H2aj (H2A.J histone) - Rat Genome Database

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Gene: H2aj (H2A.J histone) Rattus norvegicus
Analyze
Symbol: H2aj
Name: H2A.J histone
RGD ID: 1592176
Description: Predicted to enable nucleosomal DNA binding activity. Predicted to be involved in heterochromatin formation. Predicted to be part of nucleosome. Predicted to be active in nucleus. Orthologous to human H2AJ (H2A.J histone); PARTICIPATES IN systemic lupus erythematosus pathway; INTERACTS WITH 6-propyl-2-thiouracil; acrylamide; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: H2A histone family, member J; H2a/j; H2afj; Histone H2A.J; histone H2A.J-like; LOC100910152; LOC103690002; LOC690795; similar to H2A histone family, member J
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr84171,406,922 - 171,407,406 (+)NCBIGRCr8
mRatBN7.24169,675,718 - 169,676,202 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl4169,675,752 - 169,677,006 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx4175,970,446 - 175,970,930 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.04171,752,185 - 171,752,669 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.04170,376,110 - 170,376,594 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.04170,766,900 - 170,767,384 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl4170,766,900 - 170,767,382 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0 Ensembl4170,149,029 - 170,149,418 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.04234,409,181 - 234,409,665 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.44173,818,670 - 173,819,154 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera4158,259,247 - 158,259,731 (+)NCBICelera
Cytogenetic Map4q43NCBI
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
nucleosome  (IBA)
nucleus  (IBA)

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:12477932   PMID:15489334   PMID:20458337   PMID:23533145   PMID:32357304   PMID:35352799  


