Macroh2a2 (macroH2A.2 histone) - Rat Genome Database

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Gene: Macroh2a2 (macroH2A.2 histone) Rattus norvegicus
Analyze
Symbol: Macroh2a2
Name: macroH2A.2 histone
RGD ID: 1561371
Description: Predicted to enable RNA polymerase II transcription regulatory region sequence-specific DNA binding activity and nucleosomal DNA binding activity. Predicted to be involved in several processes, including establishment of protein localization to chromatin; negative regulation of macromolecule biosynthetic process; and positive regulation of keratinocyte differentiation. Predicted to act upstream of or within sex-chromosome dosage compensation. Part of chromatin. Orthologous to human MACROH2A2 (macroH2A.2 histone); PARTICIPATES IN histone modification pathway; systemic lupus erythematosus pathway; INTERACTS WITH 1,3-dinitrobenzene; 2,3,7,8-tetrachlorodibenzodioxine; 6-propyl-2-thiouracil.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: core histone macro-H2A.2; H2A histone family, member Y2; H2afy2; LOC361844; RGD1561371; similar to macroH2A2
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr82030,220,975 - 30,270,652 (-)NCBIGRCr8
mRatBN7.22029,678,194 - 29,727,867 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2029,678,222 - 29,727,891 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx2030,689,165 - 30,738,841 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.02030,080,380 - 30,129,756 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.02030,822,865 - 30,872,538 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.02031,352,924 - 31,402,483 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2031,352,960 - 31,402,483 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02033,152,549 - 33,200,486 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42029,104,096 - 29,154,482 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera2031,104,770 - 31,153,499 (-)NCBICelera
Cytogenetic Map20q11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. MacroH2A histone variants act as a barrier upon reprogramming towards pluripotency. Gaspar-Maia A, etal., Nat Commun. 2013;4:1565. doi: 10.1038/ncomms2582.
2. 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.
3. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
4. GOA pipeline RGD automated data pipeline
5. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
6. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
7. Comprehensive gene review and curation RGD comprehensive gene curation
8. Histone variants: dynamic punctuation in transcription. Weber CM and Henikoff S, Genes Dev. 2014 Apr 1;28(7):672-82. doi: 10.1101/gad.238873.114.
Additional References at PubMed
PMID:11331621   PMID:12477932   PMID:19135898   PMID:19734898   PMID:22871113   PMID:23376485   PMID:23533145   PMID:23595991   PMID:24071584  


