Tpm4 (tropomyosin 4) - Rat Genome Database
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Gene: Tpm4 (tropomyosin 4) Rattus norvegicus
Analyze
Symbol: Tpm4
Name: tropomyosin 4
RGD ID: 3899
Description: Exhibits actin filament binding activity; protein heterodimerization activity; and protein homodimerization activity. Predicted to be involved in actin filament organization and muscle contraction. Localizes to actin cytoskeleton. Orthologous to human TPM4 (tropomyosin 4); PARTICIPATES IN dilated cardiomyopathy pathway; hypertrophic cardiomyopathy pathway; INTERACTS WITH (+)-schisandrin B; 1-naphthyl isothiocyanate; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: TM-4; Tpm4.2; Tpm4.2cy; Tropomycin 4; tropomyosin alpha-4 chain; tropomyosin-4
Orthologs:
Homo sapiens (human) : TPM4 (tropomyosin 4)  HGNC  Alliance
Mus musculus (house mouse) : Tpm4 (tropomyosin 4)  MGI  Alliance
Chinchilla lanigera (long-tailed chinchilla) : Tpm4 (tropomyosin 4)
Pan paniscus (bonobo/pygmy chimpanzee) : TPM4 (tropomyosin 4)
Canis lupus familiaris (dog) : TPM4 (tropomyosin 4)
Ictidomys tridecemlineatus (thirteen-lined ground squirrel) : Tpm4 (tropomyosin 4)
Sus scrofa (pig) : TPM4 (tropomyosin 4)
Chlorocebus sabaeus (African green monkey) : TPM4 (tropomyosin 4)
Heterocephalus glaber (naked mole-rat) : Tpm4 (tropomyosin 4)
more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.01619,385,810 - 19,399,851 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1619,385,736 - 19,399,903 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01619,244,141 - 19,258,182 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41618,108,914 - 18,122,956 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11618,108,911 - 18,122,954 (-)NCBI
Celera1617,899,051 - 17,913,092 (-)NCBICelera
Cytogenetic Map16p14NCBI
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
(+)-schisandrin B  (EXP)
1,1-dichloroethene  (ISO)
1,2-dimethylhydrazine  (ISO)
1-naphthyl isothiocyanate  (EXP)
17beta-estradiol  (ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,2',5,5'-tetrachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4-dinitrotoluene  (EXP)
2-methylcholine  (ISO)
3,3',5,5'-tetrabromobisphenol A  (ISO)
3-chloropropane-1,2-diol  (EXP)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
4,4'-diaminodiphenylmethane  (EXP)
4,4'-sulfonyldiphenol  (ISO)
4-hydroxyphenyl retinamide  (ISO)
5-aza-2'-deoxycytidine  (ISO)
acetamide  (EXP)
afimoxifene  (ISO)
aflatoxin B1  (ISO)
all-trans-retinoic acid  (ISO)
ammonium chloride  (EXP)
ampicillin  (ISO)
Aroclor 1254  (ISO)
arsenous acid  (ISO)
asbestos  (ISO)
atrazine  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
bexarotene  (EXP)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
bleomycin A2  (EXP)
bleomycin A5  (ISO)
buspirone  (EXP)
butan-1-ol  (ISO)
cadmium atom  (ISO)
cadmium dichloride  (EXP,ISO)
carbon nanotube  (ISO)
choline  (ISO)
cisplatin  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
copper(II) sulfate  (ISO)
cyclosporin A  (ISO)
decabromodiphenyl ether  (EXP)
dexamethasone  (ISO)
diarsenic trioxide  (ISO)
dibutyl phthalate  (EXP,ISO)
dioxygen  (ISO)
diuron  (EXP)
dopamine  (EXP)
dorsomorphin  (ISO)
doxorubicin  (EXP,ISO)
enzyme inhibitor  (ISO)
fenamidone  (ISO)
fenoldopam  (EXP)
folic acid  (ISO)
geldanamycin  (ISO)
gentamycin  (EXP)
glafenine  (EXP)
indometacin  (ISO)
ketamine  (EXP)
L-methionine  (ISO)
leflunomide  (EXP,ISO)
methylmercury chloride  (ISO)
microcystin RR  (ISO)
monosodium L-glutamate  (ISO)
N-nitrosodiethylamine  (EXP)
N-nitrosodimethylamine  (EXP)
N-nitrosomorpholine  (EXP)
nefazodone  (EXP)
nickel atom  (ISO)
nimesulide  (EXP)
ochratoxin A  (EXP)
paracetamol  (ISO)
paraoxon  (ISO)
phenethyl isothiocyanate  (ISO)
pirinixic acid  (ISO)
quercetin  (ISO)
resveratrol  (ISO)
SB 431542  (ISO)
silicon dioxide  (ISO)
silver atom  (ISO)
silver(0)  (ISO)
Soman  (EXP)
sulforaphane  (ISO)
sunitinib  (ISO)
tetrachloromethane  (EXP,ISO)
thimerosal  (ISO)
thioacetamide  (EXP)
torcetrapib  (ISO)
tributylstannane  (ISO)
trichostatin A  (ISO)
triphenyl phosphate  (EXP)
triphenylstannane  (ISO)
urethane  (ISO)
valproic acid  (ISO)
vancomycin  (ISO)
vinclozolin  (EXP)
vincristine  (ISO)
vorinostat  (ISO)
zinc atom  (EXP)
zinc sulfate  (EXP)
zinc(0)  (EXP)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:16210410   PMID:16236705   PMID:16765662   PMID:20458337   PMID:21423176   PMID:24625528   PMID:25002582   PMID:25369766   PMID:28259758   PMID:29476059   PMID:30361391  


