H3f3b (H3.3 histone B) - Rat Genome Database

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Gene: H3f3b (H3.3 histone B) Rattus norvegicus
Analyze
Symbol: H3f3b (Ensembl: H3f3a)
Name: H3.3 histone B (Ensembl:H3.3 histone A)
RGD ID: 621095
Description: Predicted to enable RNA polymerase II cis-regulatory region sequence-specific DNA binding activity; RNA polymerase II core promoter sequence-specific DNA binding activity; and nucleosomal DNA binding activity. Predicted to be a structural constituent of chromatin. Involved in response to hormone. Predicted to be located in chromosome, telomeric region and nucleoplasm. Predicted to be part of nucleosome. Predicted to be active in nucleus. Orthologous to human H3-3B (H3.3 histone B); PARTICIPATES IN histone modification pathway; systemic lupus erythematosus pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,6-dinitrotoluene; 4-tert-Octylphenol.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: H3 histone family member 3B; H3 histone, family 3B; H3-3b; H3.3B; histone H3.3; MGC105794
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr810101,755,404 - 101,764,616 (-)NCBIGRCr8
mRatBN7.210101,256,484 - 101,258,716 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl10101,256,480 - 101,258,709 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx10106,317,943 - 106,320,175 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.010105,781,026 - 105,783,258 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.010101,177,427 - 101,179,659 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.010104,573,666 - 104,575,890 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl10104,573,664 - 104,575,890 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.010103,709,482 - 103,711,706 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.410106,130,320 - 106,132,544 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.110106,144,823 - 106,147,045 (-)NCBI
Celera1099,830,619 - 99,832,836 (-)NCBICelera
Cytogenetic Map10q32.1NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,2-dichloroethane  (ISO)
1,2-dimethylhydrazine  (ISO)
17alpha-ethynylestradiol  (ISO)
17beta-estradiol  (ISO)
2,3',4,4',5-Pentachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4-diaminotoluene  (ISO)
2,6-dinitrotoluene  (EXP)
2-methylcholine  (ISO)
3-methylcholanthrene  (ISO)
4-tert-Octylphenol  (EXP)
5-methoxy-2-\{[(4-methoxy-3,5-dimethylpyridin-2-yl)methyl]sulfinyl\}-1H-benzimidazole  (EXP)
6-propyl-2-thiouracil  (EXP)
acrolein  (ISO)
acrylamide  (EXP)
aflatoxin B1  (EXP)
all-trans-retinoic acid  (ISO)
alpha-pinene  (ISO)
amiodarone  (EXP)
ammonium chloride  (EXP)
amphetamine  (EXP)
antirheumatic drug  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
atrazine  (EXP)
benzbromarone  (EXP)
benzene  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
bis(2-chloroethyl) sulfide  (ISO)
bisphenol A  (ISO)
cadmium atom  (ISO)
cadmium dichloride  (ISO)
carbamazepine  (ISO)
CGP 52608  (ISO)
chlorpyrifos  (EXP,ISO)
chromium(6+)  (ISO)
ciguatoxin CTX1B  (ISO)
cisplatin  (ISO)
clofibrate  (EXP,ISO)
copper(II) sulfate  (ISO)
coumestrol  (ISO)
DDE  (ISO)
Dibutyl phosphate  (ISO)
dibutyl phthalate  (EXP,ISO)
dicrotophos  (ISO)
diethylstilbestrol  (EXP)
diuron  (EXP)
dorsomorphin  (ISO)
doxorubicin  (ISO)
Enterolactone  (ISO)
ethanol  (ISO)
flutamide  (EXP)
folic acid  (ISO)
formaldehyde  (ISO)
fumonisin B1  (ISO)
gentamycin  (EXP)
L-ethionine  (EXP)
lead diacetate  (ISO)
Mesaconitine  (EXP)
methotrexate  (ISO)
nefazodone  (EXP)
omeprazole  (EXP)
ozone  (ISO)
p-tert-Amylphenol  (EXP)
paracetamol  (EXP,ISO)
perfluorooctane-1-sulfonic acid  (ISO)
perfluorooctanoic acid  (EXP)
PhIP  (EXP)
pinosylvin  (ISO)
pirinixic acid  (EXP,ISO)
pregnenolone 16alpha-carbonitrile  (ISO)
resveratrol  (EXP,ISO)
SB 431542  (ISO)
silicon dioxide  (ISO)
Soman  (EXP)
succimer  (ISO)
tamoxifen  (ISO)
tetrachloromethane  (EXP,ISO)
thioacetamide  (EXP)
titanium dioxide  (ISO)
trans-pinosylvin  (ISO)
trichostatin A  (ISO)
triphenyl phosphate  (ISO)
valproic acid  (ISO)
zinc atom  (ISO)
zinc(0)  (ISO)

