Dmd (dystrophin) - Rat Genome Database

Send us a Message



 Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Search RGD Grant Resources Citing RGD About Us Contact Us
Genes QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) RatMine GViewer (Genome Viewer) Overgo Probe Designer ACP Haplotyper Genome Scanner VCMap
Aging & Age-Related Disease Cancer Cardiovascular Disease COVID-19 Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease
Find Models   new Genetic Models Autism Models PhenoMiner (Quantitative Phenotypes) Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes GERRC (Gene Editing Rat Resource Center) Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive
Pathways
Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Poster Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
Gene: Dmd (dystrophin) Rattus norvegicus
Analyze
Symbol: Dmd
Name: dystrophin
RGD ID: 2507
Description: Exhibits several functions, including PDZ domain binding activity; integrin binding activity; and lamin binding activity. Involved in several processes, including nervous system development; regulation of neuron differentiation; and response to denervation involved in regulation of muscle adaptation. Localizes to several cellular components, including mitochondrial membrane; neurofilament; and secretory vesicle. Used to study Duchenne muscular dystrophy; brain edema; and dilated cardiomyopathy. Biomarker of muscular atrophy; retinal degeneration; and status epilepticus. Human ortholog(s) of this gene implicated in cognitive disorder; dilated cardiomyopathy (multiple); intellectual disability; and muscular dystrophy (multiple). Orthologous to human DMD (dystrophin); INTERACTS WITH (+)-pilocarpine; 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: apodystrophin-3; apodystrophin-I; DNADMD1; dystrophin transcript variant Dp71e; dystrophin, muscular dystrophy; dystrophin-related; RATDMD; RNDNADMD1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: Dmdem1Kykn   Dmdem1Ang  
Genetic Models: SD-Dmdem1Ang W-Dmdem1Kykn
Is Marker For: Strains:   W-Dmdem2Kykn   W-Dmdem3Kykn  
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2X47,272,324 - 49,504,219 (+)NCBI
Rnor_6.0 EnsemblX51,286,737 - 53,519,259 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0X51,149,358 - 53,519,271 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0X51,475,950 - 53,700,033 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X71,501,362 - 71,671,414 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1X71,574,653 - 71,744,706 (+)NCBI
CeleraX49,967,398 - 50,127,432 (+)NCBICelera
Cytogenetic MapXq21NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View
Animal Disease Models  (ISO)
arrhythmogenic right ventricular cardiomyopathy  (ISO)
Ataxia  (ISO)
autistic disorder  (ISO)
Becker muscular dystrophy  (ISO)
Benign Pseudohypertrophic Muscular Dystrophy  (ISO)
brain edema  (IDA)
calcinosis  (ISO)
Cardiac Fibrosis  (IMP)
Cardiomegaly  (ISO)
cardiomyopathy  (ISO)
cataract  (ISO)
cognitive disorder  (ISO)
colorectal cancer  (ISO)
congestive heart failure  (ISO)
Dehydration  (IEP)
dilated cardiomyopathy  (IMP,ISO)
dilated cardiomyopathy 1A  (ISO)
dilated cardiomyopathy 1B  (ISO)
Dilated Cardiomyopathy with Left Ventricular Noncompaction  (ISO)
Duchenne muscular dystrophy  (IMP,ISO)
Duchenne Muscular Dystrophy, Mental Retardation, and Absence of ERG B-wave  (ISO)
embryonal rhabdomyosarcoma  (ISO)
Exertional Myalgia, Muscle Stiffness and Myoglobinuria  (ISO)
Experimental Seizures  (IEP)
familial hypertrophic cardiomyopathy  (ISO)
Funnel Chest  (ISO)
gastrointestinal stromal tumor  (ISO)
genetic disease  (ISO)
Heart Block  (ISO)
hypertrophic cardiomyopathy  (ISO)
intellectual disability  (ISO)
isolated elevated serum creatine phosphokinase levels  (ISO)
leiomyosarcoma  (ISO)
long QT syndrome  (ISO)
Malformations of Cortical Development, Group II  (ISO)
Muscle Cramp  (ISO)
Muscle Weakness  (ISO)
muscular atrophy  (IEP)
muscular dystrophy  (ISO)
Muscular Dystrophy, Animal  (ISO)
myocarditis  (ISO)
myopathy  (ISO)
Necrosis  (ISO)
Neoplasm Invasiveness  (ISO)
Neoplasm Metastasis  (ISO)
Neurodevelopmental Disorders  (ISO)
ornithine carbamoyltransferase deficiency  (ISO)
polycystic ovary syndrome  (ISO)
restrictive cardiomyopathy  (ISO)
retinal degeneration  (IEP)
schizophrenia  (ISO)
status epilepticus  (IEP,ISO)
syndromic X-linked intellectual disability Lubs type  (ISO)
Ventricular Dysfunction  (ISO)
X-linked adrenal hypoplasia congenita  (ISO)
X-linked dilated cardiomyopathy  (ISO)

