H2ac4 (H2A clustered histone 4) - Rat Genome Database

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Gene: H2ac4 (H2A clustered histone 4) Rattus norvegicus
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Symbol: H2ac4
Name: H2A clustered histone 4
RGD ID: 1589461
Description: Predicted to be a structural constituent of chromatin. Predicted to be involved in heterochromatin formation and negative regulation of cell population proliferation. Predicted to be part of CENP-A containing nucleosome. Predicted to be active in nucleus. Orthologous to human H2AC4 (H2A clustered histone 4); PARTICIPATES IN systemic lupus erythematosus pathway; INTERACTS WITH 6-propyl-2-thiouracil; bisphenol A; Cuprizon.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: Hist1h2ak; histone cluster 1, H2ak; LOC680615; similar to histone 2a
RGD Orthologs
Human
Mouse
Green Monkey
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81747,495,624 - 47,496,127 (-)NCBIGRCr8
mRatBN7.21742,799,884 - 42,800,387 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1742,799,652 - 42,800,381 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1744,849,530 - 44,849,922 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01749,608,630 - 49,609,022 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01744,099,555 - 44,099,947 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01744,840,990 - 44,841,382 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1744,840,990 - 44,841,382 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01758,624,879 - 58,625,271 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41750,436,332 - 50,436,724 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1753,661,266 - 53,661,658 (+)NCBICelera
Cytogenetic Map17p11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

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:16319397   PMID:16457589   PMID:23956221  


Genomics

Comparative Map Data
H2ac4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81747,495,624 - 47,496,127 (-)NCBIGRCr8
mRatBN7.21742,799,884 - 42,800,387 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1742,799,652 - 42,800,381 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1744,849,530 - 44,849,922 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01749,608,630 - 49,609,022 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01744,099,555 - 44,099,947 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01744,840,990 - 44,841,382 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1744,840,990 - 44,841,382 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01758,624,879 - 58,625,271 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41750,436,332 - 50,436,724 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1753,661,266 - 53,661,658 (+)NCBICelera
Cytogenetic Map17p11NCBI
H2AC4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38626,033,092 - 26,033,618 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl626,033,092 - 26,033,618 (-)EnsemblGRCh38hg38GRCh38
GRCh37626,033,320 - 26,033,846 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36626,141,299 - 26,141,775 (-)NCBINCBI36Build 36hg18NCBI36
Build 34626,141,298 - 26,141,775NCBI
Celera627,260,544 - 27,261,020 (-)NCBICelera
Cytogenetic Map6p22.2NCBI
HuRef625,976,385 - 25,976,861 (-)NCBIHuRef
CHM1_1626,035,593 - 26,036,069 (-)NCBICHM1_1
T2T-CHM13v2.0625,899,048 - 25,899,577 (-)NCBIT2T-CHM13v2.0
H2ac4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391323,935,061 - 23,935,577 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1323,935,109 - 23,935,581 (+)EnsemblGRCm39 Ensembl
GRCm381323,751,088 - 23,751,592 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1323,751,126 - 23,751,598 (+)EnsemblGRCm38mm10GRCm38
MGSCv371323,842,957 - 23,843,462 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361323,758,553 - 23,759,058 (+)NCBIMGSCv36mm8
Celera1323,982,859 - 23,983,364 (+)NCBICelera
Cytogenetic Map13A3.1NCBI
cM Map139.91NCBI
LOC119626805
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Vero_WHO_p1.0NW_02366604425,967,970 - 25,968,956 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0