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. H1(0) and H3.3B mRNA levels in developing rat brain. Castiglia D, etal., Neurochem Res 1994 Dec;19(12):1531-7.
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. Every amino acid matters: essential contributions of histone variants to mammalian development and disease. Maze I, etal., Nat Rev Genet. 2014 Apr;15(4):259-71. doi: 10.1038/nrg3673. Epub 2014 Mar 11.
4. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
5. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
6. GOA pipeline RGD automated data pipeline
7. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
8. Comprehensive gene review and curation RGD comprehensive gene curation
9. Posttranscriptional regulation of H1 zero and H3.3B histone genes in differentiating rat cortical neurons. Scaturro M, etal., Neurochem Res. 1995 Aug;20(8):969-76.
10. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
Additional References at PubMed
PMID:7534202   PMID:9582357   PMID:12560483   PMID:14718166   PMID:15273246   PMID:15489334   PMID:15607978   PMID:15746254   PMID:19135898   PMID:19633671   PMID:20094059   PMID:20110566  
PMID:20458337   PMID:20513656   PMID:21274551   PMID:21630459   PMID:21636898   PMID:22371606   PMID:22705305   PMID:22871113   PMID:23570311   PMID:23903189   PMID:24747049   PMID:25615412  
PMID:25675407   PMID:26159997   PMID:26388943   PMID:35352799  


