Nfyb (nuclear transcription factor Y subunit beta)

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Gene: Nfyb (nuclear transcription factor Y subunit beta) Rattus norvegicus

Analyze

Symbol:

Nfyb

Name:

nuclear transcription factor Y subunit beta

RGD ID:

3172

Description:

Is predicted to contribute to RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in cellular response to leukemia inhibitory factor and positive regulation of transcription by RNA polymerase II. Localizes to CCAAT-binding activity factor complex. Orthologous to human NFYB (nuclear transcription factor Y subunit beta); PARTICIPATES IN altered p53 signaling pathway; antigen processing and presentation pathway; tuberculosis pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,4-dinitrotoluene; 2,6-dinitrotoluene.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Also known as:

CAAT box DNA-binding protein subunit B; CAAT-box DNA-binding protein subunit B; CBF-A; CBF-B; CBFB; CCAAT binding transcription factor of CBF-B/NFY-B; CCAAT-binding transcription factor subunit A; CCAAT-binding transcription factor subunit B; MGC108654; NF-YB; Nfya; nuclear transcription factor - Y beta; nuclear transcription factor Y subunit B; nuclear transcription factor-Y beta

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 Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	7	20,964,988 - 20,980,569 (+)	NCBI
Rnor_6.0 Ensembl	7	27,081,667 - 27,097,479 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	7	27,081,667 - 27,097,481 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	7	27,200,204 - 27,216,018 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	7	23,190,295 - 23,205,611 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	7	23,210,565 - 23,225,880 (+)	NCBI
Celera	7	18,145,883 - 18,161,286 (+)	NCBI		Celera
Cytogenetic Map	7	q13	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

(-)-epigallocatechin 3-gallate (ISO)

(S)-nicotine (ISO)

1,2-dichloroethane (ISO)

1,2-dimethylhydrazine (ISO)

17alpha-ethynylestradiol (ISO)

2,2',4,4',5,5'-hexachlorobiphenyl (ISO)

2,2',5,5'-tetrachlorobiphenyl (ISO)

2,3,7,8-tetrachlorodibenzodioxine (EXP,ISO)

2,4-dinitrotoluene (EXP)

2,6-dinitrotoluene (EXP)

2-naphthylamine (ISO)

3,4-methylenedioxymethamphetamine (ISO)

3-isobutyl-1-methyl-7H-xanthine (ISO)

3H-1,2-dithiole-3-thione (EXP)

4-hydroxyphenyl retinamide (ISO)

5-fluorouracil (ISO)

acrylamide (EXP)

aflatoxin B1 (ISO)

aflatoxin M1 (ISO)

all-trans-retinoic acid (ISO)

ammonium chloride (EXP)

antirheumatic drug (ISO)

Aroclor 1254 (ISO)

benzo[a]pyrene (ISO)

bisphenol A (EXP,ISO)

carbon nanotube (ISO)

choline (ISO)

ciguatoxin CTX1B (ISO)

cisplatin (ISO)

cobalt dichloride (ISO)

cocaine (ISO)

copper(II) sulfate (ISO)

cyclosporin A (ISO)

dexamethasone (ISO)

dibutyl phthalate (ISO)

dicrotophos (ISO)

dorsomorphin (ISO)

ethanol (ISO)

fluoranthene (ISO)

folic acid (ISO)

geraniol (ISO)

indometacin (ISO)

L-methionine (ISO)

manganese atom (ISO)

manganese(0) (ISO)

manganese(II) chloride (ISO)

methoxyacetic acid (ISO)

methylmercury chloride (ISO)

methylparaben (ISO)

Monobutylphthalate (ISO)

N-methyl-N'-nitro-N-nitrosoguanidine (ISO)

nicotine (ISO)

oxaliplatin (EXP)

paracetamol (ISO)

PCB138 (ISO)

pentachlorophenol (ISO)

perfluorooctane-1-sulfonic acid (EXP)

phenobarbital (EXP,ISO)

phenylmercury acetate (ISO)

pirinixic acid (ISO)

potassium chromate (ISO)

propiconazole (ISO)

SB 431542 (ISO)

Soman (EXP)

sunitinib (ISO)

tamibarotene (ISO)

tert-butyl hydroperoxide (ISO)

thimerosal (ISO)

topotecan (EXP)

trabectedin (ISO)

trichostatin A (ISO)

triphenyl phosphate (EXP)

valproic acid (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

cellular response to leukemia inhibitory factor (ISO)

positive regulation of transcription by RNA polymerase II (IEA,ISO)

positive regulation of transcription, DNA-templated (ISO)

regulation of transcription by RNA polymerase II (IBA)

regulation of transcription, DNA-templated (ISO)

transcription by RNA polymerase II (IC)