Variants

.
Variants in H2ac4
1 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:24
Count of miRNA genes:23
Interacting mature miRNAs:23
Transcripts:ENSRNOT00000059328
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.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
631497Bp98Blood pressure QTL 983.66arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)174135465160463643Rat
1354581Bp247Blood pressure QTL 2474.5arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)17169599340Rat
1358295Aocep1Aortic cell protein QTL 16.17e-07thoracic aorta cellular protein amount (VT:0010598)aortic cell percentage174099000585990005Rat
1354640Scl32Serum cholesterol level QTL 325.4blood HDL cholesterol amount (VT:0000184)blood high density lipoprotein cholesterol level (CMO:0000052)171578159260781592Rat
152023626Bp403Blood pressure QTL 4033.86arterial blood pressure trait (VT:2000000)172393042179524188Rat
2301412Kidm40Kidney mass QTL 400.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)173747984782479847Rat
9590107Sffal7Serum free fatty acids level QTL 74.810.001blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)172840914773409147Rat
2302377Scl61Serum cholesterol level QTL 614.36blood HDL cholesterol amount (VT:0000184)serum high density lipoprotein cholesterol level (CMO:0000361)172738994653481766Rat
70157Niddm32Non-insulin dependent diabetes mellitus QTL 324.34blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)172245492450909196Rat
724549Niddm56Non-insulin dependent diabetes mellitus QTL 560.03blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)173199078476990784Rat
1354651Lmblg2Limb length QTL 26tibia length (VT:0004357)tibia length (CMO:0000450)17429913069599340Rat
1598871Memor5Memory QTL 55.3exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)174054004180387013Rat
1354628Stl13Serum triglyceride level QTL 133.8blood triglyceride amount (VT:0002644)blood triglyceride level (CMO:0000118)172129303960781592Rat
1581512Cm55Cardiac mass QTL 552.80.05heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)172702794956836890Rat
10054088Scort28Serum corticosterone level QTL 282.040.0102blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)17452803849528038Rat
1354630Cm34Cardiac mass QTL 348.7heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)17429913069599340Rat
61394Bp8Blood pressure QTL 82.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)172308056759555013Rat
1559055Bp278Blood pressure QTL 2780.04arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)172365318468653184Rat
10450503Bp386Blood pressure QTL 3860.28arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)173136839162109574Rat
152025238Slep14Serum leptin concentration QTL 144.62blood leptin amount (VT:0005667)172418489079524188Rat
1354638Insul1Insulin level QTL 14.8blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)17429913069599340Rat
2313854Bp343Blood pressure QTL 3433.9life span trait (VT:0005372)age at time of death (CMO:0001193)173199078450909196Rat
2317054Aia12Adjuvant induced arthritis QTL 124.24joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)173828150983281509Rat
1354635Bp245Blood pressure QTL 2456arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)174207316069599340Rat
1331765Hrtrt15Heart rate QTL 154.094heart pumping trait (VT:2000009)heart rate (CMO:0000002)171533061355836425Rat
8552928Pigfal9Plasma insulin-like growth factor 1 level QTL 99blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)172840914773409147Rat
1300148Bp192Blood pressure QTL 1923.47arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)173455084373951021Rat
2317060Aia26Adjuvant induced arthritis QTL 263.22joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)173828150983281509Rat
2303627Vencon8Ventilatory control QTL 80.001respiration trait (VT:0001943)tidal volume (CMO:0000222)17452803849528038Rat
12903980Cm120Cardiac mass QTL 1200.002heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)172365318468653184Rat
12903981Am17Aortic mass QTL 170.001aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)172365318468653184Rat
4889955Bss93Bone structure and strength QTL 934.4tibia size trait (VT:0100001)tibia cortical bone volume to tibia total bone volume ratio (CMO:0001727)172702794960463643Rat
2303561Bw91Body weight QTL 912body mass (VT:0001259)body weight (CMO:0000012)17886846253868462Rat
12903982Kidm70Kidney mass QTL 700.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)172365318470974005Rat
12903978Cm118Cardiac mass QTL 1180.001heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)172365318468653184Rat
2324621Coatc5Coat color QTL 5coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)173136839173951021Rat
12903979Cm119Cardiac mass QTL 1190.001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)172365318468653184Rat
1354619Bp242Blood pressure QTL 2426.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)172459934069599340Rat
1354596Bw32Body weight QTL 324.5body mass (VT:0001259)body weight (CMO:0000012)17429913060781592Rat
1354662Rf49Renal function QTL 492.9blood creatinine amount (VT:0005328)plasma creatinine level (CMO:0000537)17169599340Rat
152023740Bp406Blood pressure QTL 4066.06arterial blood pressure trait (VT:2000000)172393042179524188Rat
1354663Bvd5Brain ventricular dilatation QTL 53.510.001brain ventricle morphology trait (VT:0000822)hydrocephalus severity score (CMO:0001881)173199078481292925Rat
7488966Bp370Blood pressure QTL 3700.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)172365318457246843Rat
1354658Spl8Serum phospholipid level QTL 83.8blood VLDL phospholipid amount (VT:0010507)blood very low density lipoprotein phospholipid level (CMO:0001571)17160781592Rat
152023737Bp405Blood pressure QTL 4055.06arterial blood pressure trait (VT:2000000)2393042179524188Rat
1354659Scl68Serum cholesterol level QTL 683.9blood VLDL cholesterol amount (VT:0005144)blood very low density lipoprotein cholesterol level (CMO:0000648)171578159260781592Rat
152023736Bp404Blood pressure QTL 4043.78arterial blood pressure trait (VT:2000000)172393042179524188Rat
724528Uae4Urinary albumin excretion QTL 44.90.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)173583708569599340Rat


