Neurog3 (neurogenin 3) - Rat Genome Database

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Gene: Neurog3 (neurogenin 3) Rattus norvegicus
Analyze
Symbol: Neurog3
Name: neurogenin 3
RGD ID: 631350
Description: Enables DNA-binding transcription activator activity, RNA polymerase II-specific and double-stranded DNA binding activity. Involved in central nervous system development; positive regulation of neuron differentiation; and regulation of DNA-templated transcription. Predicted to be active in nucleus. Human ortholog(s) of this gene implicated in congenital malabsorptive diarrhea 4; glucose intolerance; and type 2 diabetes mellitus. Orthologous to human NEUROG3 (neurogenin 3); PARTICIPATES IN maturity-onset diabetes of the young pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 3H-1,2-dithiole-3-thione; ammonium chloride.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: neurogenin-3; Ngn3; Relax; transcriptional regulator, Relax
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr82030,622,533 - 30,624,015 (+)NCBIGRCr8
mRatBN7.22030,079,780 - 30,081,262 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2030,079,780 - 30,081,262 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx2031,090,729 - 31,092,211 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.02030,481,622 - 30,483,104 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.02031,224,416 - 31,225,898 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.02031,761,419 - 31,762,893 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2031,761,405 - 31,762,893 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02033,556,854 - 33,558,331 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42029,522,778 - 29,524,261 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.12029,536,585 - 29,538,061 (+)NCBI
Celera2031,503,365 - 31,504,847 (+)NCBICelera
Cytogenetic Map20q11NCBI
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
Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
nucleus  (IBA,ISO)

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Ngn3 expression during postnatal in vitro beta cell neogenesis induced by the JAK/STAT pathway. Baeyens L, etal., Cell Death Differ. 2006 Nov;13(11):1892-9. Epub 2006 Mar 3.
2. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
3. Polymorphic variations in the neurogenic differentiation-1, neurogenin-3, and hepatocyte nuclear factor-1alpha genes contribute to glucose intolerance in a South Indian population. Jackson AE, etal., Diabetes. 2004 Aug;53(8):2122-5.
4. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
5. NEUROG3 variants and type 2 diabetes in Italians. Milord E and Gragnoli C, Minerva Med. 2006 Oct;97(5):373-8.
6. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
7. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
8. Relax, a novel rat bHLH transcriptional regulator transiently expressed in the ventricular proliferating zone of the developing central nervous system. Ravassard P, etal., J Neurosci Res 1997 Apr 15;48(2):146-58.
9. Relax promotes ectopic neuronal differentiation in Xenopus embryos. Ravassard P, etal., Proc Natl Acad Sci U S A. 1997 Aug 5;94(16):8602-5.
10. GOA pipeline RGD automated data pipeline
11. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
12. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
13. Islet cell differentiation in liver by combinatorial expression of transcription factors neurogenin-3, BETA2, and RIPE3b1. Song YD, etal., Biochem Biophys Res Commun. 2007 Mar 9;354(2):334-9. Epub 2007 Jan 10.
14. Gene Therapy with Neurogenin 3 and Betacellulin Reverses Major Metabolic Problems in Insulin-Deficient Diabetic Mice. Yechoor V, etal., Endocrinology. 2009 Oct 9.
Additional References at PubMed
PMID:10868931   PMID:12080087   PMID:12490199   PMID:12921743   PMID:14576336   PMID:15793245   PMID:16511571   PMID:17376780   PMID:17928203   PMID:18506085   PMID:19759004   PMID:19882138  
PMID:20807725   PMID:21734788   PMID:21818269   PMID:24925797   PMID:24969979  