Genomics

Comparative Map Data
H3f3b
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr810101,755,404 - 101,764,616 (-)NCBIGRCr8
mRatBN7.210101,256,484 - 101,258,716 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl10101,256,480 - 101,258,709 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx10106,317,943 - 106,320,175 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.010105,781,026 - 105,783,258 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.010101,177,427 - 101,179,659 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.010104,573,666 - 104,575,890 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl10104,573,664 - 104,575,890 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.010103,709,482 - 103,711,706 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.410106,130,320 - 106,132,544 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.110106,144,823 - 106,147,045 (-)NCBI
Celera1099,830,619 - 99,832,836 (-)NCBICelera
Cytogenetic Map10q32.1NCBI
H3-3B
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381775,776,434 - 75,779,779 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1775,776,434 - 75,785,893 (-)EnsemblGRCh38hg38GRCh38
GRCh371773,772,515 - 73,775,860 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361771,284,110 - 71,287,455 (-)NCBINCBI36Build 36hg18NCBI36
Build 341771,284,111 - 71,287,455NCBI
Celera1770,362,565 - 70,365,910 (-)NCBICelera
Cytogenetic Map17q25.1NCBI
HuRef1769,198,034 - 69,201,379 (-)NCBIHuRef
CHM1_11773,837,589 - 73,840,931 (-)NCBICHM1_1
T2T-CHM13v2.01776,669,660 - 76,678,707 (-)NCBIT2T-CHM13v2.0
H3f3b
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3911115,912,787 - 115,921,313 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl11115,912,738 - 115,918,788 (-)EnsemblGRCm39 Ensembl
GRCm3811116,021,961 - 116,026,039 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl11116,021,912 - 116,027,962 (-)EnsemblGRCm38mm10GRCm38
MGSCv3711115,883,275 - 115,885,818 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv3611115,837,018 - 115,840,587 (-)NCBIMGSCv36mm8
Celera11127,784,227 - 127,786,770 (-)NCBICelera
Cytogenetic Map11E2NCBI
cM Map1180.91NCBI
H3f3b
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555066,474,727 - 6,482,244 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049555066,475,336 - 6,478,781 (+)NCBIChiLan1.0ChiLan1.0
LOC100988671
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21991,821,558 - 91,824,038 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11796,646,832 - 96,648,754 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01769,728,165 - 69,730,519 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11775,277,614 - 75,281,106 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1775,277,614 - 75,281,106 (-)Ensemblpanpan1.1panPan2
LOC101963257
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_0244056025,450,377 - 5,452,805 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936594958,049 - 961,708 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_004936594959,493 - 961,703 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
H3-3B
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl125,632,365 - 5,634,726 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1125,632,326 - 5,634,977 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2125,578,702 - 5,581,109 (+)NCBISscrofa10.2Sscrofa10.2susScr3
LOC103243033
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11645,903,252 - 45,905,605 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1645,902,980 - 45,904,929 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366607716,660,280 - 16,662,641 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
LOC101698172
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248015,668,661 - 5,672,164 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in H3f3b
5 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:219
Count of miRNA genes:123
Interacting mature miRNAs:165
Transcripts:ENSRNOT00000050223
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
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
2303118Mamtr7Mammary tumor resistance QTL 70.003mammary gland integrity trait (VT:0010552)mammary tumor growth rate (CMO:0000344)109658275104670812Rat
631268Cia21Collagen induced arthritis QTL 213.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1014487011104060283Rat
2316949Gluco60Glucose level QTL 603.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1014487011107057807Rat
61354Pia10Pristane induced arthritis QTL 100.01joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023444813104060283Rat
631267Cia20Collagen induced arthritis QTL 203.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023444813104060283Rat
61325Aia5Adjuvant induced arthritis QTL 50.01joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023444813104060283Rat
1331791Cm31Cardiac mass QTL 313.84606heart mass (VT:0007028)heart wet weight (CMO:0000069)1029299504107211142Rat
1576308Schws1Schwannoma susceptibility QTL 10.0041nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)1040035094102359817Rat
631269Cia22Collagen induced arthritis QTL 228.9joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1040035094104060283Rat
631270Cia23Collagen induced arthritis QTL 233.9joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1040035094104060283Rat
1298078Stresp5Stress response QTL 52.990.00025blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)1042045676104670812Rat
61387Bp1Blood pressure QTL 15.1arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1051770177107211142Rat
61387Bp1Blood pressure QTL 15.1arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)1051770177107211142Rat
70171Cari1Carrageenan-induced inflammation QTL 14.90.0005hypodermis integrity trait (VT:0010550)inflammatory exudate volume (CMO:0001429)1053797385107211142Rat
2312662Slep8Serum leptin concentration QTL 80.05blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)1057134272102134272Rat
2312668Scl65Serum cholesterol level QTL 650.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)1057134272102134272Rat
2312672Insul15Insulin level QTL 150.01blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)1057134272102134272Rat
1549831Bss6Bone structure and strength QTL 64lumbar vertebra strength trait (VT:0010574)vertebra ultimate force (CMO:0001678)1057576521102576521Rat
2293698Bss43Bone structure and strength QTL 435.330.0001lumbar vertebra size trait (VT:0010518)lumbar vertebra cross-sectional area (CMO:0001689)1059209888104209888Rat
2313103Bss80Bone structure and strength QTL 8020.0001tibia strength trait (VT:1000284)tibia midshaft endosteal cross-sectional area (CMO:0001716)1062057807107057807Rat
2313105Bss79Bone structure and strength QTL 791.80.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)1062057807107057807Rat
61449Ciaa2CIA Autoantibody QTL 27.1blood autoantibody amount (VT:0003725)calculated serum anti-type 2 collagen antibody titer (CMO:0001279)1063221094107211142Rat
2317029Aia19Adjuvant induced arthritis QTL 192.98joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)1066978955107211142Rat
2317039Aia6Adjuvant induced arthritis QTL 64.31joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)1066978955107211142Rat
10450498Bp384Blood pressure QTL 3840.002arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1067750049107211142Rat
1642980Bp300Blood pressure QTL 300arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1068383129107211142Rat
61396Bp9Blood pressure QTL 94.80.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1068420376107211142Rat
2300172Bmd57Bone mineral density QTL 579.80.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)1069738412107211142Rat
2293646Bss25Bone structure and strength QTL 2510.960.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)1069738412107211142Rat
2293663Bss33Bone structure and strength QTL 339.340.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)1069738412107211142Rat
6893366Bw106Body weight QTL 1060.30.47body mass (VT:0001259)body weight (CMO:0000012)1070199100107211142Rat
70193Mcs7Mammary carcinoma susceptibility QTL 72.38mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)1072224939107211142Rat
2298548Neuinf7Neuroinflammation QTL 73.4nervous system integrity trait (VT:0010566)spinal cord RT1-B protein level (CMO:0002132)1072224939107211142Rat
2292438Bp311Blood pressure QTL 311arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1076246085107211142Rat
1302404Cia27Collagen induced arthritis QTL 272.60.0045joint integrity trait (VT:0010548)experimental arthritis severity measurement (CMO:0001459)1076452683107211142Rat
4889492Pancm2Pancreatic morphology QTL 23.2pancreatic beta cell morphology trait (VT:0005217)ratio of insulin-positive cell area to total area of splenic region of pancreas (CMO:0001814)1076748906107211142Rat
6893357Bw102Body weight QTL 1020.50.36body mass (VT:0001259)body weight (CMO:0000012)1080515287101325465Rat
2303589Bw87Body weight QTL 872body mass (VT:0001259)body weight (CMO:0000012)1081285008107211142Rat
2317754Glom25Glomerulus QTL 253.5urine protein amount (VT:0005160)urine protein level (CMO:0000591)1082685200107211142Rat
1600367Mcs15Mammary carcinoma susceptibility QTL 154.5mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)1085565469103884409Rat
631538Oia5Oil induced arthritis QTL 5joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1087055121107211142Rat
61363Oia3Oil induced arthritis QTL 30.001joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1087307617107211142Rat
634320Niddm49Non-insulin dependent diabetes mellitus QTL 494.41blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)1088539139107211142Rat
12880395Cm109Cardiac mass QTL 1090.001heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)1090404397107211142Rat
12880396Am13Aortic mass QTL 130.001aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)1090404397107211142Rat
12880398Kidm67Kidney mass QTL 670.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)1090404397107211142Rat
12880384Cm107Cardiac mass QTL 1070.001heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)90404397107211142Rat
12880385Cm108Cardiac mass QTL 1080.001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)90404397107211142Rat
1579915Bp280Blood pressure QTL 2800.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1090404397107211142Rat
1300137Bp186Blood pressure QTL 1863.57arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)1090627439107057807Rat
724530Bp149Blood pressure QTL 1490.0001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1090627439107211142Rat
61436Cia5Collagen induced arthritis QTL 54.9joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1091228102104060283Rat
1354641Bvd2Brain ventricular dilatation QTL 26.360.001brain ventricle morphology trait (VT:0000822)hydrocephalus severity score (CMO:0001881)1093223816107057807Rat
10450493Bp382Blood pressure QTL 3820.002arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1094759759107211142Rat
2292436Bp310Blood pressure QTL 310arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1094759759107211142Rat
1576307Cia28Collagen induced arthritis QTL 28joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1096120911104060283Rat
1576313Pia25Pristane induced arthritis QTL 25joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1096120911104060283Rat
1578663Bss18Bone structure and strength QTL 183.6femur width (VT:1000666)femoral neck width (CMO:0001695)1096703043107057807Rat
1578672Bmd16Bone mineral density QTL 166.2femur mineral mass (VT:0010011)compact volumetric bone mineral density (CMO:0001730)1096703043107057807Rat
631539Oia6Oil induced arthritis QTL 6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1097010147104670812Rat

