H2bc18 (H2B clustered histone 18) - Rat Genome Database

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Gene: H2bc18 (H2B clustered histone 18) Rattus norvegicus
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Symbol: H2bc18
Name: H2B clustered histone 18
RGD ID: 6487821
Description: Predicted to enable DNA binding activity and protein heterodimerization activity. Predicted to be a structural constituent of chromatin. Predicted to be involved in antimicrobial humoral immune response mediated by antimicrobial peptide and innate immune response in mucosa. Predicted to be located in cytosol; extracellular space; and nucleoplasm. Predicted to be part of nucleosome. Orthologous to human H2BC18 (H2B clustered histone 18); INTERACTS WITH (+)-catechin (ortholog); (-)-alpha-phellandrene (ortholog); 2,3,7,8-tetrachlorodibenzodioxine (ortholog).
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: Hist2h2bb; histone cluster 2, H2bb; histone H2B type 2-B-like; histone H2B type 2-F; histone H2B-3; LOC100912338; RGD1561543
RGD Orthologs
Human
Mouse
Bonobo
Pig
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr82186,527,197 - 186,531,634 (+)NCBIGRCr8
mRatBN7.22183,838,331 - 183,842,769 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2183,838,334 - 183,841,529 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.02198,418,625 - 198,419,131 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.02217,903,956 - 217,904,890 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42191,082,471 - 191,089,600 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera2176,365,871 - 176,366,377 (+)NCBICelera
Cytogenetic Map2q34NCBI
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

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. GOA pipeline RGD automated data pipeline
2. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:10524764   PMID:12477932   PMID:15632090  


Genomics

Comparative Map Data
H2bc18
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr82186,527,197 - 186,531,634 (+)NCBIGRCr8
mRatBN7.22183,838,331 - 183,842,769 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2183,838,334 - 183,841,529 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.02198,418,625 - 198,419,131 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.02217,903,956 - 217,904,890 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42191,082,471 - 191,089,600 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera2176,365,871 - 176,366,377 (+)NCBICelera
Cytogenetic Map2q34NCBI
H2BC18
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381149,782,689 - 149,812,370 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1149,782,689 - 149,812,373 (-)EnsemblGRCh38hg38GRCh38
GRCh371149,754,245 - 149,783,925 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361148,048,739 - 148,050,535 (-)NCBINCBI36Build 36hg18NCBI36
Cytogenetic Map1q21.2NCBI
HuRef1121,197,320 - 121,212,967 (+)NCBIHuRef
CHM1_11151,150,815 - 151,180,499 (-)NCBICHM1_1
T2T-CHM13v2.01148,906,835 - 148,936,505 (-)NCBIT2T-CHM13v2.0
H2bc18
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39396,177,016 - 96,177,508 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl396,177,068 - 96,177,448 (+)EnsemblGRCm39 Ensembl
GRCm38396,269,700 - 96,270,192 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl396,269,752 - 96,270,132 (+)EnsemblGRCm38mm10GRCm38
MGSCv37396,073,623 - 96,074,115 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36396,355,105 - 96,355,597 (+)NCBIMGSCv36mm8
Celera397,699,275 - 97,699,767 (+)NCBICelera
Cytogenetic Map3F2.1NCBI
cM Map341.71NCBI
LOC100984497
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21100,027,232 - 100,083,798 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1199,781,994 - 99,838,733 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01125,100,206 - 125,156,882 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11128,805,429 - 128,834,845 (-)NCBIpanpan1.1PanPan1.1panPan2
H2BC18
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl499,216,452 - 99,219,698 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1499,216,737 - 99,219,700 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1

