Tfam (transcription factor A, mitochondrial) - Rat Genome Database

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Gene: Tfam (transcription factor A, mitochondrial) Rattus norvegicus
Analyze
Symbol: Tfam
Name: transcription factor A, mitochondrial
RGD ID: 620682
Description: Enables heat shock protein binding activity and transcription coactivator binding activity. Involved in response to hypoxia and response to nutrient. Located in mitochondrial matrix. Biomarker of obesity and status epilepticus. Human ortholog(s) of this gene implicated in Alzheimer's disease; Huntington's disease; Parkinson's disease; amyotrophic lateral sclerosis; and mitochondrial DNA depletion syndrome 15. Orthologous to human TFAM (transcription factor A, mitochondrial); PARTICIPATES IN Huntington's disease pathway; INTERACTS WITH (+)-pilocarpine; (R)-noradrenaline; 17beta-estradiol.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: Mttfa
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr82017,355,373 - 17,367,422 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl2017,355,363 - 17,369,877 (+)EnsemblGRCr8
mRatBN7.22017,356,243 - 17,368,293 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2017,356,197 - 17,368,292 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx2018,082,918 - 18,094,966 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.02017,437,916 - 17,449,964 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.02017,910,581 - 17,922,629 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.02018,594,057 - 18,606,106 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2018,594,037 - 18,606,151 (+)Ensemblrn6Rnor6.0
Rnor_5.02020,760,402 - 20,772,301 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.42018,100,629 - 18,112,682 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera2018,754,951 - 18,766,964 (+)NCBICelera
RGSC_v3.12018,114,428 - 18,126,482 (+)NCBI
Cytogenetic Map20p11NCBI
JBrowse:




Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-pilocarpine  (EXP)
(-)-epigallocatechin 3-gallate  (ISO)
(3,4-dihydroxyphenyl)acetic acid  (ISO)
(R)-lipoic acid  (ISO)
(R)-noradrenaline  (EXP)
1,2-dichloroethane  (ISO)
1,2-dimethylhydrazine  (ISO)
1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine  (ISO)
17alpha-ethynylestradiol  (ISO)
17beta-estradiol  (EXP,ISO)
1H-[1,2,4]oxadiazolo[4,3-a]quinoxalin-1-one  (EXP,ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (EXP)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3,7,8-Tetrachlorodibenzofuran  (EXP)
2,4-dinitrotoluene  (EXP)
3'-amino-3'-deoxy-N(6),N(6)-dimethyladenosine  (EXP)
3-chloropropane-1,2-diol  (EXP)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
3-methyladenine  (ISO)
4,4'-sulfonyldiphenol  (ISO)
4-hydroxyphenyl retinamide  (ISO)
5-methyl-4-oxido-2-pyrazin-4-iumcarboxylic acid  (ISO)
6-chloro-2,3,4,9-tetrahydro-1H-carbazole-1-carboxamide  (ISO)
7,12-dimethyltetraphene  (ISO)
8-bromo-3',5'-cyclic GMP  (ISO)
acadesine  (ISO)
acetamide  (EXP)
acetylsalicylic acid  (ISO)