Genomics

Comparative Map Data
Tpm4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.01619,385,810 - 19,399,851 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1619,385,736 - 19,399,903 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01619,244,141 - 19,258,182 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41618,108,914 - 18,122,956 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11618,108,911 - 18,122,954 (-)NCBI
Celera1617,899,051 - 17,913,092 (-)NCBICelera
Cytogenetic Map16p14NCBI
TPM4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1916,067,021 - 16,103,002 (+)EnsemblGRCh38hg38GRCh38
GRCh381916,067,507 - 16,103,005 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371916,178,317 - 16,213,815 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361916,048,325 - 16,074,408 (+)NCBINCBI36hg18NCBI36
Build 341916,048,324 - 16,074,408NCBI
Celera1916,080,322 - 16,115,740 (+)NCBI
Cytogenetic Map19p13.12-p13.11NCBI
HuRef1915,749,181 - 15,784,766 (+)NCBIHuRef
CHM1_11916,177,722 - 16,213,291 (+)NCBICHM1_1
Tpm4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39872,889,132 - 72,906,986 (+)NCBI
GRCm38872,135,288 - 72,153,142 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl872,130,174 - 72,153,142 (+)EnsemblGRCm38mm10GRCm38
MGSCv37874,659,191 - 74,677,028 (+)NCBIGRCm37mm9NCBIm37
MGSCv36875,064,281 - 75,082,118 (+)NCBImm8
Celera876,490,967 - 76,508,585 (+)NCBICelera
Cytogenetic Map8B3.3NCBI
Tpm4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555241,415,848 - 1,432,139 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049555241,419,061 - 1,432,114 (-)NCBIChiLan1.0ChiLan1.0
TPM4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11916,540,805 - 16,575,675 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1916,540,805 - 16,575,312 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01915,557,683 - 15,593,143 (+)NCBIMhudiblu_PPA_v0panPan3
TPM4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl2046,355,736 - 46,376,425 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.12046,354,808 - 46,376,489 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Tpm4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049365964,406,301 - 4,423,775 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TPM4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl261,453,721 - 61,476,781 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1261,453,721 - 61,476,781 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2261,150,543 - 61,173,575 (+)NCBISscrofa10.2Sscrofa10.2susScr3
Pig Cytomap2q24-q29NCBI
TPM4
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1 Ensembl614,566,869 - 14,598,934 (+)Ensembl
ChlSab1.1614,566,958 - 14,604,754 (+)NCBI
Tpm4
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046249081,135,240 - 1,155,175 (-)NCBI

Position Markers
D16Mgh4  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01619,398,187 - 19,398,306NCBIRnor6.0
Rnor_5.01619,256,518 - 19,256,637UniSTSRnor5.0
RGSC_v3.41618,121,292 - 18,121,411UniSTSRGSC3.4
RGSC_v3.41618,121,291 - 18,121,411RGDRGSC3.4
RGSC_v3.11618,121,289 - 18,121,409RGD
Celera1617,911,428 - 17,911,547UniSTS
Cytogenetic Map16p14UniSTS
RH 3.4 Map16213.1UniSTS
RH 3.4 Map16213.1RGD
RH 2.0 Map16200.5RGD
FHH x ACI Map1612.2099RGD
D16Wox10  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01619,398,173 - 19,398,285NCBIRnor6.0
Rnor_5.01619,256,504 - 19,256,616UniSTSRnor5.0
RGSC_v3.41618,121,277 - 18,121,390RGDRGSC3.4
RGSC_v3.41618,121,278 - 18,121,390UniSTSRGSC3.4
RGSC_v3.11618,121,275 - 18,121,388RGD
Celera1617,911,414 - 17,911,526UniSTS
Cytogenetic Map16p14UniSTS
D16Wox11  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01619,398,181 - 19,398,342NCBIRnor6.0
Rnor_5.01619,256,512 - 19,256,673UniSTSRnor5.0
RGSC_v3.41618,121,286 - 18,121,447UniSTSRGSC3.4
RGSC_v3.41618,121,285 - 18,121,447RGDRGSC3.4
RGSC_v3.11618,121,283 - 18,121,445RGD
Celera1617,911,422 - 17,911,583UniSTS
Cytogenetic Map16p14UniSTS
RH 3.4 Map16180.5UniSTS
RH 3.4 Map16180.5RGD
RH 2.0 Map16164.4RGD
D16Arb9  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01619,391,435 - 19,391,652NCBIRnor6.0
Rnor_5.01619,249,766 - 19,249,983UniSTSRnor5.0
RGSC_v3.41618,114,539 - 18,114,756UniSTSRGSC3.4
RGSC_v3.41618,114,538 - 18,114,756RGDRGSC3.4
RGSC_v3.11618,114,536 - 18,114,754RGD
