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

Name: H3f3b
Creator: Rat Genome Database
License: Creative Commons CC BY 4.0
Keywords: Rat Gene RGD Genome

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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 ...

More Info

Species	Gene symbol and name	Data Source	Assertion derived from	less info ...
Orthologs ¹				less info ...
Homo sapiens (human):	H3-3B (H3.3 histone B)	RGD	RGD
Mus musculus (house mouse):	H3f3b (H3.3 histone B)	RGD	RGD
Chinchilla lanigera (long-tailed chinchilla):	H3f3b (H3 histone, family 3B)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	LOC100988671 (histone H3.3A)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	H3-3B (H3.3 histone B)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	LOC101963257 (histone H3.3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	LOC100521680 (histone H3.3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (African green monkey):	LOC103243033 (histone H3.3A)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	LOC101698172 (histone H3.3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Other homologs ²
Homo sapiens (human):	H3-3A (H3.3 histone A)	HGNC	HomoloGene, Inparanoid, Panther, PhylomeDB
Homo sapiens (human):	H3-5 (H3.5 histone)	HGNC	Ensembl, Panther
Homo sapiens (human):	H3Y1 (H3.Y histone 1)	HGNC	OrthoDB
Alliance orthologs ³
Homo sapiens (human):	H3-3B (H3.3 histone B)	Alliance	DIOPT (HGNC\|OMA)
Drosophila melanogaster (fruit fly):	His3.3A	Alliance	DIOPT (Ensembl Compara\|OMA\|TreeFam)
Saccharomyces cerevisiae (baker's yeast):	HHT2	Alliance	DIOPT (Ensembl Compara\|OMA\|TreeFam)

Latest Assembly:

Rnor_6.0 - RGSC Genome Assembly v6.0

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Rnor_6.0	10	104,573,666 - 104,575,890 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	10	104,573,664 - 104,575,890 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	10	103,709,482 - 103,711,706 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	10	106,130,320 - 106,132,544 (-)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	10	106,144,823 - 106,147,045 (-)	NCBI
Celera	10	99,830,619 - 99,832,836 (-)	NCBI		Celera
Cytogenetic Map	10	q32.1	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

Animal Mammary Neoplasms (ISO)

carcinoma (ISO)

chondroblastoma (ISO)

genetic disease (ISO)

Mammary Neoplasms, Experimental (ISO)

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)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

brain development (IEP)

cell population proliferation (ISO)

DNA replication-independent nucleosome assembly (ISO)

embryo implantation (ISO)

male gonad development (ISO)

multicellular organism growth (ISO)

muscle cell differentiation (ISO)

negative regulation of chromosome condensation (ISO)

nucleosome assembly (ISO)

nucleus organization (ISO)

oogenesis (ISO)

osteoblast differentiation (ISO)

pericentric heterochromatin assembly (ISO)

positive regulation of cell growth (ISO)

regulation of centromere complex assembly (ISO)

response to hormone (IEP)

single fertilization (ISO)

spermatid development (ISO)

spermatogenesis (ISO)

subtelomeric heterochromatin assembly (ISO)

Cellular Component

cellular_component (ND)

chromosome, telomeric region (ISO)

nuclear chromosome (ISO)

nucleosome (ISO)

nucleus (IBA,ISO)

protein-containing complex (ISO)

Molecular Function

molecular_function (ND)

nucleosomal DNA binding (ISO)

protein binding (ISO)

protein heterodimerization activity (IEA)

RNA polymerase II cis-regulatory region sequence-specific DNA binding (ISO)

RNA polymerase II core promoter sequence-specific DNA binding (ISO)

Molecular Pathway Annotations Click to see Annotation Detail View

histone modification pathway (ISO)

systemic lupus erythematosus pathway (IEA)

References

References - curated


1.	Castiglia D, etal., Neurochem Res 1994 Dec;19(12):1531-7.
2.	Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
3.	Maze I, etal., Nat Rev Genet. 2014 Apr;15(4):259-71. doi: 10.1038/nrg3673. Epub 2014 Mar 11.
4.	NCBI rat LocusLink and RefSeq merged data July 26, 2002
5.	Pipeline to import KEGG annotations from KEGG into RGD
6.	RGD automated data pipeline
7.	RGD automated import pipeline for gene-chemical interactions
8.	RGD comprehensive gene curation
9.	Scaturro M, etal., Neurochem Res. 1995 Aug;20(8):969-76.
10.	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

