Neurod1 (neuronal differentiation 1) - Rat Genome Database

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Gene: Neurod1 (neuronal differentiation 1) Rattus norvegicus
Analyze
Symbol: Neurod1
Name: neuronal differentiation 1
RGD ID: 3165
Description: Exhibits double-stranded DNA binding activity. Involved in several processes, including cellular response to glucose stimulus; positive regulation of neuron differentiation; and positive regulation of transcription by RNA polymerase II. Localizes to cytoplasm and nucleus. Human ortholog(s) of this gene implicated in glucose intolerance; hyperglycemia; maturity-onset diabetes of the young type 6; type 1 diabetes mellitus; and type 2 diabetes mellitus. Orthologous to human NEUROD1 (neuronal differentiation 1); PARTICIPATES IN maturity-onset diabetes of the young pathway; INTERACTS WITH 17alpha-ethynylestradiol; 6-propyl-2-thiouracil; ammonium chloride.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: basic helix-loop-helix factor 1; BHF-1; neurogenic differentiation 1; neurogenic differentiation factor 1
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
mRatBN7.2364,360,222 - 64,363,526 (-)NCBI
Rnor_6.0 Ensembl366,414,308 - 66,417,741 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0366,414,314 - 66,417,617 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0372,974,876 - 72,978,179 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4362,224,633 - 62,227,936 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1362,121,017 - 62,124,302 (-)NCBI
Celera363,819,711 - 63,823,202 (-)NCBICelera
Cytogenetic Map3q24NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
amacrine cell differentiation  (ISO,ISS)
anterior/posterior pattern specification  (ISO)
camera-type eye development  (ISO)
cell fate commitment  (ISO)
cellular response to glucose stimulus  (IDA)
cerebellum development  (IEP,ISO)
dentate gyrus development  (ISO,ISS)
embryonic organ morphogenesis  (ISO)
endocrine pancreas development  (ISO,ISS)
enteroendocrine cell differentiation  (ISO,ISS)
glucose homeostasis  (ISO)
hindbrain development  (ISO)
inner ear development  (ISO,ISS)
insulin secretion  (ISO)
negative regulation of receptor signaling pathway via JAK-STAT  (ISO)
negative regulation of type B pancreatic cell apoptotic process  (ISO)
neuron development  (IEA)
neuron differentiation  (IBA)
nitric oxide mediated signal transduction  (ISO)
nucleocytoplasmic transport  (IDA)
pancreatic A cell fate commitment  (ISO)
pancreatic PP cell fate commitment  (ISO)
positive regulation of apoptotic process  (ISO,ISS)
positive regulation of cell differentiation  (ISO,ISS)
positive regulation of DNA-binding transcription factor activity  (ISO)
positive regulation of neuron differentiation  (IDA,ISO)
positive regulation of transcription by RNA polymerase II  (IDA,ISO)
positive regulation of transcription regulatory region DNA binding  (ISO)
positive regulation of transcription, DNA-templated  (ISO,ISS)
regulation of intestinal epithelial structure maintenance  (ISO,ISS)
regulation of neuron differentiation  (ISO)
regulation of transcription by RNA polymerase II  (IBA)
response to drug  (IEP)
response to glucose  (ISO)
signal transduction involved in regulation of gene expression  (ISO)