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-pilocarpine  (EXP)
(-)-demecolcine  (ISO)
1,2-dimethylhydrazine  (ISO)
17beta-estradiol  (ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,2',5,5'-tetrachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP)
2,3,7,8-Tetrachlorodibenzofuran  (EXP)
2,6-dinitrotoluene  (EXP)
3,3',4,4',5-pentachlorobiphenyl  (EXP)
3,4-methylenedioxymethamphetamine  (ISO)
4,4'-diaminodiphenylmethane  (ISO)
4,4'-sulfonyldiphenol  (ISO)
4-hydroxyphenyl retinamide  (ISO)
6-propyl-2-thiouracil  (EXP)
6alpha-methylprednisolone  (ISO)
acetaldehyde  (ISO)
acrylamide  (ISO)
aflatoxin B1  (ISO)
all-trans-retinoic acid  (ISO)
ammonium chloride  (EXP)
antirheumatic drug  (ISO)
apocynin  (ISO)
arsenite(3-)  (ISO)
ATP  (ISO)
benzo[a]pyrene  (EXP,ISO)
benzo[a]pyrene diol epoxide I  (ISO)
bis(2-chloroethyl) sulfide  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
calcium atom  (ISO)
calcium(0)  (ISO)
cannabidiol  (ISO)
carbon nanotube  (ISO)
clofibrate  (ISO)
copper(II) chloride  (ISO)
crocidolite asbestos  (ISO)
cyclosporin A  (ISO)
daunorubicin  (ISO)
DDT  (EXP)
dibutyl phthalate  (ISO)
dinophysistoxin 1  (ISO)
dioxygen  (ISO)
dobutamine  (ISO)
doxorubicin  (ISO)
endosulfan  (EXP)
ethanol  (ISO)
etoposide  (ISO)
fenofibrate  (ISO)
flusilazole  (ISO)
folic acid  (ISO)
formaldehyde  (ISO)
geldanamycin  (ISO)
genistein  (ISO)
gentamycin  (ISO)
graphite  (EXP)
hydrogen peroxide  (ISO)
isoprenaline  (EXP,ISO)
lead(0)  (ISO)
lead(2+)  (ISO)
menadione  (ISO)
methamphetamine  (ISO)
mitomycin C  (ISO)
mitoxantrone  (ISO)
mono(2-ethylhexyl) phthalate  (ISO)
N-ethyl-N-nitrosourea  (ISO)
nickel atom  (ISO)
nifedipine  (ISO)
paracetamol  (ISO)
paraquat  (ISO)
PCB138  (EXP,ISO)
pirinixic acid  (ISO)
progesterone  (ISO)
propanal  (ISO)
resveratrol  (ISO)
serpentine asbestos  (ISO)
silicon dioxide  (ISO)
sodium arsenate  (ISO)
spermine  (ISO)
taurine  (ISO)
tetrachloromethane  (ISO)
tioguanine  (ISO)
trichostatin A  (ISO)
triptonide  (ISO)
valproic acid  (ISO)
vinclozolin  (EXP)
vincristine  (ISO)
vorinostat  (ISO)
zidovudine  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
aging  (IEP)
cardiac muscle cell action potential  (ISO)
cardiac muscle contraction  (ISO)
cell differentiation  (IEP)
cellular protein localization  (ISO)
cellular protein-containing complex assembly  (ISO)
cerebral cortex development  (IEP)
establishment of blood-nerve barrier  (ISO)
establishment of glial blood-brain barrier  (ISO)
muscle cell cellular homeostasis  (ISO)
muscle cell differentiation  (IEP)
muscle fiber development  (ISO)
muscle organ development  (ISO)
myotube cell development  (ISO)
negative regulation of ERK1 and ERK2 cascade  (ISO)
negative regulation of neuron differentiation  (IMP)
negative regulation of peptidyl-cysteine S-nitrosylation  (ISO)
negative regulation of peptidyl-serine phosphorylation  (ISO)
neuron differentiation  (IEP)
neuron projection morphogenesis  (IMP)
neurotransmitter receptor metabolic process  (ISO)
nucleus localization  (ISO)
olfactory nerve structural organization  (ISO)
peptide biosynthetic process  (ISO)
positive regulation of cell population proliferation  (IMP)
positive regulation of cell-matrix adhesion  (ISO)
positive regulation of neuron differentiation  (IMP,ISO)
positive regulation of neuron projection development  (IMP,ISO)
positive regulation of sodium ion transmembrane transporter activity  (ISO)
regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion  (ISO)
regulation of cell cycle  (IMP)
regulation of cellular response to growth factor stimulus  (IMP,ISO)
regulation of gene expression  (ISO)
regulation of heart rate  (ISO)
regulation of membrane potential  (ISO)
regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum  (ISO)
regulation of ryanodine-sensitive calcium-release channel activity  (ISO)
regulation of skeletal muscle contraction  (ISO)
regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion  (ISO)
regulation of transcription, DNA-templated  (ISO)
regulation of voltage-gated calcium channel activity  (ISO)
response to denervation involved in regulation of muscle adaptation  (IEP)
response to muscle stretch  (ISO)
response to water deprivation  (IEP)
skeletal muscle tissue development  (ISO)
skeletal muscle tissue regeneration  (IEP)