Cellular Component

CCAAT-binding factor complex (IBA,IDA,IEA,ISO)

nucleoplasm (ISO,TAS)

nucleus (ISO)

protein-DNA complex (ISO)

RNA polymerase II transcription regulator complex (ISO)

Molecular Function

DNA binding (ISO)

DNA-binding transcription activator activity, RNA polymerase II-specific (IEA,ISO)

DNA-binding transcription factor activity (ISO)

DNA-binding transcription factor activity, RNA polymerase II-specific (IBA)

DNA-binding transcription factor binding (IEA,ISO)

protein binding (ISO)

protein heterodimerization activity (IEA)

protein-containing complex binding (IDA)

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

sequence-specific DNA binding (IEA,ISO)

transcription cis-regulatory region binding (ISO)

Molecular Pathway Annotations Click to see Annotation Detail View

altered p53 signaling pathway (ISO)

antigen processing and presentation pathway (IEA)

tuberculosis pathway (IEA)

References

References - curated


1.	Freed-Pastor WA and Prives C, Genes Dev. 2012 Jun 15;26(12):1268-86. doi: 10.1101/gad.190678.112.
2.	Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
3.	MGD data from the GO Consortium
4.	Muller PA and Vousden KH, Nat Cell Biol. 2013 Jan;15(1):2-8. doi: 10.1038/ncb2641.
5.	NCBI rat LocusLink and RefSeq merged data July 26, 2002
6.	Pipeline to import KEGG annotations from KEGG into RGD
7.	RGD automated data pipeline
8.	RGD automated import pipeline for gene-chemical interactions
9.	Sinha S, etal., Proc Natl Acad Sci U S A 1995 Feb 28;92(5):1624-8.
10.	Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
11.	Vuorio T, etal., J Biol Chem 1990 Dec 25;265(36):22480-6.

Additional References at PubMed

PMID:1698608	PMID:11256944	PMID:12477932	PMID:15220343	PMID:15243141	PMID:15516209	PMID:15601870	PMID:15721292	PMID:15964792	PMID:18247329	PMID:19223331	PMID:19734906
PMID:20439489

Genomics

Comparative Map Data

Nfyb
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	7	20,964,988 - 20,980,569 (+)	NCBI
Rnor_6.0 Ensembl	7	27,081,667 - 27,097,479 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	7	27,081,667 - 27,097,481 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	7	27,200,204 - 27,216,018 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	7	23,190,295 - 23,205,611 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	7	23,210,565 - 23,225,880 (+)	NCBI
Celera	7	18,145,883 - 18,161,286 (+)	NCBI		Celera
Cytogenetic Map	7	q13	NCBI

NFYB
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38.p13 Ensembl	12	104,117,086 - 104,138,241 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	12	104,117,086 - 104,138,241 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	12	104,510,864 - 104,531,988 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	12	103,034,988 - 103,056,170 (-)	NCBI	NCBI36		hg18	NCBI36
Build 34	12	103,013,324 - 103,034,507	NCBI
Celera	12	104,174,600 - 104,195,782 (-)	NCBI
Cytogenetic Map	12	q23.3	NCBI
HuRef	12	101,570,544 - 101,591,726 (-)	NCBI		HuRef
CHM1_1	12	104,476,772 - 104,497,954 (-)	NCBI		CHM1_1

Nfyb
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	10	82,584,534 - 82,599,985 (-)	NCBI	GRCm39		mm39
GRCm39 Ensembl	10	82,584,535 - 82,599,978 (-)	Ensembl
GRCm38	10	82,748,700 - 82,764,151 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	10	82,748,701 - 82,764,144 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	10	82,211,445 - 82,226,886 (-)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	10	82,178,499 - 82,193,940 (-)	NCBI			mm8
Celera	10	84,733,247 - 84,748,605 (-)	NCBI		Celera
Cytogenetic Map	10	C1	NCBI
cM Map	10	40.25	NCBI

Nfyb
(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_004955405	38,771,837 - 38,789,536 (-)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955405	38,773,690 - 38,789,534 (-)	NCBI	ChiLan1.0	ChiLan1.0

NFYB
(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	12	105,089,028 - 105,108,825 (-)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	12	105,089,028 - 105,108,825 (-)	Ensembl	panpan1.1		panPan2
Mhudiblu_PPA_v0	12	101,693,559 - 101,714,057 (-)	NCBI	Mhudiblu_PPA_v0		panPan3