Genomics

Comparative Map Data
H2aj
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr84171,406,922 - 171,407,406 (+)NCBIGRCr8
mRatBN7.24169,675,718 - 169,676,202 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl4169,675,752 - 169,677,006 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx4175,970,446 - 175,970,930 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.04171,752,185 - 171,752,669 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.04170,376,110 - 170,376,594 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.04170,766,900 - 170,767,384 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl4170,766,900 - 170,767,382 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0 Ensembl4170,149,029 - 170,149,418 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.04234,409,181 - 234,409,665 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.44173,818,670 - 173,819,154 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera4158,259,247 - 158,259,731 (+)NCBICelera
Cytogenetic Map4q43NCBI
H2AJ
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381214,774,405 - 14,778,002 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1214,774,405 - 14,778,002 (+)EnsemblGRCh38hg38GRCh38
GRCh371214,927,339 - 14,930,936 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361214,818,537 - 14,822,203 (+)NCBINCBI36Build 36hg18NCBI36
Build 341214,818,561 - 14,822,201NCBI
Celera1220,072,245 - 20,075,911 (+)NCBICelera
Cytogenetic Map12p12.3NCBI
HuRef1214,696,539 - 14,700,205 (+)NCBIHuRef
CHM1_11214,893,363 - 14,897,029 (+)NCBICHM1_1
T2T-CHM13v2.01214,651,754 - 14,655,351 (+)NCBIT2T-CHM13v2.0
H2aj
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm396136,785,246 - 136,787,072 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl6136,785,242 - 136,787,072 (+)EnsemblGRCm39 Ensembl
GRCm386136,808,248 - 136,810,074 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl6136,808,244 - 136,810,074 (+)EnsemblGRCm38mm10GRCm38
MGSCv376136,756,769 - 136,758,595 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv366136,772,520 - 136,774,270 (+)NCBIMGSCv36mm8
MGSCv366137,174,895 - 137,176,645 (+)NCBIMGSCv36mm8
Celera6139,817,503 - 139,819,331 (+)NCBICelera
Cytogenetic Map6G1NCBI
cM Map666.72NCBI
LOC102027285
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541311,520,610 - 11,520,999 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495541311,520,479 - 11,521,163 (+)NCBIChiLan1.0ChiLan1.0
LOC100976242
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21020,224,247 - 20,226,929 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11220,222,619 - 20,223,690 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01214,780,257 - 14,781,331 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11215,177,159 - 15,178,239 (+)NCBIpanpan1.1PanPan1.1panPan2
H2AJ
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12731,835,433 - 31,836,150 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2731,835,623 - 31,836,012 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2714,612,886 - 14,613,592 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02732,142,187 - 32,142,896 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2732,142,377 - 32,142,766 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12732,031,419 - 32,032,127 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02731,990,164 - 31,990,874 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02714,344,929 - 14,345,636 (+)NCBIUU_Cfam_GSD_1.0
LOC101977852
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494592,971,534 - 92,972,197 (-)NCBIHiC_Itri_2
SpeTri2.0NW_0049365872,699,169 - 2,699,845 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
H2AJ
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl557,777,010 - 57,777,654 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1557,777,008 - 57,777,673 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2561,247,573 - 61,248,074 (+)NCBISscrofa10.2Sscrofa10.2susScr3
H2AFJ
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11114,673,850 - 14,674,530 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1114,673,924 - 14,674,476 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366606920,634,660 - 20,636,384 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
LOC101720535
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462475223,246,383 - 23,246,772 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462475223,246,253 - 23,246,912 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
724558Plsm2Polydactyly-luxate syndrome (PLS) morphotypes QTL 20.0003hindlimb integrity trait (VT:0010563)hind foot phalanges count (CMO:0001949)4132422778177422778Rat
1331738Bp209Blood pressure QTL 2092.979arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)4138503169179293946Rat
1298524Oia8Oil induced arthritis QTL 8joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4138503169173369699Rat
2293659Bmd35Bone mineral density QTL 354.50.0001femur strength trait (VT:0010010)femoral neck ultimate force (CMO:0001703)4137755016181392681Rat
634342Cia24Collagen induced arthritis QTL 244.5joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4146565735175236377Rat
1576316Ept5Estrogen-induced pituitary tumorigenesis QTL 53.8pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)483428419177635233Rat
1578674Bmd12Bone mineral density QTL 123.8femur mineral mass (VT:0010011)compact volumetric bone mineral density (CMO:0001730)4135699135180699135Rat
1300109Rf13Renal function QTL 133.91renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)4157710145182687754Rat
2316958Gluco58Glucose level QTL 5810blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)411320076180699135Rat
2303623Vencon2Ventilatory control QTL 23.8respiration trait (VT:0001943)minute ventilation (CMO:0000132)4135204660180204660Rat
1549827Scl46Serum cholesterol level QTL 463.5blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)4132396220177396220Rat
61362Oia2Oil induced arthritis QTL 20.001joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4138503169173369699Rat
6478718Anxrr34Anxiety related response QTL 340.00896locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4144639524182687754Rat
6478748Anxrr42Anxiety related response QTL 420.28008locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4144639524182687754Rat
6478754Anxrr43Anxiety related response QTL 430.14035locomotor behavior trait (VT:0001392)distance moved per unit of time into, out of or within a discrete space in an experimental apparatus (CMO:0001493)4144639524182687754Rat
6478778Anxrr51Anxiety related response QTL 510.25384locomotor behavior trait (VT:0001392)measurement of voluntary locomotion into, out of or within a discrete space in an experimental apparatus (CMO:0000957)4124778595169778595Rat
6478693Anxrr32Anxiety related response QTL 320.00092locomotor behavior trait (VT:0001392)measurement of voluntary locomotion into, out of or within a discrete space in an experimental apparatus (CMO:0000957)4144639524182687754Rat
6478700Anxrr33Anxiety related response QTL 330.00896locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4144639524182687754Rat
7411558Bw133Body weight QTL 13313.840.001body mass (VT:0001259)body weight gain (CMO:0000420)4125590636170590636Rat
10053718Scort25Serum corticosterone level QTL 252.150.0097blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)4155561574182687754Rat
10401796Kidm48Kidney mass QTL 48kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)4145568712182687754Rat


