouse
1357878Mastr_mmodifier of astrocytoma (mouse)Not determined114570858189818733Mouse
1300765Bbaa4_mB.burgdorferi-associated arthritis 4 (mouse)Not determined114618516780185262Mouse
1301988Bmd11_mbone mineral density 11 (mouse)Not determined114631940780319522Mouse
1301830Ssta4_msusceptibility to Salmonella typhimurium antigens 4 (mouse)Not determined115007819184078411Mouse
13524840Ppiq9a_mprepulse inhibition QTL 9a (mouse)115249438586494385Mouse
1300774Pgia7_mproteoglycan induced arthritis 7 (mouse)Not determined115339058887390737Mouse
4141084Spqq1_msperm quality QTL 1 (mouse)Not determined5406567063319522Mouse
1302186Blmpf2_mbleomycin-induced pulmonary fibrosis 2 (mouse)Not determined115406567067078411Mouse
4142148Ckdbp2_mchronic kidney disease blood pressure locus 2 (mouse)Not determined115408094165103841Mouse
4141830Pregq1_mpregnancy QTL 1 (mouse)Not determined115412675283733652Mouse
4141875Etax9_methanol induced ataxia 9 (mouse)Not determined5528498572209927Mouse
4142121Tmc1m2_mTmc1 modifier 2 (mouse)Not determined1156864027114157957Mouse
1300664Etohcta9_methanol conditioned taste aversion 9 (mouse)Not determined115775466091754758Mouse
13513917Heal54_mwound healing/ regeneration 54 (mouse)115787291759879610Mouse
10053682Eae45_mexperimental allergic encephalomyelitis susceptibility 45 (mouse)Not determined115849055574754758Mouse
1300924Ity2_mimmunity to S. typhimurium 2 (mouse)Not determined15850803087695238Mouse
4141982Skts-fp2_mskin tumor susceptibility in FVB and PWK 2 (mouse)Not determined5871926685066529Mouse


Expression


Sequence


RefSeq Acc Id: ENSMUST00000122447
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1158,852,599 - 58,853,364 (+)Ensembl
GRCm38.p6 Ensembl1158,961,812 - 58,962,222 (+)Ensembl
RefSeq Acc Id: NM_001318003   ⟹   NP_001304932
RefSeq Status: REVIEWED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm391158,852,537 - 58,853,099 (+)NCBI
GRCm381158,961,711 - 58,962,273 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001304932 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL07696 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSMUSP00001091671
  ENSMUSP00001091671.1
RefSeq Acc Id: NP_001304932   ⟸   NM_001318003
- UniProtKB: A0A8I4SYN6 (UniProtKB/TrEMBL),   A1L0V4 (UniProtKB/TrEMBL)
- Sequence:
Protein Domains
Histone H2A/H2B/H3

Promoters
RGD ID:8674806
Promoter ID:EPDNEW_M15421
Type:single initiation site
Name:Gm12260_1
Description:Mus musculus predicted gene 12260 , mRNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm381158,961,773 - 58,961,833EPDNEW

Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSMUSG00000080152 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSMUST00000122447 ENTREZGENE
  ENSMUST00000122447.3 UniProtKB/TrEMBL
Gene3D-CATH 1.10.20.10 UniProtKB/TrEMBL
InterPro Histone-fold UniProtKB/TrEMBL
  Histone_H2A/H2B/H3 UniProtKB/TrEMBL
  Histone_H3/CENP-A UniProtKB/TrEMBL
MGD MGI:3651326 ENTREZGENE
NCBI Gene 382523 ENTREZGENE
PANTHER HISTONE H3.1 UniProtKB/TrEMBL
  HISTONE H3.1T UniProtKB/TrEMBL
  PTHR11426 UniProtKB/TrEMBL
Pfam Histone UniProtKB/TrEMBL
PhenoGen H3f4 PhenoGen
PRINTS HISTONEH3 UniProtKB/TrEMBL
PROSITE HISTONE_H3_1 UniProtKB/TrEMBL
  HISTONE_H3_2 UniProtKB/TrEMBL
SMART SM00428 UniProtKB/TrEMBL
Superfamily-SCOP SSF47113 UniProtKB/TrEMBL
UniProt A0A8I4SYN6 ENTREZGENE, UniProtKB/TrEMBL
  A1L0V4 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2022-07-05 H3f4  H3.4 histone, cluster member  H3f4  H3.4 histone  Symbol and/or name change 5135510 APPROVED
2019-08-13 H3f4  H3.4 histone  Gm12260  predicted gene 12260  Symbol and/or name change 5135510 APPROVED