Celera1617,904,676 - 17,904,893UniSTS
Cytogenetic Map16p14UniSTS
SHRSP x BN Map165.71UniSTS
SHRSP x BN Map165.71RGD
FHH x ACI Map1612.1799RGD
D16Arb10  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01619,398,176 - 19,398,281NCBIRnor6.0
Rnor_5.01619,256,507 - 19,256,612UniSTSRnor5.0
RGSC_v3.41618,121,280 - 18,121,386RGDRGSC3.4
RGSC_v3.41618,121,281 - 18,121,386UniSTSRGSC3.4
RGSC_v3.11618,121,278 - 18,121,384RGD
Celera1617,911,417 - 17,911,522UniSTS
Cytogenetic Map16p14UniSTS
RH143324  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01619,399,011 - 19,399,217NCBIRnor6.0
Rnor_5.01619,257,342 - 19,257,548UniSTSRnor5.0
RGSC_v3.41618,122,116 - 18,122,322UniSTSRGSC3.4
Celera1617,912,252 - 17,912,458UniSTS
Cytogenetic Map16p14UniSTS
RH 3.4 Map16178.6UniSTS
RH140074  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01619,384,975 - 19,385,179NCBIRnor6.0
Rnor_5.01619,243,306 - 19,243,510UniSTSRnor5.0
RGSC_v3.41618,108,079 - 18,108,283UniSTSRGSC3.4
Celera1617,898,216 - 17,898,420UniSTS
Cytogenetic Map16p14UniSTS
RH 3.4 Map16180.0UniSTS
GDB:434012  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01619,392,225 - 19,392,371NCBIRnor6.0
Rnor_6.01065,106,752 - 65,106,879NCBIRnor6.0
Rnor_5.01619,250,556 - 19,250,702UniSTSRnor5.0
Rnor_5.01066,519,401 - 66,519,528UniSTSRnor5.0
RGSC_v3.41618,115,329 - 18,115,475UniSTSRGSC3.4
Celera1617,905,466 - 17,905,612UniSTS
Cytogenetic Map16p14UniSTS
TM4  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01619,391,878 - 19,391,943NCBIRnor6.0
Rnor_5.01619,250,209 - 19,250,274UniSTSRnor5.0
RGSC_v3.41618,114,982 - 18,115,047UniSTSRGSC3.4
Celera1617,905,119 - 17,905,184UniSTS
Cytogenetic Map16p14UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1600369Hcas8Hepatocarcinoma susceptibility QTL 8liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)16124228366Rat
631830Alc7Alcohol consumption QTL 72.9consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)16127556253Rat
634355Rends4Renal damage susceptibility QTL 40.05kidney blood vessel morphology trait (VT:0000530)organ lesion measurement (CMO:0000677)16127556253Rat
1582235Insul8Insulin level QTL 83.30.0063blood insulin amount (VT:0001560)calculated serum insulin level (CMO:0000359)16127556253Rat
9590151Scort8Serum corticosterone level QTL 88.450.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)16131816439Rat
2302380Slep6Serum leptin concentration QTL 63.36blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)16133160624Rat
2307172Activ4Activity QTL 43.710.00023locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)16134465490Rat
1354584Despr6Despair related QTL 63.10.0067locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)16141240937Rat
2303566Bw90Body weight QTL 902body mass (VT:0001259)body weight (CMO:0000012)16141240937Rat
631561Hcuc2Hepatic copper content QTL 22.8hepatic copper amount (VT:0003065)liver total copper weight (CMO:0001507)16141240957Rat
6903319Bw114Body weight QTL 1142.70.0037body mass (VT:0001259)body weight (CMO:0000012)1624459345244593Rat
1600378Arunc4Aerobic running capacity QTL 40.03exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)16109005486162972Rat
7411664Foco30Food consumption QTL 30110.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)16134074146340741Rat
2293343Glom16Glomerulus QTL 167.4kidney glomerulus integrity trait (VT:0010546)kidney sclerotic glomeruli count to total glomeruli count ratio (CMO:0001269)16155018749247447Rat
2312660Bw95Body weight QTL 950.05inguinal fat pad mass (VT:0010424)inguinal fat pad weight to body weight ratio (CMO:0001253)16155018763210301Rat
2312663Slep9Serum leptin concentration QTL 90.001blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)16155018763210301Rat
2312666Insul16Insulin level QTL 160.01blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)16155018763210301Rat
2312669Stl23Serum triglyceride level QTL 230.01blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)16155018763210301Rat
1354625Despr7Despair related QTL 73.160.016locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)16172829746728297Rat
1300133Rf24Renal function QTL 243.64blood creatinine amount (VT:0005328)creatinine clearance (CMO:0000765)16413635523105837Rat
2306902Bp339Blood pressure QTL 3390.01arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)16413635545905331Rat
70183BpQTLcluster13Blood pressure QTL cluster 133.654arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)16501380245905331Rat