aconitine  (ISO)
acrolein  (EXP,ISO)
afimoxifene  (ISO)
aflatoxin B1  (ISO)
aldehydo-D-glucose  (EXP,ISO)
all-trans-retinoic acid  (ISO)
alpha-D-galactose  (EXP)
AM-251  (ISO)
ammonium chloride  (EXP)
angiotensin II  (EXP)
antimycin A  (ISO)
arachidonyl-2'-chloroethylamide  (ISO)
Aroclor 1254  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenous acid  (EXP)
aspartame  (ISO)
atorvastatin calcium  (EXP,ISO)
atrazine  (EXP,ISO)
auramine O  (ISO)
baicalin  (ISO)
benzo[a]pyrene  (EXP,ISO)
benzo[a]pyrene diol epoxide I  (ISO)
beryllium sulfate  (ISO)
beta-lapachone  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
Bisphenol B  (ISO)
bisphenol F  (ISO)
Butylbenzyl phthalate  (ISO)
cadmium dichloride  (EXP,ISO)
caffeine  (ISO)
calcitriol  (EXP)
calcium dihydroxide  (ISO)
calycosin  (EXP)
carbon monoxide  (EXP,ISO)
carbon nanotube  (ISO)
CGP 52608  (ISO)
chloramphenicol  (ISO)
cisplatin  (ISO)
clenbuterol  (ISO)
cobalt dichloride  (EXP,ISO)
copper atom  (EXP)
copper(0)  (EXP)
copper(II) sulfate  (ISO)
corosolic acid  (ISO)
curcumin  (EXP)
D-glucose  (EXP,ISO)
DDE  (ISO)
dexamethasone  (ISO)
Di-n-octyl phthalate  (ISO)
diarsenic trioxide  (EXP)
Dibutyl phosphate  (ISO)
dicrotophos  (ISO)
dimethyl fumarate  (ISO)
dioxygen  (EXP,ISO)
dopamine  (ISO)
dorsomorphin  (ISO)
doxorubicin  (EXP,ISO)
elemental selenium  (EXP)
ellagic acid  (ISO)
enalapril  (EXP)
enzyme inhibitor  (ISO)
Erythropoietin  (ISO)
ethanol  (ISO)
ethidium  (ISO)
etoposide  (ISO)
finasteride  (EXP)
flavonoids  (EXP)
flutamide  (EXP)
folic acid  (ISO)
formaldehyde  (ISO)
formononetin  (EXP)
FR900359  (ISO)
fructose  (EXP)
fulvestrant  (ISO)
Fusaric acid  (ISO)
galactose  (EXP)
gamma-hexachlorocyclohexane  (ISO)
Genipin  (ISO)
gentamycin  (EXP)
Gingerenone A  (ISO)
glucose  (EXP,ISO)
hexadecanoic acid  (ISO)
homovanillic acid  (ISO)
hydrogen peroxide  (EXP,ISO)
hydroxytyrosol  (ISO)
Ile(5)-angiotensin II  (EXP)
inositol  (EXP)
kaempferol  (ISO)
Licarin A  (ISO)
lipoic acid  (ISO)
lipopolysaccharide  (ISO)
LY294002  (EXP,ISO)
lycopene  (ISO)
melatonin  (EXP,ISO)
meldonium  (EXP)
Mesaconitine  (EXP)
metformin  (ISO)
methylmercury chloride  (ISO)
MitoTEMPO  (ISO)
mono(2-ethylhexyl) phthalate  (ISO)
monocrotophos  (EXP)
monosodium L-glutamate  (ISO)
N-acetyl-L-cysteine  (EXP,ISO)
N-benzyloxycarbonyl-L-leucyl-L-leucyl-L-leucinal  (ISO)
N-methyl-4-phenylpyridinium  (ISO)
nebivolol  (ISO)
nefazodone  (EXP)
neohesperidin  (ISO)
nickel atom  (ISO)
nickel dichloride  (ISO)
nicorandil  (EXP)
nimesulide  (EXP)
nitrates  (ISO)
nitrites  (EXP)
ochratoxin A  (ISO)
oleic acid  (ISO)
oxaloacetic acid  (ISO)
oxidopamine  (ISO)
oxybenzone  (EXP,ISO)
paracetamol  (ISO)
perfluorooctanoic acid  (EXP)
Phytolaccoside E  (ISO)
picoxystrobin  (ISO)
pioglitazone  (ISO)
pirinixic acid  (ISO)
piroxicam  (ISO)
poly(guanylic acid)  (EXP)
potassium chloride  (EXP)
potassium chromate  (ISO)
potassium dichromate  (EXP)
progesterone  (EXP)
propionic acid  (ISO)
pyrroloquinoline quinone  (EXP,ISO)
pyruvic acid  (EXP)
quercetin  (EXP,ISO)
