Nfya (nuclear transcription factor Y subunit alpha) - Rat Genome Database

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Gene: Nfya (nuclear transcription factor Y subunit alpha) Rattus norvegicus
Analyze
Symbol: Nfya
Name: nuclear transcription factor Y subunit alpha
RGD ID: 70976
Description: Enables transcription coregulator binding activity. Predicted to be involved in histone H3-K4 trimethylation; regulation of histone acetylation; and regulation of transcription, DNA-templated. Predicted to act upstream of or within positive regulation of stem cell proliferation; positive regulation of transcription by RNA polymerase II; and regulation of stem cell population maintenance. Part of CCAAT-binding activity factor complex. Orthologous to human NFYA (nuclear transcription factor Y subunit alpha); PARTICIPATES IN altered p53 signaling pathway; antigen processing and presentation pathway; tuberculosis pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 6-propyl-2-thiouracil; acetamide.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: CAAT box DNA-binding protein subunit A; CAAT-box DNA-binding protein subunit A; CBF-A; CBF-B; CCAAT-binding transcription factor subunit A; CCAAT-binding transcription factor subunit B; NF-YA; nuclear transcription factor Y subunit A; nuclear transcription factor-Y alpha
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2912,587,437 - 12,613,911 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl912,586,259 - 12,613,898 (+)Ensembl
Rnor_6.0914,551,752 - 14,577,002 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl914,551,758 - 14,576,967 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0913,474,255 - 13,499,504 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.497,970,040 - 7,994,375 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.197,970,039 - 7,994,375 (+)NCBI
Celera910,361,436 - 10,385,715 (+)NCBICelera
Cytogenetic Map9q12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(-)-demecolcine  (ISO)
(-)-epigallocatechin 3-gallate  (ISO)
1,2-dimethylhydrazine  (ISO)
17beta-estradiol  (ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,2',5,5'-tetrachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
3,4-methylenedioxymethamphetamine  (ISO)
3-methylcholanthrene  (ISO)
4,4'-diaminodiphenylmethane  (ISO)
5-fluorouracil  (ISO)
6-propyl-2-thiouracil  (EXP)
acetamide  (EXP)
aflatoxin B1  (ISO)
Aflatoxin B2 alpha  (ISO)
all-trans-retinoic acid  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
benzene  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
bisphenol A  (EXP)
CGP 52608  (ISO)
chlordecone  (ISO)
cisplatin  (ISO)
copper(II) sulfate  (ISO)
crocidolite asbestos  (ISO)
curcumin  (ISO)
cyclosporin A  (ISO)
deoxynivalenol  (ISO)
diazinon  (ISO)
enzyme inhibitor  (ISO)
ethanol  (ISO)
ethyl methanesulfonate  (ISO)
folic acid  (ISO)
formaldehyde  (ISO)
hydrogen cyanide  (ISO)
L-ascorbic acid  (ISO)
lead diacetate  (ISO)
leflunomide  (ISO)
methotrexate  (ISO)
methyl methanesulfonate  (ISO)
methylmercury chloride  (ISO)
mitomycin C  (ISO)
monosodium L-glutamate  (ISO)
N-ethyl-N-nitrosourea  (ISO)
N-methyl-N'-nitro-N-nitrosoguanidine  (ISO)
N-nitrosodiethylamine  (EXP)
nickel dichloride  (ISO)
paracetamol  (EXP,ISO)
PCB138  (ISO)
phenethyl caffeate  (EXP)
phenol  (ISO)
pirinixic acid  (ISO)
potassium chromate  (ISO)
potassium cyanide  (ISO)
quercetin  (ISO)
rifampicin  (ISO)
sodium dodecyl sulfate  (ISO)
sodium fluoride  (ISO)
thioacetamide  (EXP)
trabectedin  (ISO)
tungsten  (ISO)
urethane  (ISO)
valproic acid  (ISO)
vorinostat  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Mutant p53: one name, many proteins. Freed-Pastor WA and Prives C, Genes Dev. 2012 Jun 15;26(12):1268-86. doi: 10.1101/gad.190678.112.
2. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
3. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
4. NF-Y is essential for expression of the proapoptotic bim gene in sympathetic neurons. Hughes R, etal., Cell Death Differ. 2011 Jun;18(6):937-47. doi: 10.1038/cdd.2010.166. Epub 2010 Dec 17.
5. The B subunit of a rat heteromeric CCAAT-binding transcription factor shows a striking sequence identity with the yeast Hap2 transcription factor. Maity SN, etal., Proc Natl Acad Sci U S A 1990 Jul;87(14):5378-82.
6. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
7. p53 mutations in cancer. Muller PA and Vousden KH, Nat Cell Biol. 2013 Jan;15(1):2-8. doi: 10.1038/ncb2641.
8. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
9. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
10. GOA pipeline RGD automated data pipeline
11. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
12. Interaction between the two ubiquitously expressed transcription factors NF-Y and Sp1. Roder K, etal., Gene. 1999 Jun 24;234(1):61-9.
13. Recombinant rat CBF-C, the third subunit of CBF/NFY, allows formation of a protein-DNA complex with CBF-A and CBF-B and with yeast HAP2 and HAP3. Sinha S, etal., Proc Natl Acad Sci U S A 1995 Feb 28;92(5):1624-8.
Additional References at PubMed
PMID:1569083   PMID:1698608   PMID:8306889   PMID:11022037   PMID:11256944   PMID:12659851   PMID:12730328   PMID:15243141   PMID:15516209   PMID:15601870   PMID:15964792   PMID:16087680  
PMID:20630860   PMID:20861184   PMID:22969033   PMID:24030830  