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
1. Boraska V, etal., Croat Med J. 2006 Aug;47(4):571-8.
2. Chantoux F and Francon J, Mol Cell Endocrinol. 2002 Aug 30;194(1-2):157-63.
3. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
4. GOA data from the GO Consortium
5. Gonsorcikova L, etal., Pediatr Diabetes. 2008 Aug;9(4 Pt 2):367-72. Epub 2008 Mar 5.
6. Jackson AE, etal., Diabetes. 2004 Aug;53(8):2122-5.
7. Kaneto H, etal., J Biol Chem 2002 Apr 12;277(15):12998-3006.
8. Kavvoura FK and Ioannidis JP, Hum Genet. 2005 Feb;116(3):192-9. Epub 2004 Dec 11.
9. Kawakami H, etal., Biochem Biophys Res Commun 1996 Apr 5;221(1):199-204.
10. Kristinsson SY, etal., Diabetologia. 2001 Nov;44(11):2098-103.
11. Krugel H, etal., J Neurochem. 2006 Apr;97 Suppl 1:74-81.
12. Liu L, etal., Mol Cell Biochem. 2006 Oct;290(1-2):199-204. Epub 2006 Jun 14.
13. Liu L, etal., Mol Cell Biochem. 2007 Sep;303(1-2):115-20. Epub 2007 Apr 18.
14. Malecki MT, etal., Nat Genet. 1999 Nov;23(3):323-8.
15. MGD data from the GO Consortium
16. Muharram G, etal., Biochem Biophys Res Commun. 2005 Aug 12;333(4):1153-9.
17. NCBI rat LocusLink and RefSeq merged data July 26, 2002
18. Noma T, etal., Brain Res Mol Brain Res 1999 Apr 6;67(1):53-63.
19. Oliveira CS, etal., Diabetes Metab. 2005 Dec;31(6):599-602.
20. OMIM Disease Annotation Pipeline
21. Petersen HV, etal., FEBS Lett 2002 Sep 25;528(1-3):241-5.
22. Pipeline to import KEGG annotations from KEGG into RGD
23. Plengvidhya N, etal., Clin Endocrinol (Oxf). 2009 Jun;70(6):847-53. Epub 2008 Sep 22.
24. RGD automated data pipeline
25. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
26. RGD automated import pipeline for gene-chemical interactions
27. RGD comprehensive gene curation
28. Vella A, etal., Diabetes. 2004 Apr;53(4):1158-61.
Additional References at PubMed
PMID:9308961   PMID:9512516   PMID:10398678   PMID:10639171   PMID:10804213   PMID:10868931   PMID:11152640   PMID:11861467   PMID:11891657   PMID:11981044   PMID:12368292   PMID:12477932  
PMID:14697366   PMID:14741104   PMID:14752053   PMID:15121856   PMID:15701640   PMID:15793245   PMID:16055439   PMID:16321656   PMID:16368089   PMID:17941991   PMID:17988662   PMID:18007592  
PMID:18388149   PMID:18462699   PMID:18848628   PMID:19272376   PMID:19619559   PMID:22513373   PMID:24338128  


Genomics

Comparative Map Data
Neurod1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2364,360,222 - 64,363,526 (-)NCBI
Rnor_6.0 Ensembl366,414,308 - 66,417,741 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0366,414,314 - 66,417,617 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0372,974,876 - 72,978,179 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4362,224,633 - 62,227,936 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1362,121,017 - 62,124,302 (-)NCBI