Markers in Region
RH141812  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2611,421,483 - 11,421,686 (-)MAPPERmRatBN7.2
mRatBN7.2611,421,355 - 11,421,686 (-)MAPPERmRatBN7.2
Rnor_6.066,470,748 - 6,471,111NCBIRnor6.0
Rnor_6.066,470,748 - 6,470,950NCBIRnor6.0
Rnor_5.066,427,708 - 6,427,910UniSTSRnor5.0
Rnor_5.066,427,708 - 6,428,071UniSTSRnor5.0
RGSC_v3.466,606,574 - 6,606,776UniSTSRGSC3.4
RGSC_v3.410105,493,315 - 105,493,517UniSTSRGSC3.4
Celera611,125,752 - 11,125,954UniSTS
Cytogenetic Map10q32.3UniSTS
UniSTS:224180  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.210101,256,889 - 101,257,047 (+)MAPPERmRatBN7.2
Rnor_6.010104,574,068 - 104,574,225NCBIRnor6.0
Rnor_5.010103,711,147 - 103,711,304UniSTSRnor5.0
RGSC_v3.410106,130,722 - 106,130,879UniSTSRGSC3.4
Celera1099,831,021 - 99,831,178UniSTS
Cytogenetic Map10q32.3UniSTS
RH47096  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2611,421,732 - 11,421,843 (-)MAPPERmRatBN7.2
mRatBN7.210101,257,662 - 101,257,861 (+)MAPPERmRatBN7.2
Rnor_6.066,470,591 - 6,470,701NCBIRnor6.0
Rnor_6.010104,574,841 - 104,575,039NCBIRnor6.0
Rnor_5.010103,710,333 - 103,710,531UniSTSRnor5.0
Rnor_5.066,427,551 - 6,427,661UniSTSRnor5.0
Celera1099,831,794 - 99,831,992UniSTS
Celera611,126,001 - 11,126,111UniSTS
Cytogenetic Map10q32.3UniSTS