Genomics

Comparative Map Data
Neurog3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr82030,622,533 - 30,624,015 (+)NCBIGRCr8
mRatBN7.22030,079,780 - 30,081,262 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2030,079,780 - 30,081,262 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx2031,090,729 - 31,092,211 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.02030,481,622 - 30,483,104 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.02031,224,416 - 31,225,898 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.02031,761,419 - 31,762,893 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2031,761,405 - 31,762,893 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02033,556,854 - 33,558,331 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42029,522,778 - 29,524,261 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.12029,536,585 - 29,538,061 (+)NCBI
Celera2031,503,365 - 31,504,847 (+)NCBICelera
Cytogenetic Map20q11NCBI
NEUROG3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381069,571,485 - 69,573,422 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1069,571,698 - 69,573,422 (-)EnsemblGRCh38hg38GRCh38
GRCh371071,331,454 - 71,333,178 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361071,001,797 - 71,003,128 (-)NCBINCBI36Build 36hg18NCBI36
Build 341071,001,796 - 71,003,128NCBI
Celera1064,608,651 - 64,610,070 (-)NCBICelera
Cytogenetic Map10q22.1NCBI
HuRef1065,321,715 - 65,323,132 (-)NCBIHuRef
CHM1_11071,613,524 - 71,614,943 (-)NCBICHM1_1
T2T-CHM13v2.01070,439,446 - 70,441,420 (-)NCBIT2T-CHM13v2.0
Neurog3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391061,968,869 - 61,970,542 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1061,968,869 - 61,970,542 (+)EnsemblGRCm39 Ensembl
GRCm381062,133,090 - 62,134,763 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1062,133,090 - 62,134,763 (+)EnsemblGRCm38mm10GRCm38
MGSCv371061,595,838 - 61,597,511 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361061,528,447 - 61,530,120 (+)NCBIMGSCv36mm8
Celera1063,235,605 - 63,237,278 (+)NCBICelera
Cytogenetic Map10B4NCBI
cM Map1032.35NCBI
Neurog3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_00495543721,577,896 - 21,578,546 (+)NCBIChiLan1.0ChiLan1.0
NEUROG3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2881,720,280 - 81,721,303 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11081,725,601 - 81,726,624 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01066,039,739 - 66,041,804 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11068,571,204 - 68,572,663 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1068,571,614 - 68,572,258 (-)Ensemblpanpan1.1panPan2
NEUROG3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1420,654,824 - 20,657,816 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl420,656,791 - 20,657,438 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha420,784,524 - 20,787,459 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0420,926,422 - 20,929,357 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl420,928,319 - 20,928,966 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1420,825,760 - 20,828,692 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0421,030,322 - 21,033,256 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0421,374,244 - 21,377,179 (-)NCBIUU_Cfam_GSD_1.0
Neurog3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440721360,438,787 - 60,440,954 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365218,932,998 - 8,933,645 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365218,932,998 - 8,933,645 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
NEUROG3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1472,604,467 - 72,606,360 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11472,604,203 - 72,606,362 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
NEUROG3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1961,743,562 - 61,746,884 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl961,744,332 - 61,744,979 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604822,483,580 - 22,484,779 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Neurog3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247543,817,400 - 3,818,047 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Neurog3
2 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:160
Count of miRNA genes:125
Interacting mature miRNAs:147
Transcripts:ENSRNOT00000000661
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.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
6893685Bw111Body weight QTL 1112.70.004body mass (VT:0001259)body weight (CMO:0000012)20132578807Rat
7411668Foco32Food consumption QTL 3280.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20136600972Rat
9590252Scort12Serum corticosterone level QTL 1220.460.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20136600972Rat
2305926Iddm37Insulin dependent diabetes mellitus QTL 376blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)20152784246527842Rat
1641915Colcr9Colorectal carcinoma resistance QTL 92.970.0024intestine integrity trait (VT:0010554)benign colorectal tumor number (CMO:0001795)20153065546530655Rat
1598816Memor12Memory QTL 122.4exploratory behavior trait (VT:0010471)average horizontal distance between subject and target during voluntary locomotion in an experimental apparatus (CMO:0002674)20260683647606836Rat
7411652Foco24Food consumption QTL 240.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)201175751554435887Rat
9590092Insglur9Insulin/glucose ratio QTL 918.380.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)201175751554435887Rat
4889610Pancm3Pancreatic morphology QTL 33.750.001pancreas mass (VT:0010144)pancreas wet weight (CMO:0000626)201761783247606836Rat
2317880Alcrsp25Alcohol response QTL 252.3response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)201769755054435887Rat
2303626Vencon10Ventilatory control QTL 100.001respiration trait (VT:0001943)respiration rate (CMO:0000289)201919072154435887Rat
2303578Gluco50Glucose level QTL 502blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)202510672254435887Rat
2303587Bw93Body weight QTL 9313body mass (VT:0001259)body weight (CMO:0000012)202510672254435887Rat
2300188Bmd68Bone mineral density QTL 686.40.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)202510672254435887Rat
1331747Hrtrt16Heart rate QTL 163.163heart pumping trait (VT:2000009)heart rate (CMO:0000002)202520973454435887Rat
1598869Memor6Memory QTL 63.1exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)202924438854435887Rat

