H3f3c (H3 histone, family 3C) - Rat Genome Database

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Gene: H3f3c (H3 histone, family 3C) Mus musculus
Analyze
Symbol: H3f3c
Name: H3 histone, family 3C
RGD ID: 2294834
MGI Page MGI
Description: A structural constituent of chromatin. Predicted to be involved in nucleosome assembly. Predicted to act upstream of or within chromatin organization. Located in condensed nuclear chromosome and euchromatin.
Type: protein-coding (Ensembl: processed_pseudogene)
RefSeq Status: VALIDATED
Previously known as: embryonic; Gm14384; H3-5; H3mm11; histone H3.3C; predicted gene, OTTMUSG00000016509; uncharacterized protein LOC625328
RGD Orthologs
Human
Bonobo
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCm39 - Mouse Genome Assembly GRCm39
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm392119,495,597 - 119,496,633 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl2119,496,107 - 119,496,517 (-)EnsemblGRCm39 Ensembl
GRCm382119,665,116 - 119,666,152 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl2119,665,626 - 119,666,036 (-)EnsemblGRCm38mm10GRCm38
MGSCv372119,491,362 - 119,491,864 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv362119,356,527 - 119,357,599 (-)NCBIMGSCv36mm8
Celera2120,823,569 - 120,824,143 (-)NCBICelera
Cytogenetic Map2E5NCBI
cM Map259.97NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model



  
Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
H3f3cMouse1-chloro-2,4-dinitrobenzene affects bindingISOH3Y2 (Homo sapiens)6480464Dinitrochlorobenzene binds to H3F3C proteinCTDPMID:32991956
H3f3cMouse2,3',4,4',5-Pentachlorobiphenyl increases expressionEXP 64804642 more ...CTDPMID:31388691
H3f3cMouse4-vinylcyclohexene dioxide affects expressionEXP 64804644-vinyl-1-cyclohexene dioxide affects the expression of H3F3C mRNACTDPMID:20829426


Biological Process

  
Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
H3f3cMousechromatin organization acts_upstream_of_or_withinICGO:00007912290270 PMID:26388943MGIPMID:26388943
H3f3cMousenucleosome assembly involved_inISOUniProtKB:Q71DI32290270 GO_CentralGO_REF:0000119

Cellular Component

  
Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
H3f3cMousecondensed nuclear chromosome located_inIDA 2290270 PMID:26388943MGIPMID:26388943
H3f3cMouseeuchromatin located_inIDA 2290270 PMID:26388943MGIPMID:26388943
H3f3cMousenucleoplasm located_inISOUniProtKB:Q71DI32290270 GO_CentralGO_REF:0000119
H3f3cMousenucleosome part_ofISOUniProtKB:Q71DI32290270 GO_CentralGO_REF:0000119
H3f3cMousenucleosome part_ofIEAUniProtKB-KW:KW-05442290270 UniProtGO_REF:0000043
H3f3cMousenucleus is_active_inIBAPANTHER:PTN008517671 more ...2290270 GO_CentralGO_REF:0000033
H3f3cMousenucleus located_inIEAUniProtKB-SubCell:SL-01912290270 UniProtGO_REF:0000044
H3f3cMousenucleus located_inISOUniProtKB:Q71DI32290270 GO_CentralGO_REF:0000119

Molecular Function

  
Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
H3f3cMouseDNA binding enablesIEAUniProtKB-KW:KW-02382290270 UniProtGO_REF:0000043
H3f3cMouseprotein heterodimerization activity enablesIEAInterPro:IPR0090722290270 InterProGO_REF:0000002
H3f3cMousestructural constituent of chromatin enablesIDA 2290270 PMID:26388943MGIPMID:26388943
H3f3cMousestructural constituent of chromatin enablesIEAInterPro:IPR0001642290270 InterProGO_REF:0000002

Imported Annotations - KEGG (archival)

Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
H3f3cMousesystemic lupus erythematosus pathway  IEA 6907045 KEGGmmu:05322

#
Reference Title
Reference Citation
1. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
2. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
PMID:20676102   PMID:21873635   PMID:22705305   PMID:24614311   PMID:25092339   PMID:26388943   PMID:28524856   PMID:30562941   PMID:30713523   PMID:34175335   PMID:36417873  