raloxifene  (ISO)
resveratrol  (EXP,ISO)
rotenone  (EXP,ISO)
Salvianolic acid A  (ISO)
salvianolic acid B  (ISO)
SB 431542  (ISO)
selenium atom  (EXP)
silicon atom  (ISO)
silicon dioxide  (EXP,ISO)
sirolimus  (ISO)
sodium arsenite  (EXP,ISO)
sodium benzoate  (EXP)
sodium dichromate  (EXP,ISO)
sodium fluoride  (ISO)
sodium hydrogensulfite  (EXP)
streptozocin  (ISO)
sulforaphane  (ISO)
sulfur dioxide  (EXP)
sunitinib  (ISO)
T-2 toxin  (EXP,ISO)
testosterone  (ISO)
tetrachloromethane  (EXP)
thapsigargin  (ISO)
thiram  (ISO)
titanium dioxide  (ISO)
triphenyl phosphate  (ISO)
Triptolide  (EXP,ISO)
troglitazone  (ISO)
tunicamycin  (ISO)
undecane  (EXP)
uranium atom  (ISO)
valdecoxib  (EXP)
valproic acid  (ISO)
zalcitabine  (ISO)
zidovudine  (EXP)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
cytosol  (TAS)
mitochondrial matrix  (IDA,IEA,ISO,TAS)
mitochondrial nucleoid  (IBA,IEA,ISO,ISS)
mitochondrion  (IEA,ISO)
nucleus  (IEA)
protein-containing complex  (IEA,ISO)

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Mitochondrial transcription factor A (TFAM) gene variation in Parkinson's disease. Alvarez V, etal., Neurosci Lett. 2008 Feb 13;432(1):79-82. Epub 2007 Dec 15.
2. Association study of two genetic variants in mitochondrial transcription factor A (TFAM) in Alzheimer's and Parkinson's disease. Belin AC, etal., Neurosci Lett. 2007 Jun 15;420(3):257-62. Epub 2007 May 10.
3. Impairment of PGC-1alpha expression, neuropathology and hepatic steatosis in a transgenic mouse model of Huntington's disease following chronic energy deprivation. Chaturvedi RK, etal., Hum Mol Genet. 2010 Aug 15;19(16):3190-205. Epub 2010 Jun 7.
4. Mitochondrial transcription factor A is a proinflammatory mediator in hemorrhagic shock. Chaung WW, etal., Int J Mol Med. 2012 Jul;30(1):199-203. doi: 10.3892/ijmm.2012.959. Epub 2012 Apr 2.
5. Mitochondrial transcription factor A and its downstream targets are up-regulated in a rat hepatoma. Dong X, etal., J Biol Chem 2002 Nov 8;277(45):43309-18.
6. Dysregulation of mitochondrial dynamics and the muscle transcriptome in ICU patients suffering from sepsis induced multiple organ failure. Fredriksson K, etal., PLoS One. 2008;3(11):e3686. Epub 2008 Nov 10.
7. The mitochondrial RNA polymerase contributes critically to promoter specificity in mammalian cells. Gaspari M, etal., EMBO J. 2004 Nov 24;23(23):4606-14. Epub 2004 Nov 4.
8. 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.
9. Mitochondrial transcription factor A variants and the risk of Parkinson's disease. Gaweda-Walerych K, etal., Neurosci Lett. 2010 Jan 18;469(1):24-9. doi: 10.1016/j.neulet.2009.11.037. Epub 2009 Nov 17.
10. PARK2 variability in Polish Parkinson's disease patients--interaction with mitochondrial haplogroups. Gaweda-Walerych K, etal., Parkinsonism Relat Disord. 2012 Jun;18(5):520-4. Epub 2012 Feb 22.
11. Impaired mitochondrial biogenesis in hippocampi of rats with chronic seizures. Han Y, etal., Neuroscience. 2011 Oct 27;194:234-40. Epub 2011 Aug 6.