Celera363,819,711 - 63,823,202 (-)NCBICelera
Cytogenetic Map3q24NCBI
NEUROD1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl2181,673,088 - 181,680,547 (-)EnsemblGRCh38hg38GRCh38
GRCh38.p13 Ensembl2181,673,088 - 181,680,876 (-)EnsemblGRCh38hg38GRCh38
GRCh38.p13 Ensembl2181,668,295 - 181,680,827 (-)EnsemblGRCh38hg38GRCh38
GRCh382181,668,295 - 181,680,517 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh372182,533,022 - 182,545,244 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 362182,249,439 - 182,253,626 (-)NCBINCBI36hg18NCBI36
Build 342182,366,700 - 182,370,760NCBI
Celera2176,137,248 - 176,141,434 (-)NCBI
Cytogenetic Map2q31.3NCBI
HuRef2174,397,426 - 174,401,985 (-)NCBIHuRef
CHM1_12182,546,618 - 182,551,246 (-)NCBICHM1_1
Neurod1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39279,282,981 - 79,286,980 (-)NCBIGRCm39mm39
GRCm39 Ensembl279,282,865 - 79,287,095 (-)Ensembl
GRCm38279,452,637 - 79,456,636 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl279,452,521 - 79,456,751 (-)EnsemblGRCm38mm10GRCm38
MGSCv37279,292,798 - 79,296,793 (-)NCBIGRCm37mm9NCBIm37
MGSCv36279,253,480 - 79,257,475 (-)NCBImm8
Celera281,111,974 - 81,115,969 (-)NCBICelera
Cytogenetic Map2C3NCBI
cM Map247.58NCBI
Neurod1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540315,595,888 - 15,600,040 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495540315,595,888 - 15,600,040 (+)NCBIChiLan1.0ChiLan1.0
NEUROD1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12B186,749,155 - 186,753,541 (-)NCBIpanpan1.1PanPan1.1panPan2
Mhudiblu_PPA_v02B68,939,341 - 68,943,516 (-)NCBIMhudiblu_PPA_v0panPan3
NEUROD1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13624,853,591 - 24,857,886 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3624,876,367 - 24,880,645 (-)NCBI
ROS_Cfam_1.03625,015,921 - 25,020,202 (-)NCBI
UMICH_Zoey_3.13625,105,431 - 25,109,707 (-)NCBI
UNSW_CanFamBas_1.03625,071,760 - 25,074,709 (-)NCBI
UU_Cfam_GSD_1.03625,205,991 - 25,210,288 (-)NCBI
Neurod1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405303141,867,918 - 141,872,050 (-)NCBI
SpeTri2.0NW_00493650910,421,821 - 10,425,927 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
NEUROD1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1587,175,764 - 87,179,961 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11587,175,629 - 87,179,953 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21596,661,749 - 96,664,352 (+)NCBISscrofa10.2Sscrofa10.2susScr3
NEUROD1
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11067,203,714 - 67,208,644 (-)NCBI
ChlSab1.1 Ensembl1067,205,141 - 67,206,211 (-)Ensembl
Neurod1
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248443,493,819 - 3,497,814 (-)NCBI