NFYB
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	15	42,608,067 - 42,628,816 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	15	42,609,606 - 42,629,158 (-)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	15	42,977,178 - 42,998,767 (-)	NCBI
ROS_Cfam_1.0	15	43,265,789 - 43,287,387 (-)	NCBI
UMICH_Zoey_3.1	15	42,531,537 - 42,553,082 (-)	NCBI
UNSW_CanFamBas_1.0	15	42,630,397 - 42,651,973 (-)	NCBI
UU_Cfam_GSD_1.0	15	42,901,800 - 42,923,377 (-)	NCBI

Nfyb
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HiC_Itri_2	NW_024404945	17,348,997 - 17,368,049 (+)	NCBI
SpeTri2.0	NW_004936492	10,359,387 - 10,377,537 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

NFYB
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	5	80,334,747 - 80,353,772 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	5	80,333,762 - 80,353,466 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	5	83,903,195 - 83,922,952 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3
Pig Cytomap	5	q2.3	NCBI

NFYB
(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	11	99,320,263 - 99,341,289 (-)	NCBI
ChlSab1.1 Ensembl	11	99,319,390 - 99,329,726 (-)	Ensembl

Nfyb
(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_004624750	4,600,423 - 4,616,241 (+)	NCBI

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
2298550	Neuinf6	Neuroinflammation QTL 6	3.3		nervous system integrity trait (VT:0010566)	spinal cord RT1-B protein level (CMO:0002132)	7	1	34147172	Rat
9590142	Scort5	Serum corticosterone level QTL 5	24.4	0.001	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	7	1	34828535	Rat
7411566	Bw136	Body weight QTL 136	10.4	0.001	body mass (VT:0001259)	body weight gain (CMO:0000420)	7	1	34828535	Rat
724560	Plsm3	Polydactyly-luxate syndrome (PLS) morphotypes QTL 3		0.0003	tibia length (VT:0004357)	tibia length (CMO:0000450)	7	1	37009673	Rat
2317047	Wbc4	White blood cell count QTL 4		0.01	leukocyte quantity (VT:0000217)	white blood cell count (CMO:0000027)	7	1	38119654	Rat
1300176	Hrtrt10	Heart rate QTL 10	3.19		heart pumping trait (VT:2000009)	heart rate (CMO:0000002)	7	2653138	32258115	Rat
634336	Anxrr17	Anxiety related response QTL 17	3.66		locomotor behavior trait (VT:0001392)	number of entries into a discrete space in an experimental apparatus (CMO:0000960)	7	2920071	124838025	Rat
61410	Bw19	Body weight QTL 19	6.2	0.001	body mass (VT:0001259)	body weight (CMO:0000012)	7	5911477	50911477	Rat
631503	Bp102	Blood pressure QTL 102	1.9		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	7	5951969	50951969	Rat
10755438	Coatc9	Coat color QTL 9		0	coat/hair pigmentation trait (VT:0010463)	pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)	7	9758045	54758045	Rat
9590102	Sffal5	Serum free fatty acids level QTL 5	8.62	0.001	blood free fatty acid amount (VT:0001553)	plasma free fatty acids level (CMO:0000546)	7	11647102	56647102	Rat
2298547	Neuinf5	Neuroinflammation QTL 5	3.7		nervous system integrity trait (VT:0010566)	spinal cord Cd74 protein level (CMO:0002131)	7	12328467	67193263	Rat
1643004	Pain2	Pain QTL 2	1		mechanical nociception trait (VT:0002734)	self mutilation severity score (CMO:0002145)	7	12328467	106995532	Rat
1578652	Bmd15	Bone mineral density QTL 15	5.2		femur mineral mass (VT:0010011)	trabecular volumetric bone mineral density (CMO:0001729)	7	12687850	67801690	Rat
10755440	Coatc10	Coat color QTL 10		0	coat/hair pigmentation trait (VT:0010463)	pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)	7	13952179	58952179	Rat
10059592	Kidm45	Kidney mass QTL 45	3.95	0.025	kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	7	14445685	59445685	Rat
1582260	Bw72	Body weight QTL 72	3.2	0.0043	body mass (VT:0001259)	body weight (CMO:0000012)	7	20215583	44668493	Rat
1582261	Bw69	Body weight QTL 69	3.2	0.0048	body mass (VT:0001259)	body weight (CMO:0000012)	7	20215583	44668493	Rat
1582262	Bw75	Body weight QTL 75	3	0.0038	body mass (VT:0001259)	body weight (CMO:0000012)	7	20215583	44668493	Rat
738033	Anxrr6	Anxiety related response QTL 6	4.1		exploratory behavior trait (VT:0010471)	percentage of entries into a discrete space in an experimental apparatus (CMO:0000961)	7	22168412	67168412	Rat
70207	Niddm31	Non-insulin dependent diabetes mellitus QTL 31	3.9		blood glucose amount (VT:0000188)	plasma glucose level (CMO:0000042)	7	24175337	32258115	Rat
10755451	Coatc11	Coat color QTL 11		0	coat/hair pigmentation trait (VT:0010463)	pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)	7	24731465	69731465	Rat
61369	Mcs2	Mammary carcinoma susceptibility QTL 2	3.38		mammary gland integrity trait (VT:0010552)	mammary tumor number (CMO:0000343)	7	24738680	40433335	Rat
1354644	Spl4	Serum phospholipid level QTL 4	4.9		blood phospholipid amount (VT:0006084)	blood phospholipid level (CMO:0001169)	7	25365633	57064364	Rat
1354637	Scl30	Serum cholesterol level QTL 30	3.7		blood cholesterol amount (VT:0000180)	blood total cholesterol level (CMO:0000051)	7	25365633	57064364	Rat
1354639	Spl5	Serum phospholipid level QTL 5	3.9		blood LDL phospholipid amount (VT:0010505)	blood low density lipoprotein phospholipid level (CMO:0001568)	7	25365633	60317612	Rat
1300132	Bp182	Blood pressure QTL 182	3.49		arterial blood pressure trait (VT:2000000)	blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)	7	25365633	93155402	Rat
2290372	Gluco33	Glucose level QTL 33	2.71		blood glucose amount (VT:0000188)	blood glucose level area under curve (AUC) (CMO:0000350)	7	26508887	36346595	Rat

