Nfyb (nuclear transcription factor Y subunit beta) - Rat Genome Database

Send us a Message



Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
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 AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2720,964,988 - 20,980,569 (+)NCBI
Rnor_6.0 Ensembl727,081,667 - 27,097,479 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0727,081,667 - 27,097,481 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0727,200,204 - 27,216,018 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4723,190,295 - 23,205,611 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1723,210,565 - 23,225,880 (+)NCBI
Celera718,145,883 - 18,161,286 (+)NCBICelera
Cytogenetic Map7q13NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


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)

Molecular Pathway Annotations     Click to see Annotation Detail View
References

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 AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2720,964,988 - 20,980,569 (+)NCBI
Rnor_6.0 Ensembl727,081,667 - 27,097,479 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0727,081,667 - 27,097,481 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0727,200,204 - 27,216,018 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4723,190,295 - 23,205,611 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1723,210,565 - 23,225,880 (+)NCBI
Celera718,145,883 - 18,161,286 (+)NCBICelera
Cytogenetic Map7q13NCBI
NFYB
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl12104,117,086 - 104,138,241 (-)EnsemblGRCh38hg38GRCh38
GRCh3812104,117,086 - 104,138,241 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh3712104,510,864 - 104,531,988 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 3612103,034,988 - 103,056,170 (-)NCBINCBI36hg18NCBI36
Build 3412103,013,324 - 103,034,507NCBI
Celera12104,174,600 - 104,195,782 (-)NCBI
Cytogenetic Map12q23.3NCBI
HuRef12101,570,544 - 101,591,726 (-)NCBIHuRef
CHM1_112104,476,772 - 104,497,954 (-)NCBICHM1_1
Nfyb
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391082,584,534 - 82,599,985 (-)NCBIGRCm39mm39
GRCm39 Ensembl1082,584,535 - 82,599,978 (-)Ensembl
GRCm381082,748,700 - 82,764,151 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1082,748,701 - 82,764,144 (-)EnsemblGRCm38mm10GRCm38
MGSCv371082,211,445 - 82,226,886 (-)NCBIGRCm37mm9NCBIm37
MGSCv361082,178,499 - 82,193,940 (-)NCBImm8
Celera1084,733,247 - 84,748,605 (-)NCBICelera
Cytogenetic Map10C1NCBI
cM Map1040.25NCBI
Nfyb
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540538,771,837 - 38,789,536 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495540538,773,690 - 38,789,534 (-)NCBIChiLan1.0ChiLan1.0
NFYB
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.112105,089,028 - 105,108,825 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl12105,089,028 - 105,108,825 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v012101,693,559 - 101,714,057 (-)NCBIMhudiblu_PPA_v0panPan3
NFYB
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11542,608,067 - 42,628,816 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1542,609,606 - 42,629,158 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1542,977,178 - 42,998,767 (-)NCBI
ROS_Cfam_1.01543,265,789 - 43,287,387 (-)NCBI
UMICH_Zoey_3.11542,531,537 - 42,553,082 (-)NCBI
UNSW_CanFamBas_1.01542,630,397 - 42,651,973 (-)NCBI
UU_Cfam_GSD_1.01542,901,800 - 42,923,377 (-)NCBI
Nfyb
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494517,348,997 - 17,368,049 (+)NCBI
SpeTri2.0NW_00493649210,359,387 - 10,377,537 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
NFYB
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl580,334,747 - 80,353,772 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1580,333,762 - 80,353,466 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2583,903,195 - 83,922,952 (+)NCBISscrofa10.2Sscrofa10.2susScr3
Pig Cytomap5q2.3NCBI
NFYB
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11199,320,263 - 99,341,289 (-)NCBI
ChlSab1.1 Ensembl1199,319,390 - 99,329,726 (-)Ensembl
Nfyb
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247504,600,423 - 4,616,241 (+)NCBI