Position Markers
UniSTS:158749  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2364,360,878 - 64,361,382 (+)MAPPER
Rnor_6.0366,414,971 - 66,415,474NCBIRnor6.0
Rnor_5.0372,975,533 - 72,976,036UniSTSRnor5.0
RGSC_v3.4362,225,290 - 62,225,793UniSTSRGSC3.4
Celera363,820,368 - 63,820,871UniSTS
Cytogenetic Map3q24-q32UniSTS
RH80773  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2364,360,692 - 64,360,878 (+)MAPPER
Rnor_6.0366,414,785 - 66,414,970NCBIRnor6.0
Rnor_5.0372,975,347 - 72,975,532UniSTSRnor5.0
RGSC_v3.4362,225,104 - 62,225,289UniSTSRGSC3.4
Celera363,820,182 - 63,820,367UniSTS
Cytogenetic Map3q24-q32UniSTS
U28068  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2364,360,590 - 64,360,743 (+)MAPPER
Rnor_6.0366,414,683 - 66,414,835NCBIRnor6.0
Rnor_5.0372,975,245 - 72,975,397UniSTSRnor5.0
RGSC_v3.4362,225,002 - 62,225,154UniSTSRGSC3.4
Celera363,820,080 - 63,820,232UniSTS
Cytogenetic Map3q24-q32UniSTS
PMC85623P1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2364,363,750 - 64,363,905 (+)MAPPER
Rnor_6.0366,417,842 - 66,417,996NCBIRnor6.0
Rnor_5.0372,978,404 - 72,978,558UniSTSRnor5.0
RGSC_v3.4362,228,161 - 62,228,315UniSTSRGSC3.4
Celera363,823,427 - 63,823,581UniSTS
Cytogenetic Map3q24-q32UniSTS
PMC140695P3  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2364,360,827 - 64,361,214 (+)MAPPER
Rnor_6.0366,414,920 - 66,415,306NCBIRnor6.0
Rnor_5.0372,975,482 - 72,975,868UniSTSRnor5.0
RGSC_v3.4362,225,239 - 62,225,625UniSTSRGSC3.4
Celera363,820,317 - 63,820,703UniSTS
Cytogenetic Map3q24-q32UniSTS
PMC85623P3  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2364,360,835 - 64,361,122 (+)MAPPER
Rnor_6.0366,414,928 - 66,415,214NCBIRnor6.0
Rnor_5.0372,975,490 - 72,975,776UniSTSRnor5.0
RGSC_v3.4362,225,247 - 62,225,533UniSTSRGSC3.4
Celera363,820,325 - 63,820,611UniSTS
Cytogenetic Map3q24-q32UniSTS
UniSTS:274183  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2364,361,295 - 64,361,524 (+)MAPPER
Rnor_6.0366,415,388 - 66,415,616NCBIRnor6.0
Rnor_5.0372,975,950 - 72,976,178UniSTSRnor5.0
RGSC_v3.4362,225,707 - 62,225,935UniSTSRGSC3.4
Celera363,820,785 - 63,821,013UniSTS
Cytogenetic Map3q24-q32UniSTS
Neurod1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2364,360,893 - 64,361,106 (+)MAPPER
Rnor_6.0366,414,986 - 66,415,198NCBIRnor6.0
Rnor_5.0372,975,548 - 72,975,760UniSTSRnor5.0
RGSC_v3.4362,225,305 - 62,225,517UniSTSRGSC3.4
Celera363,820,383 - 63,820,595UniSTS
Cytogenetic Map3q24-q32UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2290452Scl56Serum cholesterol level QTL 562.26blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)3195176874Rat
1358905Hrtrt17Heart rate QTL 175.90.000014heart pumping trait (VT:2000009)heart rate (CMO:0000002)31009408193415837Rat
2298542Neuinf11Neuroinflammation QTL 113.9nervous system integrity trait (VT:0010566)spinal cord complement component 1, q subcomponent, B chain mRNA level (CMO:0002126)31011931879772001Rat
1358885Bp251Blood pressure QTL 2513.8arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)310639528127023997Rat
1358888Bp264Blood pressure QTL 2644.43arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)310639528127023997Rat
631685Bp118Blood pressure QTL 1183.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)32465522569655225Rat
2302055Pia30Pristane induced arthritis QTL 303.50.001blood autoantibody amount (VT:0003725)serum immunoglobulin M-type rheumatoid factor level relative to an arbitrary reference serum (CMO:0002111)32932171474321714Rat
9590286Uminl1Urine mineral level QTL 13.50.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)32968273274682732Rat
9590136Scort3Serum corticosterone level QTL 323.370.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)32968273274682732Rat
8552950Pigfal12Plasma insulin-like growth factor 1 level QTL 127.3blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)32968273274682732Rat
8694196Abfw2Abdominal fat weight QTL 216.580.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)32968273274682732Rat
8694386Bw159Body weight QTL 1594.520.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)32968273274682732Rat
1354590Despr11Despair related QTL 110.000031locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)32990825574908255Rat
2303593Gluco46Glucose level QTL 463blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)32990825574908255Rat
737818Hcar12Hepatocarcinoma resistance QTL 122.6liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)330114912123700444Rat
70216Cm14Cardiac mass QTL 142.1heart mass (VT:0007028)heart wet weight (CMO:0000069)330846101172879276Rat
2301400Cm68Cardiac mass QTL 680.001heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)33110358972989078Rat
