H2ab2 (H2A.B variant histone 2) - Rat Genome Database

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Gene: H2ab2 (H2A.B variant histone 2) Rattus norvegicus
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Symbol: H2ab2 (Ensembl: H2ab3)
Name: H2A.B variant histone 2 (Ensembl:H2A.B variant histone 3)
RGD ID: 1561666
Description: Predicted to be a structural constituent of chromatin. Predicted to be involved in heterochromatin formation; mRNA processing; and nucleosome assembly. Predicted to be located in euchromatin. Predicted to be part of nucleosome. Predicted to be active in nucleus. Orthologous to several human genes including H2AB1 (H2A.B variant histone 1); PARTICIPATES IN systemic lupus erythematosus pathway; INTERACTS WITH C60 fullerene; 2,3,7,8-tetrachlorodibenzodioxine (ortholog); CGP 52608 (ortholog).
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: H2A histone family, member B3; H2A.B variant histone 3; H2ab3; H2afb3; LOC302783; RGD1561666; similar to Histone H2A-Bbd (H2A Barr body-deficient)
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X86,566,994 - 86,567,568 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 EnsemblX86,566,994 - 86,567,568 (+)EnsemblGRCr8
mRatBN7.2X82,362,531 - 82,363,105 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX82,362,633 - 82,362,983 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_UtxX84,053,296 - 84,053,646 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X87,474,676 - 87,475,026 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X85,034,596 - 85,034,946 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X88,602,135 - 88,602,485 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX88,602,135 - 88,602,485 (+)Ensemblrn6Rnor6.0
Rnor_5.0X88,525,854 - 88,526,204 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4X105,959,002 - 105,959,352 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
CeleraX83,583,749 - 83,584,099 (+)NCBICelera
Cytogenetic MapXq31NCBI
JBrowse:




Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
chromosome  (IEA)
euchromatin  (IEA,ISO)
nucleosome  (IBA,IEA,ISO)
nucleus  (IBA,IEA)

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:21630459   PMID:22795134  


Genomics

Comparative Map Data
H2ab2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X86,566,994 - 86,567,568 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 EnsemblX86,566,994 - 86,567,568 (+)EnsemblGRCr8
mRatBN7.2X82,362,531 - 82,363,105 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX82,362,633 - 82,362,983 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_UtxX84,053,296 - 84,053,646 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X87,474,676 - 87,475,026 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X85,034,596 - 85,034,946 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X88,602,135 - 88,602,485 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX88,602,135 - 88,602,485 (+)Ensemblrn6Rnor6.0
Rnor_5.0X88,525,854 - 88,526,204 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4X105,959,002 - 105,959,352 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
CeleraX83,583,749 - 83,584,099 (+)NCBICelera
Cytogenetic MapXq31NCBI
H2AB1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38X154,884,972 - 154,885,558 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 EnsemblX154,884,972 - 154,885,558 (+)Ensemblhg38GRCh38
GRCh37X154,113,247 - 154,113,833 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36X153,766,511 - 153,767,027 (+)NCBIBuild 36Build 36hg18NCBI36
CeleraX154,271,936 - 154,272,452 (+)NCBICelera
Cytogenetic MapXq28NCBI
HuRefX142,656,817 - 142,657,333 (+)NCBIHuRef
CHM1_1X154,025,079 - 154,025,595 (+)NCBICHM1_1
T2T-CHM13v2.0X153,121,380 - 153,121,966 (+)NCBIT2T-CHM13v2.0
H2ab2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X115,590,875 - 115,591,222 (+)NCBIGRCm39GRCm39mm39
GRCm39 EnsemblX115,590,875 - 115,591,222 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm38X116,681,178 - 116,681,525 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX116,681,178 - 116,681,525 (+)Ensemblmm10GRCm38
MGSCv37X113,794,787 - 113,795,134 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv36X112,798,122 - 112,798,469 (+)NCBIMGSCv36mm8
CeleraX103,425,578 - 103,425,925 (+)NCBICelera
Cytogenetic MapXE1NCBI
cM MapX49.55NCBI
LOC102021406
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_004955593911,641 - 911,919 (+)NCBIChiLan1.0ChiLan1.0
LOC100992822
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2X154,863,587 - 154,864,290 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1X154,867,195 - 154,867,890 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0X144,364,612 - 144,365,333 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1X154,205,452 - 154,206,043 (+)NCBIPanPan1.1PanPan1.1panPan2
H2AB1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X122,910,412 - 122,913,373 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 EnsemblX122,910,968 - 122,913,382 (+)NCBIcanFam3CanFam3.1
ROS_Cfam_1.0X126,038,484 - 126,041,082 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
UMICH_Zoey_3.1X121,785,189 - 121,788,817 (+)NCBIUMICH_Zoey_3.1
LOC101967165
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X119,873,257 - 119,874,388 (+)NCBIHiC_Itri_2
SpeTri2.0NW_004936927232,353 - 232,857 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
H2AB1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1X125,277,575 - 125,280,752 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X143,203,035 - 143,205,593 (-)NCBISscrofa10.2Sscrofa10.2susScr3
H2AB1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X129,130,005 - 129,131,069 (+)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366606567,106,492 - 67,107,273 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0