Genomics

Comparative Map Data
Macroh2a2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr82030,220,975 - 30,270,652 (-)NCBIGRCr8
mRatBN7.22029,678,194 - 29,727,867 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2029,678,222 - 29,727,891 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx2030,689,165 - 30,738,841 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.02030,080,380 - 30,129,756 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.02030,822,865 - 30,872,538 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.02031,352,924 - 31,402,483 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2031,352,960 - 31,402,483 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02033,152,549 - 33,200,486 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42029,104,096 - 29,154,482 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera2031,104,770 - 31,153,499 (-)NCBICelera
Cytogenetic Map20q11NCBI
MACROH2A2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381070,052,846 - 70,112,282 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1070,052,544 - 70,112,282 (+)EnsemblGRCh38hg38GRCh38
GRCh371071,812,602 - 71,872,038 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361071,482,363 - 71,542,046 (+)NCBINCBI36Build 36hg18NCBI36
Build 341071,482,622 - 71,542,021NCBI
Celera1065,091,467 - 65,151,152 (+)NCBICelera
Cytogenetic Map10q22.1NCBI
HuRef1065,804,968 - 65,864,674 (+)NCBIHuRef
CHM1_11072,094,360 - 72,154,062 (+)NCBICHM1_1
T2T-CHM13v2.01070,921,840 - 70,981,283 (+)NCBIT2T-CHM13v2.0
Macroh2a2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391061,574,419 - 61,620,383 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1061,574,444 - 61,619,926 (-)EnsemblGRCm39 Ensembl
GRCm381061,738,640 - 61,784,604 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1061,738,665 - 61,784,147 (-)EnsemblGRCm38mm10GRCm38
MGSCv371061,201,395 - 61,246,612 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361061,134,004 - 61,179,221 (-)NCBIMGSCv36mm8
Celera1062,840,139 - 62,885,803 (-)NCBICelera
Cytogenetic Map10B4NCBI
cM Map1032.27NCBI
LOC102017503
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495543721,126,006 - 21,186,797 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495543721,126,581 - 21,186,308 (-)NCBIChiLan1.0ChiLan1.0
LOC100974647
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2882,205,793 - 82,265,391 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11082,211,107 - 82,270,712 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01066,526,013 - 66,585,568 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11069,077,456 - 69,114,194 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1069,077,456 - 69,114,194 (+)Ensemblpanpan1.1panPan2
MACROH2A2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1421,057,935 - 21,087,097 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl421,057,947 - 21,086,730 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha421,171,443 - 21,220,082 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0421,314,237 - 21,362,993 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl421,314,237 - 21,362,438 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1421,247,163 - 21,260,687 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0421,417,215 - 21,465,849 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0421,761,518 - 21,816,628 (+)NCBIUU_Cfam_GSD_1.0
LOC101956559
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440721359,983,038 - 60,036,383 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365218,473,794 - 8,509,268 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365218,474,408 - 8,509,269 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
MACROH2A2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1473,003,117 - 73,055,229 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11473,002,385 - 73,055,228 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
H2AFY2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1961,194,887 - 61,254,361 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl961,195,431 - 61,231,228 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604821,933,593 - 21,993,269 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
LOC101712013
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247544,227,644 - 4,279,077 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247544,227,897 - 4,276,595 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Macroh2a2
235 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:49
Count of miRNA genes:44
Interacting mature miRNAs:46
Transcripts:ENSRNOT00000033529
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
6893685Bw111Body weight QTL 1112.70.004body mass (VT:0001259)body weight (CMO:0000012)20132578807Rat
7411668Foco32Food consumption QTL 3280.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20136600972Rat
9590252Scort12Serum corticosterone level QTL 1220.460.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20136600972Rat
2305926Iddm37Insulin dependent diabetes mellitus QTL 376blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)20152784246527842Rat
1641915Colcr9Colorectal carcinoma resistance QTL 92.970.0024intestine integrity trait (VT:0010554)benign colorectal tumor number (CMO:0001795)20153065546530655Rat
1598816Memor12Memory QTL 122.4exploratory behavior trait (VT:0010471)average horizontal distance between subject and target during voluntary locomotion in an experimental apparatus (CMO:0002674)20260683647606836Rat
7411652Foco24Food consumption QTL 240.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)201175751554435887Rat
9590092Insglur9Insulin/glucose ratio QTL 918.380.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)201175751554435887Rat
4889610Pancm3Pancreatic morphology QTL 33.750.001pancreas mass (VT:0010144)pancreas wet weight (CMO:0000626)201761783247606836Rat
2317880Alcrsp25Alcohol response QTL 252.3response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)201769755054435887Rat
2303626Vencon10Ventilatory control QTL 100.001respiration trait (VT:0001943)respiration rate (CMO:0000289)201919072154435887Rat
2303578Gluco50Glucose level QTL 502blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)202510672254435887Rat
2303587Bw93Body weight QTL 9313body mass (VT:0001259)body weight (CMO:0000012)202510672254435887Rat
2300188Bmd68Bone mineral density QTL 686.40.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)202510672254435887Rat
1331747Hrtrt16Heart rate QTL 163.163heart pumping trait (VT:2000009)heart rate (CMO:0000002)202520973454435887Rat
1598869Memor6Memory QTL 63.1exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)202924438854435887Rat

Markers in Region
RH142880  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22029,729,002 - 29,729,180 (+)MAPPERmRatBN7.2
Rnor_6.02031,403,619 - 31,403,796NCBIRnor6.0
Rnor_5.02033,201,622 - 33,201,799UniSTSRnor5.0
RGSC_v3.42029,155,618 - 29,155,795UniSTSRGSC3.4
Celera2031,154,635 - 31,154,812UniSTS
Cytogenetic Map20q11UniSTS
AU048438  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22029,725,311 - 29,725,444 (+)MAPPERmRatBN7.2
Rnor_6.02031,399,928 - 31,400,060NCBIRnor6.0
Rnor_5.02033,197,581 - 33,198,063UniSTSRnor5.0
Rnor_5.02033,197,581 - 33,197,713UniSTSRnor5.0
RGSC_v3.42029,151,927 - 29,152,059UniSTSRGSC3.4
Celera2031,150,709 - 31,150,841UniSTS
Cytogenetic Map20q11UniSTS