11565451Bw177Body weight QTL 1770.002body mass (VT:0001259)body weight (CMO:0000012)33110358972989078Rat
11565452Kidm57Kidney mass QTL 570.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)33110358972989078Rat
12879866Cm94Cardiac mass QTL 940.001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)33110358972989078Rat
12879867Cm95Cardiac mass QTL 950.047heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)33110358972989078Rat
12879868Am6Aortic mass QTL 60.001aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)33110358972989078Rat
61356Bp37Blood pressure QTL 373blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)33213099777130997Rat
631647Bp122Blood pressure QTL 1226.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)33213099777130997Rat
1354589Bw31Body weight QTL 313.3body mass (VT:0001259)body weight (CMO:0000012)33347735481136227Rat
1354604Bw36Body weight QTL 362.9body mass (VT:0001259)body weight (CMO:0000012)333477354108914061Rat
61419Cia11Collagen induced arthritis QTL 115.6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)334394121103141944Rat
1358362Srcrt2Stress Responsive Cort QTL 22.78blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)339248391140271184Rat
738019Anxrr10Anxiety related response QTL 103.9exploratory behavior trait (VT:0010471)number of entries into a discrete space in an experimental apparatus (CMO:0000960)34042292185422921Rat
1331777Bw24Body weight QTL 243.503body mass (VT:0001259)body weight (CMO:0000012)34052359392654473Rat
1331795Rf30Renal function QTL 303.708urine potassium amount (VT:0010539)urine potassium level (CMO:0000128)34052359392654473Rat
1354597Kidm13Kidney mass QTL 132.9kidney mass (VT:0002707)right kidney wet weight (CMO:0000082)343295930108914061Rat
2301970Bw81Body weight QTL 815.19body mass (VT:0001259)body weight (CMO:0000012)343295930163640485Rat
2301971Cm71Cardiac mass QTL 714.63heart left ventricle mass (VT:0007031)heart left ventricle weight (CMO:0000776)343295930163640485Rat
1300178Hrtrt4Heart rate QTL 43.74heart pumping trait (VT:2000009)heart rate (CMO:0000002)34540605894467785Rat
1581503Cm58Cardiac mass QTL 582.70.05heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)345406058127023997Rat
1559282Emca5Estrogen-induced mammary cancer QTL 53.9mammary gland integrity trait (VT:0010552)percentage of study population developing mammary tumors during a period of time (CMO:0000948)345406058177699992Rat
2292591Esta4Estrogen-induced thymic atrophy QTL 4thymus mass (VT:0004954)thymus wet weight (CMO:0000855)348561928155263151Rat
1358186Ept2Estrogen-induced pituitary tumorigenesis QTL 28.3pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)348562146115249962Rat
2292613Ept16Estrogen-induced pituitary tumorigenesis QTL 168.3pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)348562146115249962Rat
631665Bw8Body weight QTL 85.5body mass (VT:0001259)body weight (CMO:0000012)351821836124513579Rat
724523Tsu1Thymus enlargement suppressive QTL 13.84thymus mass (VT:0004954)thymus weight to body weight ratio (CMO:0000612)351822008120917851Rat
1582249Bw77Body weight QTL 773.20.0025epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)35463094866711785Rat
1582218Bw74Body weight QTL 743.90.0021body mass (VT:0001259)body weight (CMO:0000012)354630948119830094Rat
1582238Bw68Body weight QTL 683.20.0064body mass (VT:0001259)body weight (CMO:0000012)354630948119830094Rat
1582239Epfw1Epididymal fat weight QTL 14.50.0006epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)354630948119830094Rat
61377Edpm3Estrogen-dependent pituitary mass QTL 37.050.038pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)35463104693415673Rat
731180Bp152Blood pressure QTL 1520.03arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)35524527695176874Rat
731180Bp152Blood pressure QTL 1520.03arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)35524527695176874Rat
731180Bp152Blood pressure QTL 1520.03arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)35524527695176874Rat
1358293Bw38Body weight QTL 3860.0000031body mass (VT:0001259)body weight (CMO:0000012)356735995101735995Rat
1581568Rf53Renal function QTL 53total urine protein amount (VT:0000032)urine protein excretion rate to body weight ratio (CMO:0001099)358204463170534769Rat
8662816Vetf4Vascular elastic tissue fragility QTL 44renal artery integrity trait (VT:0010642)number of ruptures of the internal elastic lamina of the renal arteries (CMO:0002563)361241033165369047Rat
1300111Rf12Renal function QTL 123.78renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)362922868127023997Rat
631200Cm25Cardiac mass QTL 254.80.0001heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)36304905092654302Rat