Genomics

Comparative Map Data

H3f3b
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Rnor_6.0	10	104,573,666 - 104,575,890 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	10	104,573,664 - 104,575,890 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	10	103,709,482 - 103,711,706 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	10	106,130,320 - 106,132,544 (-)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	10	106,144,823 - 106,147,045 (-)	NCBI
Celera	10	99,830,619 - 99,832,836 (-)	NCBI		Celera
Cytogenetic Map	10	q32.1	NCBI

H3-3B
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38.p13 Ensembl	17	75,776,434 - 75,785,893 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	17	75,776,434 - 75,779,779 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	17	73,772,515 - 73,775,860 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	17	71,284,110 - 71,287,455 (-)	NCBI	NCBI36		hg18	NCBI36
Build 34	17	71,284,111 - 71,287,455	NCBI
Celera	17	70,362,565 - 70,365,910 (-)	NCBI
Cytogenetic Map	17	q25.1	NCBI
HuRef	17	69,198,034 - 69,201,379 (-)	NCBI		HuRef
CHM1_1	17	73,837,589 - 73,841,087 (-)	NCBI		CHM1_1

H3f3b
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	11	115,912,787 - 115,921,313 (-)	NCBI	GRCm39		mm39
GRCm38	11	116,021,961 - 116,026,039 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	11	116,021,912 - 116,027,962 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	11	115,883,275 - 115,885,818 (-)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	11	115,837,018 - 115,840,587 (-)	NCBI			mm8
Celera	11	127,784,227 - 127,786,770 (-)	NCBI		Celera
Cytogenetic Map	11	E2	NCBI

H3f3b
(Chinchilla lanigera - long-tailed chinchilla)

Chinchilla Assembly	Chr	Position (strand)	Source	Genome Browsers
Chinchilla Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChiLan1.0 Ensembl	NW_004955506	6,474,727 - 6,482,244 (+)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955506	6,475,336 - 6,478,781 (+)	NCBI	ChiLan1.0	ChiLan1.0

LOC100988671
(Pan paniscus - bonobo/pygmy chimpanzee)

Bonobo Assembly	Chr	Position (strand)	Source	Genome Browsers
Bonobo Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
PanPan1.1	17	75,277,614 - 75,281,106 (-)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	17	75,277,614 - 75,281,106 (-)	Ensembl	panpan1.1		panPan2
Mhudiblu_PPA_v0	17	69,728,165 - 69,730,519 (-)	NCBI	Mhudiblu_PPA_v0		panPan3

H3-3B
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1 Ensembl	9	4,805,650 - 4,833,503 (+)	Ensembl	CanFam3.1		canFam3	CanFam3.1
CanFam3.1	9	4,805,655 - 4,808,076 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1

LOC101963257
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
SpeTri2.0	NW_004936594	959,493 - 961,703 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

LOC100521680
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	12	5,632,365 - 5,634,726 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	12	5,632,326 - 5,634,977 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	12	5,578,702 - 5,581,109 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

LOC103243033
(Chlorocebus sabaeus - African green monkey)

Vervet Assembly	Chr	Position (strand)	Source	Genome Browsers
Vervet Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1	16	45,903,252 - 45,905,605 (+)	NCBI
ChlSab1.1 Ensembl	16	45,902,980 - 45,904,929 (+)	Ensembl

LOC101698172
(Heterocephalus glaber - naked mole-rat)

Molerat Assembly	Chr	Position (strand)	Source	Genome Browsers
Molerat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HetGla 1.0	NW_004624801	5,668,661 - 5,672,164 (-)	NCBI

Position Markers

RH141812

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	6	6,470,748 - 6,470,950	NCBI	Rnor6.0
Rnor_6.0	6	6,470,748 - 6,471,111	NCBI	Rnor6.0
Rnor_5.0	6	6,427,708 - 6,428,071	UniSTS	Rnor5.0
Rnor_5.0	6	6,427,708 - 6,427,910	UniSTS	Rnor5.0
RGSC_v3.4	6	6,606,574 - 6,606,776	UniSTS	RGSC3.4
RGSC_v3.4	10	105,493,315 - 105,493,517	UniSTS	RGSC3.4
Celera	6	11,125,752 - 11,125,954	UniSTS
Cytogenetic Map	10	q32.3	UniSTS