Genomics

Comparative Map Data
Nfya
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2912,587,437 - 12,613,911 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl912,586,259 - 12,613,898 (+)Ensembl
Rnor_6.0914,551,752 - 14,577,002 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl914,551,758 - 14,576,967 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0913,474,255 - 13,499,504 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.497,970,040 - 7,994,375 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.197,970,039 - 7,994,375 (+)NCBI
Celera910,361,436 - 10,385,715 (+)NCBICelera
Cytogenetic Map9q12NCBI
NFYA
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38641,072,974 - 41,102,403 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl641,072,974 - 41,102,403 (+)EnsemblGRCh38hg38GRCh38
GRCh37641,040,713 - 41,070,142 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36641,148,688 - 41,174,713 (+)NCBINCBI36hg18NCBI36
Build 34641,148,687 - 41,174,714NCBI
Celera642,593,388 - 42,622,828 (+)NCBI
Cytogenetic Map6p21.1NCBI
HuRef640,758,459 - 40,787,895 (+)NCBIHuRef
CHM1_1641,043,210 - 41,072,650 (+)NCBICHM1_1
T2T-CHM13v2.0640,901,531 - 40,930,960 (+)NCBI
Nfya
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391748,693,913 - 48,716,848 (-)NCBIGRCm39mm39
GRCm39 Ensembl1748,693,913 - 48,716,934 (-)Ensembl
GRCm381748,386,885 - 48,409,820 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1748,386,885 - 48,409,906 (-)EnsemblGRCm38mm10GRCm38
MGSCv371748,526,210 - 48,549,145 (-)NCBIGRCm37mm9NCBIm37
MGSCv361747,853,500 - 47,875,288 (-)NCBImm8
Celera1751,818,370 - 51,841,444 (-)NCBICelera
Cytogenetic Map17CNCBI
cM Map1723.99NCBI
Nfya
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554377,744,633 - 7,771,035 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554377,745,182 - 7,770,348 (+)NCBIChiLan1.0ChiLan1.0
NFYA
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1641,969,561 - 41,999,279 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl641,969,561 - 41,996,963 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0640,661,407 - 40,688,440 (+)NCBIMhudiblu_PPA_v0panPan3
NFYA
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1129,827,254 - 9,854,693 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl129,835,285 - 9,854,543 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha129,857,490 - 9,886,781 (+)NCBI
ROS_Cfam_1.01210,307,124 - 10,336,396 (+)NCBI
ROS_Cfam_1.0 Ensembl1210,308,079 - 10,337,166 (+)Ensembl
UMICH_Zoey_3.1129,839,014 - 9,868,509 (+)NCBI
UNSW_CanFamBas_1.0129,921,197 - 9,950,466 (+)NCBI
UU_Cfam_GSD_1.01210,015,520 - 10,045,268 (+)NCBI
Nfya
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494645,209,288 - 45,233,519 (+)NCBI
SpeTri2.0NW_00493647618,728,575 - 18,750,917 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
NFYA
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl736,385,873 - 36,409,495 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1736,385,677 - 36,409,495 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2741,682,169 - 41,705,576 (+)NCBISscrofa10.2Sscrofa10.2susScr3
NFYA
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11731,057,059 - 31,084,036 (-)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl1731,059,630 - 31,077,926 (-)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366604441,073,590 - 41,100,712 (+)NCBIVero_WHO_p1.0
Nfya
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462475417,656,036 - 17,682,624 (-)EnsemblHetGla_female_1.0hetGla2
HetGla 1.0NW_00462475417,660,134 - 17,682,604 (-)NCBIHetGla_female_1.0hetGla2