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	230
Count of miRNA genes:	149
Interacting mature miRNAs:	185
Transcripts:	ENSRNOT00000066143
Prediction methods:	Miranda, 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
Medium	3	26	57	41	19	41	8	11	74	23	35	11	8
Low		17								12	6
Below cutoff

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_031553	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_006241196	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_017594674	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039078461	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039078462	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	BC089791	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473960	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000185	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	M55045	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	M60617	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000066143 ⟹ ENSRNOP00000061405

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	7	27,081,667 - 27,097,479 (+)	Ensembl

RefSeq Acc Id:

ENSRNOT00000082398 ⟹ ENSRNOP00000071810

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	7	27,089,278 - 27,095,777 (+)	Ensembl

RefSeq Acc Id:

NM_031553 ⟹ NP_113741

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	7	20,964,999 - 20,980,569 (+)	NCBI
Rnor_6.0	7	27,081,667 - 27,097,481 (+)	NCBI
Rnor_5.0	7	27,200,204 - 27,216,018 (+)	NCBI
RGSC_v3.4	7	23,190,295 - 23,205,611 (+)	RGD
Celera	7	18,145,883 - 18,161,286 (+)	RGD

Sequence:

show sequence

CGGCCCGCGGCGGAGGGAGGGGAGGCCGAGTCCTGGAAGTGGAGCTCCGCGCTGGGACTGGTTC
CTTCGCAGCCATTTTCTGTCCAACCAAACAGCCGATTGGAGACGGGAGCCAACCAGGGCTGCAT
TGGAGGTTAAAATTGGACAAAGATCCACCACCTTTAGGACAGGTGTTCAAGAACCCTGCAGATA
ACACAATTCTGACAGTATTTCATGACAATGGATGGCGACAGCTCTACAACAGATGCTTCTCAAC
TAGGGATTTCTGCAGACTACATCGGAGGAAGTCATTATGTGATCCAGCCCCACGATGATACTGA
GGACAGCATGAATGATCATGAAGATACAAATGGTTCAAAAGAAAGTTTCAGAGAACAAGATATT
TATCTTCCCATTGCAAATGTGGCTAGGATAATGAAAAATGCCATACCTCAAACAGGAAAGATTG
CAAAGGATGCCAAAGAATGCGTTCAGGAGTGTGTGAGTGAGTTTATAAGCTTCATAACATCTGA
AGCAAGTGAGCGCTGTCACCAGGAGAAGCGGAAGACCATCAACGGGGAGGACATTCTGTTCGCC
ATGTCCACTCTCGGCTTCGACAGCTACGTGGAGCCTCTGAAACTGTACCTCCAGAAGTTCAGAG
