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

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Gene: H3-4 (H3.4 histone, cluster member) Ictidomys tridecemlineatus
Analyze
Symbol: H3-4
Name: H3.4 histone, cluster member (Ensembl:histone H3.1-like)
RGD ID: 12446506
Description: ENCODES a protein that exhibits DNA binding (inferred); protein heterodimerization activity (inferred); structural constituent of chromatin (inferred); INVOLVED IN nucleosome assembly (inferred); ASSOCIATED WITH gastrointestinal stromal tumor (ortholog); genetic disease (ortholog); intellectual disability (ortholog); FOUND IN nucleosome (ortholog)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: HIST3H3; histone H3.1; histone H3.1-like; LOC101961517
RGD Orthologs
Human
Mouse
Rat
Bonobo
Dog
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: SpeTri2.0 - Squirrel SpeTri2.0 Assembly
Position:
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
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
nucleoplasm  (IEA)
nucleosome  (IEA,ISO)
nucleus  (IEA)

Molecular Function

References
Additional References at PubMed
PMID:22301074   PMID:30032202  


Genomics

Comparative Map Data
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
(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
(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
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
(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


Expression


Sequence

Nucleotide Sequences
RefSeq Transcripts XM_005342557 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide JAESOR010002273 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSSTOT00000023780   ⟹   ENSSTOP00000021167
Type: CODING
Position:
Squirrel AssemblyChrPosition (strand)Source
SpeTri2.0 EnsemblNW_00493713530,455 - 30,865 (-)Ensembl
RefSeq Acc Id: XM_005342557   ⟹   XP_005342614
Type: CODING
Position:
Squirrel AssemblyChrPosition (strand)Source
HiC_Itri_2NW_02440721387,066,284 - 87,066,991 (+)NCBI
SpeTri2.0NW_00493713530,302 - 30,865 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs XP_005342614 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSSTOP00000021167.1
GenBank Protein KAG3265087 (Get FASTA)   NCBI Sequence Viewer  
  KAG3265088 (Get FASTA)   NCBI Sequence Viewer  
Reference Protein Sequences
RefSeq Acc Id: XP_005342614   ⟸   XM_005342557
- UniProtKB: I3N9X0 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSSTOP00000021167   ⟸   ENSSTOT00000023780
Protein Domains
Histone H2A/H2B/H3


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSSTOG00000022946 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSSTOT00000023780.1 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
NCBI Gene LOC101961517 ENTREZGENE
PANTHER HISTONE H3.1T UniProtKB/TrEMBL
  PTHR11426 UniProtKB/TrEMBL
Pfam Histone UniProtKB/TrEMBL
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 I3N9X0 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2022-06-21 H3-4  H3.4 histone, cluster member  LOC101961517  histone H3.1  Symbol and/or name change 5135510 APPROVED
2021-03-26 LOC101961517  histone H3.1  LOC101961517  histone H3.1-like  Symbol and/or name change 5135510 APPROVED