Human Gene NEUROD6 (uc003tch.4) Description and Page Index
  Description: Homo sapiens neuronal differentiation 6 (NEUROD6), mRNA.
RefSeq Summary (NM_022728): This gene is a member of the NEUROD family of basic helix-loop-helix transcription factors. The encoded protein may be involved in the development and differentiation of the nervous system. [provided by RefSeq, Nov 2012]. ##Evidence-Data-START## Transcript exon combination :: BC035048.2, AF248954.1 [ECO:0000332] RNAseq introns :: single sample supports all introns SAMEA2145743, SAMEA2154665 [ECO:0000348] ##Evidence-Data-END## ##RefSeq-Attributes-START## MANE Ensembl match :: ENST00000297142.4/ ENSP00000297142.3 RefSeq Select criteria :: based on single protein-coding transcript ##RefSeq-Attributes-END##
Transcript (Including UTRs)
   Position: hg19 chr7:31,377,075-31,380,538 Size: 3,464 Total Exon Count: 2 Strand: -
Coding Region
   Position: hg19 chr7:31,377,869-31,378,882 Size: 1,014 Coding Exon Count: 1 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr7:31,377,075-31,380,538)mRNA (may differ from genome)Protein (337 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtOMIMPubMedStanford SOURCEUniProtKB

-  Comments and Description Text from UniProtKB
  ID: NDF6_HUMAN
DESCRIPTION: RecName: Full=Neurogenic differentiation factor 6; Short=NeuroD6; AltName: Full=Class A basic helix-loop-helix protein 2; Short=bHLHa2; AltName: Full=Protein atonal homolog 2;
FUNCTION: Activates E box-dependent transcription in collaboration with TCF3/E47. May be a trans-acting factor involved in the development and maintenance of the mammalian nervous system. Transactivates the promoter of its own gene (By similarity).
SUBUNIT: Efficient DNA binding requires dimerization with another bHLH protein (By similarity).
SUBCELLULAR LOCATION: Nucleus (Probable).
SIMILARITY: Contains 1 bHLH (basic helix-loop-helix) domain.
SEQUENCE CAUTION: Sequence=AAG43167.1; Type=Frameshift; Positions=300, 307;

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): NEUROD6
CDC HuGE Published Literature: NEUROD6
Positive Disease Associations: Parietal Lobe
Related Studies:
  1. Parietal Lobe
    Sudha Seshadri et al. BMC medical genetics 2007, Genetic correlates of brain aging on MRI and cognitive test measures: a genome-wide association and linkage analysis in the Framingham Study., BMC medical genetics. [PubMed 17903297]
    Our results suggest that genes associated with clinical neurological disease also have detectable effects on subclinical phenotypes. These hypothesis generating data illustrate the use of an unbiased approach to discover novel pathways that may be involved in brain aging, and could be used to replicate observations made in other studies.

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  Common Gene Haplotype Alleles
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-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 19.75 RPKM in Brain - Frontal Cortex (BA9)
Total median expression: 77.51 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -107.10353-0.303 Picture PostScript Text
3' UTR -156.30794-0.197 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR011598 - HLH_dom
IPR022575 - Neurogenic_DUF
IPR016637 - TF_bHLH_NeuroD

Pfam Domains:
PF00010 - Helix-loop-helix DNA-binding domain
PF12533 - Neuronal helix-loop-helix transcription factor

SCOP Domains:
47459 - HLH, helix-loop-helix DNA-binding domain

ModBase Predicted Comparative 3D Structure on Q96NK8
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
 Protein Sequence    
 Alignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000978 RNA polymerase II core promoter proximal region sequence-specific DNA binding
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding
GO:0001077 transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding
GO:0003677 DNA binding
GO:0046983 protein dimerization activity

Biological Process:
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006366 transcription from RNA polymerase II promoter
GO:0007275 multicellular organism development
GO:0007399 nervous system development
GO:0021542 dentate gyrus development
GO:0030154 cell differentiation
GO:0045944 positive regulation of transcription from RNA polymerase II promoter

Cellular Component:
GO:0005634 nucleus


-  Descriptions from all associated GenBank mRNAs
  AK055238 - Homo sapiens cDNA FLJ30676 fis, clone FCBBF2000038, highly similar to ATONAL PROTEIN HOMOLOG 2.
BC022560 - Homo sapiens cDNA clone IMAGE:4818263, containing frame-shift errors.
AF136169 - Homo sapiens neuronal helix-loop-helix protein NEX-1 mRNA, complete cds.
AF248954 - Homo sapiens MATH2 protein (MATH2) mRNA, complete cds.
BC035048 - Homo sapiens neurogenic differentiation 6, mRNA (cDNA clone MGC:41788 IMAGE:5261681), complete cds.
JD305717 - Sequence 286741 from Patent EP1572962.
AK055224 - Homo sapiens cDNA FLJ30662 fis, clone FCBBF1000581, highly similar to Neurogenic differentiation factor 6.
JD328856 - Sequence 309880 from Patent EP1572962.
AF063609 - Homo sapiens brain my051 protein mRNA, complete cds.
AK289619 - Homo sapiens cDNA FLJ78237 complete cds, highly similar to Homo sapiens neurogenic differentiation 6 (NEUROD6), mRNA.
EU446880 - Synthetic construct Homo sapiens clone IMAGE:100070155; IMAGE:100012089; FLH257455.01L neurogenic differentiation 6 (NEUROD6) gene, encodes complete protein.
AB464632 - Synthetic construct DNA, clone: pF1KB9629, Homo sapiens NEUROD6 gene for neurogenic differentiation 6, without stop codon, in Flexi system.
AK299619 - Homo sapiens cDNA FLJ56829 complete cds, highly similar to Neurogenic differentiation factor 6.
JD332517 - Sequence 313541 from Patent EP1572962.
JD544716 - Sequence 525740 from Patent EP1572962.
JD080077 - Sequence 61101 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: ATOH2, BHLHA2, My051, NDF6_HUMAN, NM_022728, NP_073565, Q548T9, Q96NK8, Q9H3H6, uc003tch.3
UCSC ID: uc003tch.4
RefSeq Accession: NM_022728
Protein: Q96NK8 (aka NDF6_HUMAN)
CCDS: CCDS5434.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_022728.3
exon count: 2CDS single in 3' UTR: no RNA size: 2161
ORF size: 1014CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 1931.50frame shift in genome: no % Coverage: 100.00
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
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-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.