Human Gene BHLHA9 (ENST00000391429.2) from GENCODE V44
  Description: Homo sapiens basic helix-loop-helix family member a9 (BHLHA9), mRNA. (from RefSeq NM_001164405)
RefSeq Summary (NM_001164405): This gene is a member of the basic helix-loop-helix family. The encoded protein is a transcription factor involved in limb development. Mutations in this gene have been associated with mesoaxial synostotic syndactyly Malik-Percin type (MSSD). Copy number variation of a locus containing this gene has been linked to a form of split-hand/foot malformation with long bone deficiency (SHFLD3). [provided by RefSeq, Mar 2015].
Gencode Transcript: ENST00000391429.2
Gencode Gene: ENSG00000205899.4
Transcript (Including UTRs)
   Position: hg38 chr17:1,270,444-1,271,815 Size: 1,372 Total Exon Count: 1 Strand: +
Coding Region
   Position: hg38 chr17:1,270,564-1,271,271 Size: 708 Coding Exon Count: 1 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsRNA-Seq Expression
RNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA DescriptionsOther Names
Methods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr17:1,270,444-1,271,815)mRNA (may differ from genome)Protein (235 aa)
Gene SorterGenome BrowserOther Species FASTATable SchemaAlphaFoldBioGPS
EnsemblEntrez GeneExonPrimerGencodeGeneCardsHGNC
LynxMalacardsMGIneXtProtOMIMPubMed
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: BHA09_HUMAN
DESCRIPTION: RecName: Full=Class A basic helix-loop-helix protein 9; Short=bHLHa9; AltName: Full=Class F basic helix-loop-helix factor 42; Short=bHLHf42;
FUNCTION: Putative transcription factor (By similarity).
SUBCELLULAR LOCATION: Nucleus (By similarity).
SIMILARITY: Contains 1 bHLH (basic helix-loop-helix) domain.
SEQUENCE CAUTION: Sequence=DAA00302.1; Type=Erroneous initiation;

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: BHLHA9
Diseases sorted by gene-association score: syndactyly, mesoaxial synostotic, with phalangeal reduction* (1681), camptosynpolydactyly, complex* (578), ectrodactyly with tibial hemimelia* (25), split hand-foot malformation (24), split hand (18), split-hand/foot malformation with long bone deficiency 3 (14), split-hand/foot malformation 6 (12), synostosis (6), miller-dieker lissencephaly syndrome (6)
* = Manually curated disease association

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 0.62 RPKM in Brain - Cortex
Total median expression: 2.44 RPKM



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

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -53.80120-0.448 Picture PostScript Text
3' UTR -250.70544-0.461 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

Pfam Domains:
PF00010 - Helix-loop-helix DNA-binding domain

ModBase Predicted Comparative 3D Structure on Q7RTU4
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
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGIRGDEnsembl   
Protein SequenceProtein SequenceProtein Sequence   
AlignmentAlignmentAlignment   

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding
GO:0003677 DNA binding
GO:0005515 protein binding
GO:0046982 protein heterodimerization activity
GO:0046983 protein dimerization activity

Biological Process:
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006357 regulation of transcription from RNA polymerase II promoter
GO:0007275 multicellular organism development

Cellular Component:
GO:0005634 nucleus
GO:0005737 cytoplasm


-  Descriptions from all associated GenBank mRNAs
  AK057824 - Homo sapiens cDNA FLJ25095 fis, clone CBR00768.

-  Other Names for This Gene
  Alternate Gene Symbols: A8MSH6, BHA09_HUMAN, BHLHF42, ENST00000391429.1, NM_001164405, Q7RTU4, uc021tnd.1, uc021tnd.2, uc021tnd.3
UCSC ID: ENST00000391429.2
RefSeq Accession: NM_001164405
Protein: Q7RTU4 (aka BHA09_HUMAN)
CCDS: CCDS45560.1

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.