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2298550Neuinf6Neuroinflammation QTL 63.3nervous system integrity trait (VT:0010566)spinal cord RT1-B protein level (CMO:0002132)7134147172Rat
9590142Scort5Serum corticosterone level QTL 524.40.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)7134828535Rat
7411566Bw136Body weight QTL 13610.40.001body mass (VT:0001259)body weight gain (CMO:0000420)7134828535Rat
724560Plsm3Polydactyly-luxate syndrome (PLS) morphotypes QTL 30.0003tibia length (VT:0004357)tibia length (CMO:0000450)7137009673Rat
2317047Wbc4White blood cell count QTL 40.01leukocyte quantity (VT:0000217)white blood cell count (CMO:0000027)7138119654Rat
1300176Hrtrt10Heart rate QTL 103.19heart pumping trait (VT:2000009)heart rate (CMO:0000002)7265313832258115Rat
634336Anxrr17Anxiety related response QTL 173.66locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)72920071124838025Rat
61410Bw19Body weight QTL 196.20.001body mass (VT:0001259)body weight (CMO:0000012)7591147750911477Rat
631503Bp102Blood pressure QTL 1021.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)7595196950951969Rat
10755438Coatc9Coat color QTL 90coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)7975804554758045Rat
9590102Sffal5Serum free fatty acids level QTL 58.620.001blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)71164710256647102Rat
2298547Neuinf5Neuroinflammation QTL 53.7nervous system integrity trait (VT:0010566)spinal cord Cd74 protein level (CMO:0002131)71232846767193263Rat
1643004Pain2Pain QTL 21mechanical nociception trait (VT:0002734)self mutilation severity score (CMO:0002145)712328467106995532Rat
1578652Bmd15Bone mineral density QTL 155.2femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)71268785067801690Rat
10755440Coatc10Coat color QTL 100coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)71395217958952179Rat
10059592Kidm45Kidney mass QTL 453.950.025kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)71444568559445685Rat
1582260Bw72Body weight QTL 723.20.0043body mass (VT:0001259)body weight (CMO:0000012)72021558344668493Rat
1582261Bw69Body weight QTL 693.20.0048body mass (VT:0001259)body weight (CMO:0000012)72021558344668493Rat
1582262Bw75Body weight QTL 7530.0038body mass (VT:0001259)body weight (CMO:0000012)72021558344668493Rat
738033Anxrr6Anxiety related response QTL 64.1exploratory behavior trait (VT:0010471)percentage of entries into a discrete space in an experimental apparatus (CMO:0000961)72216841267168412Rat
70207Niddm31Non-insulin dependent diabetes mellitus QTL 313.9blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)72417533732258115Rat
10755451Coatc11Coat color QTL 110coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)72473146569731465Rat
61369Mcs2Mammary carcinoma susceptibility QTL 23.38mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)72473868040433335Rat
1354644Spl4Serum phospholipid level QTL 44.9blood phospholipid amount (VT:0006084)blood phospholipid level (CMO:0001169)72536563357064364Rat
1354637Scl30Serum cholesterol level QTL 303.7blood cholesterol amount (VT:0000180)blood total cholesterol level (CMO:0000051)72536563357064364Rat
1354639Spl5Serum phospholipid level QTL 53.9blood LDL phospholipid amount (VT:0010505)blood low density lipoprotein phospholipid level (CMO:0001568)72536563360317612Rat
1300132Bp182Blood pressure QTL 1823.49arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)72536563393155402Rat
2290372Gluco33Glucose level QTL 332.71blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)72650888736346595Rat

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

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000066143   ⟹   ENSRNOP00000061405
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl727,081,667 - 27,097,479 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000082398   ⟹   ENSRNOP00000071810
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl727,089,278 - 27,095,777 (+)Ensembl
RefSeq Acc Id: NM_031553   ⟹   NP_113741
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2720,964,999 - 20,980,569 (+)NCBI
Rnor_6.0727,081,667 - 27,097,481 (+)NCBI
Rnor_5.0727,200,204 - 27,216,018 (+)NCBI
RGSC_v3.4723,190,295 - 23,205,611 (+)RGD
Celera718,145,883 - 18,161,286 (+)RGD
Sequence:
RefSeq Acc Id: XM_006241196   ⟹   XP_006241258
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0727,082,433 - 27,097,481 (+)NCBI
Rnor_5.0727,200,204 - 27,216,018 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017594674   ⟹   XP_017450163
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2720,965,529 - 20,980,569 (+)NCBI
Rnor_6.0727,081,807 - 27,093,745 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039078461   ⟹   XP_038934389
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2720,965,529 - 20,980,569 (+)NCBI
RefSeq Acc Id: XM_039078462   ⟹   XP_038934390
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2720,964,988 - 20,980,569 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_113741   ⟸   NM_031553
- UniProtKB: P63140 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006241258   ⟸   XM_006241196
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_017450163   ⟸   XM_017594674
- Peptide Label: isoform X2
- 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 AssemblyChrPosition (strand)Source
Rnor_6.0727,081,737 - 27,081,797EPDNEW

Strain Variation

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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD: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