Position Markers
RH132935  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2912,586,272 - 12,586,470 (+)MAPPERmRatBN7.2
Rnor_6.0914,550,543 - 14,550,740NCBIRnor6.0
Rnor_5.0913,473,045 - 13,473,242UniSTSRnor5.0
RGSC_v3.497,968,825 - 7,969,022UniSTSRGSC3.4
Celera910,360,221 - 10,360,418UniSTS
RH 3.4 Map930.1UniSTS
Cytogenetic Map9q12UniSTS
RH94867  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2912,611,613 - 12,611,803 (+)MAPPERmRatBN7.2
Rnor_6.0914,574,704 - 14,574,893NCBIRnor6.0
Rnor_5.0913,497,206 - 13,497,395UniSTSRnor5.0
RGSC_v3.497,994,181 - 7,994,370UniSTSRGSC3.4
Celera910,385,521 - 10,385,710UniSTS
Cytogenetic Map9q12UniSTS
RH132381  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2912,611,580 - 12,611,789 (+)MAPPERmRatBN7.2
Rnor_6.0914,574,671 - 14,574,879NCBIRnor6.0
Rnor_5.0913,497,173 - 13,497,381UniSTSRnor5.0
RGSC_v3.497,994,148 - 7,994,356UniSTSRGSC3.4
Celera910,385,488 - 10,385,696UniSTS
RH 3.4 Map928.4UniSTS
Cytogenetic Map9q12UniSTS
RH94866  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2912,611,603 - 12,611,793 (+)MAPPERmRatBN7.2
Rnor_6.0914,574,694 - 14,574,883NCBIRnor6.0
Rnor_5.0913,497,196 - 13,497,385UniSTSRnor5.0
RGSC_v3.497,994,171 - 7,994,360UniSTSRGSC3.4
Celera910,385,511 - 10,385,700UniSTS
Cytogenetic Map9q12UniSTS
RH136693  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2912,588,286 - 12,588,409 (+)MAPPERmRatBN7.2
Rnor_6.0914,552,557 - 14,552,679NCBIRnor6.0
Rnor_5.0913,475,059 - 13,475,181UniSTSRnor5.0
RGSC_v3.497,970,839 - 7,970,961UniSTSRGSC3.4
Celera910,362,235 - 10,362,357UniSTS
Cytogenetic Map9q12UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
10054141Gmadr4Adrenal mass QTL 42.450.0074adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)9114209783Rat
70226Eae4Experimental allergic encephalomyelitis QTL 4nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)9125661317Rat
9589055Scfw5Subcutaneous fat weight QTL 55.550.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)9137999212Rat
7411592Foco8Food consumption QTL 87.40.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)9137999212Rat
9589158Gluco65Glucose level QTL 656.820.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)9137999212Rat
1300124Cm4Cardiac mass QTL 43.55heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)9140594091Rat
1298088Edpm11Estrogen-dependent pituitary mass QTL 112.5pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)9143718459Rat
1641911Alcrsp13Alcohol response QTL 13response to alcohol trait (VT:0010489)brain neurotensin receptor 1 density (CMO:0002068)9143718459Rat
10054125Srcrt7Stress Responsive Cort QTL 73.330.0011blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)9187073594Rat
1331757Cdexp1CD45RC expression in CD8 T cells QTL 14.3CD8-positive T cell quantity (VT:0008077)blood CD45RC(high) CD8 T cell count to CD45RC(low) CD8 T cell count ratio (CMO:0001990)9102453767509080Rat
1354650Despr5Despair related QTL 54.010.0017locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)9125408446254084Rat
2303559Gluco54Glucose level QTL 542blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)9125408446254084Rat
1578675Bss17Bone structure and strength QTL 173.8femur morphology trait (VT:0000559)femoral neck cortical cross-sectional area (CMO:0001702)9336865213533896Rat
61425Cia15Collagen induced arthritis QTL 154.6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)9510982642921101Rat
631211Bw4Body weight QTL45.31retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)9510982650109826Rat
11353947Bp392Blood pressure QTL 392arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)9728325252283252Rat
61450Ciaa3CIA Autoantibody QTL 36.5blood autoantibody amount (VT:0003725)calculated serum anti-type 2 collagen antibody titer (CMO:0001279)9795472022071169Rat