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 3 17 11 14 11 13 10 2
Low 43 40 30 5 30 8 11 74 22 31 9 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000044446   ⟹   ENSRNOP00000044986
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl4170,766,900 - 170,767,382 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000073287   ⟹   ENSRNOP00000064421
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl4169,675,752 - 169,677,006 (+)Ensembl
Rnor_6.0 Ensembl4170,149,029 - 170,149,418 (+)Ensembl
RefSeq Acc Id: NM_001109610   ⟹   NP_001103080
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr84171,406,922 - 171,407,406 (+)NCBI
mRatBN7.24169,675,718 - 169,676,202 (+)NCBI
Rnor_6.04170,766,900 - 170,767,384 (+)NCBI
Rnor_5.04234,409,181 - 234,409,665 (+)NCBI
RGSC_v3.44173,818,670 - 173,819,154 (+)RGD
Celera4158,259,247 - 158,259,731 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001103080 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein A9UMV8 (Get FASTA)   NCBI Sequence Viewer  
  AAI57817 (Get FASTA)   NCBI Sequence Viewer  
  EDM01605 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000064421.2
Reference Protein Sequences
RefSeq Acc Id: NP_001103080   ⟸   NM_001109610
- UniProtKB: A9UMV8 (UniProtKB/Swiss-Prot),   A0A8L2QY15 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000044986   ⟸   ENSRNOT00000044446
RefSeq Acc Id: ENSRNOP00000064421   ⟸   ENSRNOT00000073287
Protein Domains
Histone H2A C-terminal   Histone H2A/H2B/H3

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-A9UMV8-F1-model_v2 AlphaFold A9UMV8 1-129 view protein structure

Transcriptome

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

Promoters
RGD ID:13693465
Promoter ID:EPDNEW_R3990
Type:initiation region
Name:LOC103690002_1
Description:histone H2A.J
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_6.04170,766,918 - 170,766,978EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1592176 AgrOrtholog
BioCyc Gene G2FUF-42598 BioCyc
Ensembl Genes ENSRNOG00000033045 Ensembl
  ENSRNOG00000045819 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000073287.2 UniProtKB/TrEMBL
Gene3D-CATH 1.10.20.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:9034669 IMAGE-MGC_LOAD
InterPro Histone-fold UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Histone_H2A UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Histone_H2A/H2B/H3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Histone_H2A_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Histone_H2A_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:690795 UniProtKB/Swiss-Prot
MGC_CLONE MGC:187833 IMAGE-MGC_LOAD
NCBI Gene 690795 ENTREZGENE
PANTHER HISTONE H2A TYPE 1-C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR23430 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Histone UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Histone_H2A_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen H2aj PhenoGen
PRINTS HISTONEH2A UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE HISTONE_H2A UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
RatGTEx ENSRNOG00000033045 RatGTEx
  ENSRNOG00000045819 RatGTEx
SMART H2A UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF47113 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A8L2QY15 ENTREZGENE, UniProtKB/TrEMBL
  A9UMV8 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2021-03-09 H2aj  H2A.J histone  LOC103690002  histone H2A.J  Data merged from RGD:9140761 737654 PROVISIONAL
2019-09-13 H2aj  H2A.J histone  H2afj  H2A histone family, member J  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2015-07-29 H2afj  H2A histone family, member J  LOC100910152  histone H2A.J-like  Data merged from RGD:6499683 737654 PROVISIONAL
2014-08-25 LOC103690002  histone H2A.J      Symbol and Name status set to provisional 70820 PROVISIONAL
2012-07-05 LOC100910152  histone H2A.J-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2008-03-06 H2afj  H2A histone family, member J  LOC690795  similar to H2A histone family, member J  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-01-09 LOC690795  similar to H2A histone family, member J  LOC684899  similar to H2A histone family, member J  Data merged from RGD:1585499 1643240 APPROVED
2006-11-20 LOC690795  similar to H2A histone family, member J      Symbol and Name status set to provisional 70820 PROVISIONAL
2006-11-19 LOC684899  similar to H2A histone family, member J      Symbol and Name status set to provisional 70820 PROVISIONAL