UniSTS:224180

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	10	104,574,068 - 104,574,225	NCBI	Rnor6.0
Rnor_5.0	10	103,711,147 - 103,711,304	UniSTS	Rnor5.0
RGSC_v3.4	10	106,130,722 - 106,130,879	UniSTS	RGSC3.4
Celera	10	99,831,021 - 99,831,178	UniSTS
Cytogenetic Map	10	q32.3	UniSTS

RH47096

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	6	6,470,591 - 6,470,701	NCBI	Rnor6.0
Rnor_6.0	10	104,574,841 - 104,575,039	NCBI	Rnor6.0
Rnor_5.0	10	103,710,333 - 103,710,531	UniSTS	Rnor5.0
Rnor_5.0	6	6,427,551 - 6,427,661	UniSTS	Rnor5.0
Celera	10	99,831,794 - 99,831,992	UniSTS
Celera	6	11,126,001 - 11,126,111	UniSTS
Cytogenetic Map	10	q32.3	UniSTS

QTLs in Region (Rnor_6.0)

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
2303118	Mamtr7	Mammary tumor resistance QTL 7		0.003	mammary gland integrity trait (VT:0010552)	mammary tumor growth rate (CMO:0000344)	10	9841807	108540162	Rat
631268	Cia21	Collagen induced arthritis QTL 21	3.1		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	10	14827894	107857673	Rat
2316949	Gluco60	Glucose level QTL 60	3.7		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	10	14827894	110992275	Rat
1331791	Cm31	Cardiac mass QTL 31	3.84606		heart mass (VT:0007028)	heart wet weight (CMO:0000069)	10	23861015	112626471	Rat
631267	Cia20	Collagen induced arthritis QTL 20	3.2		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	10	24483076	107857673	Rat
61325	Aia5	Adjuvant induced arthritis QTL 5		0.01	joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	10	24483076	107857673	Rat
61354	Pia10	Pristane induced arthritis QTL 10		0.01	joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	10	24483076	107857673	Rat
1576308	Schws1	Schwannoma susceptibility QTL 1		0.0041	nervous system integrity trait (VT:0010566)	percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)	10	41260363	106105607	Rat
631269	Cia22	Collagen induced arthritis QTL 22	8.9		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	10	41260363	107857673	Rat
631270	Cia23	Collagen induced arthritis QTL 23	3.9		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	10	41260363	107857673	Rat
1298078	Stresp5	Stress response QTL 5	2.99	0.00025	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	10	43289657	108540162	Rat
61387	Bp1	Blood pressure QTL 1	5.1		arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	10	53621375	112626471	Rat
61387	Bp1	Blood pressure QTL 1	5.1		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	10	53621375	112626471	Rat
70171	Cari1	Carrageenan-induced inflammation QTL 1	4.9	0.0005	hypodermis integrity trait (VT:0010550)	inflammatory exudate volume (CMO:0001429)	10	55678976	112626471	Rat
1549831	Bss6	Bone structure and strength QTL 6	4		lumbar vertebra strength trait (VT:0010574)	vertebra ultimate force (CMO:0001678)	10	60450007	105450007	Rat
2312662	Slep8	Serum leptin concentration QTL 8		0.05	blood leptin amount (VT:0005667)	serum leptin level (CMO:0000780)	10	60875260	105875260	Rat
2312668	Scl65	Serum cholesterol level QTL 65		0.001	blood cholesterol amount (VT:0000180)	serum total cholesterol level (CMO:0000363)	10	60875260	105875260	Rat
2312672	Insul15	Insulin level QTL 15		0.01	blood insulin amount (VT:0001560)	serum insulin level (CMO:0000358)	10	60875260	105875260	Rat