Variants

.
Variants in H2bc18
34 total Variants

QTLs in Region (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1358356Srcrt1Stress Responsive Cort QTL13.66blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)2163997722225110681Rat
1578648Bss11Bone structure and strength QTL 114.7femur morphology trait (VT:0000559)femoral neck cortical cross-sectional area (CMO:0001702)2169358774214358774Rat
1331734Bp204Blood pressure QTL 2043.61192arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2170656145239614549Rat
631566Bp90Blood pressure QTL 900.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2149957381221199885Rat
1298074Bp164Blood pressure QTL 1640.003arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)244537979205135428Rat
1354648Bp239Blood pressure QTL 2390.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)267845370229470703Rat
1354649Kidm17Kidney mass QTL 172.9kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)283465462229820014Rat
1298076Bp166Blood pressure QTL 1660.0009arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2138595962205135428Rat
1581576Pur7Proteinuria QTL 70.0001urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)280396178220931218Rat
1581578Cm49Cardiac mass QTL 494.90.01heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)2145807215220931416Rat
631198Cm22Cardiac mass QTL 224.30.0008heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)278269809208420281Rat
1554319Bmd2Bone mineral density QTL 213.40.0001lumbar vertebra area (VT:0010570)lumbar vertebra cross-sectional area (CMO:0001689)2122597372215234002Rat
12879836Kidm61Kidney mass QTL 610.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)2154723085199723085Rat
1581569Uae32Urinary albumin excretion QTL 320.0001urine protein amount (VT:0005160)urine albumin excretion rate (CMO:0000757)280396178220931218Rat
10043136Iddm54Insulin dependent diabetes mellitus QTL 543.40.0001blood glucose amount (VT:0000188)age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)2145807215190807215Rat
12879837Am2Aortic mass QTL 20.001aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)2154723085199723085Rat
10043139Iddm55Insulin dependent diabetes mellitus QTL 553.10.0001blood glucose amount (VT:0000188)age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)2150313808195313808Rat
12879838Cm86Cardiac mass QTL 860.002heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)2154723085199723085Rat
1302793Bw16Body weight QTL 1650.0001body mass (VT:0001259)body weight (CMO:0000012)2159440891205135267Rat
12879839Cm85Cardiac mass QTL 850.001heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)2154723085199723085Rat
1549833Bp257Blood pressure QTL 2570.003arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2170652929215652929Rat
1358900Bw48Body weight QTL 484.88body mass (VT:0001259)body weight (CMO:0000012)2159440891220931218Rat
4889834Pur24Proteinuria QTL 245.80.014urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)2171994826205135428Rat
1359030Bp277Blood pressure QTL 277arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)2143565208188565208Rat
1331760Bp206Blood pressure QTL 2063.62454arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)24265106205135428Rat
12879840Bw179Body weight QTL 1790.005body mass (VT:0001259)body weight (CMO:0000012)2154723085199723085Rat
1581502Esta3Estrogen-induced thymic atrophy QTL 3thymus mass (VT:0004954)thymus wet weight (CMO:0000855)2139067258192287892Rat
9589044Scfw1Subcutaneous fat weight QTL 15.80.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)2184856304229856304Rat
8694435Bw166Body weight QTL 16614.080.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)2184856304229856304Rat
1359032Hrtrt18Heart rate QTL 18heart pumping trait (VT:2000009)heart rate (CMO:0000002)2159440760195313808Rat
2301966Bp322Blood pressure QTL 3223.58arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2144882354205135428Rat
1298080Bp163Blood pressure QTL 1630.02arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)267845182205135428Rat
1357991Ael2Aortic elastin QTL 24.20.000071aorta elastin amount (VT:0003905)aortic elastin2169227906214227906Rat
8662832Vetf7Vascular elastic tissue fragility QTL 73.5aorta elastin amount (VT:0003905)aorta wall extracellular elastin dry weight to aorta wall dry weight ratio (CMO:0002002)283400752223709938Rat
1298085Bp165Blood pressure QTL 1650.0006arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)244537979205135428Rat
8694194Abfw1Abdominal fat weight QTL 111.70.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)2184856304229856304Rat
1578671Bmd10Bone mineral density QTL 105.4femur mineral mass (VT:0010011)compact volumetric bone mineral density (CMO:0001730)2175931416220931416Rat
1641891Alcrsp17Alcohol response QTL 17response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)2151869660251712708Rat
724534Uae6Urinary albumin excretion QTL 610urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)280396034220931416Rat
61374Edpm2Estrogen-dependent pituitary mass QTL 24.420.86pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)278269809205135428Rat
2300189Bmd48Bone mineral density QTL 485.80.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)2182024327227024327Rat
8662843Vetf9Vascular elastic tissue fragility QTL 92.05thoracic aorta molecular composition trait (VT:0010568)aorta wall extracellular elastin dry weight to aorta wall extracellular collagen weight ratio (CMO:0002003)2159440760228950743Rat
2301408Kidm36Kidney mass QTL 360.002kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)2184482291229482291Rat
1331794Bp202Blood pressure QTL 2023.66819arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2143344967251712708Rat
71113Cari2Carrageenan-induced inflammation QTL 22.70.009hypodermis integrity trait (VT:0010550)inflammatory exudate volume (CMO:0001429)2143746578205135428Rat
1331805Cm29Cardiac mass QTL 293.50746heart mass (VT:0007028)heart wet weight (CMO:0000069)2143344967251712708Rat
634308Sach6Saccharin preference QTL 64.9taste sensitivity trait (VT:0001986)saccharin intake volume to total fluid intake volume ratio (CMO:0001601)2114384617215381366Rat
1598805Memor8Memory QTL 83exploratory behavior trait (VT:0010471)average horizontal distance between subject and target during voluntary locomotion in an experimental apparatus (CMO:0002674)2150096616195096616Rat
1358917Cm42Cardiac mass QTL 422.82heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)227148328206613235Rat
724568Uae13Urinary albumin excretion QTL 134.4urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)2145306936212705578Rat
1358913Cm41Cardiac mass QTL 412.73heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)227148328206613235Rat
1300165Rf9Renal function QTL 93.28kidney glomerulus integrity trait (VT:0010546)index of glomerular damage (CMO:0001135)2113746222205135428Rat
61401Niddm2Non-insulin dependent diabetes mellitus QTL 24.54blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)2147287892192287892Rat
631507Bp105Blood pressure QTL 1050.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2114384617215381366Rat
1641925Alcrsp2Alcohol response QTL 2response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)2151869660223841096Rat
1354609Niddm62Non-insulin dependent diabetes mellitus QTL 624.720.000006insulin secretion trait (VT:0003564)plasma insulin level (CMO:0000342)2117415288205135428Rat
1598833Bp295Blood pressure QTL 2953.5arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2150096616195096616Rat
61417Cia10Collagen induced arthritis QTL 103.4joint integrity trait (VT:0010548)experimental arthritis severity measurement (CMO:0001459)2182635347227635347Rat
1354622Kidm16Kidney mass QTL 163kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)283465462225110681Rat
631266Bp132Blood pressure QTL 1320.0005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)247856345205135428Rat
631522Bp74Blood pressure QTL 740.05arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2175008837220008837Rat
8694383Bw158Body weight QTL 1587.690.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)2184856304229856304Rat
7488927Bp365Blood pressure QTL 3650.008arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2165453811210453811Rat
7488925Bp364Blood pressure QTL 3640.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2163253030208253030Rat
2306901Bp337Blood pressure QTL 3370.01arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2166372086229820014Rat
1354605Rf48Renal function QTL 482.9blood creatinine amount (VT:0005328)plasma creatinine level (CMO:0000537)276328396209350714Rat