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 8 8 8 75 18 31
Medium 6 86 106 74 38 74 15 21 73 52 51 22 15
Low
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_053985 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063268315 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063268316 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC130970 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC063159 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC078759 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473948 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ215473 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ225133 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ225528 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ226787 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ227040 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ227260 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ227664 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ227957 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ228569 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ232451 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ232671 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ232852 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ234172 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ234408 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ235236 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JAXUCZ010000010 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  X73683 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

RefSeq Acc Id: ENSRNOT00000050223   ⟹   ENSRNOP00000040434
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl10101,256,480 - 101,258,709 (-)Ensembl
Rnor_6.0 Ensembl10104,573,664 - 104,575,890 (-)Ensembl
RefSeq Acc Id: NM_053985   ⟹   NP_446437
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr810101,755,404 - 101,757,636 (-)NCBI
mRatBN7.210101,256,484 - 101,258,716 (-)NCBI
Rnor_6.010104,573,666 - 104,575,890 (-)NCBI
Rnor_5.010103,709,482 - 103,711,706 (+)NCBI
RGSC_v3.410106,130,320 - 106,132,544 (-)RGD
Celera1099,830,619 - 99,832,836 (-)RGD
Sequence:
RefSeq Acc Id: XM_063268315   ⟹   XP_063124385
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr810101,755,404 - 101,764,613 (-)NCBI
RefSeq Acc Id: XM_063268316   ⟹   XP_063124386
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr810101,755,404 - 101,764,616 (-)NCBI
RefSeq Acc Id: NP_446437   ⟸   NM_053985
- UniProtKB: Q5RJM5 (UniProtKB/Swiss-Prot),   P84245 (UniProtKB/Swiss-Prot),   B0BMY8 (UniProtKB/TrEMBL),   A6HKT3 (UniProtKB/TrEMBL),   A6JGH8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000040434   ⟸   ENSRNOT00000050223
RefSeq Acc Id: XP_063124386   ⟸   XM_063268316
- Peptide Label: isoform X1
- UniProtKB: Q5RJM5 (UniProtKB/Swiss-Prot),   P84245 (UniProtKB/Swiss-Prot),   A6HKT3 (UniProtKB/TrEMBL),   A6JGH8 (UniProtKB/TrEMBL),   B0BMY8 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063124385   ⟸   XM_063268315
- Peptide Label: isoform X1
- UniProtKB: Q5RJM5 (UniProtKB/Swiss-Prot),   P84245 (UniProtKB/Swiss-Prot),   A6HKT3 (UniProtKB/TrEMBL),   A6JGH8 (UniProtKB/TrEMBL),   B0BMY8 (UniProtKB/TrEMBL)
Protein Domains
Histone H2A/H2B/H3

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-P84245-F1-model_v2 AlphaFold P84245 1-136 view protein structure