Phenotype Annotations     Click to see Annotation Detail View
References

References - curated
1. Acosta R, etal., Exp Cell Res. 2004 Jun 10;296(2):265-75.
2. Ahmad S, etal., J Clin Immunol. 2010 Jul;30(4):520-30. Epub 2010 Apr 7.
3. Aleman V, etal., Histochem Cell Biol. 2001 Mar;115(3):243-54.
4. Aragón J, etal., J Neurochem. 2011 Nov;119(4):697-707. doi: 10.1111/j.1471-4159.2011.07347.x. Epub 2011 Sep 22.
5. Biral D, etal., J Muscle Res Cell Motil. 1996 Oct;17(5):523-32.
6. Blake DJ, etal., Hum Mol Genet 1992 May;1(2):103-9.
7. Calderilla-Barbosa L, etal., J Neurochem. 2006 Aug;98(3):713-22.
8. Chamova T, etal., Balkan J Med Genet. 2013 Jun;16(1):21-30. doi: 10.2478/bjmg-2013-0014.
9. Chockalingam PS, etal., Am J Physiol Cell Physiol 2002 Aug;283(2):C500-11.
10. Chávez O, etal., Biochem Biophys Res Commun. 2000 Aug 2;274(2):275-80.
11. Cisneros B, etal., Neurosci Lett. 1996 Aug 2;213(2):107-10.
12. Claudepierre T, etal., Invest Ophthalmol Vis Sci 1999 Jun;40(7):1520-9.
13. Claudepierre T, etal., J Cell Sci. 2000 Oct;113 Pt 19:3409-17.
14. Cortes JC, etal., Neurochem Res. 2009 Mar;34(3):438-44. Epub 2008 Aug 2.
15. de Brouwer AP, etal., Eur J Hum Genet. 2014 Apr;22(4):480-5. doi: 10.1038/ejhg.2013.169. Epub 2013 Jul 31.
16. Deconinck AE, etal., Cell 1997 Aug 22;90(4):717-27.
17. Dorbani-Mamine L, etal., Neuroreport. 1998 Nov 16;9(16):3583-7.
18. Enriquez-Aragon JA, etal., Neuroreport. 2005 Feb 28;16(3):235-8.
19. Feng J, etal., Mol Genet Metab. 2002 Sep-Oct;77(1-2):119-26.
20. Flanigan KM, etal., Hum Gene Ther. 2013 Sep;24(9):797-806. doi: 10.1089/hum.2013.092.
21. Fort PE, etal., Mol Vis. 2014 Nov 4;20:1480-90. eCollection 2014.
22. Garcia-Tovar CG, etal., Acta Histochem. 2001 Apr;103(2):209-24.
23. Geng J, etal., Cytotherapy. 2009;11(7):849-63.
24. Gilgenkrantz H, etal., J Biol Chem 1992 May 25;267(15):10823-30.
25. Górecki DC, etal., Neuroscience. 1998 May;84(2):467-77.
26. Hoshino S, etal., Acta Histochem. 2002;104(2):139-47.
27. Jancsik V and Hajós F, Brain Res. 1999 Jun 12;831(1-2):200-5.
28. Jung HK, etal., Brain Res. 2012 Apr 4;1447:126-34. Epub 2012 Jan 31.
29. Kakarla SK, etal., J Gerontol A Biol Sci Med Sci. 2010 Feb;65(2):147-55. Epub 2010 Jan 7.
30. Kim JE, etal., J Comp Neurol. 2010 Nov 15;518(22):4612-28.
31. Kim TW, etal., Proc Natl Acad Sci U S A. 1992 Dec 1;89(23):11642-4.
32. Kyoi S, etal., Circ J. 2003 Aug;67(8):725-7.
33. Larcher T, etal., PLoS One. 2014 Oct 13;9(10):e110371. doi: 10.1371/journal.pone.0110371. eCollection 2014.
34. Leonoudakis D, etal., J Biol Chem. 2004 May 21;279(21):22331-46. Epub 2004 Mar 15.
