H3f3b (H3.3 histone B) - Rat Genome Database
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Gene: H3f3b (H3.3 histone B) Rattus norvegicus
Analyze
Symbol: H3f3b
Name: H3.3 histone B
RGD ID: 621095
Description: Predicted to have 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. Involved in brain development and response to hormone. Predicted to localize to nuclear chromosome, telomeric region and nuclear nucleosome. 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: PROVISIONAL
Also 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
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
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 (-)NCBIRGSC3.4rn4RGSC3.4
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


Disease Annotations     Click to see Annotation Detail View

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)
all-trans-retinoic acid  (ISO)
alpha-pinene  (ISO)
amiodarone  (EXP)
ammonium chloride  (EXP)
amphetamine  (EXP)
antirheumatic drug  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
benzbromarone  (EXP)
benzene  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
bis(2-chloroethyl) sulfide  (ISO)
bisphenol A  (ISO)
carbamazepine  (ISO)
chlorpyrifos  (EXP)
chromium(6+)  (ISO)
ciguatoxin CTX1B  (ISO)
cisplatin  (ISO)
clofibrate  (EXP,ISO)
copper(II) sulfate  (ISO)
coumestrol  (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)
L-ethionine  (EXP)
lead diacetate  (ISO)
methotrexate  (ISO)
nefazodone  (EXP)
omeprazole  (EXP)
ozone  (ISO)
p-tert-Amylphenol  (EXP)
paracetamol  (ISO)
perfluorooctanoic acid  (EXP)
PhIP  (EXP)
pinosylvin  (ISO)
pirinixic acid  (EXP,ISO)
pregnenolone 16alpha-carbonitrile  (ISO)
resveratrol  (EXP)
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)
valproic acid  (ISO)
zinc atom  (ISO)
zinc(0)  (ISO)

Molecular Pathway Annotations     Click to see Annotation Detail View
References

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  


Genomics

Comparative Map Data
H3f3b
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
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 (-)NCBIRGSC3.4rn4RGSC3.4
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
GRCh38.p13 Ensembl1775,776,434 - 75,785,893 (-)EnsemblGRCh38hg38GRCh38
GRCh381775,776,434 - 75,779,779 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371773,772,515 - 73,775,860 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361771,284,110 - 71,287,455 (-)NCBINCBI36hg18NCBI36
Build 341771,284,111 - 71,287,455NCBI
Celera1770,362,565 - 70,365,910 (-)NCBI
Cytogenetic Map17q25.1NCBI
HuRef1769,198,034 - 69,201,379 (-)NCBIHuRef
CHM1_11773,837,589 - 73,841,087 (-)NCBICHM1_1
H3f3b
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3911115,912,787 - 115,921,313 (-)NCBIGRCm39mm39
GRCm3811116,021,961 - 116,026,039 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl11116,021,912 - 116,027,962 (-)EnsemblGRCm38mm10GRCm38
MGSCv3711115,883,275 - 115,885,818 (-)NCBIGRCm37mm9NCBIm37
MGSCv3611115,837,018 - 115,840,587 (-)NCBImm8
Celera11127,784,227 - 127,786,770 (-)NCBICelera
Cytogenetic Map11E2NCBI
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
PanPan1.11775,277,614 - 75,281,106 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1775,277,614 - 75,281,106 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01769,728,165 - 69,730,519 (-)NCBIMhudiblu_PPA_v0panPan3
H3-3B
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl94,805,650 - 4,833,503 (+)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.194,805,655 - 4,808,076 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
LOC101963257
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_004936594959,493 - 961,703 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LOC100521680
(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 - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11645,903,252 - 45,905,605 (+)NCBI
ChlSab1.1 Ensembl1645,902,980 - 45,904,929 (+)Ensembl
LOC101698172
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248015,668,661 - 5,672,164 (-)NCBI

Position Markers
RH141812  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.066,470,748 - 6,470,950NCBIRnor6.0
Rnor_6.066,470,748 - 6,471,111NCBIRnor6.0
Rnor_5.066,427,708 - 6,428,071UniSTSRnor5.0
Rnor_5.066,427,708 - 6,427,910UniSTSRnor5.0
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
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
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