12. Reduced activity of mtTFA decreases the transcription in mitochondria isolated from diabetic rat heart. Kanazawa A, etal., Am J Physiol Endocrinol Metab 2002 Apr;282(4):E778-85.
13. Alternative translation initiation augments the human mitochondrial proteome. Kazak L, etal., Nucleic Acids Res. 2013 Feb 1;41(4):2354-69. doi: 10.1093/nar/gks1347. Epub 2012 Dec 28.
14. Mitochondrial transcription factor A is necessary for mtDNA maintenance and embryogenesis in mice. Larsson NG, etal., Nat Genet. 1998 Mar;18(3):231-6.
15. Genetic modification of survival in tissue-specific knockout mice with mitochondrial cardiomyopathy. Li H, etal., Proc Natl Acad Sci U S A. 2000 Mar 28;97(7):3467-72.
16. The impact of mitochondrial and nuclear DNA variants on late-onset Alzheimer's disease risk. Maruszak A, etal., J Alzheimers Dis. 2011;27(1):197-210. doi: 10.3233/JAD-2011-110710.
17. Characterization of the mtTFA gene and identification of a processed pseudogene in rat. Mezzina M, etal., Gene 2002 Mar 6;286(1):105-12.
18. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
19. Effect of mitochondrial transcription factor a overexpression on motor neurons in amyotrophic lateral sclerosis model mice. Morimoto N, etal., J Neurosci Res. 2012 Jun;90(6):1200-8. doi: 10.1002/jnr.23000. Epub 2012 Feb 22.
20. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
21. Regulation and role of the mitochondrial transcription factor in the diabetic rat heart. Nishio Y, etal., Ann N Y Acad Sci. 2004 Apr;1011:78-85.
22. Impact of exercise on mitochondrial transcription factor expression and damage in the striatum of a chronic mouse model of Parkinson's disease. Patki G and Lau YS, Neurosci Lett. 2011 Nov 21;505(3):268-72. Epub 2011 Oct 21.
23. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
24. Downregulation of Tfam and mtDNA copy number during mammalian spermatogenesis. Rantanen A, etal., Mamm Genome 2001 Oct;12(10):787-92.
25. Peroxisome proliferator-activated receptor expression is reduced in skeletal muscle in COPD. Remels AH, etal., Eur Respir J. 2007 Aug;30(2):245-52. Epub 2007 Apr 25.
26. GOA pipeline RGD automated data pipeline
27. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
28. Role of mitochondria biogenesis in the metabolic memory associated with the continued progression of diabetic retinopathy and its regulation by lipoic acid. Santos JM and Kowluru RA, Invest Ophthalmol Vis Sci. 2011 Nov 11;52(12):8791-8. Print 2011.
29. Maternal obesity promotes a proinflammatory signature in rat uterus and blastocyst. Shankar K, etal., Endocrinology. 2011 Nov;152(11):4158-70. Epub 2011 Aug 23.
30. AMP-activated protein kinase is required for exercise-induced peroxisome proliferator-activated receptor co-activator 1 translocation to subsarcolemmal mitochondria in skeletal muscle. Smith BK, etal., J Physiol. 2013 Mar 15;591(Pt 6):1551-61. doi: 10.1113/jphysiol.2012.245944. Epub 2013 Jan 7.
31. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
32. PGC-1alpha downstream transcription factors NRF-1 and TFAM are genetic modifiers of Huntington disease. Taherzadeh-Fard E, etal., Mol Neurodegener. 2011 May 19;6(1):32.
33. WY14643 improves left ventricular myocardial mitochondrial and systolic functions in obese rats under chronic persistent hypoxia via the PPARα pathway. Yan J, etal., Life Sci. 2021 Feb 1;266:118888. doi: 10.1016/j.lfs.2020.118888. Epub 2020 Dec 10.