H3f3c
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm392119,495,597 - 119,496,633 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl2119,496,107 - 119,496,517 (-)EnsemblGRCm39 Ensembl
GRCm382119,665,116 - 119,666,152 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl2119,665,626 - 119,666,036 (-)EnsemblGRCm38mm10GRCm38
MGSCv372119,491,362 - 119,491,864 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv362119,356,527 - 119,357,599 (-)NCBIMGSCv36mm8
Celera2120,823,569 - 120,824,143 (-)NCBICelera
Cytogenetic Map2E5NCBI
cM Map259.97NCBI
H3Y2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38517,490,967 - 17,492,076 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl517,490,967 - 17,492,076 (-)EnsemblGRCh38hg38GRCh38
GRCh37517,491,076 - 17,492,185 (-)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map5p15.1NCBI
HuRef517,463,812 - 17,464,219 (-)NCBIHuRef
CHM1_1517,491,508 - 17,491,915 (-)NCBICHM1_1
T2T-CHM13v2.0517,430,381 - 17,431,490 (-)NCBIT2T-CHM13v2.0
LOC129397736
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2417,724,056 - 17,729,485 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1515,877,665 - 15,883,177 (-)NCBINHGRI_mPanPan1

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Variants in H3f3c
88 total Variants

Predicted Target Of
Summary Value
Count of predictions:57
Count of miRNA genes:54
Interacting mature miRNAs:57
Transcripts:ENSMUST00000119459
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.


1 to 10 of 58 rows
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD ID
Symbol
Name
LOD
P Value
Trait
Sub Trait
Chr
Start
Stop
Species
1301905Lgth2_mbody length 2 (mouse)Not determined2111173704145173821Mouse
1302033Nsv1_mNeuroadapted Sindbis viral RNA level 1 (mouse)Not determined2111623386145623526Mouse
12904007Cfq7_mconditioned fear QTL 7 (mouse)2118356772125048872Mouse
13506762Tbvq2_mtrabecular bone volume QTL 2 (mouse)2115430481124741920Mouse
13824983Vclq1_mcurvilinear velocity QTL 1 (mouse)261830344136841920Mouse
1301909Smdq2_msegregation of mitochondrial DNA QTL 2 (mouse)Not determined292778465126778607Mouse
11039520Ltpr2h_mLeishmania tropica response 2h (mouse)2112212746146213005Mouse
11039521Ltpr2g_mLeishmania tropica response 2g (mouse)2115212857149212994Mouse
12910799Pwgrq2_mpre-weaning growth rate QTL 2 (mouse)2118589253160611165Mouse
1302174Dssc2_mdextran sodium sulfate induced colitis QTL2 (mouse)Not determined224224632148700377Mouse

1 to 10 of 58 rows
H3f3a  
Mouse AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map12D2UniSTS
Cytogenetic Map2E5UniSTS
Cytogenetic Map13D1UniSTS
Cytogenetic Map1D2.3UniSTS
Cytogenetic Map6E2UniSTS
Cytogenetic Map4C5UniSTS
Cytogenetic Map11B2UniSTS
cM Map1 UniSTS
cM Map13 UniSTS






RefSeq Transcripts NM_001370931 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AL844536 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Ensembl Acc Id: ENSMUST00000119459
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl2119,496,107 - 119,496,517 (-)Ensembl
GRCm38.p6 Ensembl2119,665,626 - 119,666,036 (-)Ensembl
RefSeq Acc Id: NM_001370931   ⟹   NP_001357860
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm392119,495,597 - 119,496,633 (-)NCBI
GRCm382119,665,116 - 119,666,152 (-)NCBI
Sequence:
Protein RefSeqs NP_001357860 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein P02301 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_001357860   ⟸   NM_001370931
- UniProtKB: P02301 (UniProtKB/Swiss-Prot),   A1L0U3 (UniProtKB/TrEMBL),   A1L0V4 (UniProtKB/TrEMBL)
Histone H2A/H2B/H3

Name Modeler Protein Id AA Range Protein Structure
AF-P02301-F1-model_v2 AlphaFold P02301 1-136 view protein structure



1 to 18 of 18 rows
Database
Acc Id
Source(s)
Ensembl Genes ENSMUSG00000082029 Ensembl
Gene3D-CATH 1.10.20.10 UniProtKB/Swiss-Prot
InterPro Histone-fold UniProtKB/Swiss-Prot
  Histone_H2A/H2B/H3 UniProtKB/Swiss-Prot
  Histone_H3/CENP-A UniProtKB/Swiss-Prot
MGD MGI:3650546 ENTREZGENE
NCBI Gene 625328 ENTREZGENE
PANTHER PTHR11426 UniProtKB/Swiss-Prot
Pfam Histone UniProtKB/Swiss-Prot
PhenoGen H3f3c PhenoGen
PRINTS HISTONEH3 UniProtKB/Swiss-Prot
PROSITE HISTONE_H3_1 UniProtKB/Swiss-Prot
  HISTONE_H3_2 UniProtKB/Swiss-Prot
SMART SM00428 UniProtKB/Swiss-Prot
Superfamily-SCOP SSF47113 UniProtKB/Swiss-Prot
UniProt A1L0U3 ENTREZGENE, UniProtKB/TrEMBL
  A1L0V4 ENTREZGENE, UniProtKB/TrEMBL
  H3C_MOUSE UniProtKB/Swiss-Prot, ENTREZGENE
1 to 18 of 18 rows