QTLs in Region (Rnor_6.0)
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)109841807108540162Rat
631268Cia21Collagen induced arthritis QTL 213.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1014827894107857673Rat
2316949Gluco60Glucose level QTL 603.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1014827894110992275Rat
1331791Cm31Cardiac mass QTL 313.84606heart mass (VT:0007028)heart wet weight (CMO:0000069)1023861015112626471Rat
631267Cia20Collagen induced arthritis QTL 203.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1024483076107857673Rat
61325Aia5Adjuvant induced arthritis QTL 50.01joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1024483076107857673Rat
61354Pia10Pristane induced arthritis QTL 100.01joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1024483076107857673Rat
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)1041260363106105607Rat
631269Cia22Collagen induced arthritis QTL 228.9joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1041260363107857673Rat
631270Cia23Collagen induced arthritis QTL 233.9joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1041260363107857673Rat
1298078Stresp5Stress response QTL 52.990.00025blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)1043289657108540162Rat
61387Bp1Blood pressure QTL 15.1arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)1053621375112626471Rat
61387Bp1Blood pressure QTL 15.1arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1053621375112626471Rat
70171Cari1Carrageenan-induced inflammation QTL 14.90.0005hypodermis integrity trait (VT:0010550)inflammatory exudate volume (CMO:0001429)1055678976112626471Rat
1549831Bss6Bone structure and strength QTL 64lumbar vertebra strength trait (VT:0010574)vertebra ultimate force (CMO:0001678)1060450007105450007Rat
2312662Slep8Serum leptin concentration QTL 80.05blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)1060875260105875260Rat
2312668Scl65Serum cholesterol level QTL 650.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)1060875260105875260Rat
2312672Insul15Insulin level QTL 150.01blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)1060875260105875260Rat
2293698Bss43Bone structure and strength QTL 435.330.0001lumbar vertebra size trait (VT:0010518)lumbar vertebra cross-sectional area (CMO:0001689)1062096293107096293Rat
61449Ciaa2CIA Autoantibody QTL 27.1blood autoantibody amount (VT:0003725)calculated serum anti-type 2 collagen antibody titer (CMO:0001279)1065590122110590122Rat
2313103Bss80Bone structure and strength QTL 8020.0001tibia strength trait (VT:1000284)tibia midshaft endosteal cross-sectional area (CMO:0001716)1065992275110992275Rat
2313105Bss79Bone structure and strength QTL 791.80.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)1065992275110992275Rat
7387312Bw125Body weight QTL 12530.0047retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight (CMO:0000356)1067880046112626471Rat
1581559Eae18Experimental allergic encephalomyelitis QTL 180.00002nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis severity score (CMO:0001419)1067988218110992091Rat
2317029Aia19Adjuvant induced arthritis QTL 192.98joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)1069385595112626471Rat
2317039Aia6Adjuvant induced arthritis QTL 64.31joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)1069385595112626471Rat
10450498Bp384Blood pressure QTL 3840.002arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1070166960112626471Rat
1642980Bp300Blood pressure QTL 300arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1070800069112626471Rat
61396Bp9Blood pressure QTL 94.80.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1071692298112626471Rat
2300172Bmd57Bone mineral density QTL 579.80.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)1073008136112626471Rat
2293646Bss25Bone structure and strength QTL 2510.960.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)1073008136112626471Rat
2293663Bss33Bone structure and strength QTL 339.340.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)1073008136112626471Rat
6893366Bw106Body weight QTL 1060.30.47body mass (VT:0001259)body weight (CMO:0000012)1073467158112626471Rat
70193Mcs7Mammary carcinoma susceptibility QTL 72.38mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)1075544754112626471Rat
2298548Neuinf7Neuroinflammation QTL 73.4nervous system integrity trait (VT:0010566)spinal cord RT1-B protein level (CMO:0002132)1075544754112626471Rat
2292438Bp311Blood pressure QTL 311arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1078970279112626471Rat
1302404Cia27Collagen induced arthritis QTL 272.60.0045joint integrity trait (VT:0010548)experimental arthritis severity measurement (CMO:0001459)1079927661112626471Rat
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)1080239190112626471Rat
