H2al3 (H2A.L variant histone 3) - Rat Genome Database

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Gene: H2al3 (H2A.L variant histone 3) Rattus norvegicus
Analyze
Symbol: H2al3 (Ensembl: LOC100363125)
Name: H2A.L variant histone 3 (Ensembl:rCG42854-like)
RGD ID: 2324764
Description: Predicted to enable nucleosomal DNA binding activity. Predicted to be involved in heterochromatin organization. Predicted to be part of nucleosome. Predicted to be active in nucleus. Orthologous to human H2AL3 (H2A.L variant histone 3); INTERACTS WITH rotenone (ortholog); triptonide (ortholog).
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: histone H2A-Bbd type 1; LOC100363125; rCG42854-like; uncharacterized protein LOC100363125
RGD Orthologs
Human
Mouse
Bonobo
Dog
Pig
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X15,577,826 - 15,578,405 (-)NCBIGRCr8
mRatBN7.2X12,905,312 - 12,905,891 (-)NCBImRatBN7.2mRatBN7.2
Rnor_6.0X13,991,860 - 13,992,606 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX13,992,064 - 13,992,429 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X14,774,446 - 14,775,119 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X25,061,576 - 25,062,149 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
CeleraX13,514,557 - 13,515,302 (-)NCBICelera
Cytogenetic MapXq12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
rotenone  (ISO)
triptonide  (ISO)

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.
Additional References at PubMed
PMID:17261847  


Genomics

Comparative Map Data
H2al3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X15,577,826 - 15,578,405 (-)NCBIGRCr8
mRatBN7.2X12,905,312 - 12,905,891 (-)NCBImRatBN7.2mRatBN7.2
Rnor_6.0X13,991,860 - 13,992,606 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX13,992,064 - 13,992,429 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X14,774,446 - 14,775,119 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X25,061,576 - 25,062,149 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
CeleraX13,514,557 - 13,515,302 (-)NCBICelera
Cytogenetic MapXq12NCBI
H2AL3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38X37,994,272 - 37,994,904 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 EnsemblX37,994,272 - 37,994,904 (+)EnsemblGRCh38hg38GRCh38
GRCh37X37,853,525 - 37,854,157 (+)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic MapXp11.4NCBI
T2T-CHM13v2.0X37,397,862 - 37,398,494 (+)NCBIT2T-CHM13v2.0
H2al3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X9,715,942 - 9,716,491 (+)NCBIGRCm39GRCm39mm39
GRCm39 EnsemblX9,715,942 - 9,716,494 (+)EnsemblGRCm39 Ensembl
GRCm38X9,849,703 - 9,850,252 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX9,849,703 - 9,850,255 (+)EnsemblGRCm38mm10GRCm38
MGSCv37X9,426,835 - 9,427,382 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36X9,426,829 - 9,427,380 (+)NCBIMGSCv36mm8
CeleraX7,563,893 - 7,564,440 (+)NCBICelera
Cytogenetic MapXA1.1NCBI
cM MapX4.62NCBI
LOC129395263
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2X39,642,285 - 39,643,030 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1X39,645,661 - 39,646,363 (+)NCBINHGRI_mPanPan1
H2AL3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X32,755,269 - 32,755,889 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_TashaX20,103,993 - 20,104,609 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0X32,801,756 - 32,802,373 (+)NCBIROS_Cfam_1.0
UMICH_Zoey_3.1X32,883,345 - 32,883,961 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0X32,854,867 - 32,855,484 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0X32,895,064 - 32,895,680 (+)NCBIUU_Cfam_GSD_1.0
H2AL1Q
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1X32,692,523 - 32,693,072 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X36,255,237 - 36,255,837 (+)NCBISscrofa10.2Sscrofa10.2susScr3

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:34
Count of miRNA genes:34
Interacting mature miRNAs:34
Transcripts:ENSRNOT00000036543
Prediction methods:Miranda, Pita, 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
731181Uae27Urinary albumin excretion QTL 272.70.0059urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)X143491017Rat
634325Bw13Body weight QTL 130body mass (VT:0001259)body weight (CMO:0000012)X144797220991088Rat
70165Bp64Blood pressure QTL 645.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)X144812931706553Rat
631204Gluco15Glucose level QTL 150.001blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)X162371522646544Rat
1298071Edpm12Estrogen-dependent pituitary mass QTL 123.2pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)X292789847927898Rat
10755455Coatc13Coat color QTL 130coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)7440600049406000Rat
631666Iddm5Insulin dependent diabetes mellitus QTL 5blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)X449454949494549Rat

Markers in Region
BF404274  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X12,905,381 - 12,905,610 (-)MAPPERmRatBN7.2
Rnor_6.0X13,992,307 - 13,992,535NCBIRnor6.0
Rnor_5.0X14,774,821 - 14,775,049UniSTSRnor5.0
RGSC_v3.4X25,061,646 - 25,061,874UniSTSRGSC3.4
CeleraX13,514,628 - 13,514,856UniSTS
RH 3.4 MapX115.0UniSTS


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 1
Medium 6
Low 1 2 1 2 2 5 1 1 5 2
Below cutoff 1 17 5 7 5 4 5 8 9 2 3 4

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000036543   ⟹   ENSRNOP00000032267
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX13,992,064 - 13,992,429 (+)Ensembl
RefSeq Acc Id: NM_001408920   ⟹   NP_001395849
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X15,577,826 - 15,578,405 (-)NCBI
mRatBN7.2X12,905,312 - 12,905,891 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001395849 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL97610 (Get FASTA)   NCBI Sequence Viewer  
Reference Protein Sequences
RefSeq Acc Id: ENSRNOP00000032267   ⟸   ENSRNOT00000036543
RefSeq Acc Id: NP_001395849   ⟸   NM_001408920
- UniProtKB: A6K025 (UniProtKB/TrEMBL)
Protein Domains
Transcription factor CBF/NF-Y/archaeal histone

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZXS7-F1-model_v2 AlphaFold D3ZXS7 1-122 view protein structure

Transcriptome

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

Promoters
RGD ID:13701722
Promoter ID:EPDNEW_R12243
Type:single initiation site
Name:LOC100363125_1
Description:rCG42854-like
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_6.0X13,992,014 - 13,992,074EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:2324764 AgrOrtholog
BioCyc Gene G2FUF-3024 BioCyc
Ensembl Genes ENSRNOG00000021470 Ensembl
Gene3D-CATH Histone, subunit A UniProtKB/TrEMBL
InterPro CBFA_NFYB_domain UniProtKB/TrEMBL
  Histone-fold UniProtKB/TrEMBL
  Histone_H2A UniProtKB/TrEMBL
NCBI Gene 100363125 ENTREZGENE
PANTHER HISTONE H2A UniProtKB/TrEMBL
  HISTONE H2A UniProtKB/TrEMBL
Pfam CBFD_NFYB_HMF UniProtKB/TrEMBL
PhenoGen H2al3 PhenoGen
PRINTS HISTONEH2A UniProtKB/TrEMBL
RatGTEx ENSRNOG00000021470 RatGTEx
SMART H2A UniProtKB/TrEMBL
Superfamily-SCOP Histone-fold UniProtKB/TrEMBL
UniProt A6K025 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2021-11-09 H2al3  H2A.L variant histone 3  LOC100363125  rCG42854-like  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2010-05-12 LOC100363125  rCG42854-like      Symbol and Name status set to provisional 70820 PROVISIONAL