AGGCCATGAAGGGAGAGAAGGGCATTGGTGGGGCCGTGTCTGCTACAGATGGACTCAGCGAGGA
GCTCACGGAAGAGGCATTCACTAACCAGTTACCGGCTGGGTTAATAACTGCAGATGGCCAACAA
CAAAACGTTATGGTTTACACGACGTCCTATCAACAGATTTCTGGTGTCCAGCAGATTCAGTTTT
CATGATATGAAGGAAGGATGGAGCCGGGCTGTGTGGAGAGCGCGAGCGAGAGTCTGACGGAGTC
TGGAGCAGAGGCATTGGGAGGAAGTGAGAGTGAGGCCGCCTCCTTGTATAATAAGTAGCTGTAA
CGTAGCTTCCTGATGCCTGACTAATTGAGGTGTTAATTCTGACTTGAGAATCTTTTTCATGAAT
GATTTTAAAAGAAAAAAATTGGATTTTAAAGGTATTAAAAATATTTTTGTTTTGTACGAGAGTG
TGTTGCTCTGTGACGCCTGTATGCATTGTATATTGCGATTTATTACTGTCAGAGATTTGTAGAC
AGTTTCTTATTTTCATATTGAATCATGTTATTTTGTAATTCAAGTAAGCAGCTGGGTTAATTCA
TAATGTTTATTACCCTTTTAATAAAATATAAGGGTAGAGTTCATTTTGAATGAAAGTTGCCTTT
ATTACGAATTTGCGTTTGTCTTAGCTATACACTATCCTGCATGGTAACTTAGCCGAATGTTTAG
CATTTATTTATTGAAAACATTTTTTTTTTTTTTTTGGTAAACAGTCATAGCTTAAGCAACGTCA
TTTTTTTAACTGAATAATTAAGTTGGATGCAGAAGCAAGTGTTGCCTGGCCTGTCAGACCTGGT
GCCTGTTGCTGTCTGTGCTGTTGAGGCAGCTTCCGTTACTGCCATGCCTGTGAGAATTCCTTTC
CCTTCCATACGGTCCTGCCACCTCTGAAATGGCCCCTTTCTTCTTCAAGTATCACAGTCCCCTT
CCTGAAGAGGGAGTTTTCAGTCCACTGATAGTCATTTCCCTTCATGGAAAGGTCAGGTCCCTGT
CGGGCTGTGGGAGCCGAGCAGTGGGCGTGGTTCTGTGCAGATGCTGCAGGTGAGAGCAAGTGAG
CGGAGGAGCGGTGAGGCAGGGGAGCAGCCAGCACTTGGAATCAGGAGACACGGAGCCTTTTGGT
GTGCTGTCACACCATCTGCAGTAAGCTAGCATTAGTTGATGTAGCGTGGTTTCTTTTTTAAAGT
GAAGATTTCTATTTTCTCATCTAGTCTTTTTAGTAATACTTCCTTTGAATTTTTGTGTATGTAG
TGTGGTAGTTTTAGCCCTATCAAAAATGGCTTATTGTATAGTTTGTCCAGAGGAAATTTTGGGG
CTCCAGTGGACAAAAGCAAGCAGTTCCCTAGGTCCAGGCTGATCAGTAATGGCCACTTGCCAAG
AGTCTTGTGGAACACAGCTAGCTACTCTGAGATTAAATAATTCCCCCTTCTCCTTCCTCCTTTC
CTTTTCAGTAGTCACCTTCTGTGTAGGAGATGCACATAGGGAAGAACGGGAGGTGACGGTCAAG
CAGAACCAGCAGTCGTCCTACTGTGCTGAAGTAACAATGTTAATATTTTGATAACTCATTTGTC
CTTTTACTTTGCTAAATATGTATATTTTTATAAAGATGGGCTCGTGTTGTGCACACTGTTTTGT
AACTCGTTTTTCACTTAATACATTGTGAACATCTTTCCCAGGTCATGCATGATCTTCTGCATCA
TTTTTACTGGGTTTTTATTCTGTTATATGACTGAATCATGATTAATTTATTTAATTGCCTATTG
CACAGTTTGACCTTTTTCCATCTCTTCATAGTTATAAACATAGTTATATAAGTTCACTGAATCT
TGTGTACATCGTAACTTTTCTTGAAATAAATTCTTAGAAGTAGAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAA

hide sequence

RefSeq Acc Id:

XM_006241196 ⟹ XP_006241258

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0	7	27,082,433 - 27,097,481 (+)	NCBI
Rnor_5.0	7	27,200,204 - 27,216,018 (+)	NCBI

