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: Exhibits heat shock protein binding activity and transcription coactivator binding activity. Predicted to be involved in mitochondrial respiratory chain complex assembly; positive regulation of transcription, DNA-templated; and transcription initiation from mitochondrial promoter. Localizes to mitochondrion. Biomarker of 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
Also known as: Mttfa
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
mRatBN7.22017,356,243 - 17,368,293 (+)NCBI
Rnor_6.0 Ensembl2018,594,037 - 18,606,151 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.02018,594,057 - 18,606,106 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.02020,760,402 - 20,772,301 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42018,100,629 - 18,112,682 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.12018,114,428 - 18,126,482 (+)NCBI
Celera2018,754,951 - 18,766,964 (+)NCBICelera
Cytogenetic Map20p11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-pilocarpine  (EXP)
(-)-epigallocatechin 3-gallate  (ISO)
(3,4-dihydroxyphenyl)acetic 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)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3,7,8-Tetrachlorodibenzofuran  (EXP)
2,4-dinitrotoluene  (EXP)
2,6-di-tert-butyl-4-methylphenol  (ISO)
3'-amino-3'-deoxy-N(6),N(6)-dimethyladenosine  (EXP)
3-isobutyl-1-methyl-7H-xanthine  (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)
8-bromo-3',5'-cyclic GMP  (ISO)
acetamide  (EXP)
acrolein  (ISO)
afimoxifene  (ISO)
aflatoxin B1  (ISO)
aldehydo-D-glucose  (EXP,ISO)
alpha-D-galactose  (EXP)
AM-251  (ISO)
ammonium chloride  (EXP)
Aroclor 1254  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
aspartame  (ISO)
atorvastatin calcium  (EXP,ISO)
atrazine  (EXP,ISO)
auramine O  (ISO)
benzo[a]pyrene  (EXP,ISO)
benzo[a]pyrene diol epoxide I  (ISO)
bisphenol A  (EXP,ISO)
Butylbenzyl phthalate  (ISO)
cadmium dichloride  (ISO)
calcitriol  (EXP)
calcium dihydroxide  (ISO)
carbon monoxide  (EXP,ISO)
chloramphenicol  (ISO)
clenbuterol  (ISO)
cobalt dichloride  (EXP,ISO)
copper atom  (EXP)
copper(0)  (EXP)
copper(II) sulfate  (ISO)
curcumin  (EXP)
D-glucose  (EXP,ISO)
DDE  (ISO)
dexamethasone  (ISO)
dicrotophos  (ISO)
dimethyl fumarate  (ISO)
dioxygen  (EXP,ISO)
dopamine  (ISO)
dorsomorphin  (ISO)
doxorubicin  (EXP,ISO)
elemental selenium  (EXP)
ellagic acid  (ISO)
enzyme inhibitor  (ISO)
Erythropoietin  (ISO)
ethanol  (ISO)
ethidium  (ISO)
etoposide  (ISO)
finasteride  (EXP)
flavonoids  (EXP)
flutamide  (EXP)
folic acid  (ISO)
formaldehyde  (ISO)
fructose  (EXP)
fulvestrant  (ISO)
Fusaric acid  (ISO)
galactose  (EXP)
gamma-hexachlorocyclohexane  (ISO)
Genipin  (ISO)
gentamycin  (EXP)
glucose  (EXP,ISO)
hexadecanoic acid  (ISO)
homovanillic acid  (ISO)
hydrogen peroxide  (EXP,ISO)
hydroxytyrosol  (ISO)
kaempferol  (ISO)
Licarin A  (ISO)
lipopolysaccharide  (ISO)
LY294002  (EXP,ISO)
melatonin  (EXP,ISO)
meldonium  (EXP)
metformin  (ISO)
methylmercury chloride  (ISO)
mono(2-ethylhexyl) phthalate  (ISO)
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)
nickel dichloride  (ISO)
nimesulide  (EXP)
nitrites  (EXP)
oleic acid  (ISO)
oxaloacetic acid  (ISO)
oxidopamine  (ISO)
oxybenzone  (EXP)
paracetamol  (ISO)
perfluorooctanoic acid  (EXP)
pioglitazone  (ISO)
pirinixic acid  (ISO)
piroxicam  (ISO)
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)
selenium atom  (EXP)
silicon dioxide  (ISO)
sodium arsenite  (EXP,ISO)
sodium benzoate  (EXP)
sodium dichromate  (EXP,ISO)
sodium fluoride  (ISO)
sodium hydrogensulfite  (EXP)
sulforaphane  (ISO)
sulfur dioxide  (EXP)
sunitinib  (ISO)
T-2 toxin  (EXP,ISO)
tetrachloromethane  (EXP)
thapsigargin  (ISO)
Triptolide  (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