9589133Insul26Insulin level QTL 2617.960.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)9895256053952560Rat
7411609Foco16Food consumption QTL 1625.60.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)9895256053952560Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:49
Count of miRNA genes:42
Interacting mature miRNAs:48
Transcripts:ENSRNOT00000017157
Prediction methods: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
Medium 3 28 31 22 18 22 59 27 36 11
Low 15 26 19 1 19 8 11 15 8 5 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000017157   ⟹   ENSRNOP00000017157
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl912,596,294 - 12,606,263 (+)Ensembl
Rnor_6.0 Ensembl914,551,758 - 14,574,898 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000091532   ⟹   ENSRNOP00000075707
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl912,587,482 - 12,613,892 (+)Ensembl
Rnor_6.0 Ensembl914,560,504 - 14,576,967 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000115817   ⟹   ENSRNOP00000078156
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl912,586,259 - 12,613,898 (+)Ensembl
RefSeq Acc Id: NM_012865   ⟹   NP_036997
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2912,587,488 - 12,611,808 (+)NCBI
Rnor_6.0914,551,758 - 14,574,898 (+)NCBI
Rnor_5.0913,474,255 - 13,499,504 (+)NCBI
RGSC_v3.497,970,040 - 7,994,375 (+)RGD
Celera910,361,436 - 10,385,715 (+)RGD
Sequence:
RefSeq Acc Id: XM_006244409   ⟹   XP_006244471
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2912,587,437 - 12,613,911 (+)NCBI
Rnor_6.0914,551,752 - 14,577,002 (+)NCBI
Rnor_5.0913,474,255 - 13,499,504 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006244410   ⟹   XP_006244472
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2912,587,437 - 12,611,589 (+)NCBI
Rnor_6.0914,551,753 - 14,577,002 (+)NCBI
Rnor_5.0913,474,255 - 13,499,504 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006244411   ⟹   XP_006244473
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2912,587,437 - 12,613,911 (+)NCBI
Rnor_6.0914,551,753 - 14,577,002 (+)NCBI
Rnor_5.0913,474,255 - 13,499,504 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006244412   ⟹   XP_006244474
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2912,587,437 - 12,613,911 (+)NCBI
Rnor_6.0914,551,753 - 14,577,002 (+)NCBI
Rnor_5.0913,474,255 - 13,499,504 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006244413   ⟹   XP_006244475
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2912,587,437 - 12,613,908 (+)NCBI
Rnor_6.0914,551,754 - 14,577,002 (+)NCBI
Rnor_5.0913,474,255 - 13,499,504 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017596305   ⟹   XP_017451794
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2912,587,437 - 12,611,589 (+)NCBI
Rnor_6.0914,551,754 - 14,577,002 (+)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_036997   ⟸   NM_012865
- UniProtKB: P18576 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006244471   ⟸   XM_006244409
- Peptide Label: isoform X1
- UniProtKB: A0A0G2KB97 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006244472   ⟸   XM_006244410
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_006244475   ⟸   XM_006244413
- Peptide Label: isoform X5
- Sequence:
RefSeq Acc Id: XP_006244473   ⟸   XM_006244411
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_006244474   ⟸   XM_006244412
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_017451794   ⟸   XM_017596305
- Peptide Label: isoform X6
- Sequence:
RefSeq Acc Id: ENSRNOP00000017157   ⟸   ENSRNOT00000017157
RefSeq Acc Id: ENSRNOP00000075707   ⟸   ENSRNOT00000091532
RefSeq Acc Id: ENSRNOP00000078156   ⟸   ENSRNOT00000115817