Sequence:

show sequence

GATGCGCTCCGCGGGGCCGCCCGGGCACCTGCGAGCCGAGGCGGCGGGTCCCCGCGAGGAACGA
GCGGCCTGGCGGGTCCCCGACCCGCTCCGCGCCTACAGCATGCAGCCATCTGGCGGCTGGCTCG
CCCCGGACTTGCCCCGAAGGTTAAAATTGGACAAAGATCCACCACCTTTAGGACAGGTGTTCAA
GAACCCTGCAGATAACACAATTCTGACAGTATTTCATGACAATGGATGGCGACAGCTCTACAAC
AGATGCTTCTCAACTAGGGATTTCTGCAGACTACATCGGAGGAAGTCATTATGTGATCCAGCCC
CACGATGATACTGAGGACAGCATGAATGATCATGAAGATACAAATGGTTCAAAAGAAAGTTTCA
GAGAACAAGATATTTATCTTCCCATTGCAAATGTGGCTAGGATAATGAAAAATGCCATACCTCA
AACAGGAAAGATTGCAAAGGATGCCAAAGAATGCGTTCAGGAGTGTGTGAGTGAGTTTATAAGC
TTCATAACATCTGAAGCAAGTGAGCGCTGTCACCAGGAGAAGCGGAAGACCATCAACGGGGAGG
ACATTCTGTTCGCCATGTCCACTCTCGGCTTCGACAGCTACGTGGAGCCTCTGAAACTGTACCT
CCAGAAGTTCAGAGAGGCCATGAAGGGAGAGAAGGGCATTGGTGGGGCCGTGTCTGCTACAGAT
GGACTCAGCGAGGAGCTCACGGAAGAGGCATTCACTAACCAGTTACCGGCTGGGTTAATAACTG
CAGATGGCCAACAACAAAACGTTATGGTTTACACGACGTCCTATCAACAGATTTCTGGTGTCCA
GCAGATTCAGTTTTCATGATATGAAGGAAGGATGGAGCCGGGCTGTGTGGAGAGCGCGAGCGAG
AGTCTGACGGAGTCTGGAGCAGAGGCATTGGGAGGAAGTGAGAGTGAGGCCGCCTCCTTGTATA
ATAAGTAGCTGTAACGTAGCTTCCTGATGCCTGACTAATTGAGGTGTTAATTCTGACTTGAGAA
TCTTTTTCATGAATGATTTTAAAAGAAAAAAATTGGATTTTAAAGGTATTAAAAATATTTTTGT
TTTGTACGAGAGTGTGTTGCTCTGTGACGCCTGTATGCATTGTATATTGCGATTTATTACTGTC
AGAGATTTGTAGACAGTTTCTTATTTTCATATTGAATCATGTTATTTTGTAATTCAAGTAAGCA
GCTGGGTTAATTCATAATGTTTATTACCCTTTTAATAAAATATAAGGGTAGAGTTCATTTTGAA
TGAAAGTTGCCTTTATTACGAATTTGCGTTTGTCTTAGCTATACACTATCCTGCATGGTAACTT
AGCCGAATGTTTAGCATTTATTTATTGAAAACATTTTTTTTTTTTTTTTGGTAAACAGTCATAG
CTTAAGCAACGTCATTTTTTTAACTGAATAATTAAGTTGGATGCAGAAGCAAGTGTTGCCTGGC
CTGTCAGACCTGGTGCCTGTTGCTGTCTGTGCTGTTGAGGCAGCTTCCGTTACTGCCATGCCTG
TGAGAATTCCTTTCCCTTCCATACGGTCCTGCCACCTCTGAAATGGCCCCTTTCTTCTTCAAGT
ATCACAGTCCCCTTCCTGAAGAGGGAGTTTTCAGTCCACTGATAGTCATTTCCCTTCATGGAAA
GGTCAGGTCCCTGTCGGGCTGTGGGAGCCGAGCAGTGGGCGTGGTTCTGTGCAGATGCTGCAGG
TGAGAGCAAGTGAGCGGAGGAGCGGTGAGGCAGGGGAGCAGCCAGCACTTGGAATCAGGAGACA
CGGAGCCTTTTGGTGTGCTGTCACACCATCTGCAGTAAGCTAGCATTAGTTGATGTAGCGTGGT
TTCTTTTTTAAAGTGAAGATTTCTATTTTCTCATCTAGTCTTTTTAGTAATACTTCCTTTGAAT
TTTTGTGTATGTAGTGTGGTAGTTTTAGCCCTATCAAAAATGGCTTATTGTATAGTTTGTCCAG
AGGAAATTTTGGGGCTCCAGTGGACAAAAGCAAGCAGTTCCCTAGGTCCAGGCTGATCAGTAAT
GGCCACTTGCCAAGAGTCTTGTGGAACACAGCTAGCTACTCTGAGATTAAATAATTCCCCCTTC
TCCTTCCTCCTTTCCTTTTCAGTAGTCACCTTCTGTGTAGGAGATGCACATAGGGAAGAACGGG
AGGTGACGGTCAAGCAGAACCAGCAGTCGTCCTACTGTGCTGAAGTAACAATGTTAATATTTTG
ATAACTCATTTGTCCTTTTACTTTGCTAAATATGTATATTTTTATAAAGATGGGCTCGTGTTGT
GCACACTGTTTTGTAACTCGTTTTTCACTTAATACATTGTGAACATCTTTCCCAGGTCATGCAT
GATCTTCTGCATCATTTTTACTGGGTTTTTATTCTGTTATATGACTGAATCATGATTAATTTAT
TTAATTGCCTATTGCACAGTTTGACCTTTTTCCATCTCTTCATAGTTATAAACATAGTTATATA
AGTTCACTGAATCTTGTGTACATCGTAACTTTTCTTGAAATAAATTCTTAGAAGTAGAA