Expression

RNA-SEQ Expression


Sequence


Ensembl Acc Id: ENSRNOT00000095604   ⟹   ENSRNOP00000078702
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2183,838,334 - 183,841,529 (+)Ensembl
RefSeq Acc Id: NM_001416314   ⟹   NP_001403243
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82186,527,197 - 186,531,634 (+)NCBI
mRatBN7.22183,838,331 - 183,842,769 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001403243 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAC98918 (Get FASTA)   NCBI Sequence Viewer  
  EDL85634 (Get FASTA)   NCBI Sequence Viewer  
  EDL85635 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000078702.1
  ENSRNOP00000092229.1
Ensembl Acc Id: ENSRNOP00000078702   ⟸   ENSRNOT00000095604
RefSeq Acc Id: NP_001403243   ⟸   NM_001416314
- UniProtKB: A0A8I6AGQ8 (UniProtKB/TrEMBL),   A0A8I5ZLH6 (UniProtKB/TrEMBL),   A6K366 (UniProtKB/TrEMBL)
Protein Domains
Histone H2A/H2B/H3

Transcriptome

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


Additional Information

Database Acc Id Source(s)
BioCyc Gene G2FUF-52040 BioCyc
Ensembl Genes ENSRNOG00000070591 Ensembl, UniProtKB/TrEMBL
  ENSRNOG00000070916 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000095604.1 UniProtKB/TrEMBL
  ENSRNOT00000097860.1 UniProtKB/TrEMBL
Gene3D-CATH 1.10.20.10 UniProtKB/TrEMBL
InterPro Histone-fold UniProtKB/TrEMBL
  Histone_H2A/H2B/H3 UniProtKB/TrEMBL
  Histone_H2B UniProtKB/TrEMBL
  HISTONE_H2B_site UniProtKB/TrEMBL
NCBI Gene LOC100912338 ENTREZGENE
PANTHER PTHR23428 UniProtKB/TrEMBL
Pfam Histone UniProtKB/TrEMBL
PhenoGen H2bc18 PhenoGen
PRINTS HISTONEH2B UniProtKB/TrEMBL
PROSITE HISTONE_H2B UniProtKB/TrEMBL
RatGTEx ENSRNOG00000070591 RatGTEx
  ENSRNOG00000070916 RatGTEx
SMART H2B UniProtKB/TrEMBL
Superfamily-SCOP SSF47113 UniProtKB/TrEMBL
UniProt A0A8I5ZLH6 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I6AGQ8 ENTREZGENE, UniProtKB/TrEMBL
  A6K366 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2023-01-26 H2bc18  H2B clustered histone 18  Hist2h2bb  histone cluster 2, H2bb  Data merged from RGD:1561543 737654 PROVISIONAL
2022-12-09 H2bc18  H2B clustered histone 18  LOC100912338  histone H2B type 2-B-like  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2012-07-05 LOC100912338  histone H2B type 2-B-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2008-02-29 Hist2h2bb  histone cluster 2, H2bb  RGD1561543_predicted  similar to histone H2b-616 (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-07 RGD1561543_predicted  similar to histone H2b-616 (predicted)  LOC295278  similar to histone H2b-616  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC295278  similar to histone H2b-616      Symbol and Name status set to provisional 70820 PROVISIONAL