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-P18576-F1-model_v2 AlphaFold P18576 1-341 view protein structure

Transcriptome

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

Promoters
RGD ID:13696488
Promoter ID:EPDNEW_R7013
Type:multiple initiation site
Name:Nfya_1
Description:nuclear transcription factor Y subunit alpha
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_6.0914,551,752 - 14,551,812EPDNEW

Strain Variation

Strain Sequence Variants (MRatBN7.2)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN-Lx/CubMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BUF/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
DA/OlaHsd (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE16/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/FarMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB10/IpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF10A/StmMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrcAek (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrcAek (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrcAek (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/NRrrcMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MWF/Hsd (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHR/OlalpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WAG/RijCrl (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:70976 AgrOrtholog
BioCyc Gene G2FUF-28309 BioCyc
Ensembl Genes ENSRNOG00000012702 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000017157 ENTREZGENE
  ENSRNOP00000075707 ENTREZGENE
  ENSRNOP00000075707.2 UniProtKB/TrEMBL
  ENSRNOP00000078156 ENTREZGENE
  ENSRNOP00000078156.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000017157 ENTREZGENE
  ENSRNOT00000091532 ENTREZGENE
  ENSRNOT00000091532.2 UniProtKB/TrEMBL
  ENSRNOT00000115817 ENTREZGENE
  ENSRNOT00000115817.1 UniProtKB/TrEMBL
InterPro CCAAT-binding_factor_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  NFYA UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:29508 UniProtKB/Swiss-Prot
NCBI Gene 29508 ENTREZGENE
PANTHER PTHR12632 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam CBFB_NFYA UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Nfya PhenoGen
PRINTS CCAATSUBUNTB UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE NFYA_HAP2_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  NFYA_HAP2_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART CBF UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0G2KB97 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I5Y9Y4_RAT UniProtKB/TrEMBL
  NFYA_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-11-20 Nfya  nuclear transcription factor Y subunit alpha  Nfya  nuclear transcription factor-Y alpha  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2002-07-09 Nfya  nuclear transcription factor-Y alpha      Symbol and Name updated to reflect Human and Mouse nomenclature 70877 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_function must heterodimerize with A component to be able to bind DNA 70612
gene_protein 341 amino acids 70612