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
nervous system
renal system
reproductive system
respiratory system
8 8 37 96 71 69 43 25 43 5 174 79 77 36 55 26

Sequence


Ensembl Acc Id: ENSRNOT00000080119   ⟹   ENSRNOP00000070475
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1744,840,990 - 44,841,382 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000110197   ⟹   ENSRNOP00000087700
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1742,799,652 - 42,800,381 (-)Ensembl
RefSeq Acc Id: NM_001109423   ⟹   NP_001102893
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81747,495,624 - 47,496,127 (-)NCBI
mRatBN7.21742,799,884 - 42,800,387 (-)NCBI
Rnor_6.01744,840,990 - 44,841,382 (-)NCBI
Rnor_5.01758,624,879 - 58,625,271 (+)NCBI
RGSC_v3.41750,436,332 - 50,436,724 (-)RGD
Celera1753,661,266 - 53,661,658 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001102893 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL84558 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000087700.1
RefSeq Acc Id: NP_001102893   ⟸   NM_001109423
- UniProtKB: Q64598 (UniProtKB/Swiss-Prot),   D3ZVK7 (UniProtKB/TrEMBL),   A6KN90 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000070475   ⟸   ENSRNOT00000080119
Ensembl Acc Id: ENSRNOP00000087700   ⟸   ENSRNOT00000110197
Protein Domains
Histone H2A C-terminal   Histone H2A/H2B/H3

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZVK7-F1-model_v2 AlphaFold D3ZVK7 1-130 view protein structure

Transcriptome

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

Promoters
RGD ID:13700491
Promoter ID:EPDNEW_R11015
Type:single initiation site
Name:Hist1h2ak_1
Description:histone cluster 1, H2ak
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_6.01744,841,424 - 44,841,484EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1589461 AgrOrtholog
BioCyc Gene G2FUF-9241 BioCyc
Ensembl Genes ENSRNOG00000052594 Ensembl
  ENSRNOG00000070010 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000110197.1 UniProtKB/TrEMBL
Gene3D-CATH 1.10.20.10 UniProtKB/TrEMBL, UniProtKB/Swiss-Prot
InterPro Histone-fold UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Histone_core_D UniProtKB/TrEMBL
  Histone_H2A UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Histone_H2A/H2B/H3 UniProtKB/Swiss-Prot
  Histone_H2A_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Histone_H2A_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:680615 UniProtKB/TrEMBL
NCBI Gene 680615 ENTREZGENE
PANTHER HISTONE H2A UniProtKB/Swiss-Prot
  HISTONE H2A TYPE 1-B/E UniProtKB/Swiss-Prot
  HISTONE H2A TYPE 1-D UniProtKB/TrEMBL
  PTHR23430 UniProtKB/TrEMBL
Pfam Histone UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Histone_H2A_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen H2ac4 PhenoGen
PRINTS HISTONEH2A UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE HISTONE_H2A UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
RatGTEx ENSRNOG00000052594 RatGTEx
  ENSRNOG00000070010 RatGTEx
SMART H2A UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP Histone-fold UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A6KN90 ENTREZGENE, UniProtKB/TrEMBL
  D3ZVK7 ENTREZGENE, UniProtKB/TrEMBL
  H2A1F_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2021-04-29 H2ac4  H2A clustered histone 4  Hist1h2ak  histone cluster 1, H2ak  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2010-04-21 Hist1h2ak  histone cluster 1, H2ak  LOC680615  similar to histone 2a  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-11-19 LOC680615  similar to histone 2a      Symbol and Name status set to provisional 70820 PROVISIONAL