2293698	Bss43	Bone structure and strength QTL 43	5.33	0.0001	lumbar vertebra size trait (VT:0010518)	lumbar vertebra cross-sectional area (CMO:0001689)	10	62096293	107096293	Rat
61449	Ciaa2	CIA Autoantibody QTL 2	7.1		blood autoantibody amount (VT:0003725)	calculated serum anti-type 2 collagen antibody titer (CMO:0001279)	10	65590122	110590122	Rat
2313103	Bss80	Bone structure and strength QTL 80	2	0.0001	tibia strength trait (VT:1000284)	tibia midshaft endosteal cross-sectional area (CMO:0001716)	10	65992275	110992275	Rat
2313105	Bss79	Bone structure and strength QTL 79	1.8	0.0001	tibia size trait (VT:0100001)	tibia midshaft cross-sectional area (CMO:0001717)	10	65992275	110992275	Rat
7387312	Bw125	Body weight QTL 125	3	0.0047	retroperitoneal fat pad mass (VT:0010430)	retroperitoneal fat pad weight (CMO:0000356)	10	67880046	112626471	Rat
1581559	Eae18	Experimental allergic encephalomyelitis QTL 18		0.00002	nervous system integrity trait (VT:0010566)	experimental autoimmune encephalomyelitis severity score (CMO:0001419)	10	67988218	110992091	Rat
2317029	Aia19	Adjuvant induced arthritis QTL 19	2.98		joint integrity trait (VT:0010548)	left rear ankle joint diameter (CMO:0002149)	10	69385595	112626471	Rat
2317039	Aia6	Adjuvant induced arthritis QTL 6	4.31		joint integrity trait (VT:0010548)	right rear ankle joint diameter (CMO:0002150)	10	69385595	112626471	Rat
10450498	Bp384	Blood pressure QTL 384		0.002	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	10	70166960	112626471	Rat
1642980	Bp300	Blood pressure QTL 300			arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	10	70800069	112626471	Rat
61396	Bp9	Blood pressure QTL 9	4.8	0.0001	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	10	71692298	112626471	Rat
2300172	Bmd57	Bone mineral density QTL 57	9.8	0.0001	femur mineral mass (VT:0010011)	volumetric bone mineral density (CMO:0001553)	10	73008136	112626471	Rat
2293646	Bss25	Bone structure and strength QTL 25	10.96	0.0001	femur morphology trait (VT:0000559)	femur cross-sectional area (CMO:0001661)	10	73008136	112626471	Rat
2293663	Bss33	Bone structure and strength QTL 33	9.34	0.0001	femur strength trait (VT:0010010)	femur midshaft polar moment of inertia (CMO:0001669)	10	73008136	112626471	Rat
6893366	Bw106	Body weight QTL 106	0.3	0.47	body mass (VT:0001259)	body weight (CMO:0000012)	10	73467158	112626471	Rat
70193	Mcs7	Mammary carcinoma susceptibility QTL 7	2.38		mammary gland integrity trait (VT:0010552)	mammary tumor number (CMO:0000343)	10	75544754	112626471	Rat
2298548	Neuinf7	Neuroinflammation QTL 7	3.4		nervous system integrity trait (VT:0010566)	spinal cord RT1-B protein level (CMO:0002132)	10	75544754	112626471	Rat
2292438	Bp311	Blood pressure QTL 311			arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	10	78970279	112626471	Rat
1302404	Cia27	Collagen induced arthritis QTL 27	2.6	0.0045	joint integrity trait (VT:0010548)	experimental arthritis severity measurement (CMO:0001459)	10	79927661	112626471	Rat
4889492	Pancm2	Pancreatic morphology QTL 2	3.2		pancreatic beta cell morphology trait (VT:0005217)	ratio of insulin-positive cell area to total area of splenic region of pancreas (CMO:0001814)	10	80239190	112626471	Rat
6893357	Bw102	Body weight QTL 102	0.5	0.36	body mass (VT:0001259)	body weight (CMO:0000012)	10	83389828	104994768	Rat