34. Rapidly increased neuronal mitochondrial biogenesis after hypoxic-ischemic brain injury. Yin W, etal., Stroke. 2008 Nov;39(11):3057-63. Epub 2008 Aug 21.
35. P53 physically interacts with mitochondrial transcription factor A and differentially regulates binding to damaged DNA. Yoshida Y, etal., Cancer Res. 2003 Jul 1;63(13):3729-34.
36. Exercise induces mitochondrial biogenesis after brain ischemia in rats. Zhang Q, etal., Neuroscience. 2012 Mar 15;205:10-7. Epub 2012 Jan 8.
Additional References at PubMed
PMID:2628167   PMID:8673128   PMID:10902920   PMID:11259653   PMID:11955630   PMID:12535660   PMID:14651853   PMID:15489334   PMID:15585199   PMID:16230352   PMID:16543724   PMID:17143337  
PMID:18063578   PMID:18614015   PMID:19060297   PMID:19304746   PMID:19656489   PMID:20410300   PMID:21113058   PMID:21575134   PMID:21630459   PMID:22037171   PMID:22658674   PMID:22681889  
PMID:23255365   PMID:24058615   PMID:24631828   PMID:24703694   PMID:26063705   PMID:27091693   PMID:27223823   PMID:29142323   PMID:29445193   PMID:30563025   PMID:31314594   PMID:31942725  


Genomics

Comparative Map Data
Tfam
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr82017,355,373 - 17,367,422 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl2017,355,363 - 17,369,877 (+)EnsemblGRCr8
mRatBN7.22017,356,243 - 17,368,293 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2017,356,197 - 17,368,292 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx2018,082,918 - 18,094,966 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.02017,437,916 - 17,449,964 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.02017,910,581 - 17,922,629 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.02018,594,057 - 18,606,106 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2018,594,037 - 18,606,151 (+)Ensemblrn6Rnor6.0
Rnor_5.02020,760,402 - 20,772,301 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.42018,100,629 - 18,112,682 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera2018,754,951 - 18,766,964 (+)NCBICelera
RGSC_v3.12018,114,428 - 18,126,482 (+)NCBI
Cytogenetic Map20p11NCBI
TFAM
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381058,385,410 - 58,399,220 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1058,385,345 - 58,399,220 (+)Ensemblhg38GRCh38
GRCh371060,145,170 - 60,158,980 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361059,815,182 - 59,825,903 (+)NCBIBuild 36Build 36hg18NCBI36
Celera1053,410,112 - 53,420,833 (+)NCBICelera
Cytogenetic Map10q21.1NCBI
HuRef1054,133,767 - 54,148,729 (+)NCBIHuRef
CHM1_11060,426,687 - 60,440,776 (+)NCBICHM1_1
T2T-CHM13v2.01059,239,514 - 59,253,326 (+)NCBIT2T-CHM13v2.0
Tfam
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391071,061,298 - 71,074,157 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1071,061,294 - 71,074,110 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm381071,225,468 - 71,238,328 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1071,225,464 - 71,238,280 (-)Ensemblmm10GRCm38
MGSCv371070,688,225 - 70,700,792 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv361070,620,777 - 70,633,344 (-)NCBIMGSCv36mm8
Celera1072,300,895 - 72,313,462 (-)NCBICelera
Cytogenetic Map10B5.3NCBI
cM Map1036.83NCBI
Tfam
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495542512,106,877 - 12,120,782 (+)Ensembl
ChiLan1.0NW_00495542512,106,506 - 12,121,625 (+)NCBIChiLan1.0ChiLan1.0
TFAM
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2870,594,983 - 70,606,152 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11070,600,391 - 70,611,474 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01054,917,578 - 54,934,124 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11057,137,911 - 57,152,102 (+)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1057,138,437 - 57,147,972 (+)EnsemblpanPan2panpan1.1
TFAM
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1410,585,320 - 10,600,664 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl410,585,480 - 10,598,058 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha410,777,843 - 10,794,098 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0410,841,889 - 10,857,973 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl410,842,146 - 10,857,106 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1410,826,103 - 10,842,176 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0410,945,723 - 10,961,973 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0411,254,972 - 11,271,059 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Tfam
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440721370,510,063 - 70,519,044 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366144,596,617 - 4,605,104 (-)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049366144,595,973 - 4,605,040 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TFAM
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1492,259,403 - 92,279,731 (-)EnsemblsusScr11Sscrofa11.1
Sscrofa11.11492,261,713 - 92,279,731 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.214100,777,168 - 100,778,350 (+)NCBISscrofa10.2Sscrofa10.2susScr3
TFAM
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1972,900,665 - 72,914,634 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl972,904,637 - 72,914,397 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366604833,803,050 - 33,817,151 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Tfam
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247915,179,195 - 5,198,611 (-)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046247915,183,276 - 5,198,986 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Tfam
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v11815,612,499 - 15,624,707 (+)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Tfam
52 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:63
Count of miRNA genes:56
Interacting mature miRNAs:62
Transcripts:ENSRNOT00000000753
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.