hide sequence

RefSeq Acc Id:

XM_017594674 ⟹ XP_017450163

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	7	20,965,529 - 20,980,569 (+)	NCBI
Rnor_6.0	7	27,081,807 - 27,093,745 (+)	NCBI

Sequence:

show sequence

TCTCGCTTCGGCCAATGATCGCTCCTAAACCGACTCCACTTTAGCTCGAATGAAATGTCCGTCT
CCTCCCGGCGCCGTCCCCGCCGCCAACGCCGCAGCGGTCGGGGGCACTCGCAGTCCGCAGCCTT
CGGGCGGGCCGGGCCTCCGGGCGAGGCCGCTGTGCTTCGGGCCGGGCCCGGCGCGGGGCGGCGG
GTGCTTTGTGCGCGGGGCCGCGAGCCCGAGCCGGGCTGGGCCGGGCGGCTGCGGGGCTCTCGCG
GCGGCAGCCCCGGGTCGGCTCCATTTTGTCCGGGTAGCCGGCGGGCGGGGAACGCGGCGCTCCG
GAGCGGCCGCTTTGTCTCCCGCATCCCGGCGGCGGCAGGCGTTGGGCGCGGGCGGCGGGGGGAT
GCGCTCCGCGGGGCCGCCCGGGCACCTGCGAGCCGAGGCGGCGGGTCCCCGCGAGGAACGAGCG
GCCTGGCGGGTCCCCGACCCGCTCCGCGCCTACAGCATGCAGCCATCTGGCGGCTGGCTCGCCC
CGGACTTGCCCCGAAGGTTAAAATTGGACAAAGATCCACCACCTTTAGGACAGGTGTTCAAGAA
CCCTGCAGATAACACAATTCTGACAGTATTTCATGACAATGGATGGCGACAGCTCTACAACAGA
TGCTTCTCAACTAGGGATTTCTGCAGACTACATCGGAGGAAGTCATTATGTGATCCAGCCCCAC
GATGATTGCAAAGGATGCCAAAGAATGCGTTCAGGAGTGTGTGAGTGAGTTTATAAGCTTCATA
ACATCTGAAGCAAGTGAGCGCTGTCACCAGGAGAAGCGGAAGACCATCAACGGGGAGGACATTC
TGTTCGCCATGTCCACTCTCGGCTTCGACAGCTACGTGGAGCCTCTGAAACTGTACCTCCAGAA
GTTCAGAGAG

hide sequence

RefSeq Acc Id:

XM_039078461 ⟹ XP_038934389

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	7	20,965,529 - 20,980,569 (+)	NCBI

RefSeq Acc Id:

XM_039078462 ⟹ XP_038934390

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	7	20,964,988 - 20,980,569 (+)	NCBI

Protein Sequences


Protein RefSeqs	NP_113741	(Get FASTA)	NCBI Sequence Viewer
	XP_017450163	(Get FASTA)	NCBI Sequence Viewer
	XP_038934389	(Get FASTA)	NCBI Sequence Viewer
	XP_038934390	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAA40887	(Get FASTA)	NCBI Sequence Viewer
	AAA40888	(Get FASTA)	NCBI Sequence Viewer
	AAH89791	(Get FASTA)	NCBI Sequence Viewer
	EDM17067	(Get FASTA)	NCBI Sequence Viewer
	EDM17068	(Get FASTA)	NCBI Sequence Viewer
	EDM17069	(Get FASTA)	NCBI Sequence Viewer
	P63140	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:

NP_113741 ⟸ NM_031553

- UniProtKB:

P63140 (UniProtKB/Swiss-Prot)