2303589	Bw87	Body weight QTL 87	2		body mass (VT:0001259)	body weight (CMO:0000012)	10	85079943	112626471	Rat
2317754	Glom25	Glomerulus QTL 25	3.5		urine protein amount (VT:0005160)	urine protein level (CMO:0000591)	10	86566908	112626471	Rat
1600367	Mcs15	Mammary carcinoma susceptibility QTL 15	4.5		mammary gland integrity trait (VT:0010552)	mammary tumor number (CMO:0000343)	10	88544136	107545372	Rat
631538	Oia5	Oil induced arthritis QTL 5			joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	10	90041957	112626471	Rat
61363	Oia3	Oil induced arthritis QTL 3		0.001	joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	10	90296897	112626471	Rat
634320	Niddm49	Non-insulin dependent diabetes mellitus QTL 49	4.41		blood glucose amount (VT:0000188)	plasma glucose level (CMO:0000042)	10	91689348	112626471	Rat
1579915	Bp280	Blood pressure QTL 280		0.001	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	10	93662786	112626471	Rat
12880395	Cm109	Cardiac mass QTL 109		0.001	heart right ventricle mass (VT:0007033)	heart right ventricle weight to body weight ratio (CMO:0000914)	10	93662786	112626471	Rat
12880396	Am13	Aortic mass QTL 13		0.001	aorta mass (VT:0002845)	aorta weight to aorta length to body weight ratio (CMO:0002722)	10	93662786	112626471	Rat
12880398	Kidm67	Kidney mass QTL 67		0.001	kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	10	93662786	112626471	Rat
12880384	Cm107	Cardiac mass QTL 107		0.001	heart mass (VT:0007028)	heart wet weight to body weight ratio (CMO:0002408)		93662786	112626471	Rat
12880385	Cm108	Cardiac mass QTL 108		0.001	heart left ventricle mass (VT:0007031)	heart left ventricle weight to body weight ratio (CMO:0000530)		93662786	112626471	Rat
1300137	Bp186	Blood pressure QTL 186	3.57		arterial blood pressure trait (VT:2000000)	blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)	10	93886117	110992275	Rat
724530	Bp149	Blood pressure QTL 149		0.0001	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	10	93886117	112626471	Rat
1558652	Bw57	Body weight QTL 57	4.2	0.0008	body mass (VT:0001259)	body weight (CMO:0000012)	10	94170766	112626471	Rat
61436	Cia5	Collagen induced arthritis QTL 5	4.9		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	10	94486204	107857673	Rat
1354641	Bvd2	Brain ventricular dilatation QTL 2	6.36	0.001	brain ventricle morphology trait (VT:0000822)	hydrocephalus severity score (CMO:0001881)	10	96520816	110992275	Rat
2292436	Bp310	Blood pressure QTL 310			arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	10	98079221	112626471	Rat
10450493	Bp382	Blood pressure QTL 382		0.002	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	10	98079221	112626471	Rat
1576307	Cia28	Collagen induced arthritis QTL 28			joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	10	99492217	107857673	Rat
1576313	Pia25	Pristane induced arthritis QTL 25			joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	10	99492217	107857673	Rat
1578663	Bss18	Bone structure and strength QTL 18	3.6		femur width (VT:1000666)	femoral neck width (CMO:0001695)	10	100155035	110992275	Rat
1578672	Bmd16	Bone mineral density QTL 16	6.2		femur mineral mass (VT:0010011)	cortical volumetric bone mineral density (CMO:0001730)	10	100155035	110992275	Rat
631539	Oia6	Oil induced arthritis QTL 6			joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	10	100460820	108540162	Rat