QTLs in Region (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
4889610Pancm3Pancreatic morphology QTL 33.750.001pancreas mass (VT:0010144)pancreas wet weight (CMO:0000626)20418947649189476Rat
2317057Aia27Adjuvant induced arthritis QTL 272.83joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)20126925056Rat
1641915Colcr9Colorectal carcinoma resistance QTL 92.970.0024intestine integrity trait (VT:0010554)benign colorectal tumor number (CMO:0001795)20133724594Rat
7387283Uae44Urinary albumin excretion QTL 440.1712urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)20126128279Rat
4889870Pur30Proteinuria QTL 30190.005urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)20804392029865039Rat
7411668Foco32Food consumption QTL 3280.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20136600300Rat
2305926Iddm37Insulin dependent diabetes mellitus QTL 376blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)20153308346533083Rat
1354642Despr15Despair related QTL 150.0027locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)20124164241Rat
1558640Prcs2Prostate cancer susceptibility QTL 23.3prostate integrity trait (VT:0010571)percentage of study population developing ventral prostate tumorous lesions during a period of time (CMO:0000943)20134066551Rat
8694189Bw153Body weight QTL 1533.130.001body mass (VT:0001259)body weight gain (CMO:0000420)20129193376Rat
4889857Pur27Proteinuria QTL 2712.20.001urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)20127341128Rat
1598870Bp289Blood pressure QTL 2892.4arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)20821635953216359Rat
9590109Sffal8Serum free fatty acids level QTL 85.320.01blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)20129193376Rat
9589155Insul32Insulin level QTL 326.380.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)20129193376Rat
9590275Scort15Serum corticosterone level QTL 153.480.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20129193376Rat
1598858Cm61Cardiac mass QTL 613.6heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)20821635953216359Rat
7411650Foco23Food consumption QTL 2320.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20129193376Rat
2317851Alcrsp22Alcohol response QTL 223.20.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20127341128Rat
1598816Memor12Memory QTL 122.4exploratory behavior trait (VT:0010471)average horizontal distance between subject and target during voluntary locomotion in an experimental apparatus (CMO:0002674)201224324249189476Rat
1641893Alcrsp7Alcohol response QTL 7response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20127341128Rat
6893685Bw111Body weight QTL 1112.70.004body mass (VT:0001259)body weight (CMO:0000012)20132578510Rat
9590252Scort12Serum corticosterone level QTL 1220.460.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20136600300Rat

Markers in Region
RH130441  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22017,367,912 - 17,368,116 (+)MAPPERmRatBN7.2
Rnor_6.02018,605,726 - 18,605,929NCBIRnor6.0
Rnor_5.02020,771,921 - 20,772,124UniSTSRnor5.0