- Sequence:

show sequence

MTMDGDSSTTDASQLGISADYIGGSHYVIQPHDDTEDSMNDHEDTNGSKESFREQDIYLPIANV
ARIMKNAIPQTGKIAKDAKECVQECVSEFISFITSEASERCHQEKRKTINGEDILFAMSTLGFD
SYVEPLKLYLQKFREAMKGEKGIGGAVSATDGLSEELTEEAFTNQLPAGLITADGQQQNVMVYT
TSYQQISGVQQIQFS

hide sequence

RefSeq Acc Id:

XP_006241258 ⟸ XM_006241196

- Peptide Label:

isoform X2

- Sequence:

show sequence

MTMDGDSSTTDASQLGISADYIGGSHYVIQPHDDTEDSMNDHEDTNGSKESFREQDIYLPIANV
ARIMKNAIPQTGKIAKDAKECVQECVSEFISFITSEASERCHQEKRKTINGEDILFAMSTLGFD
SYVEPLKLYLQKFREAMKGEKGIGGAVSATDGLSEELTEEAFTNQLPAGLITADGQQQNVMVYT
TSYQQISGVQQIQFS

hide sequence

RefSeq Acc Id:

XP_017450163 ⟸ XM_017594674

- Peptide Label:

isoform X2

- Sequence:

show sequence

MKCPSPPGAVPAANAAAVGGTRSPQPSGGPGLRARPLCFGPGPARGGGCFVRGAASPSRAGPGG
CGALAAAAPGRLHFVRVAGGRGTRRSGAAALSPASRRRQALGAGGGGMRSAGPPGHLRAEAAGP
REERAAWRVPDPLRAYSMQPSGGWLAPDLPRRLKLDKDPPPLGQVFKNPADNTILTVFHDNGWR
QLYNRCFSTRDFCRLHRRKSLCDPAPR

hide sequence

RefSeq Acc Id:

ENSRNOP00000071810 ⟸ ENSRNOT00000082398

RefSeq Acc Id:

ENSRNOP00000061405 ⟸ ENSRNOT00000066143

RefSeq Acc Id:	XP_038934390 ⟸ XM_039078462
- Peptide Label:	isoform X2

RefSeq Acc Id:	XP_038934389 ⟸ XM_039078461
- Peptide Label:	isoform X1

Protein Domains

CBFD_NFYB_HMF

Transcriptome

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

Promoters

RGD ID:

13695111

Promoter ID:

EPDNEW_R5636

Type:

initiation region

Name:

Nfyb_1

Description:

nuclear transcription factor Y subunit beta

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	7	27,081,737 - 27,081,797	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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CSV

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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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CSV

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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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CSV

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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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CSV

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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:3172	AgrOrtholog
Ensembl Genes	ENSRNOG00000010309	Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein	ENSRNOP00000061405	ENTREZGENE, UniProtKB/Swiss-Prot
	ENSRNOP00000071810	UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000066143	ENTREZGENE, UniProtKB/Swiss-Prot
	ENSRNOT00000082398	UniProtKB/TrEMBL
Gene3D-CATH	1.10.20.10	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE	IMAGE:7380395	IMAGE-MGC_LOAD
InterPro	CBFA_NFYB_domain	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Histone-fold	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Transc_fact_NFYB/HAP3	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Transcrpt_fac_NFYB/HAP3_CS	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report	rno:25336	UniProtKB/Swiss-Prot
MGC_CLONE	MGC:108654	IMAGE-MGC_LOAD
NCBI Gene	25336	ENTREZGENE
PANTHER	PTHR11064	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam	CBFD_NFYB_HMF	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen	Nfyb	PhenoGen
PROSITE	NFYB_HAP3	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP	SSF47113	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGR	TC209912
	TC223146
UniProt	A0A0G2K1E6_RAT	UniProtKB/TrEMBL
	NFYB_RAT	UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary	P22569	UniProtKB/Swiss-Prot
	Q5FVT0	UniProtKB/Swiss-Prot

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2015-11-20	Nfyb	nuclear transcription factor Y subunit beta	Nfyb	nuclear transcription factor-Y beta	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2001-07-23	Nfyb	nuclear transcription factor - Y beta			Name updated to reflect Human and Mouse nomenclature	67952	APPROVED
2001-07-23	Nfyb	CCAAT binding transcription factor of CBF-B/NFY-B			Name withdrawn	67952	WITHDRAWN

RGD Curation Notes

Note Type	Note	Reference
gene_protein	207 amino acids	728940

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)

RGD Manual Annotations

Imported Annotations - KEGG (archival)

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RGD Manual Annotations

Imported Annotations - KEGG (archival)