Neurod4 (neuronal differentiation 4) - Rat Genome Database

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Gene: Neurod4 (neuronal differentiation 4) Rattus norvegicus
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Symbol: Neurod4
Name: neuronal differentiation 4
RGD ID: 1310434
Description: Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and E-box binding activity. Involved in positive regulation of cell differentiation and retina development in camera-type eye. Predicted to be active in nucleus. Orthologous to human NEUROD4 (neuronal differentiation 4); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC288821; neurogenic differentiation 4; neurogenic differentiation factor 4
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr877,740,852 - 7,828,052 (-)NCBIGRCr8
mRatBN7.277,090,048 - 7,102,018 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl77,090,045 - 7,102,030 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx710,013,848 - 10,025,820 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0711,889,512 - 11,901,484 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.079,697,683 - 9,709,648 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.079,699,964 - 9,712,067 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl79,699,961 - 9,711,928 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.079,865,743 - 9,877,660 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.478,534,957 - 8,547,130 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.178,536,559 - 8,547,119 (-)NCBI
Celera75,307,012 - 5,318,756 (-)NCBICelera
Cytogenetic Map7q11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
nucleus  (IBA)

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Involvement of Ath3 in CNTF-mediated differentiation of the late retinal progenitors. Bhattacharya S, etal., Mol Cell Neurosci. 2004 Sep;27(1):32-43.
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. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
4. GOA pipeline RGD automated data pipeline
5. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
6. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
7. Comprehensive gene review and curation RGD comprehensive gene curation
Additional References at PubMed
PMID:11032813   PMID:11861467   PMID:15976074   PMID:29687839   PMID:32468054  


Genomics

Comparative Map Data
Neurod4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr877,740,852 - 7,828,052 (-)NCBIGRCr8
mRatBN7.277,090,048 - 7,102,018 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl77,090,045 - 7,102,030 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx710,013,848 - 10,025,820 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0711,889,512 - 11,901,484 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.079,697,683 - 9,709,648 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.079,699,964 - 9,712,067 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl79,699,961 - 9,711,928 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.079,865,743 - 9,877,660 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.478,534,957 - 8,547,130 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.178,536,559 - 8,547,119 (-)NCBI
Celera75,307,012 - 5,318,756 (-)NCBICelera
Cytogenetic Map7q11NCBI
NEUROD4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381255,019,974 - 55,030,017 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1255,019,974 - 55,030,017 (+)EnsemblGRCh38hg38GRCh38
GRCh371255,413,758 - 55,423,801 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361253,699,996 - 53,710,068 (+)NCBINCBI36Build 36hg18NCBI36
Build 341253,699,888 - 53,707,486NCBI
Celera1255,065,583 - 55,075,655 (+)NCBICelera
Cytogenetic Map12q13.2NCBI
HuRef1252,452,529 - 52,462,601 (+)NCBIHuRef
CHM1_11255,380,629 - 55,390,701 (+)NCBICHM1_1
T2T-CHM13v2.01254,986,632 - 54,996,675 (+)NCBIT2T-CHM13v2.0
Neurod4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3910130,104,021 - 130,116,123 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl10130,104,021 - 130,116,109 (-)EnsemblGRCm39 Ensembl
GRCm3810130,268,152 - 130,280,254 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl10130,268,152 - 130,280,240 (-)EnsemblGRCm38mm10GRCm38
MGSCv3710129,705,208 - 129,717,296 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv3610129,671,102 - 129,683,175 (-)NCBIMGSCv36mm8
Celera10132,642,855 - 132,654,951 (-)NCBICelera
Cytogenetic Map10D3NCBI
cM Map1077.81NCBI
Neurod4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554582,138,849 - 2,146,636 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554582,138,849 - 2,146,636 (+)NCBIChiLan1.0ChiLan1.0
NEUROD4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21039,146,944 - 39,156,972 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11239,143,713 - 39,153,741 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01233,719,986 - 33,730,012 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11234,447,026 - 34,457,083 (-)NCBIpanpan1.1PanPan1.1panPan2
NEUROD4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.127384,809 - 396,731 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl27389,095 - 390,090 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2745,848,698 - 45,858,754 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.027391,934 - 402,001 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl27394,351 - 395,346 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.127386,476 - 396,504 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.027394,850 - 404,905 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02746,253,998 - 46,264,178 (+)NCBIUU_Cfam_GSD_1.0
Neurod4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494560,809,685 - 60,820,300 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936891474,111 - 482,095 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_004936891471,576 - 482,195 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
NEUROD4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl520,046,937 - 20,059,128 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1520,046,864 - 20,057,380 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2520,909,099 - 20,919,582 (+)NCBISscrofa10.2Sscrofa10.2susScr3
NEUROD4
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11151,112,973 - 51,120,862 (+)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_023666037194,911,270 - 194,921,368 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Neurod4
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462498385,494 - 86,486 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462498379,564 - 89,114 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Neurod4
66 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:900
Count of miRNA genes:305
Interacting mature miRNAs:395
Transcripts:ENSRNOT00000011167
Prediction methods:Microtar, 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.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
61410Bw19Body weight QTL 196.20.001body mass (VT:0001259)body weight (CMO:0000012)7144782185Rat
1300176Hrtrt10Heart rate QTL 103.19heart pumping trait (VT:2000009)heart rate (CMO:0000002)766427026029351Rat
2317047Wbc4White blood cell count QTL 40.01leukocyte quantity (VT:0000217)white blood cell count (CMO:0000027)7135342956Rat
9590102Sffal5Serum free fatty acids level QTL 58.620.001blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)7532901950329019Rat
2298550Neuinf6Neuroinflammation QTL 63.3nervous system integrity trait (VT:0010566)spinal cord RT1-B protein level (CMO:0002132)7127829089Rat
631503Bp102Blood pressure QTL 1021.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)7144822433Rat
634336Anxrr17Anxiety related response QTL 173.66locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)7924703115097879Rat
10755438Coatc9Coat color QTL 90coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)7352928048529280Rat
724560Plsm3Polydactyly-luxate syndrome (PLS) morphotypes QTL 30.0003tibia length (VT:0004357)tibia length (CMO:0000450)7134000259Rat
9590142Scort5Serum corticosterone level QTL 524.40.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)7131962314Rat
7411566Bw136Body weight QTL 13610.40.001body mass (VT:0001259)body weight gain (CMO:0000420)7131962314Rat


