H2bc6 (H2B clustered histone 6) - Rat Genome Database

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Gene: H2bc6 (H2B clustered histone 6) Rattus norvegicus
Analyze
Symbol: H2bc6 (Ensembl: Hist2h2be)
Name: H2B clustered histone 6 (Ensembl:histone cluster 2 H2B family member E)
RGD ID: 2320230
Description: Predicted to enable identical protein binding activity and lipopolysaccharide binding activity. Predicted to be involved in antimicrobial humoral immune response mediated by antimicrobial peptide; innate immune response in mucosa; and negative regulation of tumor necrosis factor-mediated signaling pathway. Predicted to be located in extracellular space; nucleus; and plasma membrane. Predicted to be part of CENP-A containing nucleosome. Orthologous to human H2BC6 (H2B clustered histone 6); INTERACTS WITH (-)-demecolcine (ortholog); 17beta-estradiol (ortholog); 2,3,7,8-tetrachlorodibenzodioxine (ortholog).
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: histone cluster 1, H2bd-like; histone H2B type 1; histone H2B type 1-C/E/F/G/I; histone H2B type 1-N; LOC100364835
RGD Orthologs
Human
Mouse
Dog
Pig
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81741,948,813 - 41,949,276 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1747,392,229 - 47,449,312 (-)EnsemblGRCr8
mRatBN7.21741,520,775 - 41,521,238 (+)NCBImRatBN7.2mRatBN7.2
Rnor_6.01743,764,654 - 43,765,101 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1744,737,950 - 44,738,330 (-)Ensemblrn6Rnor6.0
Rnor_6.0 Ensembl1743,679,925 - 43,689,311 (-)Ensemblrn6Rnor6.0
Celera1741,151,671 - 41,152,146 (+)NCBICelera
Cytogenetic Map17p11NCBI
JBrowse:




Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
chromosome  (IEA)
extracellular exosome  (ISO)
extracellular space  (IBA,ISO)
nucleosome  (IBA,IEA)
nucleus  (IBA,IEA)

Molecular Function

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. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:12860195  


Genomics

Comparative Map Data
H2bc6
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81741,948,813 - 41,949,276 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1747,392,229 - 47,449,312 (-)EnsemblGRCr8
mRatBN7.21741,520,775 - 41,521,238 (+)NCBImRatBN7.2mRatBN7.2
Rnor_6.01743,764,654 - 43,765,101 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1744,737,950 - 44,738,330 (-)Ensemblrn6Rnor6.0
Rnor_6.0 Ensembl1743,679,925 - 43,689,311 (-)Ensemblrn6Rnor6.0
Celera1741,151,671 - 41,152,146 (+)NCBICelera
Cytogenetic Map17p11NCBI
H2BC6
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38626,183,761 - 26,184,230 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl626,172,059 - 26,184,655 (+)Ensemblhg38GRCh38
GRCh37626,183,989 - 26,184,458 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36626,292,003 - 26,292,437 (+)NCBIBuild 36Build 36hg18NCBI36
Build 34626,292,002 - 26,292,437NCBI
Celera627,413,325 - 27,413,759 (+)NCBICelera
Cytogenetic Map6p22.2NCBI
HuRef626,127,029 - 26,127,463 (+)NCBIHuRef
CHM1_1626,186,226 - 26,186,660 (+)NCBICHM1_1
T2T-CHM13v2.0626,051,896 - 26,052,365 (+)NCBIT2T-CHM13v2.0
H2bc6
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391323,767,653 - 23,805,091 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1323,767,653 - 23,805,107 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm381323,583,670 - 23,621,124 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1323,583,670 - 23,621,124 (-)Ensemblmm10GRCm38
MGSCv371323,675,539 - 23,712,993 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv361323,591,206 - 23,628,589 (-)NCBIMGSCv36mm8
Celera1323,815,585 - 23,852,605 (-)NCBICelera
Cytogenetic Map13A3.1NCBI
cM Map139.81NCBI
H2BC6
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13524,115,034 - 24,115,551 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3525,006,510 - 25,006,890 (+)EnsemblcanFam3CanFam3.1
CanFam3.1 Ensembl3524,131,296 - 24,131,676 (-)EnsemblcanFam3CanFam3.1
CanFam3.1 Ensembl3525,061,555 - 25,061,935 (+)EnsemblcanFam3CanFam3.1
CanFam3.1 Ensembl3524,178,933 - 24,179,313 (+)EnsemblcanFam3CanFam3.1
CanFam3.1 Ensembl3524,066,399 - 24,066,779 (-)EnsemblcanFam3CanFam3.1
CanFam3.1 Ensembl3524,999,692 - 25,000,072 (-)EnsemblcanFam3CanFam3.1
H2BC2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1720,467,395 - 20,471,314 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2721,770,167 - 21,770,838 (-)NCBISscrofa10.2Sscrofa10.2susScr3