Transcriptome

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

Promoters
RGD ID:13697901
Promoter ID:EPDNEW_R8426
Type:single initiation site
Name:H3f3b_1
Description:H3 histone family member 3B
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_6.010104,575,887 - 104,575,947EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:621095 AgrOrtholog
BioCyc Gene G2FUF-22637 BioCyc
Ensembl Genes ENSRNOG00000003220 UniProtKB/Swiss-Prot
  ENSRNOG00000006532 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOG00055012486 UniProtKB/Swiss-Prot
  ENSRNOG00055013215 UniProtKB/Swiss-Prot
  ENSRNOG00055032581 UniProtKB/Swiss-Prot
  ENSRNOG00060007048 UniProtKB/Swiss-Prot
  ENSRNOG00060025541 UniProtKB/Swiss-Prot
  ENSRNOG00060031181 UniProtKB/Swiss-Prot
  ENSRNOG00065017038 UniProtKB/Swiss-Prot
  ENSRNOG00065021089 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000004329.8 UniProtKB/Swiss-Prot
  ENSRNOT00000050223 ENTREZGENE
  ENSRNOT00000050223.4 UniProtKB/Swiss-Prot
  ENSRNOT00055021290 UniProtKB/Swiss-Prot
  ENSRNOT00055022653 UniProtKB/Swiss-Prot
  ENSRNOT00055056311 UniProtKB/Swiss-Prot
  ENSRNOT00060011575 UniProtKB/Swiss-Prot
  ENSRNOT00060044229 UniProtKB/Swiss-Prot
  ENSRNOT00060054108 UniProtKB/Swiss-Prot
  ENSRNOT00065028436 UniProtKB/Swiss-Prot
  ENSRNOT00065035867 UniProtKB/Swiss-Prot
Gene3D-CATH 1.10.20.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:6921452 IMAGE-MGC_LOAD
  IMAGE:7112262 IMAGE-MGC_LOAD
  IMAGE:7307209 IMAGE-MGC_LOAD
  IMAGE:7320825 IMAGE-MGC_LOAD
  IMAGE:7386252 IMAGE-MGC_LOAD
  IMAGE:9024967 IMAGE-MGC_LOAD
InterPro Histone-fold UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Histone_H2A/H2B/H3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Histone_H3/CENP-A UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:100361558 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  rno:117056 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
MGC_CLONE MGC:105789 IMAGE-MGC_LOAD
  MGC:105794 IMAGE-MGC_LOAD
  MGC:187497 IMAGE-MGC_LOAD
  MGC:188786 IMAGE-MGC_LOAD
  MGC:72729 IMAGE-MGC_LOAD
  MGC:93264 IMAGE-MGC_LOAD
NCBI Gene 117056 ENTREZGENE
PANTHER HISTONE H3.3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR11426 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Histone UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB H3F3B RGD
PhenoGen H3f3b PhenoGen
PRINTS HISTONEH3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE HISTONE_H3_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  HISTONE_H3_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
RatGTEx ENSRNOG00000003220 RatGTEx
  ENSRNOG00000006532 RatGTEx
  ENSRNOG00055012486 RatGTEx
  ENSRNOG00055013215 RatGTEx
  ENSRNOG00055032581 RatGTEx
  ENSRNOG00060007048 RatGTEx
  ENSRNOG00060025541 RatGTEx
  ENSRNOG00060031181 RatGTEx
  ENSRNOG00065017038 RatGTEx
  ENSRNOG00065021089 RatGTEx
SMART SM00428 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF47113 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A6HKT2_RAT UniProtKB/TrEMBL
  A6HKT3 ENTREZGENE, UniProtKB/TrEMBL
  A6JGH8 ENTREZGENE, UniProtKB/TrEMBL
  B0BMY8 ENTREZGENE
  H33_RAT UniProtKB/Swiss-Prot, ENTREZGENE
  Q5RJM5 ENTREZGENE
UniProt Secondary B0BMY8 UniProtKB/TrEMBL
  P06351 UniProtKB/Swiss-Prot
  P33155 UniProtKB/Swiss-Prot
  Q5RJM5 UniProtKB/Swiss-Prot
  Q9V3W4 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2020-10-27 H3f3b  H3.3 histone B  H3f3b  H3 histone family member 3B  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2016-08-18 H3f3b  H3 histone family member 3B  H3f3b  H3 histone, family 3B  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-11-17 H3f3b  H3 histone, family 3B      Symbol and Name status set to approved 1299863 APPROVED
2002-08-07 H3f3b  H3 histone, family 3B      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_expression mRNAs decreases from the embryonal day 18 (E18) to the postnatal day 10 (P10) 632914