35. Malhotra SB, etal., Science. 1988 Nov 4;242(4879):755-9.
36. MGD data from the GO Consortium
37. Miller G, etal., Hum Mol Genet. 2012 Oct 15;21(20):4508-20. Epub 2012 Jul 18.
38. Nakamura K, etal., Sci Rep. 2014 Jul 9;4:5635. doi: 10.1038/srep05635.
39. NCBI rat LocusLink and RefSeq merged data July 26, 2002
40. Noel G, etal., J Biol Chem. 2009 Jul 17;284(29):19694-704. Epub 2009 May 18.
41. OMIM Disease Annotation Pipeline
42. Paul AC, etal., Cell Tissue Res. 2002 May;308(2):255-65. Epub 2002 Apr 13.
43. Rapaport D, etal., Differentiation 1992 Apr;49(3):187-93.
44. RGD automated data pipeline
45. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
46. RGD automated import pipeline for gene-chemical interactions
47. Rice KM, etal., J Gerontol A Biol Sci Med Sci. 2006 Nov;61(11):1119-29.
48. Saint Martin A, etal., FEBS J. 2012 Jan;279(1):66-77. doi: 10.1111/j.1742-4658.2011.08399.x. Epub 2011 Nov 17.
49. Spitali P, etal., FASEB J. 2013 Dec;27(12):4909-16. doi: 10.1096/fj.13-232025. Epub 2013 Aug 23.
50. Tinsley JM, etal., Hum Mol Genet 1993 May;2(5):521-4.
51. Ursitti JA, etal., J Biol Chem. 2004 Oct 1;279(40):41830-8. Epub 2004 Jul 6.
52. Vatta M, etal., J Cardiovasc Med (Hagerstown). 2009 Feb;10(2):149-56. doi: 10.2459/JCM.0b013e328318954c.
53. Villarreal-Silva M, etal., PLoS One. 2011;6(8):e23504. doi: 10.1371/journal.pone.0023504. Epub 2011 Aug 19.
54. Wehling-Henricks M, etal., Hum Mol Genet. 2005 Jul 15;14(14):1921-33. doi: 10.1093/hmg/ddi197. Epub 2005 May 25.
Additional References at PubMed
PMID:6583703   PMID:7545544   PMID:7592992   PMID:7890770   PMID:7919967   PMID:8007658   PMID:8663016   PMID:9334395   PMID:10545507   PMID:10867799   PMID:10995443   PMID:11115849  
PMID:11259414   PMID:11316798   PMID:11717465   PMID:11882673   PMID:12115694   PMID:12370193   PMID:12416719   PMID:12673830   PMID:12895031   PMID:14627610   PMID:14643017   PMID:14645204  
PMID:14711029   PMID:14718391   PMID:15001448   PMID:15501597   PMID:16000376   PMID:16371353   PMID:16803572   PMID:16810681   PMID:16841465   PMID:16935300   PMID:17164264   PMID:17436058  
PMID:17993586   PMID:18468998   PMID:18586242   PMID:18687308   PMID:19027585   PMID:19198614   PMID:19535499   PMID:19681445   PMID:19784870   PMID:19924636   PMID:20080623   PMID:20097170  
PMID:20717635   PMID:21029730   PMID:21164104   PMID:21677768   PMID:22000014   PMID:23263329   PMID:25139234   PMID:25931508   PMID:26004254   PMID:26378780   PMID:26411569   PMID:27225184  
PMID:28755400   PMID:28851655   PMID:29267303   PMID:29625189   PMID:31095755   PMID:33046751  