70183BpQTLcluster13Blood pressure QTL cluster 133.654arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)16501380245905331Rat
70183BpQTLcluster13Blood pressure QTL cluster 133.654arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)16501380245905331Rat
61338Bp23Blood pressure QTL 234.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)16501380250013802Rat
737819Hcas4Hepatocarcinoma susceptibility QTL 44.43liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)16501380250169318Rat
61405Niddm6Non-insulin dependent diabetes mellitus QTL 63.660.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)16501380252144919Rat
737826Alc11Alcohol consumption QTL 113.2consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)16501380264012784Rat
61372Bp40Blood pressure QTL 402.2blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)16509870419398181Rat
631517Scl9Serum cholesterol level QTL 93.3blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)161730939622744540Rat
70205Gcr3Gastric cancer resistance QTL 32.3stomach morphology trait (VT:0000470)stomach tumor depth of invasion (CMO:0001888)161939818770590230Rat
70205Gcr3Gastric cancer resistance QTL 32.3stomach morphology trait (VT:0000470)stomach tumor depth of invasion (CMO:0001888)161939818770590230Rat
70205Gcr3Gastric cancer resistance QTL 32.3stomach morphology trait (VT:0000470)stomach tumor diameter (CMO:0001889)161939818770590230Rat
70205Gcr3Gastric cancer resistance QTL 32.3stomach morphology trait (VT:0000470)stomach tumor diameter (CMO:0001889)161939818770590230Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:79
Count of miRNA genes:63
Interacting mature miRNAs:68
Transcripts:ENSRNOT00000021073
Prediction methods:Microtar, 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: ENSRNOT00000021073   ⟹   ENSRNOP00000021073
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1619,385,736 - 19,399,903 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000089056   ⟹   ENSRNOP00000072238
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1619,389,652 - 19,399,851 (-)Ensembl
RefSeq Acc Id: NM_012678   ⟹   NP_036810
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01619,385,810 - 19,399,851 (-)NCBI
Rnor_5.01619,244,141 - 19,258,182 (-)NCBI
RGSC_v3.41618,108,914 - 18,122,956 (-)RGD
Celera1617,899,051 - 17,913,092 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_036810 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAA42291 (Get FASTA)   NCBI Sequence Viewer  
  CAA68360 (Get FASTA)   NCBI Sequence Viewer  
  EDL90830 (Get FASTA)   NCBI Sequence Viewer  
  P09495 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_036810   ⟸   NM_012678
- UniProtKB: P09495 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000072238   ⟸   ENSRNOT00000089056
RefSeq Acc Id: ENSRNOP00000021073   ⟸   ENSRNOT00000021073

Transcriptome

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

Promoters
RGD ID:13699999
Promoter ID:EPDNEW_R10513
Type:initiation region
Name:Tpm4_1
Description:tropomyosin 4
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_6.01619,399,862 - 19,399,922EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
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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:3899 AgrOrtholog
Ensembl Genes ENSRNOG00000015496 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000021073 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOP00000072238 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000021073 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOT00000089056 UniProtKB/TrEMBL
InterPro Tropomyosin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:24852 UniProtKB/Swiss-Prot
NCBI Gene 24852 ENTREZGENE
Pfam Tropomyosin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Tpm4 PhenoGen
PRINTS TROPOMYOSIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE TROPOMYOSIN UniProtKB/Swiss-Prot
TIGR TC229658
UniGene Rn.108199 ENTREZGENE
UniProt A0A0G2K2G8_RAT UniProtKB/TrEMBL
  P09495 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2002-06-10 Tpm4  Tropomycin 4      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_homology aa sequence contains 98% identity with equine platelet TM 730104
gene_protein protein contains 248 aa residues 729954
gene_transcript sequence contains 8 exons spanning approximately 16 kb 729954