RGSC_v3.42018,112,302 - 18,112,505UniSTSRGSC3.4
Celera2018,766,584 - 18,766,787UniSTS
Cytogenetic Map20p11UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
16 12 67 165 91 90 59 92 59 6 356 192 11 144 81 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000000753   ⟹   ENSRNOP00000000753
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl2017,355,363 - 17,369,877 (+)Ensembl
mRatBN7.2 Ensembl2017,356,197 - 17,368,292 (+)Ensembl
Rnor_6.0 Ensembl2018,594,037 - 18,606,151 (+)Ensembl
RefSeq Acc Id: NM_031326   ⟹   NP_112616
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82017,355,373 - 17,367,422 (+)NCBI
mRatBN7.22017,356,243 - 17,368,293 (+)NCBI
Rnor_6.02018,594,057 - 18,606,106 (+)NCBI
Rnor_5.02020,760,402 - 20,772,301 (+)NCBI
RGSC_v3.42018,100,629 - 18,112,682 (+)RGD
Celera2018,754,951 - 18,766,964 (+)RGD
Sequence:
RefSeq Acc Id: NP_112616   ⟸   NM_031326
- Peptide Label: precursor
- UniProtKB: Q91ZW1 (UniProtKB/Swiss-Prot),   Q9WTM7 (UniProtKB/Swiss-Prot),   A6JKP1 (UniProtKB/TrEMBL),   Q9ES32 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000000753   ⟸   ENSRNOT00000000753
Protein Domains
HMG box

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q91ZW1-F1-model_v2 AlphaFold Q91ZW1 1-244 view protein structure

Transcriptome

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

Promoters
RGD ID:13701554
Promoter ID:EPDNEW_R12078
Type:initiation region
Name:Tfam_1
Description:transcription factor A, mitochondrial
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_6.02018,594,050 - 18,594,110EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:620682 AgrOrtholog
BioCyc Gene G2FUF-4044 BioCyc
Ensembl Genes ENSRNOG00000000613 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000000753 ENTREZGENE
  ENSRNOT00000000753.5 UniProtKB/Swiss-Prot
Gene3D-CATH 1.10.30.10 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:5623491 IMAGE-MGC_LOAD
InterPro HMG_box_dom UniProtKB/Swiss-Prot
  HMG_box_dom_sf UniProtKB/Swiss-Prot
  HMGB UniProtKB/Swiss-Prot
KEGG Report rno:83474 UniProtKB/Swiss-Prot
MGC_CLONE MGC:72409 IMAGE-MGC_LOAD
NCBI Gene 83474 ENTREZGENE
PANTHER HIGH MOBILITY GROUP PROTEIN DSP1 UniProtKB/Swiss-Prot
  TRANSCRIPTION FACTOR A, MITOCHONDRIAL UniProtKB/Swiss-Prot
Pfam HMG_box UniProtKB/Swiss-Prot
  HMG_box_2 UniProtKB/Swiss-Prot
PhenoGen Tfam PhenoGen
PROSITE HMG_BOX_2 UniProtKB/Swiss-Prot
RatGTEx ENSRNOG00000000613 RatGTEx
SMART HMG UniProtKB/Swiss-Prot
Superfamily-SCOP SSF47095 UniProtKB/Swiss-Prot
UniProt A6JKP1 ENTREZGENE, UniProtKB/TrEMBL
  A6JKP2_RAT UniProtKB/TrEMBL
  Q91ZW1 ENTREZGENE
  Q9ES32 ENTREZGENE, UniProtKB/TrEMBL
  Q9WTM7 ENTREZGENE
  TFAM_RAT UniProtKB/Swiss-Prot
UniProt Secondary Q9WTM7 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2004-09-10 Tfam  transcription factor A, mitochondrial    transcription factor A, mitochondrial  Name updated 1299863 APPROVED
2002-08-07 Tfam  transcription factor A, mitochondrial      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_disease displays reduced binding to the D loop of mitochondrial DNA in diabetic rats 730138