6893357Bw102Body weight QTL 1020.50.36body mass (VT:0001259)body weight (CMO:0000012)1083389828104994768Rat
2303589Bw87Body weight QTL 872body mass (VT:0001259)body weight (CMO:0000012)1085079943112626471Rat
2317754Glom25Glomerulus QTL 253.5urine protein amount (VT:0005160)urine protein level (CMO:0000591)1086566908112626471Rat
1600367Mcs15Mammary carcinoma susceptibility QTL 154.5mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)1088544136107545372Rat
631538Oia5Oil induced arthritis QTL 5joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1090041957112626471Rat
61363Oia3Oil induced arthritis QTL 30.001joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1090296897112626471Rat
634320Niddm49Non-insulin dependent diabetes mellitus QTL 494.41blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)1091689348112626471Rat
1579915Bp280Blood pressure QTL 2800.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1093662786112626471Rat
12880395Cm109Cardiac mass QTL 1090.001heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)1093662786112626471Rat
12880396Am13Aortic mass QTL 130.001aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)1093662786112626471Rat
12880398Kidm67Kidney mass QTL 670.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)1093662786112626471Rat
12880384Cm107Cardiac mass QTL 1070.001heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)93662786112626471Rat
12880385Cm108Cardiac mass QTL 1080.001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)93662786112626471Rat
1300137Bp186Blood pressure QTL 1863.57arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)1093886117110992275Rat
724530Bp149Blood pressure QTL 1490.0001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1093886117112626471Rat
1558652Bw57Body weight QTL 574.20.0008body mass (VT:0001259)body weight (CMO:0000012)1094170766112626471Rat
61436Cia5Collagen induced arthritis QTL 54.9joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1094486204107857673Rat
1354641Bvd2Brain ventricular dilatation QTL 26.360.001brain ventricle morphology trait (VT:0000822)hydrocephalus severity score (CMO:0001881)1096520816110992275Rat
2292436Bp310Blood pressure QTL 310arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1098079221112626471Rat
10450493Bp382Blood pressure QTL 3820.002arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1098079221112626471Rat
1576307Cia28Collagen induced arthritis QTL 28joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1099492217107857673Rat
1576313Pia25Pristane induced arthritis QTL 25joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1099492217107857673Rat
1578663Bss18Bone structure and strength QTL 183.6femur width (VT:1000666)femoral neck width (CMO:0001695)10100155035110992275Rat
1578672Bmd16Bone mineral density QTL 166.2femur mineral mass (VT:0010011)cortical volumetric bone mineral density (CMO:0001730)10100155035110992275Rat
631539Oia6Oil induced arthritis QTL 6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)10100460820108540162Rat

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.


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
GenBank Nucleotide AAHX01066744 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  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
  X73683 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000050223   ⟹   ENSRNOP00000040434
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl10104,573,664 - 104,575,890 (-)Ensembl
RefSeq Acc Id: NM_053985   ⟹   NP_446437
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
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:
Reference Sequences
RefSeq Acc Id: NP_446437   ⟸   NM_053985
- UniProtKB: P84245 (UniProtKB/Swiss-Prot),   B0BMY8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000040434   ⟸   ENSRNOT00000050223
Protein Domains
Histone

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

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:621095 AgrOrtholog
Ensembl Genes ENSRNOG00000003220 UniProtKB/Swiss-Prot
  ENSRNOG00000006532 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000004329 UniProtKB/Swiss-Prot
  ENSRNOP00000040434 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000004329 UniProtKB/Swiss-Prot
  ENSRNOT00000050223 ENTREZGENE, 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 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
SMART SM00428 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF47113 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniGene Rn.198918 ENTREZGENE
  Rn.29857 ENTREZGENE
UniProt B0BMY8 ENTREZGENE, UniProtKB/TrEMBL
  H33_RAT UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary 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
2016-05-11 H3f3b  H3 histone, family 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