Genomics

Comparative Map Data
Dmd
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2X47,272,324 - 49,504,219 (+)NCBI
Rnor_6.0 EnsemblX51,286,737 - 53,519,259 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0X51,149,358 - 53,519,271 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0X51,475,950 - 53,700,033 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X71,501,362 - 71,671,414 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1X71,574,653 - 71,744,706 (+)NCBI
CeleraX49,967,398 - 50,127,432 (+)NCBICelera
Cytogenetic MapXq21NCBI
DMD
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 EnsemblX31,097,677 - 33,339,441 (-)EnsemblGRCh38hg38GRCh38
GRCh38.p13 EnsemblX31,097,677 - 33,339,609 (-)EnsemblGRCh38hg38GRCh38
GRCh38X31,119,219 - 33,339,460 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37X31,137,339 - 33,357,505 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36X31,047,266 - 33,267,647 (-)NCBINCBI36hg18NCBI36
Build 34X30,955,968 - 31,044,681NCBI
CeleraX35,264,860 - 37,484,992 (-)NCBI
Cytogenetic MapXp21.2-p21.1NCBI
HuRefX28,877,768 - 31,095,562 (-)NCBIHuRef
CHM1_1X31,168,731 - 33,388,091 (-)NCBICHM1_1
Dmd
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X81,858,244 - 84,248,656 (+)NCBIGRCm39mm39
GRCm39 EnsemblX81,992,476 - 84,249,747 (+)Ensembl
GRCm38X82,814,664 - 85,205,050 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX82,948,870 - 85,206,141 (+)EnsemblGRCm38mm10GRCm38
MGSCv37X80,194,209 - 82,450,389 (+)NCBIGRCm37mm9NCBIm37
MGSCv36X79,201,622 - 81,457,760 (+)NCBImm8
CeleraX74,178,103 - 76,399,942 (+)NCBICelera
Cytogenetic MapXC1NCBI
cM MapX38.38NCBI
Dmd
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555351,283,523 - 3,299,542 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049555351,283,084 - 3,297,015 (+)NCBIChiLan1.0ChiLan1.0
DMD
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1X31,279,878 - 32,974,614 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 EnsemblX31,282,415 - 33,492,733 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0X23,728,650 - 26,338,849 (-)NCBIMhudiblu_PPA_v0panPan3
DMD
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X26,290,903 - 28,444,635 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 EnsemblX26,290,910 - 28,333,576 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_TashaX31,264,482 - 33,330,008 (-)NCBI
ROS_Cfam_1.0X26,319,830 - 28,487,633 (-)NCBI
UMICH_Zoey_3.1X26,365,124 - 28,433,100 (-)NCBI
UNSW_CanFamBas_1.0X26,358,103 - 28,426,635 (-)NCBI
UU_Cfam_GSD_1.0X26,455,978 - 28,540,050 (-)NCBI
Dmd
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X19,065,166 - 21,072,605 (-)NCBI
SpeTri2.0NW_0049365537,157,526 - 7,943,703 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
DMD
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX27,028,223 - 29,181,689 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1X27,028,223 - 29,650,728 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X29,663,010 - 29,797,624 (-)NCBISscrofa10.2Sscrofa10.2susScr3
Sscrofa10.2X29,402,260 - 29,549,360 (-)NCBISscrofa10.2Sscrofa10.2susScr3
Sscrofa10.2X30,958,632 - 31,033,485 (+)NCBISscrofa10.2Sscrofa10.2susScr3
Sscrofa10.2X30,368,459 - 30,440,314 (+)NCBISscrofa10.2Sscrofa10.2susScr3
Sscrofa10.2X31,219,126 - 31,875,451 (-)NCBISscrofa10.2Sscrofa10.2susScr3
DMD
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X29,543,003 - 32,218,011 (-)NCBI
Vero_WHO_p1.0NW_02366605631,608,900 - 34,272,207 (-)NCBI
Dmd
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462476222,306,962 - 24,846,427 (+)NCBI