Variants

.
Variants in H2bc6
3 total Variants

QTLs in Region (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
8552966Pigfal18Plasma insulin-like growth factor 1 level QTL 188.7blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)171286094257860942Rat
1300123Bp194Blood pressure QTL 1942.82arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)17212084342054133Rat
2302377Scl61Serum cholesterol level QTL 614.36blood HDL cholesterol amount (VT:0000184)serum high density lipoprotein cholesterol level (CMO:0000361)17622199858177198Rat
1354654Spl7Serum phospholipid level QTL 75.5blood phospholipid amount (VT:0006084)blood phospholipid level (CMO:0001169)173803135483031354Rat
70157Niddm32Non-insulin dependent diabetes mellitus QTL 324.34blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)172266079955604694Rat
9589151Insul30Insulin level QTL 308.820.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)171286094257860942Rat
1598871Memor5Memory QTL 55.3exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)174096801789341781Rat
1354628Stl13Serum triglyceride level QTL 133.8blood triglyceride amount (VT:0002644)blood triglyceride level (CMO:0000118)172149899450592236Rat
1354629Scl31Serum cholesterol level QTL 314.1blood cholesterol amount (VT:0000180)blood total cholesterol level (CMO:0000051)173803135483031354Rat
1600398Edcs5Endometrial carcinoma susceptibility QTL 52.2uterus morphology trait (VT:0001120)percentage of study population developing endometrioid carcinoma during a period of time (CMO:0001759)173544694975762341Rat
9590154Scort9Serum corticosterone level QTL 923.570.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)171286094257860942Rat
1559055Bp278Blood pressure QTL 2780.04arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)172385892668858926Rat
152025238Slep14Serum leptin concentration QTL 144.62blood leptin amount (VT:0005667)172439059584432719Rat
1354638Insul1Insulin level QTL 14.8blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)173803135483031354Rat
1354635Bp245Blood pressure QTL 2456arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)173803135483031354Rat
1331765Hrtrt15Heart rate QTL 154.094heart pumping trait (VT:2000009)heart rate (CMO:0000002)171553702560531414Rat
7411666Foco31Food consumption QTL 3111.40.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)171286094257860942Rat
2303627Vencon8Ventilatory control QTL 80.001respiration trait (VT:0001943)tidal volume (CMO:0000222)17473353449733534Rat
4889955Bss93Bone structure and strength QTL 934.4tibia size trait (VT:0100001)tibia cortical bone volume to tibia total bone volume ratio (CMO:0001727)172723344565155015Rat
1354662Rf49Renal function QTL 492.9blood creatinine amount (VT:0005328)plasma creatinine level (CMO:0000537)17143999106Rat
1300129Rf25Renal function QTL 253.03blood creatinine amount (VT:0005328)creatinine clearance (CMO:0000765)174106235286062352Rat
152023740Bp406Blood pressure QTL 4066.06arterial blood pressure trait (VT:2000000)172413612784432719Rat
1354663Bvd5Brain ventricular dilatation QTL 53.510.001brain ventricle morphology trait (VT:0000822)hydrocephalus severity score (CMO:0001881)173219953486201342Rat
7488966Bp370Blood pressure QTL 3700.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)172385892668858926Rat
1354658Spl8Serum phospholipid level QTL 83.8blood VLDL phospholipid amount (VT:0010507)blood very low density lipoprotein phospholipid level (CMO:0001571)17143999106Rat
152023737Bp405Blood pressure QTL 4055.06arterial blood pressure trait (VT:2000000)2413612784432719Rat
152023736Bp404Blood pressure QTL 4043.78arterial blood pressure trait (VT:2000000)172413612784432719Rat
724528Uae4Urinary albumin excretion QTL 44.90.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)173604553781045537Rat
1354581Bp247Blood pressure QTL 2474.5arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)17143999106Rat
70210Cm15Cardiac mass QTL 156.5heart right ventricle mass (VT:0007033)heart right ventricle wet weight (CMO:0000072)173006647275066472Rat
152023626Bp403Blood pressure QTL 4033.86arterial blood pressure trait (VT:2000000)172413612784432719Rat
9590107Sffal7Serum free fatty acids level QTL 74.810.001blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)173310464578104645Rat
724549Niddm56Non-insulin dependent diabetes mellitus QTL 560.03blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)173219953449497050Rat
1581512Cm55Cardiac mass QTL 552.80.05heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)172723344583975845Rat
10054088Scort28Serum corticosterone level QTL 282.040.0102blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)17473353449733534Rat
61394Bp8Blood pressure QTL 82.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)172328632264246472Rat
9589057Scfw6Subcutaneous fat weight QTL 68.620.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)171286094257860942Rat
2317045Aia11Adjuvant induced arthritis QTL 114.06joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)172652205171522051Rat
10450503Bp386Blood pressure QTL 3860.28arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)172201970567019705Rat
9590088Insglur7Insulin/glucose ratio QTL 720.380.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)171286094257860942Rat
2313854Bp343Blood pressure QTL 3433.9life span trait (VT:0005372)age at time of death (CMO:0001193)173219953455604694Rat
2317053Aia25Adjuvant induced arthritis QTL 252.69joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)171060469455604694Rat
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)173310464578104645Rat
12903980Cm120Cardiac mass QTL 1200.002heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)172385892668858926Rat
12903981Am17Aortic mass QTL 170.001aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)172385892668858926Rat
4889891Eae32Experimental allergic encephalomyelitis QTL 324.80.0002nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis severity score (CMO:0001419)172723344572233445Rat
12903982Kidm70Kidney mass QTL 700.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)172385892668858926Rat
12903978Cm118Cardiac mass QTL 1180.001heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)172385892668858926Rat
12903979Cm119Cardiac mass QTL 1190.001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)172385892668858926Rat
1354619Bp242Blood pressure QTL 2426.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)173768787782687877Rat