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 24 16 6 2 6 68 22 33 2
Low 3 19 37 31 17 31 8 11 6 13 8 9 8
Below cutoff 4 4 4

Sequence


RefSeq Acc Id: ENSRNOT00000033529   ⟹   ENSRNOP00000031717
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2029,678,222 - 29,727,891 (-)Ensembl
Rnor_6.0 Ensembl2031,352,960 - 31,402,483 (-)Ensembl
RefSeq Acc Id: NM_001135807   ⟹   NP_001129279
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82030,220,975 - 30,270,652 (-)NCBI
mRatBN7.22029,678,194 - 29,727,867 (-)NCBI
Rnor_6.02031,352,924 - 31,402,483 (-)NCBI
Rnor_5.02033,152,549 - 33,200,486 (-)NCBI
RGSC_v3.42029,104,096 - 29,154,482 (-)RGD
Celera2031,104,770 - 31,153,499 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001129279 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAI61981 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000031717
  ENSRNOP00000031717.4
RefSeq Acc Id: NP_001129279   ⟸   NM_001135807
- UniProtKB: B1WC28 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000031717   ⟸   ENSRNOT00000033529
Protein Domains
Macro

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-B1WC28-F1-model_v2 AlphaFold B1WC28 1-372 view protein structure

Transcriptome

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

Promoters
RGD ID:13701608
Promoter ID:EPDNEW_R12132
Type:initiation region
Name:H2afy2_1
Description:H2A histone family, member Y2
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_6.02031,402,512 - 31,402,572EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1561371 AgrOrtholog
BioCyc Gene G2FUF-3713 BioCyc
Ensembl Genes ENSRNOG00000024751 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000033529 ENTREZGENE
  ENSRNOT00000033529.7 UniProtKB/TrEMBL
Gene3D-CATH 1.10.20.10 UniProtKB/TrEMBL
  3.40.220.10 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:9029999 IMAGE-MGC_LOAD
InterPro A1pp UniProtKB/TrEMBL
  Core_histone_macro-H2A UniProtKB/TrEMBL
  Histone-fold UniProtKB/TrEMBL
  Histone_core_D UniProtKB/TrEMBL
  Histone_H2A UniProtKB/TrEMBL
  Histone_H2A_C UniProtKB/TrEMBL
  Macro_dom-like UniProtKB/TrEMBL
  Macro_H2A UniProtKB/TrEMBL
KEGG Report rno:361844 UniProtKB/TrEMBL
MGC_CLONE MGC:187793 IMAGE-MGC_LOAD
NCBI Gene 361844 ENTREZGENE
PANTHER CORE HISTONE MACRO-H2A.2 UniProtKB/TrEMBL
  PTHR23430 UniProtKB/TrEMBL
Pfam Histone UniProtKB/TrEMBL
  Histone_H2A_C UniProtKB/TrEMBL
  Macro UniProtKB/TrEMBL
PhenoGen Macroh2a2 PhenoGen
PIRSF Core_histone_macro-H2A UniProtKB/TrEMBL
PRINTS HISTONEH2A UniProtKB/TrEMBL
PROSITE MACRO UniProtKB/TrEMBL
RatGTEx ENSRNOG00000024751 RatGTEx
SMART A1pp UniProtKB/TrEMBL
  H2A UniProtKB/TrEMBL
Superfamily-SCOP Histone-fold UniProtKB/TrEMBL
  SSF52949 UniProtKB/TrEMBL
UniProt B1WC28 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2019-08-20 Macroh2a2  macroH2A.2 histone  H2afy2  H2A histone family, member Y2  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-02-29 H2afy2  H2A histone family, member Y2  RGD1561371_predicted  similar to macroH2A2 (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-07 RGD1561371_predicted  similar to macroH2A2 (predicted)  LOC361844  similar to macroH2A2  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC361844  similar to macroH2A2      Symbol and Name status set to provisional 70820 PROVISIONAL