Position Markers
DXWox18  
Rat AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic MapXq22UniSTS
DXWox19  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0X53,517,148 - 53,517,371NCBIRnor6.0
Rnor_5.0X53,697,910 - 53,698,133UniSTSRnor5.0
RGSC_v3.4X71,671,410 - 71,671,633UniSTSRGSC3.4
CeleraX50,127,428 - 50,127,649UniSTS
Cytogenetic MapXq22UniSTS
DXMit8.3  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0X53,517,228 - 53,517,405NCBIRnor6.0
Rnor_5.0X53,697,990 - 53,698,167UniSTSRnor5.0
RGSC_v3.4X71,671,490 - 71,671,667UniSTSRGSC3.4
CeleraX50,127,506 - 50,127,683UniSTS
Cytogenetic MapXq22UniSTS
DMD  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0X52,122,081 - 52,122,179NCBIRnor6.0
Rnor_5.0X52,308,276 - 52,308,374UniSTSRnor5.0
RGSC_v3.4X70,237,157 - 70,237,255UniSTSRGSC3.4
CeleraX48,737,083 - 48,737,181UniSTS
Cytogenetic MapXq22UniSTS
BE121015  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0X53,424,378 - 53,424,575NCBIRnor6.0
Rnor_5.0X53,605,142 - 53,605,339UniSTSRnor5.0
RGSC_v3.4X71,566,440 - 71,566,637UniSTSRGSC3.4
CeleraX50,034,719 - 50,034,916UniSTS
RH 3.4 MapX658.4UniSTS
Cytogenetic MapXq22UniSTS
DMD  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0X53,418,677 - 53,418,744NCBIRnor6.0
Rnor_5.0X53,599,441 - 53,599,508UniSTSRnor5.0
RGSC_v3.4X71,560,750 - 71,560,817UniSTSRGSC3.4
CeleraX50,029,018 - 50,029,085UniSTS
Cytogenetic MapXq22UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
61430Cia18Collagen induced arthritis QTL 183.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X15688119127888215Rat
71116Niddm16Non-insulin dependent diabetes mellitus QTL 167.81blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)X1815335263153352Rat
1598837Memor13Memory QTL 133.2exploratory behavior trait (VT:0010471)difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)X44320616158345622Rat
738035Stresp1Stress response QTL 14.960.000011stress-related behavior trait (VT:0010451)defensive burying - copingX44557974120045269Rat