miRNA Target Status

Confirmed Target Of
miRNA GeneMature miRNAMethod NameResult TypeData TypeSupport TypePMID
Mir383rno-miR-383-5pMirtarbaseexternal_infoMicroarrayFunctional MTI (Weak)18258830
Mir30c1rno-miR-30c-5pMirtarbaseexternal_infoMicroarrayFunctional MTI (Weak)18258830

Predicted Target Of
Summary Value
Count of predictions:84
Count of miRNA genes:63
Interacting mature miRNAs:80
Transcripts:ENSRNOT00000007662
Prediction methods:Miranda, 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 endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system reproductive system respiratory system appendage
High
Medium 55
Low 3 19 6
Below cutoff 6 4 3 4 5 5 15 3 5

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000007662   ⟹   ENSRNOP00000007662
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl366,414,308 - 66,417,741 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000086507
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl366,414,318 - 66,417,611 (-)Ensembl
RefSeq Acc Id: NM_019218   ⟹   NP_062091
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2364,360,222 - 64,363,526 (-)NCBI
Rnor_6.0366,414,314 - 66,417,617 (-)NCBI
Rnor_5.0372,974,876 - 72,978,179 (-)NCBI
RGSC_v3.4362,224,633 - 62,227,936 (-)RGD
Celera363,819,711 - 63,823,202 (-)RGD
Sequence:
Reference Sequences
RefSeq Acc Id: NP_062091   ⟸   NM_019218
- UniProtKB: Q64289 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000007662   ⟸   ENSRNOT00000007662
Protein Domains
bHLH

Transcriptome

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

Promoters
RGD ID:13692176
Promoter ID:EPDNEW_R2692
Type:single initiation site
Name:Neurod1_1
Description:neuronal differentiation 1
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_6.0366,417,629 - 66,417,689EPDNEW

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)
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)
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
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)
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
F344/NRrrc (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
FHH/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)
FHH/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
FHL/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)
FHL/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
GH/OmrMcwi (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)
GK/Ox (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
LE/Stm (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
LEW/Crl (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
LEW/NCrlBR (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
LH/MavRrrc (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
LL/MavRrrc (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
LN/MavRrrc (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
M520/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
MHS/Gib (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
MNS/Gib (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
MR/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
SBH/Ygl (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: SBH/Ygl sequenced by MCW
SBH/Ygl (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
SBN/Ygl (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: SBN/Ygl sequenced by MCW
SBN/Ygl (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
SHR/NHsd (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
SHRSP/Gcrc (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
SR/JrHsd (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: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (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
SS/Jr (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
SS/JrHsdMcwi (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)
SS/JrHsdMcwi (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
WAG/Rij (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
WKY/Gcrc (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
WKY/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
WKY/NCrl (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
WKY/NHsd (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
WN/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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:3165 AgrOrtholog
Ensembl Genes ENSRNOG00000005609 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000007662 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000007662 ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH 4.10.280.10 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7312547 IMAGE-MGC_LOAD
  IMAGE:7318277 IMAGE-MGC_LOAD
InterPro bHLH_dom UniProtKB/Swiss-Prot
  HLH_DNA-bd_sf UniProtKB/Swiss-Prot
  Neurod1 UniProtKB/Swiss-Prot
  Neurogenic_DUF UniProtKB/Swiss-Prot
  TF_bHLH_NeuroD UniProtKB/Swiss-Prot
KEGG Report rno:29458 UniProtKB/Swiss-Prot
MGC_CLONE MGC:105447 IMAGE-MGC_LOAD
  MGC:105448 IMAGE-MGC_LOAD
NCBI Gene 29458 ENTREZGENE
PANTHER PTHR19290:SF88 UniProtKB/Swiss-Prot
Pfam HLH UniProtKB/Swiss-Prot
  Neuro_bHLH UniProtKB/Swiss-Prot
PhenoGen Neurod1 PhenoGen
PIRSF bHLH_NeuroD UniProtKB/Swiss-Prot
PROSITE BHLH UniProtKB/Swiss-Prot
SMART HLH UniProtKB/Swiss-Prot
Superfamily-SCOP SSF47459 UniProtKB/Swiss-Prot
UniProt NDF1_RAT UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary Q569P0 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2012-10-05 Neurod1  neuronal differentiation 1  Neurod1  neurogenic differentiation 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2002-06-10 Neurod1  neurogenic differentiation 1      Name updated 70584 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_process activates Adenylate kinase isozyme 1 (AK1) expression in PC12 cells 727267