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
nervous system
renal system
reproductive system
respiratory system
9 10 47 113 59 58 27 25 27 6 182 93 93 45 55 31

Sequence


Ensembl Acc Id: ENSRNOT00000011167   ⟹   ENSRNOP00000011167
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl77,090,045 - 7,102,030 (-)Ensembl
Rnor_6.0 Ensembl79,699,961 - 9,711,928 (-)Ensembl
RefSeq Acc Id: NM_001105942   ⟹   NP_001099412
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr877,740,852 - 7,752,824 (-)NCBI
mRatBN7.277,090,048 - 7,102,018 (-)NCBI
Rnor_6.079,699,964 - 9,711,916 (-)NCBI
Rnor_5.079,865,743 - 9,877,660 (-)NCBI
RGSC_v3.478,534,957 - 8,547,130 (-)RGD
Celera75,307,012 - 5,318,756 (-)RGD
Sequence:
RefSeq Acc Id: XM_063263094   ⟹   XP_063119164
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr877,740,853 - 7,828,052 (-)NCBI
RefSeq Acc Id: XM_063263095   ⟹   XP_063119165
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr877,740,853 - 7,754,701 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001099412 (Get FASTA)   NCBI Sequence Viewer  
  XP_063119164 (Get FASTA)   NCBI Sequence Viewer  
  XP_063119165 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL89112 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000011167.3
RefSeq Acc Id: NP_001099412   ⟸   NM_001105942
- UniProtKB: D4A7M5 (UniProtKB/TrEMBL),   A6K842 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000011167   ⟸   ENSRNOT00000011167
RefSeq Acc Id: XP_063119164   ⟸   XM_063263094
- Peptide Label: isoform X1
- UniProtKB: D4A7M5 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063119165   ⟸   XM_063263095
- Peptide Label: isoform X1
- UniProtKB: D4A7M5 (UniProtKB/TrEMBL)
Protein Domains
bHLH

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D4A7M5-F1-model_v2 AlphaFold D4A7M5 1-330 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1310434 AgrOrtholog
BioCyc Gene G2FUF-35078 BioCyc
Ensembl Genes ENSRNOG00000008449 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000011167.7 UniProtKB/TrEMBL
Gene3D-CATH 4.10.280.10 UniProtKB/TrEMBL
InterPro bHLH_transcription_factors UniProtKB/TrEMBL
  HLH_DNA-bd UniProtKB/TrEMBL
  HLH_DNA-bd_sf UniProtKB/TrEMBL
  Neurogenic_DUF UniProtKB/TrEMBL
  TF_bHLH_NeuroD UniProtKB/TrEMBL
KEGG Report rno:288821 UniProtKB/TrEMBL
NCBI Gene 288821 ENTREZGENE
PANTHER BASIC HELIX-LOOP-HELIX PROTEIN NEUROGENIN-RELATED UniProtKB/TrEMBL
  PTHR19290:SF86 UniProtKB/TrEMBL
Pfam HLH UniProtKB/TrEMBL
  Neuro_bHLH UniProtKB/TrEMBL
PhenoGen Neurod4 PhenoGen
PIRSF bHLH_NeuroD UniProtKB/TrEMBL
PROSITE HLH UniProtKB/TrEMBL
RatGTEx ENSRNOG00000008449 RatGTEx
SMART HLH UniProtKB/TrEMBL
Superfamily-SCOP HLH_basic UniProtKB/TrEMBL
UniProt A6K842 ENTREZGENE, UniProtKB/TrEMBL
  D4A7M5 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2012-10-05 Neurod4  neuronal differentiation 4  Neurod4  neurogenic differentiation 4  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Neurod4  neurogenic differentiation 4   Neurod4_predicted  neurogenic differentiation 4 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Neurod4_predicted  neurogenic differentiation 4 (predicted)      Symbol and Name status set to approved 70820 APPROVED