Related Rat Strains
The following Strains have been annotated to Dmd


Genetic Models
This gene Dmd is modified in the following models/strains
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:267
Count of miRNA genes:176
Interacting mature miRNAs:209
Transcripts:ENSRNOT00000034372
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 30 5 8 9 34 21 8 8
Low 3 13 57 41 14 41 2 40 35 20 3
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001005244 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001005246 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001370876 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_012698 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008773252 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008773253 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017601907 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017601908 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017601909 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017601910 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017601911 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017601912 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039099484 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039099485 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC094963 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AC097383 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AC108338 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AC111223 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AC112355 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AC112800 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AC113761 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AC117871 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AC125680 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AC125768 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AC127605 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AC131219 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AC136037 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY326947 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY326948 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY326949 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY390386 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CB750007 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CB808044 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473966 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000400 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JF510048 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KP798809 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  L01540 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  M86233 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  S38777 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  X07000 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  X65468 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  X69767 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000034372   ⟹   ENSRNOP00000032859
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX53,360,839 - 53,517,142 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000035692   ⟹   ENSRNOP00000029969
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX51,286,737 - 53,519,259 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000058357   ⟹   ENSRNOP00000055159
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX53,053,609 - 53,123,476 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000081061   ⟹   ENSRNOP00000072441
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX53,360,839 - 53,517,142 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000091467   ⟹   ENSRNOP00000074105
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX53,360,839 - 53,517,142 (+)Ensembl
RefSeq Acc Id: NM_001005244   ⟹   NP_001005244
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X49,345,362 - 49,501,764 (+)NCBI
Rnor_6.0X53,360,808 - 53,516,814 (+)NCBI
Rnor_5.0X51,475,950 - 53,700,033 (+)NCBI
RGSC_v3.4X71,501,362 - 71,671,414 (+)RGD
CeleraX49,967,398 - 50,127,094 (+)NCBI
Sequence:
RefSeq Acc Id: NM_001005246   ⟹   NP_001005246
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X49,345,393 - 49,502,102 (+)NCBI
Rnor_6.0X53,360,839 - 53,517,152 (+)NCBI
Rnor_5.0X51,475,950 - 53,700,033 (+)NCBI
RGSC_v3.4X71,501,362 - 71,671,414 (+)RGD
CeleraX49,967,429 - 50,127,432 (+)NCBI
Sequence:
RefSeq Acc Id: NM_001370876   ⟹   NP_001357805
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X47,272,324 - 49,504,219 (+)NCBI
RefSeq Acc Id: NM_012698   ⟹   NP_036830
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X49,345,362 - 49,501,764 (+)NCBI
Rnor_6.0X53,360,808 - 53,516,814 (+)NCBI
Rnor_5.0X51,475,950 - 53,700,033 (+)NCBI
RGSC_v3.4X71,501,362 - 71,671,414 (+)RGD
CeleraX49,967,398 - 50,127,094 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008773252   ⟹   XP_008771474
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X49,345,318 - 49,504,219 (+)NCBI
Rnor_6.0X53,360,777 - 53,519,271 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008773253   ⟹   XP_008771475
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X49,345,318 - 49,504,219 (+)NCBI
Rnor_6.0X53,360,778 - 53,517,016 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017601907   ⟹   XP_017457396
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0X51,149,358 - 53,519,271 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017601908   ⟹   XP_017457397
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0X51,286,674 - 53,519,271 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017601909   ⟹   XP_017457398
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X47,272,506 - 49,504,219 (+)NCBI
Rnor_6.0X51,286,674 - 53,519,271 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017601910   ⟹   XP_017457399
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0X51,286,674 - 53,517,016 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017601911   ⟹   XP_017457400
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0X52,158,340 - 53,517,016 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017601912   ⟹   XP_017457401
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0X53,053,433 - 53,517,016 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039099484   ⟹   XP_038955412
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X47,677,704 - 49,504,219 (+)NCBI
RefSeq Acc Id: XM_039099485   ⟹   XP_038955413
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X49,345,317 - 49,442,066 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_001005244   ⟸   NM_001005244
- Peptide Label: isoform Dp71ab
- UniProtKB: Q7TPH3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: NP_036830   ⟸   NM_012698
- Peptide Label: isoform Dp71a
- UniProtKB: Q7TPH4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: NP_001005246   ⟸   NM_001005246
- Peptide Label: isoform Dp71c
- UniProtKB: Q7TPH2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008771475   ⟸   XM_008773253
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_008771474   ⟸   XM_008773252
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_017457396   ⟸   XM_017601907
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017457397   ⟸   XM_017601908
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_017457398   ⟸   XM_017601909
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017457399   ⟸   XM_017601910
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_017457400   ⟸   XM_017601911
- Peptide Label: isoform X5
- Sequence:
RefSeq Acc Id: XP_017457401   ⟸   XM_017601912
- Peptide Label: isoform X6
- Sequence:
RefSeq Acc Id: ENSRNOP00000029969   ⟸   ENSRNOT00000035692
RefSeq Acc Id: ENSRNOP00000074105   ⟸   ENSRNOT00000091467
RefSeq Acc Id: ENSRNOP00000055159   ⟸   ENSRNOT00000058357
RefSeq Acc Id: ENSRNOP00000032859   ⟸   ENSRNOT00000034372
RefSeq Acc Id: ENSRNOP00000072441   ⟸   ENSRNOT00000081061
RefSeq Acc Id: NP_001357805   ⟸   NM_001370876
- Peptide Label: isoform 1
RefSeq Acc Id: XP_038955412   ⟸   XM_039099484
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038955413   ⟸   XM_039099485
- Peptide Label: isoform X5
Protein Domains
Calponin-homology (CH)   WW   ZZ-type

Transcriptome

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

Promoters
RGD ID:13701832
Promoter ID:EPDNEW_R12353
Type:initiation region
Name:Dmd_2
Description:dystrophin
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R12355  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0X51,286,704 - 51,286,764EPDNEW
RGD ID:13701831
Promoter ID:EPDNEW_R12355
Type:multiple initiation site
Name:Dmd_1
Description:dystrophin
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R12353  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0X53,360,806 - 53,360,866EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)