Markers in Region
PMC85623P2  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22030,080,643 - 30,080,876 (+)MAPPERmRatBN7.2
Rnor_6.02031,762,275 - 31,762,507NCBIRnor6.0
Rnor_5.02033,557,713 - 33,557,945UniSTSRnor5.0
RGSC_v3.42029,523,643 - 29,523,875UniSTSRGSC3.4
Celera2031,504,229 - 31,504,461UniSTS
Cytogenetic Map20q11UniSTS
UniSTS:462689  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22030,080,312 - 30,080,870 (+)MAPPERmRatBN7.2
Rnor_6.02031,761,944 - 31,762,501NCBIRnor6.0
Rnor_5.02033,557,382 - 33,557,939UniSTSRnor5.0
RGSC_v3.42029,523,312 - 29,523,869UniSTSRGSC3.4
Celera2031,503,898 - 31,504,455UniSTS
Cytogenetic Map20q11UniSTS


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 renal system reproductive system respiratory system appendage
High
Medium
Low 2 2 2 2 8 5
Below cutoff 1 3 2 2 2 1 1 15 12 8 10 1

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000000661   ⟹   ENSRNOP00000000661
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2030,079,780 - 30,081,262 (+)Ensembl
Rnor_6.0 Ensembl2031,761,405 - 31,762,893 (+)Ensembl
RefSeq Acc Id: NM_021700   ⟹   NP_067732
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82030,622,533 - 30,624,015 (+)NCBI
mRatBN7.22030,079,780 - 30,081,262 (+)NCBI
Rnor_6.02031,761,419 - 31,762,893 (+)NCBI
Rnor_5.02033,556,854 - 33,558,331 (+)NCBI
RGSC_v3.42029,522,778 - 29,524,261 (+)RGD
Celera2031,503,365 - 31,504,847 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_067732 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein CAA71630 (Get FASTA)   NCBI Sequence Viewer  
  EDL92993 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000000661
  ENSRNOP00000000661.2
Reference Protein Sequences
RefSeq Acc Id: NP_067732   ⟸   NM_021700
- UniProtKB: O08718 (UniProtKB/TrEMBL),   F7EPK2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000000661   ⟸   ENSRNOT00000000661
Protein Domains
bHLH

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-O08718-F1-model_v2 AlphaFold O08718 1-214 view protein structure

Transcriptome

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

Promoters
RGD ID:13701609
Promoter ID:EPDNEW_R12133
Type:single initiation site
Name:Neurog3_1
Description:neurogenin 3
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_6.02031,761,395 - 31,761,455EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:631350 AgrOrtholog
BioCyc Gene G2FUF-3702 BioCyc
Ensembl Genes ENSRNOG00000024413 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000000661 ENTREZGENE
  ENSRNOT00000000661.6 UniProtKB/TrEMBL
Gene3D-CATH 4.10.280.10 UniProtKB/TrEMBL
InterPro HLH_DNA-bd_sf UniProtKB/TrEMBL
  HLH_DNA_bd UniProtKB/TrEMBL
  Ngn3 UniProtKB/TrEMBL
KEGG Report rno:60329 UniProtKB/TrEMBL
NCBI Gene 60329 ENTREZGENE
PANTHER BASIC HELIX-LOOP-HELIX PROTEIN NEUROGENIN-RELATED UniProtKB/TrEMBL
  PTHR19290:SF94 UniProtKB/TrEMBL
Pfam HLH UniProtKB/TrEMBL
PhenoGen Neurog3 PhenoGen
PROSITE HLH UniProtKB/TrEMBL
RatGTEx ENSRNOG00000024413 RatGTEx
SMART HLH UniProtKB/TrEMBL
Superfamily-SCOP HLH_basic UniProtKB/TrEMBL
UniProt F7EPK2 ENTREZGENE, UniProtKB/TrEMBL
  O08718 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2006-03-30 Neurog3  neurogenin 3    transcriptional regulator, Relax  Name updated 1299863 APPROVED
2004-09-10 Neurog3  transcriptional regulator, Relax  Ngn3    Symbol and Name updated 1299863 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_expression expressed exclusively in the central nervous system 633362