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

View RNA-SEQ Expression Data

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 Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	10	104,573,664 - 104,575,890 (-)	Ensembl

RefSeq Acc Id:

NM_053985 ⟹ NP_446437

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0	10	104,573,666 - 104,575,890 (-)	NCBI
Rnor_5.0	10	103,709,482 - 103,711,706 (+)	NCBI
RGSC_v3.4	10	106,130,320 - 106,132,544 (-)	RGD
Celera	10	99,830,619 - 99,832,836 (-)	RGD

Sequence:

show sequence

GGGGCGCAGAGCGGTTTGGTCGTTCGTTGGAGGAGCTTCGTCTTGTTCTGCTCTGCGATTGCGG
CGCTTGTTCGAGCGCTTACAGCGGCGCGTCGGTCCCAGCAAGGGCCTCAGACTTCAGCTTTGGG
TGAGAGAAGATGGCCCGAACCAAGCAGACCGCTAGGAAGTCCACCGGAGGGAAAGCCCCCCGCA
AACAGCTGGCCACCAAGGCGGCCCGGAAAAGCGCGCCCTCTACTGGCGGGGTGAAGAAACCTCA
TCGCTACAGGCCCGGGACCGTGGCTCTAAGAGAGATCCGTCGTTACCAGAAATCGACTGAGCTG
CTCATCCGGAAGCTACCCTTCCAGAGGTTGGTGAGGGAGATCGCCCAGGATTTCAAAACCGACT
TGAGGTTTCAAAGTGCAGCCATCGGTGCCCTTCAGGAGGCTAGCGAGGCATACCTGGTGGGGTT
GTTTGAAGATACCAATCTGTGTGCCATCCACGCCAAGAGAGTCACCATCATGCCCAAAGACATC
CAGTTGGCTCGCCGGATACGGGGGGAGAGAGCTTAAGTTGAAGCGATTTTTATGGCATTTTGTA
GTAAATTCTGTAAAATACTTTGGTTTAATTTGTGACTTTTTTTGTAAGAAATTGTTTATAATAT
GTTGCATTTGTACTTAAGTCATTCCATCTTTCACTCAGGATGAATGGAAAGAGTGACTGTTCAC
AGACCTCAGTGATGTGAGCACTGTGGCTCAGGAGTGACAAGTTGCTAATATGCAGAAGGGATGG
GTGATACTTCTTGCTTCTCATGATGCATGTTTCTGTATGTTAATGACTTGTTGGGTAGCTATTA
AGGTACTAGAATTGATAAATGTGTACAGGGTCCTTTTGCAATAAAACTGGTTATGACTTGATCC
AAGTGTTTAACCATACATCACTGTGATAGAATGTGGGCTTTTTCAAAGGTTGAAGATACAAGTT
TTAGCCACAGTGTAACAGTTTCCTTTAAAAAAAAAAAGTAAACCTGGCAGCTATAGAATACACT
ATGTGCATTTATAATAGCTATTTTATATATTGTAGTGTTCAACATTTTTAAATTAAATGTTTTA
CATTCACAAGTGGTGGGGAGTCTTGTCATTAAGGTGTGTGTAATTTAGTCCAGTTGGTATTTCT
GACTAGACTGCATTTGTTTTTAACAAAGTAGAAGAATGCTATGCGTATTAAACCTTGCATAAGT
CCTCATTCTACCACATGTTCACTAACCCCTGACCCTCTGGCTGGTAACACAAAACACTAACGGG
GATTTTCTTTAAGGGCTCTAGAGTAAAACAACAAGCTATTCACACCAGCATCATCTGTTCCTAA
TCTAGTTAGTGAGCTTTTCATTGTGTTTGGTCTTACGCCTAGACTGAGTTTGGTTTTGTTTTTA
ATCTTTAAGGGGGAAAACTGTACAAGGTTTGCTTTTCCTTGTGGAGTTTATAAACATGGGGGTA
AGAGTACAGCTTGAGCTTATTGGACTCTGCCAATGAAGATGGGTTAGGTTACACCTGGTTACTA
TCCTGGCAAAAAAATCCCTTTTATAGAGATGGCCTTCAAGTGGTTTTTAAAAGTATCCTATTGA
AGTTTTTAGGTCAATTATGTATGTTGACTAAATTTACAAATAAACTTGTTTATCCAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAA

hide sequence

Protein Sequences


Protein RefSeqs	NP_446437	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAH63159	(Get FASTA)	NCBI Sequence Viewer
	AAH78759	(Get FASTA)	NCBI Sequence Viewer
	CAA52035	(Get FASTA)	NCBI Sequence Viewer
	EDM06637	(Get FASTA)	NCBI Sequence Viewer
	EDM06638	(Get FASTA)	NCBI Sequence Viewer
	P84245	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:	NP_446437 ⟸ NM_053985
- UniProtKB:	P84245 (UniProtKB/Swiss-Prot), B0BMY8 (UniProtKB/TrEMBL)
- Sequence:	show sequence MARTKQTARKSTGGKAPRKQLATKAARKSAPSTGGVKKPHRYRPGTVALREIRRYQKSTELLIR KLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLA RRIRGERA hide 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 Assembly	Chr	Position (strand)	Source
Rnor_6.0	10	104,575,887 - 104,575,947	EPDNEW

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)

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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/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)

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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

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

External Database Links

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

Gene Annotator (Functional Annotation) unavailable	Gene Annotator (Annotation Distribution) unavailable	Variant Visualizer (Genomic Variants) unavailble Variant Visualizer (Genomic Variants) unavailable
Gene Annotator (Functional Annotation)	Gene Annotator (Annotation Distribution)	Variant Visualizer (Genomic Variants)

InterViewer (Protein-Protein Interactions) unavailable	Gviewer (Genome Viewer) unavailable	Variant Visualizer (Damaging Variants) unavailble Variant Visualizer (Damaging Variants) unavailable
InterViewer (Protein-Protein Interactions)	GViewer (Genome Viewer)	Variant Visualizer (Damaging Variants)

Gene Annotator (Annotation Comparison) unavailable	OLGA (Gene List Generator) unavailable
Gene Annotator (Annotation Comparison)	OLGA (Gene List Generator)	Excel (Download)

MOET (Multi-Ontology Enrichement) unavailable	GOLF (Gene-Ortholog Location Finder) unavailable
MOET (Multi-Ontology Enrichement)	GOLF (Gene-Ortholog Location Finder)

Imported Disease Annotations - ClinVar

Imported Disease Annotations - CTD

RGD Manual Annotations

Imported Annotations - KEGG (archival)