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
1. Alvarez V, etal., Neurosci Lett. 2008 Feb 13;432(1):79-82. Epub 2007 Dec 15.
2. Belin AC, etal., Neurosci Lett. 2007 Jun 15;420(3):257-62. Epub 2007 May 10.
3. Chaturvedi RK, etal., Hum Mol Genet. 2010 Aug 15;19(16):3190-205. Epub 2010 Jun 7.
4. Chaung WW, etal., Int J Mol Med. 2012 Jul;30(1):199-203. doi: 10.3892/ijmm.2012.959. Epub 2012 Apr 2.
5. Dong X, etal., J Biol Chem 2002 Nov 8;277(45):43309-18.
6. Fredriksson K, etal., PLoS One. 2008;3(11):e3686. Epub 2008 Nov 10.
7. Gaspari M, etal., EMBO J. 2004 Nov 24;23(23):4606-14. Epub 2004 Nov 4.
8. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
9. 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. Gaweda-Walerych K, etal., Parkinsonism Relat Disord. 2012 Jun;18(5):520-4. Epub 2012 Feb 22.
11. Han Y, etal., Neuroscience. 2011 Oct 27;194:234-40. Epub 2011 Aug 6.
12. Kanazawa A, etal., Am J Physiol Endocrinol Metab 2002 Apr;282(4):E778-85.
13. Larsson NG, etal., Nat Genet. 1998 Mar;18(3):231-6.
14. Li H, etal., Proc Natl Acad Sci U S A. 2000 Mar 28;97(7):3467-72.
15. Maruszak A, etal., J Alzheimers Dis. 2011;27(1):197-210. doi: 10.3233/JAD-2011-110710.
16. Mezzina M, etal., Gene 2002 Mar 6;286(1):105-12.
17. MGD data from the GO Consortium
18. Morimoto N, etal., J Neurosci Res. 2012 Jun;90(6):1200-8. doi: 10.1002/jnr.23000. Epub 2012 Feb 22.
19. NCBI rat LocusLink and RefSeq merged data July 26, 2002
20. Nishio Y, etal., Ann N Y Acad Sci. 2004 Apr;1011:78-85.
21. Patki G and Lau YS, Neurosci Lett. 2011 Nov 21;505(3):268-72. Epub 2011 Oct 21.
22. Pipeline to import KEGG annotations from KEGG into RGD
23. Rantanen A, etal., Mamm Genome 2001 Oct;12(10):787-92.
24. Remels AH, etal., Eur Respir J. 2007 Aug;30(2):245-52. Epub 2007 Apr 25.
25. RGD automated data pipeline
26. RGD automated import pipeline for gene-chemical interactions
27. Santos JM and Kowluru RA, Invest Ophthalmol Vis Sci. 2011 Nov 11;52(12):8791-8. Print 2011.
28. Shankar K, etal., Endocrinology. 2011 Nov;152(11):4158-70. Epub 2011 Aug 23.
29. Smith BK, etal., J Physiol. 2013 Mar 15;591(Pt 6):1551-61. doi: 10.1113/jphysiol.2012.245944. Epub 2013 Jan 7.
30. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
31. Taherzadeh-Fard E, etal., Mol Neurodegener. 2011 May 19;6(1):32.
32. Yin W, etal., Stroke. 2008 Nov;39(11):3057-63. Epub 2008 Aug 21.
33. Yoshida Y, etal., Cancer Res. 2003 Jul 1;63(13):3729-34.
34. 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
mRatBN7.22017,356,243 - 17,368,293 (+)NCBI
Rnor_6.0 Ensembl2018,594,037 - 18,606,151 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.02018,594,057 - 18,606,106 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.02020,760,402 - 20,772,301 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42018,100,629 - 18,112,682 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.12018,114,428 - 18,126,482 (+)NCBI
Celera2018,754,951 - 18,766,964 (+)NCBICelera
Cytogenetic Map20p11NCBI
TFAM
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1058,385,345 - 58,399,220 (+)EnsemblGRCh38hg38GRCh38
GRCh381058,385,409 - 58,399,220 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371060,145,170 - 60,158,980 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361059,815,182 - 59,825,903 (+)NCBINCBI36hg18NCBI36
Celera1053,410,112 - 53,420,833 (+)NCBI
Cytogenetic Map10q21.1NCBI
HuRef1054,133,767 - 54,148,729 (+)NCBIHuRef
CHM1_11060,426,687 - 60,440,776 (+)NCBICHM1_1
Tfam
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391071,061,298 - 71,074,157 (-)NCBIGRCm39mm39
GRCm39 Ensembl1071,061,294 - 71,074,110 (-)Ensembl
GRCm381071,225,468 - 71,238,328 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1071,225,464 - 71,238,280 (-)EnsemblGRCm38mm10GRCm38
MGSCv371070,688,225 - 70,700,792 (-)NCBIGRCm37mm9NCBIm37
MGSCv361070,620,777 - 70,633,344 (-)NCBImm8
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 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495542512,106,506 - 12,121,625 (+)NCBIChiLan1.0ChiLan1.0
TFAM
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11057,137,911 - 57,152,102 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1057,138,437 - 57,147,972 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01054,917,578 - 54,934,124 (+)NCBIMhudiblu_PPA_v0panPan3
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 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha410,777,843 - 10,794,098 (+)NCBI
ROS_Cfam_1.0410,841,889 - 10,857,973 (+)NCBI
UMICH_Zoey_3.1410,826,103 - 10,842,176 (+)NCBI
UNSW_CanFamBas_1.0410,945,723 - 10,961,973 (+)NCBI
UU_Cfam_GSD_1.0411,254,972 - 11,271,059 (+)NCBI
Tfam
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440721370,510,063 - 70,519,044 (-)NCBI
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 - 92,279,550 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11492,261,713 - 92,279,731 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.214100,777,168 - 100,778,350 (+)NCBISscrofa10.2Sscrofa10.2susScr3
TFAM
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1972,900,665 - 72,914,634 (-)NCBI
ChlSab1.1 Ensembl972,904,637 - 72,914,397 (-)Ensembl
Tfam
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247915,183,276 - 5,198,986 (-)NCBI