Variants

.
Variants in H2ab2
1 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:124
Count of miRNA genes:99
Interacting mature miRNAs:106
Transcripts:ENSRNOT00000043727
Prediction methods:Microtar, Miranda, Pita, 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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
61430Cia18Collagen induced arthritis QTL 183.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X80434318125434318Rat
738035Stresp1Stress response QTL 14.960.000011stress-related behavior trait (VT:0010451)defensive burying - copingX45182909117740458Rat
1598837Memor13Memory QTL 133.2exploratory behavior trait (VT:0010471)difference between duration of physical contact or close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)X4493088389930883Rat


Expression

RNA-SEQ Expression

reproductive system
32

Sequence


Ensembl Acc Id: ENSRNOT00000043727   ⟹   ENSRNOP00000045522
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 EnsemblX86,566,994 - 86,567,568 (+)Ensembl
mRatBN7.2 EnsemblX82,362,633 - 82,362,983 (+)Ensembl
Rnor_6.0 EnsemblX88,602,135 - 88,602,485 (+)Ensembl
RefSeq Acc Id: NM_001106969   ⟹   NP_001100439
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X86,566,994 - 86,567,568 (+)NCBI
mRatBN7.2X82,362,531 - 82,363,105 (+)NCBI
Rnor_6.0X88,602,135 - 88,602,485 (+)NCBI
Rnor_5.0X88,525,854 - 88,526,204 (+)NCBI
RGSC_v3.4X105,959,002 - 105,959,352 (+)RGD
CeleraX83,583,749 - 83,584,099 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001100439 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDM07065 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000045522
  ENSRNOP00000045522.2
RefSeq Acc Id: NP_001100439   ⟸   NM_001106969
- UniProtKB: D4ACM0 (UniProtKB/TrEMBL),   A6IVB5 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000045522   ⟸   ENSRNOT00000043727

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D4ACM0-F1-model_v2 AlphaFold D4ACM0 1-116 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen

Promoters
RGD ID:13701920
Promoter ID:EPDNEW_R12444
Type:single initiation site
Name:H2afb3_1
Description:H2A histone family, member B3
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0X88,602,204 - 88,602,264EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1561666 AgrOrtholog
BioCyc Gene G2FUF-1791 BioCyc
Ensembl Genes ENSRNOG00000029736 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000043727 ENTREZGENE
  ENSRNOT00000043727.4 UniProtKB/TrEMBL
Gene3D-CATH 1.10.20.10 UniProtKB/TrEMBL
InterPro Histone-fold UniProtKB/TrEMBL
  Histone_H2A UniProtKB/TrEMBL
KEGG Report rno:302783 UniProtKB/TrEMBL
NCBI Gene 302783 ENTREZGENE
PANTHER PTHR23430 UniProtKB/TrEMBL
PhenoGen H2ab2 PhenoGen
PRINTS HISTONEH2A UniProtKB/TrEMBL
RatGTEx ENSRNOG00000029736 RatGTEx
SMART H2A UniProtKB/TrEMBL
Superfamily-SCOP Histone-fold UniProtKB/TrEMBL
UniProt A6IVB5 ENTREZGENE, UniProtKB/TrEMBL
  D4ACM0 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2025-07-14 H2ab2  H2A.B variant histone 2  H2ab3  H2A.B variant histone 3  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2020-12-10 H2ab3  H2A.B variant histone 3  H2afb3  H2A histone family, member B3  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-02-29 H2afb3  H2A histone family, member B3  RGD1561666_predicted  similar to Histone H2A-Bbd (H2A Barr body-deficient) (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-07 RGD1561666_predicted  similar to Histone H2A-Bbd (H2A Barr body-deficient) (predicted)  LOC302783  similar to Histone H2A-Bbd (H2A Barr body-deficient)  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC302783  similar to Histone H2A-Bbd (H2A Barr body-deficient)      Symbol and Name status set to provisional 70820 PROVISIONAL