Markers in Region
UniSTS:490542  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21742,752,517 - 42,752,898 (+)MAPPERmRatBN7.2
Rnor_6.01743,817,378 - 43,817,745NCBIRnor6.0
Rnor_6.01744,793,456 - 44,793,836NCBIRnor6.0
Rnor_5.01758,672,745 - 58,673,125UniSTSRnor5.0
Cytogenetic Map17q11UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
hemolymphoid system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
sensory system
visual system
7 1 15 39 54 111 75 7 42 29 30 10 10

Sequence


RefSeq Acc Id: NM_001409097   ⟹   NP_001396026
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81741,948,813 - 41,949,276 (+)NCBI
mRatBN7.21741,520,775 - 41,521,238 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001396026 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000084910.2
  ENSRNOP00000099611.1
RefSeq Acc Id: NP_001396026   ⟸   NM_001409097
- UniProtKB: G3V8B3 (UniProtKB/TrEMBL),   A6KLP6 (UniProtKB/TrEMBL),   G3V9C7 (UniProtKB/TrEMBL),   A0A8I6AGQ8 (UniProtKB/TrEMBL),   A6KNB9 (UniProtKB/TrEMBL)
Protein Domains
Histone H2A/H2B/H3

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-G3V8B3-F1-model_v2 AlphaFold G3V8B3 1-126 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:2320230 AgrOrtholog
BioCyc Gene G2FUF-9372 BioCyc
Ensembl Genes ENSRNOG00000021198 Ensembl
  ENSRNOG00000059382 Ensembl
  ENSRNOG00000070916 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000049785.7 UniProtKB/TrEMBL
  ENSRNOT00000122723.1 UniProtKB/TrEMBL
Gene3D-CATH Histone, subunit A UniProtKB/TrEMBL
InterPro Histone-fold UniProtKB/TrEMBL
  Histone_H2A/H2B/H3 UniProtKB/TrEMBL
  Histone_H2B UniProtKB/TrEMBL
  HISTONE_H2B_site UniProtKB/TrEMBL
NCBI Gene 100364835 ENTREZGENE
PANTHER HISTONE H2B UniProtKB/TrEMBL
Pfam Histone UniProtKB/TrEMBL
PhenoGen H2bc6 PhenoGen
PRINTS HISTONEH2B UniProtKB/TrEMBL
PROSITE HISTONE_H2B UniProtKB/TrEMBL
RatGTEx ENSRNOG00000021198 RatGTEx
  ENSRNOG00000059382 RatGTEx
  ENSRNOG00000070916 RatGTEx
SMART H2B UniProtKB/TrEMBL
Superfamily-SCOP Histone-fold UniProtKB/TrEMBL
UniProt A0A8I6A2W1_RAT UniProtKB/TrEMBL
  A0A8I6AGQ8 ENTREZGENE
  A0ABK0LER6_RAT UniProtKB/TrEMBL
  A6KLP6 ENTREZGENE
  A6KNB9 ENTREZGENE, UniProtKB/TrEMBL
  G3V8B3 ENTREZGENE
  G3V9C7 ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2022-12-06 H2bc6  H2B clustered histone 6  LOC100364835  histone cluster 1, H2bd-like  Name and Symbol changed 629549 APPROVED
2010-05-05 LOC100364835  histone cluster 1, H2bd-like      Symbol and Name status set to provisional 70820 PROVISIONAL