Position Markers
RH130441  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22017,367,912 - 17,368,116 (+)MAPPER
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


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1354642Despr15Despair related QTL 150.0027locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)20124652101Rat
1600382Edcs3Endometrial carcinoma susceptibility QTL33.50.003uterus morphology trait (VT:0001120)percentage of study population developing endometrioid carcinoma during a period of time (CMO:0001759)20125653396Rat
1641893Alcrsp7Alcohol response QTL 7response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20126305996Rat
2317851Alcrsp22Alcohol response QTL 223.20.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20126305996Rat
7387283Uae44Urinary albumin excretion QTL 440.1712urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)20127357423Rat
9590275Scort15Serum corticosterone level QTL 153.480.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20128375393Rat
9589155Insul32Insulin level QTL 326.380.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)20128375393Rat
9590109Sffal8Serum free fatty acids level QTL 85.320.01blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)20128375393Rat
7411650Foco23Food consumption QTL 2320.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20128375393Rat
8694189Bw153Body weight QTL 1533.130.001body mass (VT:0001259)body weight gain (CMO:0000420)20128375393Rat
6893685Bw111Body weight QTL 1112.70.004body mass (VT:0001259)body weight (CMO:0000012)20133300419Rat
9590252Scort12Serum corticosterone level QTL 1220.460.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20137550487Rat
7411668Foco32Food consumption QTL 3280.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20137550487Rat
2305926Iddm37Insulin dependent diabetes mellitus QTL 376blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)20201865447018654Rat
1641915Colcr9Colorectal carcinoma resistance QTL 92.970.0024intestine integrity trait (VT:0010554)benign colorectal tumor number (CMO:0001795)20299970747999707Rat
2317057Aia27Adjuvant induced arthritis QTL 272.83joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)20340211127968216Rat
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)20403911318872273Rat
4889857Pur27Proteinuria QTL 2712.20.001total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)20403911318872273Rat
1598816Memor12Memory QTL 122.4exploratory behavior trait (VT:0010471)average horizontal distance in proximity to the target during voluntary locomotion in an experimental apparatus (CMO:0002674)20410895649108956Rat
70154Insul2Insulin level QTL 23.75blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)20587544818739210Rat
1581577Pur15Proteinuria QTL 154.380.0002total urine protein amount (VT:0000032)urine protein excretion rate (CMO:0000759)20865434118872273Rat
4889870Pur30Proteinuria QTL 30190.005total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)20865434130991290Rat
9590092Insglur9Insulin/glucose ratio QTL 918.380.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)201383430956205956Rat
7411652Foco24Food consumption QTL 240.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)201383430956205956Rat
2317880Alcrsp25Alcohol response QTL 252.3response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)201782709656205956Rat

miRNA Target Status

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.


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 43 57 41 19 41 8 11 74 35 36 11 8
Low 5
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000000753   ⟹   ENSRNOP00000000753
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
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
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:
Reference Sequences
RefSeq Acc Id: NP_112616   ⟸   NM_031326
- Peptide Label: precursor
- Sequence:
RefSeq Acc Id: ENSRNOP00000000753   ⟸   ENSRNOT00000000753

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

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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:620682 AgrOrtholog
Ensembl Genes ENSRNOG00000000613 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000000753 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000000753 ENTREZGENE, 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
KEGG Report rno:83474 UniProtKB/Swiss-Prot
MGC_CLONE MGC:72409 IMAGE-MGC_LOAD
NCBI Gene 83474 ENTREZGENE
Pfam HMG_box UniProtKB/Swiss-Prot
  HMG_box_2 UniProtKB/Swiss-Prot
PhenoGen Tfam PhenoGen
PROSITE HMG_BOX_2 UniProtKB/Swiss-Prot
SMART HMG UniProtKB/Swiss-Prot
Superfamily-SCOP SSF47095 UniProtKB/Swiss-Prot
UniProt Q91ZW1 ENTREZGENE, 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